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CNValidatron, automated validation of CNV calls using computer vision | 10.1101/2024.09.09.612035 | Montalbano, S.; Ingason, A.; Werge, T.; Gaadin, J.; Stefansson, H.; Walters, B.; Jonsson, G.; Stefansson, K. | Motivation For more than a decade, running PennCNV on SNP array data has been the gold standard for detecting Copy Number Variants (CNVs, deletions and duplications). It is generally assumed that PennCNV has high sensitivity but poor specificity, leading to a large portion of CNV calls being false positives. Researchers often rely on manual inspection of the raw data trends to validate CNV calls. However, this approach is not feasible for more than a handful of loci in large collections. Results Here we present an R package implementing a convolutional neural network capable of automating CNV validation with an accuracy comparable to a trained human analyst. We also present an in-depth analysis into PennCNV false positive and false negative rates. Finally, we propose an algorithm to simplify the analysis of genome-wide CNV calls computing CNV regions. Availability and implementation The code is available on GitHub https://github.com/SinomeM/CNValidatron_fl. | 2024-09-13 | |
CNValidatron, automated validation of CNV calls using computer vision | 10.1101/2024.09.09.612035 | Montalbano, S.; Walters, B.; Jonsson, G.; Gaadin, J.; Werge, T.; Stefansson, H.; Stefansson, K.; Ingason, A. | Motivation For more than a decade, running PennCNV on SNP array data has been the gold standard for detecting Copy Number Variants (CNVs, deletions and duplications). It is generally assumed that PennCNV has high sensitivity but poor specificity, leading to a large portion of CNV calls being false positives. Researchers often rely on manual inspection of the raw data trends to validate CNV calls. However, this approach is not feasible for more than a handful of loci in large collections. Results Here we present an R package implementing a convolutional neural network capable of automating CNV validation with an accuracy comparable to a trained human analyst. We also present an in-depth analysis into PennCNV false positive and false negative rates. Finally, we propose an algorithm to simplify the analysis of genome-wide CNV calls computing CNV regions. Availability and implementation The code is available on GitHub https://github.com/SinomeM/CNValidatron_fl. | 2024-09-14 | |
bayesReact: Expression-coupled regulatory motif analysis detects microRNA activity in cancer and at the single cell level | 10.1101/2024.09.10.612047 | Rasmussen, A. M.; Bouchard-Cote, A.; Pedersen, J. S. | Motivation: Regulatory constraints are crucial in maintaining tissue and cell integrity, and play important roles during developmental processes and environmental responses. Yet many regulatory mechanisms remain unobserved at the single-cell level and statistical inference may, in some cases, help elucidate their condition-specific activity and perturbation during disease progression. Results: We introduce bayesReact (BAYESian modeling of Regular Expression ACTivity), a generative model of motif occurrence across experimentally ranked sequences to infer motif-based regulatory activities. The method is evaluated for microRNAs (miRNAs), which perform post-transcriptional regulation through target mRNA destabilization and translational repression. Inferred miRNA activities positively correlate with the observed miRNA expressions in primary tumors from The Cancer Genome Atlas (TCGA) and mouse stem cells. The top miRNA activity profiles are as informative for TCGA cancer-type cluster identification as the top miRNA or mRNA expression profiles. The activity captures tissue-specific miRNA patterns observed in the matched expression, e.g., the expression of miR-122-5p in the liver and miR-124-3p in low-grade gliomas (LGG). We observe a negative association between the activity of the two miRNAs and their target gene expressions, including between the miR-124-3p activity and the anti-neuronal REST expression in LGG. bayesReact outperforms the existing method, miReact, on sparse count data, and shows a higher correlation with the miRNA expression in single-cell data. The method recovers temporal activities of prominent miRNAs during murine stem cell differentiation, including miR-298-5p, miR-92-2-5p, and the large Sfmbt2 cluster (miR-297-669). The bayesReact model is probabilistic and quantifies the uncertainty of all provided estimates. It is unsupervised and permits screens of bulk or single-cell data to identify condition-specific regulatory motif candidates. It further improves miRNA activity inference in single-cell data. Availability and implementation: bayesReact is implemented as an R-package, uses a Hamiltonian Monte-Carlo sampler for posterior approximation, and is available at https://github.com/astamr/bayesReact. | 2024-09-13 | |
niiv: Fast Self-supervised Neural ImplicitIsotropic Volume Reconstruction | 10.1101/2024.09.07.611785 | Troidl, J.; Liang, Y.; Beyer, J.; Tavakoli, M.; Danzl, J. G.; Hadwiger, M.; Pfister, H.; Tompkin, J. | Three-dimensional (3D) microscopy data often is anisotropic with significantly lower resolution (up to 8x) along the z axis than along the xy axes. Computationally generating plausible isotropic resolution from anisotropic imaging data would benefit the visual analysis of large-scale volumes. This paper proposes niiv, a self-supervised method for isotropic reconstruction of 3D microscopy data that can quickly produce images at arbitrary (continuous) output resolutions. Within a neural field, the representation embeds a learned latent code that describes the implicit higher-resolution isotropic image region. Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution lateral image pairs to reconstruct an isotropic volume from low-resolution axial images. We evaluate our method on simulated and real anisotropic electron (EM) and light microscopy (LM) data. Compared to a state-of-the-art diffusion-based method, niiv shows improved reconstruction quality (+1dB PSNR) and is over three orders of magnitude faster (2,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume in 1/10th of a second, renderable at varying (continuous) high resolutions for display. | 2024-09-13 | |
Inferring cell differentiation maps from lineage tracing data | 10.1101/2024.09.09.611835 | Sashittal, P.; Zhang, R.; Law, B.; Strzalkowski, A.; Schmidt, H.; Bolondi, A.; Chan, M.; Raphael, B. | During development, mulitpotent cells differentiate through a hierarchy of increasingly restricted progenitor cell types until they realize specialized cell types. A cell differentiation map describes this hierarchy, and inferring these maps is an active area of research spanning traditional single marker lineage studies to data-driven trajectory inference methods on single-cell RNA-seq data. Recent high-throughput lineage tracing technologies profile lineages and cell types at scale, but current methods to infer cell differentiation maps from these data rely on simple models with restrictive assumptions about the developmental process. We introduce a mathematical framework for cell differentiation maps based on the concept of potency, and develop an algorithm, Carta, that infers an optimal cell differentiation map from single-cell lineage tracing data. The key insight in Carta is to balance the trade-off between the complexity of the cell differentiation map and the number of unobserved cell type transitions on the lineage tree. We show that Carta more accurately infers cell differentiation maps on both simulated and real data compared to existing methods. In models of mammalian trunk development and mouse hematopoiesis, Carta identifies important features of development that are not revealed by other methods including convergent differentiation of specialized cell types, progenitor differentiation dynamics, and the refinement of routes of differentiation via new intermediate progenitors. | 2024-09-13 | |
Parameter estimation in the Montijano-Bergues-Bory-Gompertz stochastic model for unperturbed tumor growth | 10.1101/2024.09.09.611959 | Bonilla-Capilla, B.; Cabrales, L. E. B. | Different sources of noises endogenous and exogenous to the cancer are involved in its stochastic growth. The aim of this study is to propose the stochastic version of Montijano-Bergues-Bory-Gompertz equation for the unperturbed tumor growth kinetics. The maximum likelihood estimators for the intrinsic tumor growth rate and the growth decelerating factor, and their respective discrete time approximations were analytically calculated. Different simulations of the deterministic and stochastic of this equation were made for different values of their respective parameters. Limit conditions for the average diffusion coefficient and the growth decelerating factor were established. The tumor volume at the infinite was calculated for several values of parameters of the stochastic Montijano-Bergues-Bory-Gompertz equation. Furthermore, descriptive statistic for the maximum likelihood estimators of the intrinsic tumor growth rate was computed for several parameters of this equation. The results evidenced that solid tumors there are for values of the average diffusion coefficient and the growth decelerating factor less than their respective limit values. The transition between avascular and vascular phases of the unperturbed tumor growth kinetics was revealed in the plot of the discrete time approximation for the maximum likelihood estimator of the growth decelerating factor versus the discrete time approximation for the maximum likelihood estimator of the intrinsic tumor growth rate. These results were connected with different findings in the literature. In conclusion, the stochastic Montijano-Bergues-Bory-Gompertz equation may be applied in the experiment to describe the unperturbed tumor growth kinetics, as previously demonstrated for its deterministic version, in order to estimate the parameters of this equation and their connection with processes involved in the growth, progression and metastasis of unperturbed solid tumors. | 2024-09-13 | |
Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis | 10.1101/2024.09.09.612077 | Baron, C. S.; Mitchell, O.; Avagyan, S.; Menard, R.; Yang, S.; Robertson, A. L.; Potluri, R.; Shendure, J.; Madelaine, R.; McKenna, A.; Zon, L. I. | Hematopoietic stem cells are regulated by endothelial and mesenchymal stromal cells in the marrow niche1-3. Leukemogenesis was long believed to be solely driven by genetic perturbations in hematopoietic cells but introduction of genetic mutations in the microenvironment demonstrated the ability of niche cells to drive disease progression4-8. The mechanisms by which the stem cell niche induces leukemia remain poorly understood. Here, using cellular barcoding in zebrafish, we found that clones of niche endothelial and stromal cells are significantly expanded in leukemic marrows. The pro-angiogenic peptide apelin secreted by leukemic cells induced sinusoidal endothelial cell clonal selection and transcriptional reprogramming towards an angiogenic state to promote leukemogenesis in vivo. Overexpression of apelin in normal hematopoietic stem cells led to clonal amplification of the niche endothelial cells and promotes clonal dominance of blood cells. Knock-out of apelin in leukemic zebrafish resulted in a significant reduction in disease progression. Our results demonstrate that leukemic cells remodel the clonal and transcriptional landscape of the marrow niche to promote leukemogenesis and provide a potential therapeutic opportunity for anti-apelin treatment. | 2024-09-13 | |
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis | 10.1101/2024.09.10.612045 | Lim, B.; Kamal, A.; Gomez Ramos, B.; Adrian Segarra, J.; Ibarra, I.; Dignas, L.; Kindinger, T.; Volz, K.; Rahbari, M.; Rahbari, N.; Poisel, E.; Kafetzopoulou, K.; Bose, L.; Breinig, M.; Heide, D.; Gallage, S.; Barragan Avila, J.; Wiethoff, H.; Berest, I.; Schnabellehner, S.; Schneider, M.; Becker, J.; Helm, D.; Grimm, D.; Makinen, T.; Tschaharganeh, D.; Heikenwalder, M.; Zaugg, J. B.; Mall, M. | Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether unwanted plasticity is actively suppressed by lineage-specific repressors. Here, we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that Prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternate fate master regulators. In mice, Prox1 was required for efficient hepatocyte regeneration after injury and acted as a tumour suppressor in multiple liver cancer models. In line with patient data, Prox1 depletion caused hepatocyte fate loss in vivo, and promoted transition of hepatocellular carcinoma to cholangiocarcinoma, conversely, overexpression promoted cholangiocarcinoma to hepatocellular carcinoma transdifferentiation. Our findings provide mechanistic evidence for PROX1 as a hepatocyte-specific safeguard and support a model where individual cell type-specific repressors actively suppress plasticity throughout life to safeguard lineage choice and prevent disease. | 2024-09-13 | |
Sequential ATR and PARP Inhibition Overcomes Acquired DNA Damaging Agent Resistance in Pancreatic Ductal Adenocarcinoma | 10.1101/2024.09.09.609499 | Herbert, K. J.; Upstill-Goddard, R.; Dreyer, S. B.; Rebus, S.; Australian Pancreatic Cancer Genome Initiative, ; Pilarsky, C.; Mukhopadhyay, D.; Lord, C. J.; Genomics Innovation Alliance, ; Biankin, A. V.; Froeling, F. E. M.; Chang, D. K. | Pancreatic ductal adenocarcinoma (PDAC) remains the most lethal cancer and will soon be the second most common cause of cancer related death. While regimens containing DNA damaging agents such as FOLFIRINOX and PARP inhibitors have derived clinical benefits for some patients, their efficacy invariably fails over time. This presents a significant clinical challenge, and thus there is an urgent need for novel therapeutic strategies which are able to overcome the acquisition of resistance in PDAC. Clinically relevant models of treatment resistance were generated from patient-derived cell lines by extended exposure to chemotherapy agents. Synergy scoring, clonogenicity assays, flow cytometry, immunofluorescence and transcriptomic analysis were used to investigate the efficacy of combined ATR and PARP inhibition in re-sensitising resistant PDAC to treatment. Acquisition of resistance was associated with transcriptomic shifts in cell cycle checkpoint regulation, metabolic control, DNA damage response (DDR), programmed cell death and the replication stress response. Additionally, combined treatment with the ATR inhibitor (ceralasertib), and the PARP inhibitor (olaparib) was synergistic in all models of acquired resistance. Sequential treatment using ceralasertib prior to olaparib was highly effective at low dose for DDR proficient cell lines, whereas DDR deficient models responded better when treated with olaparib first. We provide in vitro evidence of a novel therapeutic strategy to overcome acquired PARP inhibitor and platinum resistance in PDAC by using sequential exposure to ceralasertib and olaparib. A sequential regimen may be more tolerable and should be investigated clinically to circumvent dose limiting toxicity in concurrent combinations. | 2024-09-13 | |
An integrated stress response-independent role of GCN2 prevents excessive ribosome biogenesis and mRNA translation | 10.1101/2024.09.10.611650 | Roman-Trufero, M.; Kleijn, I. T.; Blighe, K.; Zhou, J.; Saavedra-Garcia, P.; Gaffar, A.; Christoforou, M.; Bellotti, A.; Abrahams, J.; Atrih, A.; Lamont, D. J.; Gierlinski, M.; Jayaprakash, P.; Michel, A. M.; Aboagye, E.; Yuneva, M.; Masson, G. R.; Shahrezaei, V.; Auner, H. W. | The Integrated Stress Response (ISR) is a corrective physiological program to restore cellular homeostasis that is based on the attenuation of global protein synthesis and a resource-enhancing transcriptional programme. GCN2 is the oldest of four kinases that are activated by diverse cellular stresses to trigger the ISR and acts as the primary responder to amino acid shortage and ribosome collisions. Here, using a broad multi-omic approach, we uncover an ISR-independent role of GCN2. GCN2 inhibition or depletion in the absence of discernible stress causes excessive protein synthesis and ribosome biogenesis, perturbs the cellular translatome, and results in a dynamic and broad loss of metabolic homeostasis. Cancer cells that rely on GCN2 to keep protein synthesis in check under conditions of full nutrient availability depend on GCN2 for survival and unrestricted tumour growth. Our observations define an ISR-independent role of GCN2 in regulating the cellular proteome and translatome and suggest new avenues for cancer therapies based on unleashing excessive mRNA translation. | 2024-09-13 | |
Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer | 10.1101/2024.09.12.611189 | Moss, D. Y.; Brown, C.; Shaw, A.; McCann, C.; Lewis, N.; Phillips, A.; Gallagher, S.; McDaid, W. J.; Roe, A.; Coughlan, A. Y.; Cavanagh, B.; Ormsby, C.; Falcone, F.; McCole, R.; Monteith, S.; Rogan, E.; Downs, M.; Malla, S. B.; Emerson, A. J.; Mohammed-Smith, L.; Sharkey, S.; Gallagher, P. F.; Banerjee, A.; Pandor, S.; Greer, B.; Elliott, C.; Ryan, A.; Dunne, P. D.; Coyle, V.; Mills, I. G.; McDade, S. S.; Sansom, O.; Ni Chonghaile, T.; Longley, D. B.; LaBonte, M. J.; Kerr, E. M. | Therapy resistance is attributed to over 80% of cancer deaths per year emphasizing the urgent need to overcome this challenge for improved patient outcomes. Despite its widespread use in colorectal cancer (CRC) treatment, resistance to 5-fluorouracil (5FU) remains poorly understood. Here, we investigate the transcriptional responses of CRC cells to 5FU treatment, revealing significant metabolic reprogramming towards heightened mitochondrial activity. Utilizing CRC models, we demonstrate sustained enhancement of mitochondrial biogenesis and function following 5FU treatment, leading to resistance in both in vitro and in vivo settings. Furthermore, we show that targeting mitochondrial metabolism, specifically by inhibiting Complex I (CI), sensitizes CRC cells to 5FU, resulting in delayed tumour growth and prolonged survival in preclinical models. Additionally, our analysis of patient data suggests that oxidative metabolism signatures may predict responses to 5FU-based chemotherapy. These findings shed light on mechanisms underlying 5FU resistance and propose a rational strategy for combination therapy in CRC, emphasizing the potential clinical benefit of targeting mitochondrial metabolism to overcome resistance and enhance patient outcomes. | 2024-09-13 | |
Merkel cell carcinoma-derived macrophage migration inhibitory factor (MIF) may promote persistence of Chronic Lymphocytic Leukemia | 10.1101/2024.09.09.611517 | Alencar, G. F.; Rodriguez, H. J.; Pulliam, T. H.; Remington, A. S.; Gilmour, M. W.; Alam, R.; Jabbour, A. J.; Mullen, L. J.; DeBuysscher, B. L.; Nghiem, P.; Taylor, J. J. | While concurrent diagnoses of Merkel cell carcinoma (MCC) and other cancers, like Chronic lymphocytic leukemia (CLL), are rare, patients with MCC have a 30-fold higher incidence of CLL. While these increases have been attributed to the ability of CLL to suppress immune responses allowing for the emergence of MCC, here we found evidence that MCC could support the persistence of CLL. Using single cell sequencing approaches and computational analyses of MCC and CLL from a patient where both cancers were present in the same lymph node, we found that production of macrophage migration inhibitory factor (MIF) by MCC could promote the persistence of CLL through stimulation of CD74 and CXCR4. These results may explain why blood cell counts rapidly normalized after treatment for MCC and were maintained at normal levels despite the absence of treatment for CLL. | 2024-09-13 | |
Evolutionary acquisition of a primitive light-dependent nuclear relocation in Marchantia polymorpha | 10.1101/2024.09.11.611950 | Iwabuchi, K.; Yagi, H.; Moriya, K. C.; Komatsu, A.; Suetsugu, N.; Sakai, Y.; Shimada, T.; Nishihama, R.; Kohchi, T.; Harada, A.; Watanabe, Y.-h.; Ueda, H.; Hara-Nishimura, I. | Arabidopsis thaliana is known to position nuclei on the bottom wall of leaf cells, distancing genetic material from external stresses, and, in response to intense blue light, it relocates them to the side walls to escape UV-induced DNA damage. However, how this protective system evolved in land plants remains unclear. Here, we show that Chara corallina, the charophyte alga, has no light-dependent nuclear relocation and that Marchantia polymorpha, a modern relative of the earliest land plants, has a nuclear positioning system distinct from that of Arabidopsis: it positions nuclei on the upper walls of the epidermal cells of the young thalli in the dark and even in prolonged intense light. We also show that, in response to intense blue light, M. polymorpha has the ability to immediately move nuclei from the upper to the side walls in an actin filament-dependent manner similarly to Arabidopsis. However, the relocation is transient and the nuclei return to the upper walls depending on two cytoskeletal components (actin filaments and microtubules). Together, these findings suggest that light-dependent nuclear relocation was initially established in bryophytes and then diverged as land plants evolved. | 2024-09-13 | |
Improvement of Antibody Affinity and Using PURE Ribosome Display and Microbial Secretion System | 10.1101/2024.09.13.612811 | Kihara, M.; Okuda, R.; Okada, A.; Ojima-Kato, T.; Nakano, H. | A method has been developed for efficiently enriching and analyzing high-affinity antibody variants by combining the PURE ribosome display (ribosome display using purified cell-free protein synthesis components) with next-generation sequencing (NGS) and the Brevibacillus choshinensis secretion system, using the NZ-1 antibody, which targets the PA tag peptide (GVAMPGAEDDVV), as a model antibody. An artificial DNA encoding the single-chain fragment of binding (scFab) of the NZ-1 antibody was synthesized and actively expressed by cell-free protein synthesis system (CFPS). Region-specific saturation mutations were introduced into the scFab gene based on its structural information. The resulting scFab library was selected against the PA tag through two rounds of PURE ribosome display, followed by Illumina sequencing to identify potential scFab variants with higher affinity. The candidates were expressed as Fab fragments using the B. choshinensis secretion system. These Fab fragments were then purified from the culture supernatant using two-step column chromatography. The binding affinity of the purified Fab was evaluated using a biolayer interferometry assay, revealing a variant Fab with higher affinity than the wild-type Fab. These results demonstrate that integrating PURE ribosome display with NGS analysis and the B. choshinensis secretion expression system enables the rapid identification and analysis of high-affinity antibody variants. | 2024-09-13 | |
RoCi - A Single Step Multi-Copy Integration System Based on Rolling-Circle Replication | 10.1101/2024.09.13.612835 | Antsotegi-Uskola, M.; D'Ambrosio, V.; Jarczynska, Z. D.; Vanegas, K. G.; Morera-Gomez, M.; Wang, X.; Larsen, T. O.; Mouillon, J.-M.; Mortensen, U. H. | Fungi are often used as cell factories for homologous and heterologous production of enzymes and metabolites. One strategy to obtain high yielding strains is to enhance the expression level of the gene(s) responsible for production of the product by inserting multiple copies of the gene-expression cassette. Typically, this is achieved by transforming non-homologous end-joining proficient strains with large amounts of a DNA vector, which randomly integrates in multiple copies at different loci, or more often, into a single locus with copies arranged as mixed orientation repeats. The majority of strains produced in this manner are unstable and substantial screening is necessary to identify strains with high and stable production. Moreover, the randomness of the insertion processes makes it difficult to determine how and where the copies are positioned in the genome. To this end, we envisioned that the instability of gene clusters made by the classical method is mostly due to the presence of a mixture of directly and inverted repeats. In such clusters, hairpins formed by inverted repeats may cause frequent recombinogenic lesions during replication to induce gene-expression cassette copy-loss by direct-repeat recombination. It is therefore possible that strains with gene-expression cassette clusters made solely by direct repeats would be more stable. Using Aspergillus nidulans as a model, we tested this idea and developed RoCi, a simple and efficient method to facilitate integration of multiple directly repeated gene-expression cassettes into a defined genomic locus through rolling-circle replication without pre-engineering requirements for strain preparation. In addition, we demonstrate that RoCi can be performed without E. coli based cloning, making it compatible with medium-high throughput experiments. Analyzing strains produced by RoCi, we have constructed strains bearing up to 68 mRFP GECs and we show that an mRFP multi-copy gene-array supports high and stable mRFP production for at least ~150 generations on solid medium. In liquid culture we observed a minor average copy loss at 1 L scale. This loss could be eliminated by extending the gene-expression cassette with a crippled selection marker. To demonstrate the strength of the method, we used it to produce stable and high yielding cell factories for production of the specialized metabolite cordycepin on solid medium and of the enzyme {beta}-glucuronidase in submerged culture. Finally, we show that RoCi can also be applied in the industrial workhorses A. niger and A. oryzae indicating that RoCi is generally applicable in fungi. | 2024-09-13 | |
Phenotype Prediction Using BEN-Based Predictive Modeling (BPM) | 10.1101/2024.09.07.611838 | Song, D.; Wang, Z. | Functional connectivity (FC) has been successfully used to predict cognitive functions, behaviors, and other phenotypes using connectome-based predictive modeling (CPM). One limitation is that FC reflects the covariation or synchrony relationship of the temporal profile in two regions and neglects the local temporal features of the brain activity. In this study, we used brain entropy (BEN) mapping to characterize regional brain activity and developed a BEN-Based Predictive Modeling (BPM) to predict phenotype. BEN measures the disorder and complexity of brain activity and has been shown to effectively capture brain activity features related to cognition and neurological disorders. Using data from the HCP 7T fMRI and corresponding 3T structural images, we calculated gray matter volume (GMV) as well as BEN from resting state and movie-watching data. We constructed prediction models based on BEN and GMV using different numbers of parcellation of the brain atlas, applying 10-fold cross-validation. Our results indicated that the BEN-based predictive model not only outperformed GMV-based predictive modeling but also achieved prediction accuracy comparable to that of CPM. Our study demonstrates that BEN can capture extensive brain activity information for accurate phenotype prediction, providing information at least as valuable as that from connectome. Additionally, our research lays the groundwork for future applications of BPM in developmental and clinical practice. | 2024-09-13 | |
Development of sensorimotor responses in larval zebrafish: a comparison between wild-type and GCaMP6s transgenic line | 10.1101/2024.09.10.612316 | Caperaa, M.; Roland-Caveriviere, M.; Herdman, C.; Imloul, N.; Poulin, S.; Lemieux, M.; De Koninck, P.; Bosse, G. D. | During early development, zebrafish larvae exhibit stereotypical behaviors, which rapidly become more complex. Thus, the generation of mutant transgenic lines that maintain transparency throughout their larval stage and that can be used to record brain activity has offered strategic opportunities to investigate the underlying neural correlates of behavior establishment. However, few studies have documented the behavioral profile of these lines during larval development. Here, we set up a behavioral characterization using diverse stimuli (light and vibration) throughout larval development to compare the responses of a transgenic strain expressing a pan-neuronal calcium indicator (GCaMP6s) with that of a wild-type strain. Interestingly, we report a drastic switch in behavioral responses to light transitions at 11 days post-fertilization (dpf) and to vibration stimuli at 14 dpf in both lines. These data highlight a specific time window of behavioral complexification. Meanwhile, we found no major difference in the maturation of sensorimotor responses between GCaMP6s and wild-type strains. Thus, these results support using GCaMP6s strain in investigating the neural mechanisms underlying the developmental maturation of sensorimotor responses. We observed nevertheless some minor differences that suggest careful attention should be taken when using mutant/transgenic lines for behavioral studies. | 2024-09-13 | |
Predicting speech-in-noise ability with static and dynamic auditory figure-ground analysis using structural equation modelling | 10.1101/2024.09.08.611859 | Guo, X.; Benzaquen, E.; Holmes, E.; Berger, J. I.; Brühl, I.; Sedley, W.; Rushton, S.; Griffiths, T. | Auditory figure-ground paradigms assess the ability to extract a foreground figure from a random background, a crucial part of central hearing. Previous studies have shown that the ability to extract static figures (with fixed frequencies) predicts real-life listening: speech-in-noise ability. In this study we assessed both fixed and dynamic figures: the latter comprised component frequencies that vary over time like natural speech. 159 participants (aged 18-79) with a range of peripheral hearing sensitivity were studied. We used hierarchal linear regression and structural equation modelling to examine how well speech-in-noise ability (for words and sentences) could be predicted by age, peripheral hearing, and static and dynamic figure-ground. Regression demonstrated that in addition to the audiogram and age, the low-frequency dynamic figure-ground accounted for significant variance of speech-in-noise, higher than the static figure-ground. The structural models showed that a combination of all types of figure-ground tasks predicted speech-in-noise with a higher effect size than the audiogram or age. Age influenced word perception in noise directly but sentence perception indirectly via effects on peripheral and central hearing. Overall, this study demonstrates that dynamic figure-ground explains more variance of real-life listening than static figure-ground, and the combination of both predicts real-life listening better than hearing sensitivity or age. | 2024-09-13 | |
Predicting speech-in-noise ability with static and dynamic auditory figure-ground analysis using structural equation modelling | 10.1101/2024.09.08.611859 | Guo, X.; Benzaquen, E.; Holmes, E.; Berger, J. I.; Brühl, I.; Sedley, W.; Rushton, S.; Griffiths, T. | Auditory figure-ground paradigms assess the ability to extract a foreground figure from a random background, a crucial part of central hearing. Previous studies have shown that the ability to extract static figures (with fixed frequencies) predicts real-life listening: speech-in-noise ability. In this study we assessed both fixed and dynamic figures: the latter comprised component frequencies that vary over time like natural speech. 159 participants (aged 18-79) with a range of peripheral hearing sensitivity were studied. We used hierarchal linear regression and structural equation modelling to examine how well speech-in-noise ability (for words and sentences) could be predicted by age, peripheral hearing, and static and dynamic figure-ground. Regression demonstrated that in addition to the audiogram and age, the low-frequency dynamic figure-ground accounted for significant variance of speech-in-noise, higher than the static figure-ground. The structural models showed that a combination of all types of figure-ground tasks predicted speech-in-noise with a higher effect size than the audiogram or age. Age influenced word perception in noise directly but sentence perception indirectly via effects on peripheral and central hearing. Overall, this study demonstrates that dynamic figure-ground explains more variance of real-life listening than static figure-ground, and the combination of both predicts real-life listening better than hearing sensitivity or age. | 2024-09-14 | |
Stronger premicrosaccadic sensitivity enhancement for dark contrasts in the primate superior colliculus | 10.1101/2024.09.08.611886 | Wu, W.; Hafed, Z. M. | Microsaccades are associated with enhanced visual perception and neural sensitivity right before their onset, and this has implications for interpreting experiments involving the covert allocation of peripheral spatial attention. However, the detailed properties of premicrosaccadic enhancement are not fully known. Here we investigated how such enhancement in the superior colliculus depends on luminance polarity. Rhesus macaque monkeys fixated a small spot while we presented either dark or bright image patches of different contrasts within the recorded neurons' response fields. Besides replicating premicrosaccadic enhancement of visual sensitivity, we observed stronger enhancement for dark contrasts. This was especially true at moderate contrast levels (such as 10-20%), and it occurred independent of an individual neuron's preference for either darks or brights. On the other hand, postmicrosaccadic visual sensitivity suppression was similar for either luminance polarity. Our results reveal an intriguing asymmetry in the properties of perimicrosaccadic modulations of superior colliculus visual neural sensitivity. | 2024-09-13 | |
Mutations in PSEN1 predispose inflammation in an astrocyte model of familial Alzheimer's disease through disrupted regulated intramembrane proteolysis | 10.1101/2024.09.09.611621 | Ziff, O. J.; Jolly, S.; Casey, J. M.; Granat, L.; Samra, S.; Seto-Salvia, N.; Alatza, A.; Phadke, L.; Galet, B.; Ravassard, P.; Potier, M.-C.; Fox, N. C.; Hardy, J.; Salih, D.; Whiting, P.; Ducotterd, F.; Patani, R.; Wray, S.; Arber, C. | Mutations in PSEN1 cause familial Alzheimer's disease with almost complete penetrance. Age at onset is highly variable between different PSEN1 mutations and even within families with the same mutation. Current research into late onset Alzheimer's disease implicates inflammation in both disease onset and progression. PSEN1 is the catalytic subunit of gamma-secretase, responsible for regulated intramembrane proteolysis of numerous substrates that include cytokine receptors. For this reason, we tested the hypothesis that mutations in PSEN1 impact inflammatory responses in astrocytes, thereby contributing to disease progression. Here, using iPSC-astrocytes, we show that PSEN1 is upregulated in response to inflammatory stimuli, and this upregulation is disrupted by pathological PSEN1 mutations. Using transcriptomic analyses, we demonstrate that PSEN1 mutant astrocytes have an augmented inflammatory profile in their basal state, concomitant with an upregulation of genes coding for regulated intramembrane proteolytic and robust activation of JAK-STAT signalling. Using JAK-STAT2 as an example signalling pathway, we show altered phosphorylation cascades in PSEN1 mutant astrocytes, reinforcing the notion of altered cytokine signalling cascades. Finally, we use small molecule modulators of gamma-secretase to confirm a role for PSEN1/gamma-secretase in regulating the astrocytic response to inflammatory stimuli. Together, these data suggest that mutations in PSEN1 enhance cytokine signalling via impaired regulated intramembrane proteolysis, thereby predisposing astrocytic inflammatory profiles. These findings support a two-hit contribution of PSEN1 mutations to fAD pathogenesis, not only impacting APP and Abeta processing but also altering the cellular response to inflammation. | 2024-09-13 | |
Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding | 10.1101/2024.09.09.612073 | Fang, C.; Lindsey, J.; Aronov, D.; Abbott, L.; Chettih, S. N. | Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an "index" --- a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ("barcodes") that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually-appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems. | 2024-09-13 | |
Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding | 10.1101/2024.09.09.612073 | Fang, C.; Lindsey, J.; Abbott, L.; Aronov, D.; Chettih, S. N. | Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an "index" --- a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ("barcodes") that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually-appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems. | 2024-09-14 | |
Modulatory Effects of M3 Muscarinic Acetylcholine Receptor on Inflammatory Profiles of Human Memory T Helper Cells | 10.1101/2024.09.08.611875 | Gholizadeh, F.; Hajiaghayi, M.; Choi, J. S.; Little, S. R.; Rahbari, N.; Brotto, K.; Han, E.; Shih, S. C. C.; Darlington, P. J. | Memory T helper (Th) cells, generated after immunogenic challenge, are crucial in directing the adaptive immune response. Muscarinic ACh receptor (mAChR) subtypes expressed by immune cells can be stimulated with acetylcholine or muscarinic-selective drug oxotremorine-M. Cholinergic signaling can influence immune cells, but it is not known how cholinergic stimuli regulate memory Th cells. This study focused on the role of mAChRs, specifically the M3 muscarinic ACh receptor (M3R), in the cytokine profile and NF-{kappa}B p65 activity of primary human memory Th cells. Memory Th cells (CD3+CD4+CD45RA-CD45RO+) were isolated from healthy participants' peripheral blood. Cell culture was performed with anti-CD3/anti-CD28/anti-CD2 reagent, oxotremorine-M (M1R-M5R agonist), atropine (M1R-M5R antagonist), and J104129 (M3R-selective antagonist). MR1-MR5 genes CHRM1-CHRM5 were measured with RT-qPCR. Protein expression of M3R and phosphorylated NF-{kappa}B p65 were quantified by Western blot. The secretion of IFN-{gamma}, IL-17A, and IL-4 was assessed by ELISA and intracellular cytokine staining flow cytometry. CHRM3, encoding M3R, was knocked out using CRISPR-Cas9 gene targeting. Memory Th cells expressed all five mAChR subtypes. Oxotremorine-M increased IFN-{gamma} and IL-17A while reducing IL-4 in an atropine-sensitive manner. Stimulation of mAChRs in cells with CHRM3-knockout or M3R blockade prevented increases in IFN-{gamma} and IL-17A but continued to inhibit IL-4. mAChR stimulation enhanced NF-{kappa}B p65 activity without affecting cell proliferation, viability, or M3R expression. This investigation demonstrates that muscarinic signaling increases the pro-inflammatory profile of memory Th cells, including NF-{kappa}B p65, IFN-{gamma}, and IL-17A, with a reduction in IL-4. Focusing on M3R blockers could modulate adaptive immune responses and alleviate immune-related conditions. | 2024-09-13 | |
Non-canonical IL-22 receptor signaling remodels the mucosal barrier during fungal immunosurveillance | 10.1101/2024.09.08.611873 | Millet, N.; Sekar, J.; Solis, N. V.; Millet, A.; Aggor, F. E. Y.; Wildeman, A.; Lionakis, M. S.; Gaffen, S. L.; Jendzjowsky, N.; Filler, S. G.; Swidergall, M. | Mucosal barrier integrity is vital for homeostasis with commensal organisms while preventing pathogen invasion. We unexpectedly found that fungal-induced immunosurveillance enhances resistance to fungal outgrowth and tissue invasion by remodeling the oral mucosal epithelial barrier in mouse models of adult and neonatal Candida albicans colonization. Epithelial subset expansion and tissue remodeling were dependent on interleukin-22 (IL-22) and signal transducer and activator of transcription 3 (STAT3) signaling, through a non-canonical receptor complex composed of glycoprotein 130 (gp130) coupled with IL-22RA1 and IL-10RB. Immunosurveillance-induced epithelial remodeling was restricted to the oral mucosa, whereas barrier architecture was reset once fungal-specific immunity developed. Collectively, these findings identify fungal-induced transient mucosal remodeling as a critical determinant of resistance to mucosal fungal infection during early stages of microbial colonization. | 2024-09-13 | |
Wilting Wildflowers and Bummed-Out Bees: Climate Change Threatens U.S. State Symbols | 10.1101/2024.09.08.611901 | Ge, X.; Zou, Y.; Hager, H. A.; Newman, J. A. | Species designated as state symbols in the United States carry cultural importance and embody historical heritage. However, they are threatened by climate change and even face the risk of local or global extinction. The responses of these species to climate change have received little attention. In this study, we examine the effects of climate change on state flowers and insects in the United States by employing correlative species distribution models (SDMs). We select a variety of commonly used SDM algorithms to construct an ensemble forecasting framework aimed at predicting the potential habitats for each species under both historical and future climate scenarios, and how these changes might influence the distributions of state flower and insect species. Our results show that more than half of the state flowers (66%) and insects (51%) are predicted to experience a substantial decrease in regions with favorable climates within the states they represent. Conversely, only a small number (Flowers: 2%; Insects: 10%) are projected to see an increase in habitat suitability in the future. Certain states may no longer possess suitable habitats for their state-designated species. Our findings indicate that cultural heritage might be at risk due to reduced habitat suitability and local extinctions driven by climate change. These findings can provide guidance regarding the protection or replacement of state species to preserve cultural heritage. | 2024-09-13 | |
In multi-strain inoculations, mutation of Medicago symbiosis genes creates a complex selective landscape for naturally-occurring genetic variation in rhizobia | 10.1101/2024.09.11.612462 | Guha, S.; Bledsoe, R. B.; Sutherland, J.; Epstein, B.; Fry, G. M.; Young, N. D.; Tiffin, P.; Burghardt, L. T. | In the mutualism between leguminous plants and rhizobia bacteria, rhizobia live inside root nodules, creating the potential for host genes to shape the rhizobial selective environment. Single-strain screens have identified many host genes influencing symbiosis. However, it's unknown whether these genes influence which rhizobial strains colonize and thrive inside nodules during multi-strain inoculations. In this study, we inoculated 18 Medicago truncatula symbiotic mutants (including mutations that alter NCR peptide production, plant defence, and nodule number regulation) with a mixture of 86 Sinorhizobium meliloti strains. In multi-strain inoculations, most mutations led to reduced host benefits but widely varying effects on host investment and rhizobial benefit (i.e., strain relative fitness), revealing widespread host gene by strain fitness interactions. Genome-wide association studies identify genetic variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations. While most top variants only affected rhizobial fitness when one host gene was disrupted, we identified ten variant groups with pervasive effects across six or more host mutations. These variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and a few metabolic genes. In contrast to the limited-effect variants, variants with pervasive positive effects in mutants tended to adversely affect strain fitness in wild-type hosts. Our results reveal how host symbiosis genes perturb the selective landscape and symbiotic outcomes for rhizobia and set the stage for improving rhizobial inoculants and breeding legume hosts better adapted for multi-strain environments. | 2024-09-13 | |
Mind the polar sun: Solar radiations trigger frequent heat stress in breeding king penguins, despite relatively cool air temperatures. | 10.1101/2024.09.09.611977 | Noiret, A.; Lewden, A.; Lemonnier, C.; Bocquet, C.; Montblanc, M.; Bertile, F.; Hoareau, M.; Marcon, E.; Robin, J.-P.; Viblanc, V. A.; Stier, A. | Polar and sub-polar animals evolved to thrive in cold climates and may thus be particularly vulnerable to the rising temperatures associated with climate change. Polar and sub-polar penguins may be especially vulnerable due to their dual habitat, alternating between foraging in cold waters and breeding/moulting on an increasingly warm land. Here, we characterized heat stress occurrence in breeding king penguins through behavioural observations and subcutaneous body temperature measurements. We show that heat stress is frequent (> 20% of observations at mid-day) in king penguins breeding in the sub-Antarctic region, and that thermoregulatory mechanisms appear insufficient to maintain stable sub-cutaneous temperature. Air temperature alone was a poor predictor of heat stress occurrence, while the combination of high solar radiations, low wind speed and high temperatures was its best predictor. Importantly, reproductive failure occurred on days warmer than average, suggesting potential significant sublethal effects of heat stress being likely to affect population dynamics. | 2024-09-13 | |
Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk | 10.1101/2024.09.07.611794 | Wang, L.; Baek, S.; Prasad, G.; Wildenthal, J.; Guo, K.; Sturgill, D.; Truongvo, T.; Char, E.; Pegoraro, G.; McKinnon, K.; The Pancreatic Cancer Cohort Consortium, ; The Pancreatic Cancer Case-Control Consortium, ; Hoskins, J. W.; Amundadottir, L. T.; Arda, E. | Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies. Despite recent advances, linking enhancer elements to target genes and predicting transcriptional outcomes of enhancer dysfunction remain significant challenges. Using 3D chromatin conformation assays, we generated an extensive enhancer interaction dataset for the human pancreas, encompassing more than 20 donors and five major cell types, including both exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating a quantitative, genome-wide analysis of enhancer connectivity. With these tree models, we developed a machine learning algorithm to estimate the impact of enhancer perturbations on cell type- specific gene expression in the human pancreas. Orthogonal to our computational approach, we perturbed enhancer function in primary human pancreas cells using CRISPR interference and quantified the effects at the single-cell level through RNA FISH coupled with high-throughput imaging. Our enhancer tree models enabled the annotation of common germline risk variants associated with pancreas diseases, linking them to putative target genes in specific cell types. For pancreatic ductal adenocarcinoma, we found a stronger enrichment of disease susceptibility variants within acinar cell regulatory elements, despite ductal cells historically being assumed as the primary cell-of-origin. Our integrative approach -- combining cell type-specific enhancer-promoter interaction mapping, computational models and single-cell enhancer perturbation assays -- produced a robust resource for studying the genetic basis of pancreas disorders. | 2024-09-13 | |
A chromosome level reference genome of Diviners sage (Salvia divinorum) provides insight into salvinorin A biosynthesis | 10.1101/2024.09.08.611878 | Ford, S. A.; Ness, R. W.; Kwon, M.; Ro, D.-K.; Phillips, M. A. | Background: Diviners sage (Salvia divinorum; Lamiaceae) is the source of the powerful hallucinogen salvinorin A (SalA). This neoclerodane diterpenoid is an agonist of the human kappa opioid receptor with potential medical applications in the treatment of chronic pain, addiction, and post-traumatic stress disorder. Only two steps of the approximately twelve step biosynthetic sequence leading to SalA have been resolved to date. Results: To facilitate pathway elucidation in this ethnomedicinal plant species, here we report a chromosome level genome assembly. A high-quality genome sequence was assembled with an N50 value of 41.4 Mb and a BUSCO completeness score of 98.4%. The diploid (2n = 22) genome of ~541 Mb is comparable in size and ploidy to most other members of this genus. Two diterpene biosynthetic gene clusters were identified and are highly enriched in previously unidentified cytochrome P450s as well as crotonolide G synthase, which forms the dihydrofuran ring early in the SalA pathway. Coding sequences for other enzyme classes with likely involvement in downstream steps of the SalA pathway (BAHD acyl transferases, alcohol dehydrogenases, and O-methyl transferases) were scattered throughout the genome with no clear indication of clustering. Differential gene expression analysis suggests that most of these genes are not inducible by methyl jasmonate treatment. Conclusions: This genome sequence and associated gene annotation are among the highest resolution in Salvia, a genus well known for the medicinal properties of its members. Here we have identified the cohort of genes responsible for the remaining steps in the SalA pathway. This genome sequence and associated candidate genes will facilitate the elucidation of SalA biosynthesis and enable an exploration of its full clinical potential. | 2024-09-13 | |
Idiosyncrasy in gestural communication: a case study of hand-clapping in a Barbary macaque (Macaca sylvanus) | 10.1101/2024.09.09.611981 | Bosshard, T. C.; Hirel, M.; Meunier, H.; Fischer, J. | While it is well established that apes invent or individually learn new gestures, cases of development and use of novel gestures in monkeys are more rarely described. We report a case of a novel, idiosyncratic gesture in a Barbary macaque (Macaca sylvanus) at 'La Foret des Singes', Rocamadour, France. One adult male, Jomanix, was observed hand-clapping. To our knowledge, hand-clapping has never been described before in this species. To hand-clap, the male briefly shifted his weight onto his legs, lifted his upper body, and clapped both hands together. We recorded 30 instances of hand-clapping. Twenty-five of these hand-claps occurred in combination with other agonistic signals, such as lunges and open mouth threats. Recipients either responded with counter-aggression (N = 9) or a submissive response (N = 16). In five of the 30 events, the context was unclear. These observations suggest that the gesture constitutes an agonistic signal. According to the staff at 'La Foret des Singes', the hand-clapping may have been copied from staff members who occasionally hand-clap to shoo the animals away from areas where they were not supposed to be, but that notion remains speculative. In the meantime, another subject from the same group reportedly started to hand-clap, but the subject had passed away before we could document the behaviour. The observations show that Jomanix can flexibly combine a novel gesture with other established communicative signals. The hand-clap is goal-directed and fulfils the criteria for first-order intentional communication. This case, as well as anecdotal reports from a Tonkean macaque (Macaca tonkeana) hand-clapping to get attention, reveals greater flexibility in the gestural communication of this genus than previously assumed but also underscores that social learning of the production of communicative gestures occurs rarely in this taxon. | 2024-09-13 | |
Nicotine interacts with DNA lesions induced by alpha radiation which may contribute to erroneous repair in human lung epithelial cells | 10.1101/2024.09.07.611801 | Boroumand, N. | Purpose: Epidemiological studies show that radon and cigarette smoke interact in inducing lung cancer, but the contribution of nicotine in response to alpha radiation emitted by radon is not well understood. Materials and methods: Bronchial epithelial BEAS 2B cells were either pre-treated with 2 uM nicotine during 16 h, exposed to radiation, or the combination. DNA damage, cellular and chromosomal alterations, oxidative stress as well as inflammatory responses were assessed to investigate the role of nicotine in modulating responses. Results: Less {gamma}H2AX foci were detected at 1 h after alpha radiation exposure (1 2 Gy) in the combination group versus alpha radiation alone, whereas nicotine alone had no effect. Comet assay showed less DNA breaks already just after combined exposure, supported by reduced p-ATM, p DNA PK, p p53 and RAD51 at 1 h, compared to alpha radiation alone. Yet the frequency of translocations was higher in the combination group at 27 h after irradiation. Although nicotine did not alter G2 arrest at 24 h, it assisted in cell cycle progression at 48 h post radiation. A slightly faster recovery was indicated in the combination group based on cell viability kinetics and viable cell counts, and significantly using colony formation assay. Pan-histone acetyl transferase inhibition using PU139 blocked the reduction in p p53 and {gamma}H2AX activation, suggesting a role for nicotine-induced histone acetylation in enabling rapid DNA repair. Nicotine had a modest effect on reactive oxygen species induction but tended to increase alpha particle induced pro inflammatory IL 6 and IL 1{beta} (4 Gy). Interestingly, nicotine did not alter gamma radiation induced {gamma}H2AX foci. Conclusions: This study provides evidence that nicotine modulates alpha radiation response by causing a faster but more error prone repair, as well as rapid recovery, which may allow expansion of cells with genomic instabilities. These results hold implications for estimating radiation risk among nicotine users. | 2024-09-13 | |
Inkjet-printed graphene multielectrode arrays: an accessible platform for in vitro cardiac electrophysiology | 10.1101/2024.09.09.611887 | Lumpuy-Castillo, J.; Fu, Y.; Avila, A.; Solodka, K.; Li, J.; Lorenzo, O.; Zeglio, E.; Garma, L. D. | In vitro models have now become a realistic alternative to animal models for cardiotoxicity assessment. However, the cost and expertise required to implement in vitro electrophysiology systems to study cardiac cells poses a strong obstacle to their widespread use. This study presents a novel, cost-effective approach for in vitro cardiac electrophysiology using fully-printed graphene-based microelectrode arrays (pGMEAs) coupled with an open-source signal acquisition system. We characterized the pGMEAs' electrical properties and biocompatibility, observing low impedance values and cell viability. We demonstrated the platform's capability to record spontaneous electrophysiological activity from HL-1 cell cultures, and we monitored and quantified their responses to chemical stimulation with noradrenaline. This study demonstrates the feasibility of producing fully-printed, graphene-based devices for in vitro electrophysiology. The accessible and versatile platform we present here represents a step further in the development of alternative methods for cardiac safety screening. | 2024-09-13 | |
Novae: a graph-based foundation model for spatial transcriptomics data | 10.1101/2024.09.09.612009 | Blampey, Q.; Benkirane, H.; Bercovici, N.; Andre, F.; Cournede, P.-H. | Spatial transcriptomics is advancing molecular biology by providing high-resolution insights into gene expression within the spatial context of tissues. This context is essential for identifying spatial domains, enabling the understanding of micro-environment organizations and their implications for tissue function and disease progression. To improve current model limitations on multiple slides, we have designed Novae (https://github.com/MICS-Lab/novae), a graph-based foundation model that extracts representations of cells within their spatial contexts. Our model was trained on a large dataset of nearly 30 million cells across 18 tissues, allowing Novae to perform zero-shot domain inference across multiple gene panels, tissues, and technologies. Unlike other models, it also natively corrects batch effects and constructs a nested hierarchy of spatial domains. Furthermore, Novae supports various downstream tasks, including spatially variable gene or pathway analysis and spatial domain trajectory analysis. Overall, Novae provides a robust and versatile tool for advancing spatial transcriptomics and its applications in biomedical research. | 2024-09-13 | |
Phylogeny-based selection of representative variants with Navargator: Proof of principle using humoral cross-reactivity data from two immunization studies | 10.1101/2024.09.08.611914 | Curran, D. M.; Ng, D.; Parkinson, J.; Moraes, T.; Gray-Owen, S.; Fegan, J. E. | Background The accessibility to the immune system of bacterial surface proteins makes them attractive targets for subunit vaccines. However, this same property also means they tend to exhibit high sequence variability. Achieving broad cross-protection usually necessitates that antigens from multiple isolates are included, but the choice of sequence variant is a non-trivial problem. Visual inspection of phylogenetic trees is the norm, but this is subjective and can be greatly influenced by the choice of viewing software. This has real-world implications, as groups have shown that the selection of non-optimal antigens likely led to lower cross-protection in the commercially available vaccines against Neisseria meningitidis serogroup B. Aim / Methods To address this problem, we have developed Navargator, bioinformatics software that takes a phylogenetic tree as input and identifies the variants that are the most similar to the greatest number of other sequences. The underlying premise is that cross-reactivity will be correlated with phylogenetic distances extracted from the tree; this was validated by several rodent immunization studies with the proteins transferrin-binding protein B and factor H binding protein from N. meningitidis and N. gonorrhoeae, measuring antibody-based cross-reactivity between an antigen panel using a custom high-throughput ELISA. Results Navargator has been made freely available both as an online tool and as source code for local installation. We implemented several different clustering methods, with exact algorithms for smaller datasets, and heuristics suitable for large trees of thousands of sequences. Our immunization studies have shown that this approach is sound, and that cross-reactivity is predicted well by phylogenetic distances in a sigmoidal manner. Conclusions The complexity of vaccine development rises sharply with each additional antigen included, so using the minimal number required is an important consideration. Navargator attempts to facilitate this in a systematic and generalizable manner. The user can run the analysis by selecting their desired number of representatives, or they can provide any form of cross-reactivity data and have the program identify a minimum reactivity threshold via correlation with the phylogenetic tree. The program will then identify the smallest number of representatives required to satisfy this threshold. | 2024-09-13 | |
G2PDeep-v2: a web-based deep-learning framework for phenotype prediction and biomarker discovery using multi-omics data | 10.1101/2024.09.10.612292 | Zeng, S.; Adusumilli, T.; Awan, S. Z.; Immadi, M. S.; Xu, D.; Joshi, T. | The G2PDeep-v2 server is a web-based platform powered by deep learning, for phenotype prediction and markers discovery from multi-omics data in any organisms including humans, plants, animals, and viruses. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases and other biological processes. The G2PDeep-v2 server is publicly available at https://g2pdeep.org/. | 2024-09-13 | |
BEGAN: Boltzmann-Reweighted Data Augmentation for Enhanced GAN-Based Molecule Design in Insect Pheromone Receptors | 10.1101/2024.09.07.611826 | Dai, J.; Zhang, Y.; Shi, C.; Liu, Y.; Xiu, P.; Wang, Y. | Identifying molecules that bind strongly to target proteins in rational drug design is crucial. Machine learning techniques, such as generative adversarial networks (GAN), are now essential tools for generating such molecules. In this study, we present an enhanced method for molecule generation using objective-reinforced GANs. Specifically, we introduce BEGAN (Boltzmann-Enhanced GAN), a novel approach that adjusts molecule occurrence frequencies during training based on the Boltzmann distribution exp(-{triangleup}U/{tau}), where {triangleup}U represents the estimated binding free energy derived from docking algorithms and {tau} is a temperature-related scaling hyperparameter. This Boltzmann reweighting process shifts the generation process towards molecules with higher binding affinities, allowing the GAN to explore molecular spaces with superior binding properties. The reweighting process can also be refined through multiple iterations without altering the overall distribution shape. To validate our approach, we apply it to the design of sex pheromone analogs targeting Spodoptera frugiperda pheromone receptor SfruOR16, illustrating that the Boltzmann reweighting significantly increases the likelihood of generating promising sex pheromone analogs with improved binding affinities to SfruOR16, further supported by atomistic molecular dynamics simulations. Furthermore, we conduct a comprehensive investigation into parameter dependencies and propose a reasonable range for the hyperparameter {tau}. Our method offers a promising approach for optimizing molecular generation for enhanced protein binding, potentially increasing the efficiency of drug discovery pipelines. | 2024-09-13 | |
Pyjacker identifies enhancer hijacking events in acute myeloid leukemia including MNX1 activation via deletion 7q | 10.1101/2024.09.11.611224 | Sollier, E.; Riedel, A.; Toprak, U. H.; Wierzbinska, J. A.; Weichenhan, D.; Schmid, J. P.; Hakobyan, M.; Touzart, A.; Jahn, E.; Vick, B.; Brown-Burke, F.; Kelly, K.; Kelekci, S.; Pejkovska, A.; Goyal, A.; Baehr, M.; Breuer, K.; Chen, M.-J. M.; Llamazares-Prada, M.; Hartmann, M.; Schoenung, M.; Correia, N.; Trumpp, A.; Abdullah, Y.; Klingmueller, U.; Mughal, S. S.; Brors, B.; Westermann, F.; Schlesner, M.; Vosberg, S.; Herold, T.; Greif, P. A.; Pfeifer, D.; Luebbert, M.; Fischer, T.; Heidel, F.; Gebhard, C.; Walter, W.; Haferlach, T.; Eisfeld, A.-K.; Mrozek, K.; Nicolet, D.; Bullinger, L.; Smee | Acute myeloid leukemia with complex karyotype (ckAML) is characterized by high genomic complexity, including frequent TP53 mutations and chromothripsis. We hypothesized that the numerous genomic rearrangements could reposition active enhancers near proto-oncogenes, leading to their aberrant expression. We developed pyjacker, a computational tool for the detection of enhancer hijacking events, and applied it to a cohort of 39 ckAML samples. Pyjacker identified motor neuron and pancreas homeobox 1 (MNX1), a gene aberrantly expressed in 1.4% of AML patients, often as a result of del(7)(q22q36) associated with hijacking of a CDK6 enhancer. MNX1-activated cases show significant co-occurrence with BCOR mutations and a gene signature shared with t(7;12)(q36;p13) pediatric AML. We demonstrated that MNX1 is a dependency gene, as its knockdown in a xenograft model reduces leukemia cell fitness. In conclusion, enhancer hijacking is a frequent mechanism for oncogene activation in AML. | 2024-09-13 | |
DNA Damage Response Deficiency Enhances Neuroblastoma Progression and Sensitivity to Combination PARP and ATR Inhibition | 10.1101/2024.09.09.612065 | Hayes, M. N.; Cohen-Gogo, S.; Kee, L.; Weiss, A.; Layeghifard, M.; Ladumor, Y.; Valencia-Sama, I.; Rajaselvam, A.; Kaplan, D. R.; Villani, A.; Shlien, A.; Morgenstern, D. R.; Irwin, M. S. | Next generation sequencing of neuroblastoma (NB) tumors have revealed frequent somatic and germline genetic alterations in genes encoding proteins involved in DNA damage response (DDR) pathways. Despite being well-studied in many adult cancers, roles for DDR disruption in pediatric solid tumors remains poorly understood. To address this, patient-relevant loss-of-function mutations in DDR pathway components including Brca2, Atm, and Palb2 were incorporated into an established zebrafish MYCN transgenic model (Tg(dbh:EGFP-MYCN)). These mutations were found to enhance NB formation and metastasis in vivo, and result in upregulation of proliferation, cell cycle checkpoint and DNA damage repair transcriptional signatures, revealing potential molecular vulnerabilities in DDR-deficient NB. Zebrafish DDR-deficient NB and human NB cells with DDR protein knock-down were sensitive to the poly(ADP-ribose)-polymerase (PARP) inhibitor olaparib, and this effect was further enhanced by inhibition of the ataxia telangiectasia and rad3 related (ATR) kinase. Altogether, our data supports a functional role for DDR-deficiency in NB in vivo and therapeutic potential for combination PARP + ATR inhibition in NB patients with alterations in DDR genes. | 2024-09-13 | |
High-efficiency discovery and structure-activity-relationship analysis of non-substrate-based covalent inhibitors of S-adenosylmethionine decarboxylase | 10.1101/2024.09.07.611751 | Ai, Y.; Xu, S.; Zhang, Y.; Liu, Z.; Liu, S. | Targeted covalent inhibitors (TCIs) form covalent bonds with targets following initial non-covalent binding. The advantages of TCIs have driven a resurgence in rational TCI design over the past decade, resulting in the approval of several blockbuster covalent drugs. To support TCI discovery, various computational methods have been developed. However, accurately predicting TCI reactivity remains challenging due to interference between non-covalent scaffolds and reactive warheads, leading to inefficiencies in computational screening and high experimental costs. In this study, we enhanced the SCARdock protocol, a validated computational screening tool developed by our lab, by incorporating quantum chemistry-based warhead reactivity calculations. By integrating these calculations with non-covalent docking scores, docking ranks, and bonding-atom distances, non-covalent and covalent inhibitors of S-adenosylmethionine decarboxylase (AdoMetDC) were correctly classified. Using the optimized SCARdock, we successfully identified twelve new AdoMetDC covalent inhibitors from 17 compounds, achieving a 70.6% hit rate. From these novel inhibitors, we analyzed the contributions of non-covalent interactions and covalent bonding, enabling a structure-activity relationship (SAR) analysis for AdoMetDC covalent inhibitors, which was previously unexplored with substrate-based inhibitors. Overall, this work presents an efficient computational protocol for TCI discovery and offers new insights into AdoMetDC inhibitor design. We anticipate that this approach will stimulate TCI development by improving computational screening efficiency and reducing experimental costs. | 2024-09-13 | |
Aging-associated vacuolation of multi-ciliated cells in the distal mouse oviduct reflects unique cell identity and luminal microenvironment | 10.1101/2024.09.07.611808 | Harwalkar, K.; Yamanaka, N.; Pacis, A. S.; Zhao, S.; Teng, K.; Pitman, W.; Taskar, M.; Lynn, V.; Thornton, A. F.; Ford, M. J.; Yamanaka, Y. | The female reproductive organs present with the earliest aging characteristics, such as a decline in fertility and estrous cyclicity. While age-related changes in the ovary are well-documented, it is unclear if any age-associated changes occur in the other female reproductive organs, such as the oviduct/fallopian tube. The recent recognition of the distal end of the fallopian tube as the tissue of origin of high-grade serous tubal ovarian carcinomas (HGSCs), and that its patient demographic is strongly biased to postmenopausal women, motivated us to investigate age-associated changes in this organ. At the distal end of aged oviducts in mice, we found vacuolated multi-ciliated cells (MCCs) with a severely apically displaced and deformed nucleus. This phenotype was unique to the distal oviduct epithelium - infundibulum (INF) and ampulla (AMP). Ovariectomy did not affect the timeline of MCC vacuolation, suggesting little involvement of ovulation and hormonal regulation. MCC vacuolation was induced in hypoxia or hydroxyurea treatments in in vitro organotypic culture of all oviduct regions, not limited to the INF/AMP epithelium. This suggests high oxygen demand in MCCs, compared to other cell types, and a uniquely stressed INF/AMP epithelial microenvironment in vivo. We found that the blood circulation of INF/AMP depended on the ovarian artery, different from the rest of the oviduct epithelium and its circulation declined along with ovarian activities. We conclude that a decline in local blood circulation and distinct cellular identity of the INF/AMP epithelium caused age-associated MCC vacuolation, reflecting its mild, chronically stressed microenvironment. | 2024-09-13 | |
Downy mildew effector HaRxL106 interacts with the transcription factor BIM1 altering plant growth, BR signaling and susceptibility to pathogens | 10.1101/2024.09.09.612066 | Bogino, M. F.; Senz, J. M. L.; Kourdova, L. T.; Tamagnone, N.; Romanowski, A.; Wirthmueller, L.; Fabro, G. | Hyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen that causes downy mildew disease on Arabidopsis. This obligate biotroph manipulates the homeostasis of its host plant by secreting numerous effector proteins, among which are the RxLR-effectors. Identifying the host targets of effectors and understanding how their manipulation facilitates colonization of plants is key to improve plant resistance to pathogens. Here we characterize the interaction between the RxLR effector HaRxL106 and BIM1, an Arabidopsis transcription factor (TF) involved in Brassinosteroid (BR) signaling. We report that HaRxL106 interacts with BIM1 in vitro and in planta. BIM1 is required by the effector to increase the host plant susceptibility to (hemi)biotrophic pathogens, and thus can be regarded as a susceptibility factor. Mechanistically, HaRxL106 requires BIM1 to induce the transcriptional activation of BR-responsive genes and cause alterations in plant growth patterns that phenocopy the shade avoidance syndrome. Our results support previous observations of antagonistic interactions between activation of BR signaling and suppression of plant immune responses and reveal that BIM1, a new player in this crosstalk, is manipulated by the pathogenic effector HaRxL106. | 2024-09-13 | |
The Arabidopsis histone H3K4me3-binding ALFIN-like proteins mediate histone H2A ubiquitination and coordinate diverse chromatin modifications | 10.1101/2024.09.12.612777 | Su, X.-M.; Yuan, D.-Y.; Li, L.; Yang, M.; Chen, S.; Zhou, Y.; He, X.-J. | The histone H3K4 trimethylation (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications remains poorly understood in plants. In this study, we find that the Arabidopsis thaliana H3K4me3-binding ALFIN-LIKE (AL) proteins are associated with H3K4me3-enriched genes at the whole-genome level. The AL proteins contain a C-terminal PHD finger, which has a conserved role in recognizing H3K4me3, and a PHD-associated AL (PAL) domain, which is responsible for binding to diverse chromatin-related proteins. We demonstrate that the AL proteins not only act as subunits of the Polycomb repressive complex 1 (PRC1) to mediate H2A ubiquitination at H3K4me3-enriched genes but also interact with a variety of other chromatin-related proteins. Furthermore, we elucidate the mechanisms by which AL proteins interact with other chromatin-associated proteins to integrate H3K4me3, H2A ubiquitination, H2A.Z deposition, H3K27 demethylation, and chromatin accessibility across the genome. These findings underscore the critical role of AL proteins in linking H3K4me3 with a variety of other chromatin modifications in plants. | 2024-09-13 | |
Leveraging large language models for metabolic engineering design | 10.1101/2024.09.09.612023 | Li, X.; Liang, Z.; Guo, Z.; Liu, Z.; Wu, K.; Luo, J.; Zhang, Y.; Liu, L.; Sun, M.; Huang, Y.; Tang, H.; Chen, Y.; Yu, T.; Nielsen, J.; Li, F. | Establishing efficient cell factories involves a continuous process of trial and error due to the intricate nature of metabolism. This complexity makes predicting effective engineering targets a challenging task. Therefore, it is vital to learn from the accumulated successes of previous designs for advancing future cell factory development. In this study, we developed a method based on large language models (LLMs) to extract metabolic engineering strategies from research articles on a large scale. We created a database containing over 29006 metabolic engineering entries, 1210 products and 751 organisms. Using this extracted data, we trained a hybrid model combining deep learning and mechanistic approaches to predict engineering targets. Our model outperformed traditional metabolic engineering target prediction algorithms, excelled in predicting the effects of gene modifications, and generalized well to out-of-distribution products and multiple gene combinations. Our study provides a valuable dataset, a chatbot, and an engineering target prediction model for the metabolic engineering field and exemplifies an efficient method for leveraging existing knowledge for future predictions. | 2024-09-13 | |
Trace Elements in Fish: Assessment of bioaccumulation and associated health risks. | 10.1101/2024.09.08.611911 | Naz, S.; Ullah, Q.; Fouad, D.; Qadeer, A.; Lateef, M.; Hassan, M. W.; Chatha, A. M. M. | Industrial and agricultural water run-off are polluting the aquatic ecosystem by depositing different toxic trace elements (TTEs) in riverine system. It has become a global concern impacting not only the well-being of aquatic organisms but human health as well. Current study evaluated the impact of four TTEs (Cadmium (Cd), copper (Cu), lead (Pb), and nickel (Ni)) in three organs (liver, gills, and muscles) of five fish species viz, Rita rita, Sperata sarwari, Wallago attu, Mastacembelus armatus, and Cirrhinus mrigala collected from right and left banks of Punjnad headworks during winter, spring and summer. We investigated accumulation (mg/kg) of these TTEs in fish in addition to the human health risk assessment by estimating exposure hazards, hazardous index (THQ and TTHQ) and metal pollution index (MPI). The obtained results showed that W. attu accumulated significantly more TTEs (p < 0.00) as compared to other fish. Among seasons, summer had significantly more (p < 0.00) accumulation of TTEs than other seasons. Lead (Pb) accumulation was highest across TTEs in fish liver as compared to gills and muscles. Right bank showed higher accumulation (p < 0.00) of all TTEs in all fish species in contrast to the left bank. The human health risk assessment showed that Cd and Pb had higher exposure levels than Cu and Ni. Furthermore, the THQ was in the order of Cd > Pb > Ni > Cu. All fish species had THQ 1 for Cd and Pb and TTHQ > 1 for all fish. MPI index showed moderate to high level of TTE contamination if all fish species. The study concluded that right bank has higher metal accumulation than left bank. However, fish consumption from both of the study site was not safe for human consumption. | 2024-09-13 | |
Effects of fasting on heat-stressed broiler chickens: part I- growth performance, meat quality, gut histomorphological and microbial responses | 10.1101/2024.09.08.611910 | Ahmed, T.; Hashem, M. A.; Afrin, A.; Lahiry, A.; Rahman, S.; Bungo, T.; Das, S. C. | The current study aimed to optimize the fasting duration in order to mitigate the detrimental effects of heat stress on broilers raised in hot and humid climatic environments. A total of 500 broiler DOCs were assigned to five distinct treatment groups: T0= Non-fasted controlled temperature (24-26 oC) (NF-CT), T1= Non-fasted heat stressed (30-38 oC) (NF-HS), T2= 6 hours fasted heat stressed (6-h FHS), T3= 8 hours fasted heat stressed (8-h FHS), and T4= 10 hours fasted heat stressed (10-h FHS). Each treatment was replicated five times, with 20 birds in each replicate group. As expected, the birds in NF-CT group showed significantly better performances for all the growth parameters, although birds who fasted for 8-h under heat stress exerted better growth and FCR in comparison to the other HS groups. Fasting of birds under heat stress significantly showed the lowest mortality. Like the NF-CT group, birds in 8-h FHS achieved significantly higher dressing percentage, breast meat, liver yields, and the lowest abdominal fat. Fasting for 8- and 10-h significantly increased breast meat pH and water holding capacity and thus reduced cooking loss. Fasting also improved the breast meat color quality by increasing redness (a*) and reducing the hue angle values comparable with the NF-CT group. A significantly upward trend in villi height (VH), width (VW) and crypt depth (CD) of gut segments was also observed in the birds of the 8-h FHS group. Total bacterial and coliform counts in cecum contents were reduced significantly with the increase in the fasting period. Benefit-cost analysis showed better profitability in the 8-h FHS group than other HS groups. Taken altogether, it can be concluded that broiler chicken exposed to 8-h fasting period is an effective approach to mitigate heat stress under hot and humid climatic conditions. | 2024-09-13 | |
The neurotrophin artemin and its receptor GFRα3 mediate migraine-like pain via the ion channel TRPM8 | 10.1101/2024.09.09.611532 | Yang, C.; Wei, C.; Alam, S.; Chen, X.; McKemy, D. D. | Background Migraine has a strong genetic foundation, including both monogenic and polygenic types. The former are rare, with most migraine considered polygenic, supported by genome-wide association studies (GWAS) identifying numerous genetic variants associated with migraine risk. Surprisingly, some of the most common mutations are associated with TRPM8, a non-selective cation channel that is the primary sensor of cold temperatures in primary afferent neurons of the somatosensory system. However, it is unlikely that the temperature sensitivity of TRPM8 underlies its role in migraine pathogenesis. To define the basis of the channels involvement, we reasoned that cellular processes that increase cold sensitivity in the skin, such as the neurotrophin artemin, via its receptor GFR3, also mediate TRPM8-associated migraine-like pain in the meninges. Methods To investigate the role of artemin and GFR3 in preclinical rodent migraine models, we infused nitroglycerin acutely and chronically, and measured changes in periorbital and hind paw mechanical sensitivity in male and female mice lacking GFR3, after neutralization of free artemin with specific monoclonal antibodies, or by systemic treatment with a TRPM8-specific antagonist. Further, in wildtypes and mice lacking either GFR3 or TRPM8, we tested the effects of supradural infusions of a mix of inflammatory mediators, artemin, and a TRPM8-specific agonist on migraine-related pain in mice. Results We find that mechanical allodynia induced by systemic nitroglycerin, or supradural infusion of inflammatory mediators, involves GFR3. In addition, neutralization of circulating artemin reduces the nitroglycerin phenotype, demonstrating the importance of this neurotrophic pathway. Further, we show TRPM8 expression in the meninges and that direct supradural infusion of either a TRPM8-specific agonist or artemin itself produces mechanical allodynia, the latter dependent on TRPM8 and ameliorated by concurrent treatment with sumatriptan. Conclusions These results indicate that neuroinflammatory events in the meninges can produce migraine-like pain in mice via artemin and GFR3, likely acting upstream of TRPM8, providing a novel pathway that may contribute to migraine pathogenesis. | 2024-09-13 | |
Sex differences in contextual fear expression are associated with altered medial prefrontal cortex activity | 10.1101/2024.09.07.611834 | Vazquez, K.; Parsons, R. G. | Understanding the neural basis of fear expression in rodents has implications for understanding pathological fear responses that characterize posttraumatic stress disorder. Even though posttraumatic stress disorder is more common in females, little is known about the neural circuit interactions supporting fear expression in female rodents. In this study, we were interested in determining whether neural activity associated with the expression of contextual fear differed between males and females within the projections from the medial prefrontal cortex to the ventrolateral periaqueductal gray, and in the medial prefrontal cortex in neurons that do not project to the periaqueductal gray. We infused a viral retrograde tracer into the ventrolateral periaqueductal gray in male and female rats and trained them in a contextual fear conditioning task. The following day rats were re-exposed to the conditioning context and were sacrificed shortly thereafter. Neural activity was measured using EGR1 immunofluorescence. The behavioral results showed that males exhibited higher levels of freezing during the context test than females. Male rats that underwent training and testing showed an increase in the proportion of viral infected cells that express EGR1 in the PL compared to rats that had only received context exposure. Trained female rats were not different than controls, however a direct comparison between sexes was not different. In cells not labeled by the tracer, males showed higher levels of fear-induced EGR1 expression in the prelimbic cortex than females. Conversely, females showed higher levels of EGR1 expression in the infralimbic cortex following testing as compared to males. These results suggest that sex differences in the expression of contextual fear may involve differences in the relative activity levels of the prelimbic and infralimbic cortex. | 2024-09-13 | |
Population coding of auditory space in the dorsal inferior colliculus persists with altered binaural cues | 10.1101/2024.09.13.612867 | Rogalla, M. M.; Quass, G. L.; Yardley, H.; Martinez-Voigt, C.; Ford, A. N.; Wallace, G.; Dileepkumar, D.; Corfas, G.; Apostolides, P. F. | Sound localization is critical for real-world hearing, such as segregating overlapping sound streams. For optimal flexibility, central representations of auditory space must adapt to peripheral changes in binaural cue availability, such as following asymmetric hearing loss in adulthood. However, whether the mature auditory system can reliably encode spatial auditory representations upon abrupt changes in binaural input is unclear. Here we use 2-photon Ca2+ imaging in awake head-fixed mice to determine how the higher-order shell layers of the inferior colliculus (IC) encode sound source location in the frontal azimuth, under binaural conditions and after acute monaural hearing loss induced by an ear plug ipsilateral to the imaged hemisphere. Spatial receptive fields were typically broad and not exclusively contralateral: Neurons responded reliably to multiple positions in the contra- and ipsilateral hemifields, with preferred positions tiling the entire frontal azimuth. Ear plugging broadened receptive fields and reduced spatial selectivity in a subset of neurons, in agreement with an inhibitory influence of ipsilateral sounds. However ear plugging also enhanced spatial tuning and/or unmasked receptive fields in other neurons, shifting the distribution of preferred angles ipsilaterally with minimal impact on the neuronal population's overall spatial resolution; these effects occurred within 2 hours of ear plugging. Consequently, linear classifiers trained on fluorescence data from control and ear-plugged conditions had similar classification accuracy when tested on held out data from within, but not across hearing conditions. Spatially informative neuronal population codes therefore arise rapidly following monaural hearing loss, in absence of overt experience. | 2024-09-13 | |
Differential Impact of Multiple Sensory Deprivation on Spatial-coding Cells in Medial Entorhinal Cortex | 10.1101/2024.09.09.611946 | Tian, J.; Wen, S.; Zhou, Y.; Yao, S.; Zhang, X.; Miao, C. | Spatial navigation depends on anchoring internal spatial maps to external environments, guided by sensory cues such as visual and tactile stimuli. The Medial Entorhinal Cortex (MEC) is crucial for integrating these sensory inputs during the formation of spatial maps. While the responsiveness of many spatial-coding cells to visual stimuli is well-established, the role of tactile sensation in spatial representation is less understood. Rodents primarily gather tactile information through their whiskers, which provide essential spatial and textural details via whisking movements, potentially vital for constructing accurate spatial map. In our study, we employed advanced miniature two-photon microscopy to monitor neural activity in the MEC of freely moving mice subjected to sensory deprivation. Our findings revealed that head direction cells and border cells exhibited impaired spatial representation after either light deprivation or whisker trimming. In contrast, grid cells and speed cells were less affected by whisker trimming compared to visual deprivation, suggesting a stronger dependence on visual cues for these cell types. Notably, distinct subpopulations within each type of spatial-coding cell exhibited varying sensitivity to sensory deprivation-some neurons significantly changed their spatial-coding patterns, while others remained unaffected. This indicates that cells within the MEC may differ in their spatial-coding based on their sensitivity to external sensory inputs. Additionally, we observed a strong correlation between the activity of certain MEC neurons and whisker movement. Collectively, these findings enhance our understanding of how the MEC processes spatial information, particularly in relation to tactile sensation. | 2024-09-13 | |
Burst firing optimizes invariant coding of natural communication signals by electrosensory neural populations | 10.1101/2024.09.09.611671 | Metzen, M. G.; Akhshi, A.; Bashivan, P.; Khadra, A.; Chacron, M. J. | Accurate perception of objects within the environment independent of context is essential for the survival of an organism. While neurons that respond in an invariant manner to identity-preserving transformations of objects are thought to provide a neural correlate of context-independent perception, how these emerge in the brain remains poorly understood. Here we demonstrate that burst firing in neural populations can give rise to an invariant representation of highly heterogeneous natural communication stimuli. Multi-unit recordings from central sensory neural populations showed that considering burst spike trains led to invariant representations at the population but not the single neuron level. Computational modeling further revealed that optimal invariance is achieved for levels of burst firing seen experimentally. Taken together, our results demonstrate a novel function for burst firing towards establishing invariant representations of sensory input in neural populations. | 2024-09-13 | |
Virally encoded single-chain antibody fragments targeting alpha-synuclein protect against motor impairments and neuropathology in a mouse model of synucleinopathy | 10.1101/2024.09.09.612044 | Castonguay, A.-M.; Morin, B.; Parent, M.; Durcan, T. M.; Luo, W.; Shlaifer, I.; Julien, J.-P.; Gravel, C.; Levesque, M. | Parkinson's disease (PD) is a neurodegenerative disorder mainly characterized by the loss of dopaminergic neurons from the substantia nigra. Affected neurons exhibit intracellular aggregates primarily composed of misfolded and phosphorylated alpha-synuclein (aSyn). In pathological conditions, this presynaptic protein has been shown to be transmitted from cell to cell in a prion-like manner, which contributes to the progression of the disease. Single-chain variable fragments (scFvs) are small polypeptides derived from the binding domains of antibodies that are less immunogenic and have better tissue penetration compared to full antibodies. In this work, we aimed to demonstrate the potential of extracellular scFvs to slow down the propagation of pathological aSyn in an in vivo model of synucleinopathy. We generated scFvs that target aSyn, and tested two of them in a PD mouse model consisting of transgenic M83 mice injected with human aSyn pre-formed fibrils (PFFs). The sequence encoding each anti-aSyn scFv was cloned in a self-complementary AAV2 viral vector, and purified particles were administered intravenously. CNS expression of either scFv protected against the development of paralysis and limb weakness, in addition to significantly reducing pathologic aggregates of phosphorylated aSyn in the brain. Moreover, in vitro results in human iPSCs-derived dopaminergic neurons suggest that the scFvs can mitigate aSyn spreading by preventing its internalization. Overall, our findings demonstrate that single-chain antibody fragments exhibit strong therapeutic potential in a preclinical mouse model. Thus, our minimally invasive, gene-mediated immunotherapy approach has the potential to serve as an effective treatment for halting the progression of Lewy body diseases. | 2024-09-13 | |
IL-1b-mediated Immunometabolic Adaptation in Corneal Epithelial Cells | 10.1101/2024.09.08.611874 | Sanches, J. M.; Ramachandran, R. A.; Mussi, N.; Baniasadi, H.; Robertson, D. M. | Purpose: As an external mucosal surface, the corneal epithelium is subject to a barrage of stressors that are known to trigger inflammation. IL-1b, a master regulator of inflammation, is secreted into the preocular tear film by ocular surface epithelial cells and infiltrating immune cells. While increased levels of IL-1b have been associated with corneal disease, the effects of IL-1b on mitochondrial function in corneal epithelial cells (CECs) is unknown. Methods: To investigate the effects of IL-1b on mitochondrial function, telomerase immortalized human CECs were cultured in either 50 ng/mL or 100 ng/mL IL-1b for short term (24 hours) or prolonged (72 hours) time periods. Cells were assessed for ROS, inflammatory cytokine production, mitochondrial polarization and ultrastructure, mitophagy, and changes in the metabolite composition. Lipid drops were examined using light and fluorescent microscopy. Results: Short term exposure to IL-1b triggered an increase in IL-8 and ROS levels that corresponded to a reduction in mitochondrial membrane potential. Long term exposure also showed increased levels of IL-8 and IL-6 and further increased ROS. After long term exposure however, there was a paradoxical increase in mitochondrial membrane potential that was associated an increase in spare respiratory capacity and mitochondrial hyperfusion. Metabolomics confirmed an upregulation of the pentose phosphate pathway and the TCA cycle. Fumarate was also increased, suggesting an increase in flux through complex II. Changes in lipid metabolism included an upregulation in cardiolipin and de novo triacylglyceride biosynthesis, along with increasing numbers of lipid droplets. Conclusion: Prolonged exposure to IL-1b induces metabolic rewiring in CECs that results in an increase in spare respiratory capacity. These findings suggest that the corneal epithelium is able to adapt to certain levels of chronic inflammation and may have important implications in our understanding of immune tone and cellular stress responses in ocular surface epithelia. | 2024-09-13 | |
Meningococcal vaccine Bexsero elicits a robust cellular immune response that targets but is not consistently protective against Neisseria gonorrhoeae during murine vaginal infection | 10.1101/2024.09.08.611931 | Zeppa, J. J.; Fegan, J. E.; Maiello, P.; Islam, E. A.; Lee, I. S.; Pham, C.; Caruso, L.-L.; Gray-Owen, S. D. | Retrospective epidemiological studies suggest that the licensed serogroup B meningococcal vaccine 4CMenB (Bexsero) provides some protection against the closely related pathogen Neisseria gonorrhoeae in humans. This result has been replicated in murine models of gonococcal colonization, with a gonococci-reactive humoral response and more rapid clearance of vaginal infection. However, immunization with Bexsero consistently elicits a robust humoral response but does not protect all individuals, so the correlates of protection remain undefined. Herein, we exploit the fact that Bexsero promotes clearance in only a subset of immunized mice to perform a broad analysis of the adaptive response in animals that are or are not protected. We observe that Bexsero vaccination induces high levels of anti-neisserial antibodies in both serum and the vaginal lumen, and a robust cellular response highlighted by an increase in both conventional naive and memory populations as well as unconventional lymphocyte subsets. Multiplex and flow cytometry results show that Bexsero vaccination generates a robust, multi-faceted cytokine response that spans numerous T cell subsets (TH1, TH2, Treg and TH17 responses) and that non-T non-B lymphocytes play an important role in this response, as indicated by an unbiased principal component analysis. Together, this work provides the first comprehensive analysis of the robust humoral and complex cellular response to Bexsero so as to reveal the effector mechanisms that may contribute to immunity against vaginal gonococcal infection. | 2024-09-13 | |
IFT and BBSome proteins are required for Leishmania mexicana pathogenicity, but flagellar motility is dispensable | 10.1101/2024.09.13.612850 | Beneke, T.; Neish, R.; Catta-Preta, C. M. C.; Smith, J.; Valli, J.; McCoy, C. J.; Albuquerque-Wendt, A.; Mottram, J. C.; Gluenz, E. | Protists of the order Kinetoplastida possess a single multifunctional flagellum, which powers cellular displacement and mediates attachment to tissues of the arthropod vector. The kinetoplastid flagellar cytoskeleton consists of a nine-microtubule doublet axoneme; further structural elaborations, which can vary between species and life cycle stages, include the assembly of axonemal dynein complexes, a pair of singlet microtubules and the extra-axonemal paraflagellar rod. The intracellular amastigote forms of Leishmania spp. build a short, non-motile cilium whose function has remained enigmatic. Here we used a panel of 25 barcoded promastigote cell lines, including mutants lacking genes encoding flagellar assembly proteins, cytoskeletal proteins required for normal motility, or flagellar membrane proteins to examine how these defects impact on their virulence in macrophages and mice. Mutants lacking intraflagellar transport (IFT) protein 88 were severely attenuated indicating that assembly of a flagellum is necessary to allow for Leishmania survival in a mammalian host. A similarly severe loss of virulence was observed upon deletion of BBS2, a core component of the BBSome complex, which may act as a cargo adapter for IFT. By contrast, promastigotes that were unable to beat their flagella due to loss of PF16 could establish an infection and only showed a small reduction of parasite burden in vivo compared to the parental cell lines. These results confirm that flagellar motility is not necessary for mammalian infection but flagellum assembly and the integrity of the BBSome are essential for pathogenicity. | 2024-09-13 | |
Cost-benefit analysis across smallholder rice farmers reveals that existing fertilization practices severely compromise their income | 10.1101/2024.09.10.612194 | Chen, J.; Mola, M.; Liu, X.; Lee, T. M.; Monokrousos, N.; Veresoglou, S. D. | Modernizing agricultural practices of smallholder farmers can increase considerably global food produce. Smallholder farmers are, nevertheless, often unwilling to adopt practices unfamiliar to them. Increases in the cost of fertilizers, can nonetheless render existing practices unsustainable, raising concerns of food injustice. We addressed here the potential to which we can increase yield through popularizing existing best practice agricultural approaches. We worked over a network of 40 smallholder farmers in the Danxia Mountain region, Guangdong province, China. We divided them into two crop-rotation treatments and gave them the freedom to implement agricultural management practices the way they usually do. We subsequently clustered them into three groups based on the management history. Over the final growth season, on which the clustering was based, there was an over 30% increase in crop yield between the most and the least efficient clusters. More importantly we show that the use of fertilizers not only did not promote rice production but it also had adverse effects. We finally present a cost-benefit analysis. Through familiarizing of the smallholder farmers` existing management practices, policy makers could make integrating new farming guidelines easier to adopt than purely dishing out modern farming practice recommendations. We thus propose that any attempts to transition agricultural practices should involve the extensive monitoring of existing practices at the very beginning. This should effectively close existing yield gaps in relation to industrial farmers. | 2024-09-13 | |
Apparent timescaling of fossil diversification rates is caused by sampling bias | 10.1101/2024.09.11.612481 | Reijenga, B. R.; Close, R. A. | Negative scaling relationships between both speciation and extinction rates on the one hand, and the age or duration of organismal groups on the other, are pervasive and recovered in both molecular phylogenetic and fossil time series. The consistency between molecular and fossil data hints at a universal cause, and potentially to incongruence between micro- and macroevolution. However, the existence of negative rate scaling in fossil time series has not undergone the same level of scrutiny as in molecular data. Here, we analyse the marine fossil record across the last ~535 Ma of the Phanerozoic to investigate the presence and strength of negative rate scaling. We find that negative rate scaling arises under commonly applied age range-based per-capita rates, which do not control for sampling bias, but are severely reduced or absent when metrics are used that do correct for sampling. We further show by simulation that even moderate incomplete sampling of species occurrences through time may induce rate scaling. We thus conclude that there are no significant scaling relationships present in these fossil clades, and that any apparent trend is caused by taxonomic practices and sampling artefacts. If rate scaling appears genuinely in molecular phylogenies, the absence of such a relationship in the fossil record will provide a valuable benchmark and constraint on what processes can cause it. | 2024-09-13 | |
Caves as species pumps: key innovations, isolation, and periodic introgression drive the world's largest cavefish radiation in a dynamic karstic landscape | 10.1101/2024.09.12.612638 | Mao, T.; Liu, Y.; Vasconcellos, M. M.; Zhou, S.; Ellepola, G.; Yang, J.; Pie, M. R.; Meegaskumbura, M. | Species diversification is shaped by intricate interactions among biotic drivers, including gene flow, hybridization, and key innovations, and abiotic drivers, such as historical climate change, geological events, and ecological opportunity. However, the relative contributions of these drivers in large radiations remain poorly understood. We investigate the interplay among these factors in the diversification of Sinocyclocheilus, a cavefish radiation comprising 79 species. Sinocyclocheilus include typical surface-dwelling forms, with well-developed eyes and pigmentation, to cave-dwelling forms with regressed eyes, reduced pigmentation, and the presence of a horn and a hump. Using reduced representation genomic data (RADseq), we show extensive gene flow events across different species, with introgression playing a key role compared to incomplete lineage sorting in creating phylogenetic discordance and contributing genetic variation for cave adaptation and diversification in this group. Key traits such as eye degeneration, reduced pigmentation, and horn evolved independently multiple times, as adaptations for effectively exploiting cave environments. Furthermore, the uplift of the Tibetan plateau and the late Miocene cooling also significantly impacted speciation rates. Demographic analyses suggest population expansions during the Gonghe Movement and stability during the Last Glacial Maximum, possibly due to cave refugia. Periodic events of introgression promoted by isolation and reconnections due to the changing climate and geological activity, combined with the repeated evolution of key cave-adapted traits, are the primary drivers of this radiation. Our findings underscore the complex interplay of biotic and abiotic factors in the evolution of Sinocyclocheilus fish, offering new insights into the mechanisms of cave adaptation and diversification. | 2024-09-13 | |
A Newborn F-box Gene Blocks Gene Flow by Selectively Degrading Phosphoglucomutase in Species Hybrids | 10.1101/2024.09.11.612556 | Xie, D.; Ma, Y.; Ye, P.; Liu, Y.; Ding, Q.; Huang, G.; Felix, M.-A.; Cai, Z.; Zhao, Z. | The establishment of reproductive barriers such as postzygotic hybrid incompatibility (HI) remains the key to speciation. Gene duplication followed by differential functionalization has long been proposed as a major model underlying HI, but few supporting evidence exists. Here, we demonstrate that a new-born F-box gene, Cni-neib-1, of the nematode Caenorhabditis nigoni specifically inactivates an essential phosphoglucomutase encoded by Cbr-shls-1 in its sister species C. briggsae and their hybrids. Zygotic expression of Cni-neib-1 specifically depletes Cbr-SHLS-1, but not Cni-SHLS-1, in approximately 40 minutes starting from gastrulation, causing embryonic death. Cni-neib-1 is one of thirty-three paralogues emerging from a recent surge in F-box gene duplication events within C. nigoni, all of which are evolving under positive selection. Cni-neib-1 undergoes turnover even among C. nigoni populations. Differential expansion of F-box genes between the two species could reflect their distinctive innate immune responses. Collectively, we demonstrate how recent duplication of genes involved in protein degradation can cause unintended destruction of targets in hybrids that leads to HI, providing an invaluable insight into mechanisms of speciation. | 2024-09-13 | |
Strong Selection, but low repeatability: Temperature-specific effects on genomic predictions of adaptation | 10.1101/2024.09.12.612579 | Rego, A.; Baur, J.; Girard-Tercieux, C.; de la Paz Celorio-Mancera, M.; Stelkens, R.; Berger, D. | Evolution should be more predictable when natural selection is strong and favors the same outcome. Climate warming is increasing temperatures beyond the optima of many ectotherms, which, due to the inherent non-linear relationship between temperature and the rate of cellular processes, is predicted to impose stronger selection compared to corresponding shifts toward cold temperatures. This suggests that adaptation to climate warming should be relatively predictable. Here, we tested this hypothesis from the level of single-nucleotide polymorphisms to life-history traits, by conducting an evolve-and-resequence experiment on three genetic backgrounds of the seed beetle, Callosobruchus maculatus. Indeed, phenotypic evolution was faster and more repeatable at hot, relative to cold, temperature. However, at the genomic level, adaptation to heat was less repeatable than to cold, especially when comparing responses between backgrounds. As a result, genomic predictions of phenotypic (mal)adaptation in populations exposed to hot temperature were highly accurate within, but inaccurate between, genetic backgrounds. These results seem best explained by an increased importance of epistasis during adaptation to heat and imply that the same biophysical mechanisms that increase the repeatability of phenotypic evolution by exerting strong selection at hot temperature, reduce repeatability at the genome level. Thus, predictions of adaptation in key phenotypes from genomic data may become increasingly difficult as climates warm. | 2024-09-13 | |
Somatic evolution of cancer genes in sex chromosomes | 10.1101/2024.09.11.612525 | Marco, A.; Akachukwu, A. C.; Ratcliff, J. S. | Genes on sex chromosomes have higher evolutionary rates than those on autosomes. However, this does not necessarily apply to somatic evolution in cancer. Many dominant mutations have been described in the so-called proto-oncogenes (OGs), while recessive mutations are typically described in tumor-suppressor genes (TSGs). Evidence indicates that mutations in X-chromosome TSGs are more likely to contribute to cancer than those in autosomal TSGs. Here, we formalize this in several dynamic models and predict, as expected, that mutations spread faster in TSGs located on the X chromosome than on autosomes (faster-X effect). Conversely, mutations in OGs spread faster on autosomes than on the X chromosome, but under high selective pressure, this difference is negligible. Published genomic screenings of cancer samples show evidence of the faster-X effect in TSGs. This pattern is observed in both sexes, suggesting that the maintenance of X-chromosome inactivation during cancer progression plays an important role in the evolution of TSGs. Strikingly, the relative mutation incidence in X-linked TSGs among females across individual studies is bimodal, with one group of studies showing a faster-X effect and another group showing similar incidences for X-linked and autosomal TSGs. This differentiation between cancer samples is not associated with the specific type of cancer or the tissue of origin. This may indicate that X-chromosome inactivation plays a differential role in the involvement of X-linked TSGs across individual cancers. | 2024-09-13 | |
Haplotype-resolved genomes provide insights into the origin and function of genome diversity in bivalves | 10.1101/2024.09.09.611967 | Liu, S.; Shi, C.; Chen, C.; Tan, Y.; Tian, Y.; Macqueen, D.; Li, Q. | Most bivalve genomes exhibit extensive heterozygosity and diversity, yet the origin and function of these genomic features remain unclear. As an ancient bivalve group, oysters demonstrate high ecological adaptability with diverse genomes, which serve as a good model for studies in genome diversity and evolution. Here, we report the significant contraction but highly divergent genomic landscape of Crassostrea species and highlight the association of transposable elements (TEs) activity with this genomic feature. By constructing a haplotype-resolved genome of C. sikamea, we identified the widespread presence of high divergence sequences (HDS) between the haplotype genome. Combined with population resequencing data, we underscore the role of genome divergence driven by TEs in shaping and maintaining oyster genomic diversity. By comparing haplotype genomes across C. sikamea, Pinctada fucata, Arcuatula senhousia, and Mimachlamys varia, we find that while haplotype divergence is common, its mechanisms of occurrence and maintenance differ significantly among bivalve species. Furthermore, our results show that the widespread presence of HDS not only contributes to substantial genetic variation but also influences the regulation of gene expression in oysters. The lack of conservation in allele-specific expression among individuals in oysters suggests high plasticity in haplotype polymorphism, allowing significant variation in gene regulation to supporting high phenotype plasticity and environment adaption. Overall, these findings offer novel insights into the connection between the unique genomic features and their role in adaptive evolution. | 2024-09-13 | |
METTL3 Modulates Radiation-Induced Cardiac Fibrosis via the Akt/mTOR Pathway | 10.1101/2024.09.07.611836 | Gu, X.-s. | BACKGROUND: Radiation therapy for cancer treatment frequently leads to radiation-induced heart disease (RIHD), characterized as cardiac fibrosis and heart failure. The enzyme METTL3, a key player in RNA methylation, is known to influence various cellular processes, while its specific role and mechanism in RIHD are not well understood. OBJECTIVES: The purpose of this study was to explore the potential mechanism of METTL3 in regulating cardiac fibrosis induced by radiation. METHODS: We constructed an X-ray-modulated RIHD mice models to investigate the role of METTL3 in cardiac fibroblasts. In parallel, METTL3 overexpression and silence were conducted on fibroblasts and mice heart to evaluate pro-fibrotic protein expression, cardiac fibrosis, and heart function. RESULTS: Elevated METTL3 expression was observed in both irradiated cardiac tissues and fibroblasts. Moreover, overexpression of METTL3 in cardiac fibroblasts was associated with increased expression of pro-fibrotic proteins and exacerbated fibrosis, whereas METTL3 silencing attenuated these adverse effects. Likewise, METTL3 knockdown ameliorated cardiac dysfunction and reduced fibrosis. Taken together, METTL3 could induce cardiac fibrosis via activating the Akt/mTOR signaling pathway to promote fibroblast proliferation and myofibroblast differentiation. CONCLUSIONS: METTL3 is a critical of RICD through modulating the Akt/mTOR pathway, hence targeting METTL3 presents a promising therapeutic strategy to mitigate the adverse cardiac effects of radiation therapy in cancer patients. | 2024-09-13 | |
NRF2 translation block by inhibition of cap-dependent initiation sensitizes lymphoma cells to ferroptosis and CAR-T immunotherapy | 10.1101/2024.09.09.612133 | Manara, P.; Newsam, A. D.; Saralamma, V. V.; Russo, M. V.; Martinez, A. B.; Fattakhov, N.; Cunningham, T. A.; Alaoui, A. Y.; Chahar, D.; Carbone, A. M.; Lightfuss, O. B.; Barroso, A. M.; Hoffman, K. S.; Maura, F.; Bilbao, D.; Schatz, J. H. | Cancers coopt stress-response pathways to drive oncogenesis, dodge immune surveillance, and resist cytotoxic therapies. Several of these provide protection from ferroptosis, iron-mediated oxidative cell death. Here, we found dramatic sensitization to ferroptosis upon disruption of cap-dependent translation in diffuse large B-cell lymphoma (DLBCL). Specifically, rocaglate inhibitors of the eIF4A1 RNA helicase synergized with pharmacologic ferroptosis inducers, driven by a collapse of glutathione production that protects polyunsaturated fatty acids from ferroptotic oxidation. These effects occur despite initial up-regulation of specific protective factors. We find lost translation of NRF2, oncogenic master regulator of antioxidant gene-expression, is a key consequence of eIF4A1 inhibition. In vivo, combination of the clinical rocaglate zotatifin with a pharmacologically optimized ferroptosis inducer eradicated DLBCL patient derived xenografts. Moreover, we found zotatifin pre-exposure sensitized DLBCL to CD19-directed chimeric antigen receptor (CAR-19) T cells. Translational disruption therefore provides new opportunities to leverage therapeutic impacts of ferroptosis inducers including cytotoxic immunotherapies. | 2024-09-13 | |
A genome-wide association screen for genes affecting leaf trichome development and epidermal metal accumulation in Arabidopsis | 10.1101/2024.09.10.612273 | Bezvoda, R.; Landeo-Rios, Y. M.; Kubatova, Z.; Kollarova, E.; Kulich, I.; Busch, W.; Zarsky, V.; Cvrckova, F. | We characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution patterns, compositional characteristics of the trichome cell wall (callose contents, mechanical attachment strength and autofluorescence), and on histologically detectable metal ion distribution. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including five genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Several large gene families were overrepresented among the candidates, suggesting epidermal development-related functions. In particular, DUF1262, DUF3741 and receptor-like kinases associated with trichome shape traits, cytochrome P450 paralogs with cell wall composition, Cys/His-rich C1 domain proteins with trichome shape and metal deposition, and formin, DUF674, DUF784 and DUF1985 gene families with metal deposition. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development. | 2024-09-13 | |
Programmed cell death and stomatal density regulate anther opening in response to ambient humidity | 10.1101/2024.09.09.612018 | Kampova, A.; Nowack, M. K.; Fendrych, M.; Vosolsobe, S. | Anther dehiscence is the process that facilitates pollen release from mature anthers in flowering plants. Despite its crucial importance to reproduction, the underlying molecular regulations and the integration of environmental information remain poorly understood. Using controlled humidity treatments of Arabidopsis thaliana flowers, we show here that high humidity prevents anthers from opening. Lower and higher stomatal densities correlate with slower and faster dehiscence dynamics, respectively, suggesting that controlled transpiration regulates anther opening. Furthermore, analyses of subcellular markers revealed that specific anther tissues undergo a spatially controlled programmed cell death (PCD) process as anthers open. Notably, genetic inhibition of PCD networks delays, whereas precocious PCD induction promotes, anther dehiscence. Our data shed new light on the interplay between ambient humidity, controlled transpiration, and PCD processes in regulating timely pollen release in the model plant Arabidopsis. | 2024-09-13 | |
Ethylene Modulates the Phenylpropanoid Pathway by Enhancing VvMYB14 Expression via the ERF5-Melatonin-ERF104 Pathway in Grape Seeds | 10.1101/2024.09.10.612321 | Gao, S.; Wang, F.; Wang, S.; Lan, S.; Xu, Y.; Lyu, X.; Kang, H.; Yao, Y. | Ethylene plays a crucial role in regulating polyphenol metabolism, however the underlying mechanism remains largely unknown. This work demonstrated that ethylene release occurred earlier than melatonin during seed ripening. Ethylene treatment increased the VvASMT expression and melatonin content. VvERF5 was elucidated to bind to the ERE element in the VvASMT promoter. VvERF5 overexpression increased ASMT expression and melatonin content while its suppression generated the opposite results in grape seeds, calli and/or Arabidopsis seeds. Using the promoter of VvMYB14, which was strongly induced by melatonin, a melatonin responsive element (MTRE) was identified. VvERF104 was revealed not only to be strongly induced by melatonin but to bind to the MTRE of the VvMYB14. VvERF104 overexpression and suppression largely increased and decreased the MYB14 expression, respectively, in grape seeds, calli and/or Arabidopsis seeds. VvMYB14 overexpression widely modified the expression of genes in phenylpropanoid pathway and phenolic compound content in grape seeds. DAP-seq revealed that the MEME-1 motif was the most likely binding sites of VvMYB14. VvPAL, VvC4H and VvCHS were verified to be the target genes of VvMYB14. Additionally, the roles of VvERF5, VvASMT and VvERF104 in mediating ethylene-induced changes in phenylpropanoid pathway were elucidated using their suppressing seeds. Collectively, ethylene increased the VvMYB14 expression via the pathway of ERF5-melatonin-ERF104 and thereby modified phenylpropanoid pathway. | 2024-09-13 | |
An endogenous peptide PEP2 modulates Iron-deficiency signalling and root growth in Arabidopsis. | 10.1101/2024.09.10.612258 | Shikha, D.; Mishra, S.; Satbhai, S. B. | Iron (Fe) is an essential element for most of the living organisms including plants and humans, where plants serve as the primary source of our dietary iron intake. The availability of Fe determines plant fitness and yield. Thus, understanding of iron uptake, its acquisition and utilization is of critical importance to reap nutritional benefits from plant breeding. Despite significant progress in uncovering how iron homeostasis is regulated by transcription factors and phytohormones, molecular pathways that mediate Fe deficiency through the action of signalling peptides remain elusive. In this work, we reported the role of PROPEP2 (Plant Elicitor Peptide 2) and PEPR (Perception of Arabidopsis danger signal peptide receptor) in regulating plant growth and development under Fe-deprived conditions. We revealed that a Damage Associated Molecular Pattern (DAMP) such as PROPEP2 is significantly induced under Fe deficiency. We also show that PEP2 modulates the expression of Iron Regulated Transporter 1 (IRT1) and Ferric-Reduction Oxidase (FRO2) under Fe deficiency. Furthermore, we showed that PEPR2 perceives PEP2 to positively regulate reactive oxygen species (ROS) content and negatively regulate the primary root growth, iron content and rhizosphere acidification. Our findings reveal the complex interplay between Fe and DAMP signalling pathways in plants. | 2024-09-13 | |
Revisiting the cytogenetics of Vellozia Vand.: immunolocalization of KLN1 elucidates the chromosome number for the genus | 10.1101/2024.09.10.612026 | Braz, G. T.; Riboldi, L. B.; Pinto, M. S.; Forni-Martins, E. R.; Yassitepe, J. E. C. T.; Dante, R. A.; Gerhardt, I. R. | Chromosome number is the most fundamental trait of a karyotype. Accurate chromosome counting is essential for further analyses including cytogenomics, taxonomic, evolutionary, and genomic studies. Despite its importance, miscounting is common, especially in early publications on species with small and morphologically similar chromosomes. Vellozia Vand. is a genus mainly distributed throughout South America belonging to the angiosperm family Velloziaceae, a dominant taxon in the Brazilian ''campos rupestres''. Cytogenetic studies within the group have been rare and have shown conflicting chromosome counts, even within the same species. These discrepancies are associated with the presence of a few small chromosome-like structures, which were previously classified as possible satellites. Here, to accurately determine the chromosome number of species belonging to the genus, we used different cytogenomics approaches, including the immunostaining of the KNL1 kinetochore protein combined with chromosome spread preparation using tissue culture-derived samples. Our results revealed 2n = 18 chromosomes for all six species studied. This finding suggests that the basic chromosome number for Vellozia is x = 9 and not x = 8, as previously proposed. The immunolocalization of functional centromeres was fundamental for undoubtedly identifying the smaller chromosome pair as real chromosomes and accurately determining the correct chromosome number of these species. This will provide substantial support for further studies, including investigations into karyotype evolution and the generation of reference genomes for the species of the family. | 2024-09-13 | |
CLIMATE BRAIN - Questionnaires, Tasks and the Neuroimaging Dataset | 10.1101/2024.09.12.612592 | Zaremba, D. A.; Kossowski, B.; Wypych, M.; Jednorog, K.; Michalowski, J. M.; Klockner, C. A.; Wierzba, M.; Marchewka, A. | Climate change presents a fundamental threat to human populations and ecosystems across the globe. Neuroscience researchers have recently started developing ways to advance research on this topic. However, validated questionnaires, experimental stimuli, and fMRI tasks are still needed. Here we describe the CLIMATE BRAIN dataset, a multimodal collection of questionnaire, behavioural, and neuroimaging data related to climate change, acquired from 160 healthy individuals. In particular, it includes data from (1) various questionnaire measures, including the Inventory of Climate Emotions (ICE); (2) a neuroimaging task for measuring emotional reactions to standardized Emotional Climate Change Stories (ECCS); and (3) a neuroimaging task based on Carbon Emission Task (CET) to measure climate action-taking. For technical validation, we provide image quality metrics and show the evidence for the effectiveness of tasks consistent with prior studies. To our knowledge, the proposed dataset is currently the only publicly available resource specifically designed to investigate human brain responses to climate change. | 2024-09-13 | |
Neutrophil NADPH oxidase breaks the inflammatory IL-1beta/IL-17A circuit to enhance pathogen clearance during respiratory virus infections. | 10.1101/2024.09.12.612505 | Sofoluwe, A.; Petropoulos, A.; Goomanee, A. S.; Ali-Khan, Z. F.; Warnatsch, A. | Respiratory virus infections are invariably accompanied by an increase in oxidative stress, characterised by elevated production of Reactive Oxygen Species (ROS) in the lung, which plays a pivotal role in both pathogenesis and host defence. Using a mouse model, neutrophil NADPH Oxidase 2 (Nox2) emerges as a key player, primarily responsible for generation of ROS during the early phases of Influenza A Virus (IAV) infection. Neutrophil Nox2-derived ROS display a multifaceted role, not only unleashing oxidative stress but in turn curbing Neutrophil-derived IL-1beta signalling. Absence of neutrophil Nox2 triggered heightened production of IL-1{beta}, promoting the proliferation of IL-17-producing gamma delta (gamma delta) T cells. This early self-amplified augmentation of the IL-beta/IL-17 axis counteracted the antiviral interferon response against IAV infection in mice. We extended our findings to humans. Similar patterns of ROS production and cytokine regulation were observed in human neutrophils when exposed to virus analogue poly(I:C) and SARS-CoV-2. Our discovery highlights that ROS, often associated with harm, play a dual role by regulating cytokine signalling and thus influencing the immune response against respiratory viruses. | 2024-09-13 | |
The orphan nuclear receptor NR4A3 is dispensable for resident memory CD8+ T cell generation | 10.1101/2024.09.09.612076 | Odagiu, L.; Boulet, S.; Maurice-De Sousa, D.; Daudelin, J.-F.; Labrecque, N. | Different memory CD8+ T cell subsets are generated following acute responses: central, effector and resident (Trm). CD8+ Trm cells established residency at the sites of infection and provide an efficient and rapid frontline defense against re-infection. The NR4A family members (NR4A1, NR4A2 and NR4A3) of orphan nuclear receptor are transiently expressed following TCR signaling and NR4As were shown to influence CD8+ T cell response. Interestingly, Nr4a1, Nr4a2 and Nr4a3 have been reported to be transcribed by CD8+ Trm cells. In absence of NR4A1, less CD8+ Trm cells are present in the liver, lungs, small intestine intra-epithelial lymphocytes (IELs) and Peyers patches. NR4A2 was shown to play a role in the generation of small intestine IEL CD8+ Trm cells. However, evidence is still lacking for the contribution of NR4A3 during CD8+ Tm cell differentiation. In this study, we evaluated the role of NR4A3 in the differentiation and maintenance of CD8+ Trm cells. Our data demonstrate that in contrast to the other family members NR4A1 and NR4A2, NR4A3 is dispensable for the generation of CD8+ Trm cells in both epithelial and non-epithelial sites. | 2024-09-13 | |
Preventing surgery induced immune suppression and metastases by inhibiting PI3K-gamma signalling in Myeloid-Derived Suppressor Cells. | 10.1101/2024.09.08.611916 | Angka, L.; Tennakoon, G.; Cook, D. P.; Martel, A. B.; Market, M. R.; Tanese de Souza, C.; Cummins, E.; Samudio, I.; Kekre, N.; Ardolino, M.; Vanderhyden, B.; Kennedy, M. A.; Auer, R. C. | Myeloid derived suppressor cells (MDSCs) have a dominating presence in the postoperative period and mediate the suppression of Natural Killer (NK) cells and promotion of cancer metastases after surgery. However, their functional characteristics and effect on cellular immunity after surgery have not been comprehensively investigated. Here, we characterize the expansion of surgery-induced (sx) MDSCs via multi-colour flow cytometry, single-cell RNA sequencing, and functional ex vivo NK cell suppression assays. We then screened a small molecule library using our sx-MDSC:NK cell suppression assay to identify compounds that could inhibit sx-MDSCs. These studies provide evidence that PI3K-{gamma} signalling is upregulated in sx-MDSCs and blockade with PI3K-{gamma} specific inhibitors attenuates NK cell suppression in humans and mice and reduces postoperative metastases in murine models. Upregulated PI3K-{gamma} in sx-MDSCs is a potential pathway amenable to therapeutic targeting in the postoperative period. | 2024-09-13 | |
IL-34 empowers regulatory T cells with novel non-canonical function to safeguard brain barrier integrity during neuro-inflammation. | 10.1101/2024.09.09.611994 | Van Hoecke, L.; Verreycken, J.; Van Acker, L.; Amelinck, L.; Xie, J.; Castelein, J.; Van Wonterghem, E.; Van Imschoot, G.; Burgelman, M.; Vanherle, S.; Dewachter, I.; Baeten, P.; Broux, B.; Vandenbroucke, R. E. | In efforts to find reparative strategies for brain damage, brain-associated regulatory T cells (Tregs) have gained increasing attention in recent years. Beyond their textbook immunoregulatory function, Tregs have emerged as key players in the response to brain trauma and the restoration of damaged brain tissue. Here, we are the first to describe a novel, non-canonical function of Tregs in maintaining the sealing capacity of both the blood-brain barrier (BBB) and the blood-cerebrospinal fluid (CSF) barrier. Moreover, we identified the cytokine IL-34 as a critical determinant in this newly unveiled Treg function. Mechanistically, IL-34 exerts its influence by modulating the expression and localization of the tight junction protein ZO-1 in both BBB endothelial cells and choroid plexus epithelial cells, thereby reinforcing the strength of the brain barriers. Given the well-established notion of leaky brain barriers and the involvement of immunological components in neurological diseases such as Alzheimer's disease (AD) and multiple sclerosis (MS), we further demonstrate diminished IL-34 expression in Tregs derived from patients with relapsing-remitting MS (RR-MS) and patients with AD and even mild cognitive impairment (MCI). Remarkably, our study reveals the potential of IL-34 treatment in reinstating the integrity of brain barriers within murine models mimicking these neurological disorders. These ground-breaking findings shed light on the intricate relationship between Tregs, IL-34, and the integrity of brain barriers. They offer novel avenues for therapeutic approaches to ameliorate brain barrier dysfunction in the context of neurological disorders. | 2024-09-13 | |
Detecting microbial engraftment after FMT: sorting signals from noise using placebo sequencing and culture-enriched metagenomics | 10.1101/2024.09.11.612315 | Shekarriz, S.; Szamosi, J. C.; Whelan, F. J.; Lau, J. T.; Libertucci, J.; Rossi, L.; Shah, M.; Wolfe, M.; Lee, C. H.; Moayyedi, P.; Surette, M. G. | Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient microbiome. Previous studies have reported microbial engraftment following FMT in various disease contexts but with inconsistent results between studies. Here we investigate engraftment in UC patients receiving FMT from a single donor applying amplicon-based profiling, shotgun metagenomics and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort. | 2024-09-13 | |
Landscape-wide metabarcoding of the invasive bumblebee (Bombus terrestris) shows interactions among the gut microbiome and pollenbiome | 10.1101/2024.09.08.611921 | Haque, S.; Gamage, H. K.; Kardum Hjort, C.; Ponton, F.; Encinas-Viso, F.; Paulsen, I.; Dudaniec, R. Y. | Many species of social insects introduced to regions beyond their native ranges have become highly invasive. The introduction of the eusocial European buff-tailed bumblebee, Bombus terrestris, to the island of Tasmania (Australia) ~30 years ago is of concern due to its ecological impacts and its potential to spill over pathogens to native bees or commercially important honeybees. The health of B. terrestris is intricately connected with its gut microbiome and diet; however, environmental variables may also interact, particularly during invasion into novel environments. Using landscape-wide sampling and a metabarcoding approach to characterize the gut bacteria (16S rRNA) and diet composition from foraged pollen (ITS2: floristic diversity of pollen baskets), this study investigates how the gut microbiota of B. terrestris workers is affected by nutritional diversity (pollenbiome) and environmental variation across diverse landscapes of its invasive range in Tasmania. Gut bacterial community composition and diversity were significantly predicted by site annual precipitation and percentage of pasture. Further, a positive interaction between site annual precipitation and site annual temperature significantly predicted gut bacterial diversity. The interaction effect of pollen diversity and average summer wind velocity was also significantly and positively related to gut bacterial diversity. Following comparison of Akaike information criterion (AIC) and sum of weights, the percentage of pasture was identified as the most strongly weighted variable, which, along with pollen diversity, had a negative impact on gut bacterial diversity. These insights help to uncover how environmental interactions affect the gut microbiome of B. terrestris in an invaded landscape with novel nutritional resources. This knowledge contributes to understanding the factors that predict the spread and persistence of invasive bumblebees. | 2024-09-13 | |
The resilience of the oral microbiome and lability of the hair microbiome across host environments in wild and captive lemurs | 10.1101/2024.09.09.612164 | Burten, R. B.; Lawler, R. R.; Ratsirarson, J.; Ranaivonasy, J.; Leduc, R. C.; Bhagat, A.; Lopez, A.; Kamilar, J. M. | Microbiome diversity and composition in mammals is affected by the hosts environment and has been linked to important immune and physiological host functions, yet most of these data come from the gut microbiome. Research on the oral and hair microbiome in nonhuman primates has been far less common, and information from wild primates is even rarer. These overlooked patterns of environmental effects on microbial communities across the body may have important implications for a range of host functions. Therefore, in this study we characterized the gut, oral, and hair microbiomes across nine different captive and wild lemur species: Eulemur collaris, Eulemur coronatus, Eulemur mongoz, Lemur catta, Microcebus griseorufus, Microcebus murinus, Propithecus coquereli, and Varecia rubra. We explored how host environment affects the microbiome diversity of these three body regions using 16S rRNA sequencing and found significant differences in microbiome composition, diversity, and environmental influence across body regions. The oral microbiome was least diverse and most resilient to different environmental effects; conversely, the hair microbiome was both most diverse and most labile. Differentially abundant bacterial taxa across oral, gut, and hair microbiota may also reflect selective regimes unique to each body region. These results emphasize the importance of accounting for body region when conducting microbiome studies. | 2024-09-13 | |
Demographic responses to climatic changes during the Final Palaeolithic in Europe | 10.1101/2024.09.11.612499 | Schmidt, I.; Gehlen, B.; Winkler, K.; Arrizabalaga, A.; Arts, N.; Bicho, N.; Crombe, P.; Eriksen, B. V.; Grimm, S. B.; Kapustka, K.; Langlais, M.; Mevel, L.; Naudinot, N.; Nerudova, Z.; Niekus, M.; Peresani, M.; Riede, F.; Sauer, F.; Schön, W.; Sobkowiak-Tabaka, I.; Vandendriessche, H.; Weber, M.-J.; Zander, A.; Zimmermann, A.; Maier, A. | The European Final Palaeolithic witnessed marked changes in almost all societal domains. Despite a rich body of evidence, our knowledge of palaeodemographic processes and regional population dynamics still needs to be improved. In this study, we present regionally differentiated estimates of absolute numbers and population densities for the Greenland Interstadial 1d-a (GI-1d-a; 14-12.7 ka BP) and the Greenland Stadial 1 (GS-1; 12.7-11.6 ka BP) for western and central Europe. The data were obtained by applying the Cologne Protocol, a geostatistical approach for estimating prehistoric population size and density, to a newly compiled dataset of Final Palaeolithic sites. On a large spatio-temporal scale, we observe a shift of the main areas of human occupation from the Franco-Cantabrian region, which was intensely occupied during most phases of the preceding Upper Palaeolithic, to regions north of the Alps. At smaller scales, we observe divergent regional trends in the Final Palaeolithic meta-population: during GI 1d-a, a decreasing population in southwestern Europe and an increasing population in north-eastern Central Europe. For the first time since the dispersal of anatomically modern humans into Europe, we see that Central Europe becomes the dominant demographic growth area. Subsequently, the climatic cooling of GS-1 coincides with a pronounced population decline in most parts of the study area. An apparent increase in population density occurs only in north-eastern Central Europe and north-eastern Italy. Our estimates suggest that the total population was reduced by half. Similar results, with a relationship between decreasing temperatures and decreasing populations, have already been observed for the late phase of the Gravettian, when populations were reduced to only one third of those estimated for the early phase. Yet, in contrast to the collapse of local populations during the late Gravettian, the increase in population densities in central Europe during GS-1 indicates population movements eastwards, possibly in response to deteriorating climatic conditions, particularly in western regions during the Younger Dryas. | 2024-09-13 | |
The effect of nitrogen on the growth of Calluna vulgaris and Avenella flexuosa in a dune heath ecosystem: competition and frequency-dependence | 10.1101/2024.09.12.612621 | Damgaard, C.; Kaae, M. E.; Bak, J. L. | Nitrogen was manipulated in a dune heath ecosystem and using time-series pin-point data it was demonstrated that both Lotka-Volterra type interspecific competition and frequency dependency play significant roles in determining plant growth. For modelling simplicity, plant taxa were divided into heather, wavy hair-grass, and all other vascular species. Significant interspecific competition was observed among all species, except wavy hair-grass on the growth of all other vascular species, and nitrogen addition was found to increase the competitive effect of heather on the growth of all other vascular species. Both heather and wavy hair-grass showed positive feedback dynamics on growth when they were relatively dominant at the plot scale and the effect increased with added nitrogen. Such positive feedback dynamics may lead to the formation of patches, which are a characteristic feature of heath ecosystems. Oppositely, there was a beneficial effect of being relatively rare on the growth of all other vascular species in plots with added nitrogen. The study highlights the importance of the combined effects of interspecific competition and frequency dependency in regulating plant communities, and consequently undermine both theoretical and empirical conclusions of modern coexistence theory. | 2024-09-13 | |
Crop productivity of Central European Permaculture is within the range of organic and conventional agriculture. | 10.1101/2024.09.09.611985 | Reiff, J.; Jungkunst, H. F.; Antes, N.; Entling, M. H. | Permaculture is a promising framework to design and manage sustainable food production systems. However, there is still a lack of scientific evidence especially on the crop productivity of permaculture systems. In this first study on permaculture yield, we collected yield data of eleven permaculture sites, that work according to organic guidelines, in Germany and surrounding countries. We used the Land Equivalent Ratio (LER) as index to compare mixed cropping systems of permaculture sites with average monoculture yield data of total and organic German agriculture. An LER of 1 indicates equal yields of the compared polyculture and monoculture. Mean permaculture LER as compared to total German agriculture was 0.80 {+/-} 0.27 and 1.44 {+/-} 0.52 as compared to German organic agriculture, both with no significant difference to 1. Our results imply, that yields of permaculture sites are comparable to predominant industrial agriculture. Provided that future studies will support our findings, permaculture could combine soil, biodiversity and climate protection with agricultural productivity. Most importantly, the variables that determine the difference in crop productivity amoung permaculture sites need to be identified and evaluated. | 2024-09-13 | |
Context- and sex-dependent links between sire sexual success and offspring pathogen resistance | 10.1101/2024.09.10.611971 | Liao, A.; Kawecki, T. J. | Sexual selection has been proposed to promote genetic variants that improve resistance to pathogens (a special case of the "good genes" hypothesis). Yet, experimental tests of this hypothesis are scarce and equivocal. It is often assumed that additive genetic correlation between sexual traits and pathogen resistance is generated by their shared dependence on genetically variable "condition" of the organism. However, an alternative scenario posits condition-independent genetic variation in pathogen resistance; individuals more resistant to currently prevalent pathogens remain healthier and can invest more in sexual traits, but this advantage disappears in the absence of pathogens. Here, we tested whether Drosophila melanogaster males that are more sexually competitive (in terms of paternity share) sire offspring that are more resistant to the fungal pathogen Metarhizium brunneum. Furthermore, to investigate the importance of epidemiological context, we exposed sires to either an infection or a sham treatment before mating, to test whether the sire-offspring relationship depends on the presence of pathogens during sexual selection. We found that the relationship between sires sexual success and offspring pathogen resistance not only depended on sires exposure to the pathogen, but also on offspring sex. Sires that were more sexually successful in the absence of the pathogen had less resistant offspring whereas no relationship was detected for sires that competed for paternity after pathogen exposure. For daughters, the relationship tended to be negative irrespective of sire pathogen exposure. In no case was a positive correlation predicted by the "good genes" hypothesis detected. Thus, while sexual selection may act on genes affecting resistance in a context- and sex-dependent manner, we found no circumstances under which it promoted resistance. | 2024-09-13 | |
Timing of starvation determines its effects on susceptibility to infection in Drosophila melanogaster females independent of host evolutionary history | 10.1101/2024.09.11.612402 | Basu, A.; Singh, A.; Prasad, N. G. | An organism's susceptibility to pathogens is contingent on various environmental factors, including the availability of nutrition. Starvation can alter host susceptibility to infections, either directly via depletion of resources essential for proper functioning of the immune system, or indirectly via the various physiological changes it induces within the host body. We tested if the susceptibility of Drosophila melanogaster populations to Enterococcus faecalis infection is affected by (a) whether the hosts are starved before or after the infection, and (b) the evolutionary history of the host. Hosts from laboratory fly populations that have been experimentally evolved to be more resistant to E. faecalis, and their corresponding control populations, were subjected to infection with or without being starved prior to and after being infected. We found that the effect of starvation on susceptibility to E. faecalis changed with the timing of starvation: starvation after infection improved survival of infected hosts, irrespective of how they were treated before infection, while starving only prior to infection (and not after) compromised post-infection survival. The changes in infection susceptibility were uniform in both the evolved and the control populations, suggesting that the effects of starvation are not dependent on pre-existing resistance to the infecting pathogen. | 2024-09-13 | |
Development of a Platform for High-Resolution Ion Mobility Separations Coupled with Messenger Tagging Infrared Spectroscopy for High-Precision Structural Characterizations | 10.1101/2024.09.06.611750 | Harrilal, C.; Garimella, S.; Norheim, R.; Ibrahim, Y. | The ability to uniquely identify a compound requires highly precise and orthogonal measurements. Here we describe a newly developed analytical platform that uniquely integrates high resolution ion mobility and cryogenic vibrational ion spectroscopy for high-precision structural characterizations. This platform allows for the temporal separation of isomeric/isobaric ions and provides a highly sensitive description of the ions adopted geometry in the gas phase. The combination of these orthogonal structural measurements yields precise descriptors that can be used to resolve between and confidently identify highly similar ions. The unique benefit of our instrument, which integrates a structures for lossless ion manipulations ion mobility (SLIM IM) device with messenger tagging infrared spectroscopy, include increased resolution and the ability to record the IR spectra of all ions simultaneously. The SLIM IM device, with its 13m separation path length, allows for multipass experiments to be performed for increased resolution as needed. It is integrated with an Agilent qTOF MS where the collision cell was retrofitted with a cryogenically (30 K) held TW SLIM device. The cryo-SLIM is operated in a novel manner that allows ions to be streamed through the device and collisionally cooled to a temperature where they can form non-covalently bound N2 complexes that are maintained as they exit the device and are detected by the TOF mass analyzer. The instrument can be operated in two modes: IMS+IR where the IR spectra for mobility-selected ions can be recorded and IR-only mode where the IR spectra for all mass-resolved ions can be recorded. In IR-only mode, IR spectra (400 cm-1 spectral range) can be recorded in as short as 2 seconds for high throughput measurements. This work details the construction of the instrument, modes of operation, and provides initial benchmarking of CCS and IR measurements to demonstrate the utility of this instrument for targeted and untargeted approaches. | 2024-09-13 | |
genomesizeR: An R package for genome size prediction | 10.1101/2024.09.08.611926 | Mercier, C.; Elleouet, J.; Garrett, L.; Wakelin, S. A. | The genome size of organisms present in an environment can provide many insights into evolutionary and ecological processes at play in that environment. The genomic revolution has enabled a rapid expansion of our knowledge of genomes in many living organisms, and most of that knowledge is classified and readily available in the databases of the National Center for Biotechnology Information (NCBI). The genomesizeR tool leverages the wealth of taxonomic and genomic information present in NCBI databases to infer the genome size of Archeae, Bacteria, or Eukaryote organisms identified at any taxonomic level. This R package uses statistical modelling on data from the most up-to-date NCBI databases and provides three statistical methods for genome size prediction of a given taxon, or group of taxa. A straightforward 'weighted mean' method identifies the closest taxa with available genome size information in the taxonomic tree, and averages their genome sizes using weights based on taxonomic distance. A frequentist random effect model uses nested genus and family information to output genome size estimates. Finally a third option provides predictions from a distributional Bayesian multilevel model which uses taxonomic information from genus all the way to superkingdom, therefore providing estimates and uncertainty bounds even for under-represented taxa. All three methods use: - A list of queries; a query being a taxon or a list of several taxa. The package was designed to make it easy to use with data coming from environmental DNA experiments, but works with any table of taxa. - A reference database containing all the known genome sizes, built from the NCBI databases, with associated taxa, provided in an archive to download. - A taxonomic tree structure as built by the NCBI, provided in the same archive. genomesizeR retrieves the taxonomic classification of input queries, estimates the genome size of each query, and provides 95% confidence intervals for each estimate. | 2024-09-13 | |
Morphology of softening and translucency in the stems of tomato and eggplant seedlings due to infection by Ralstonia pseudosolanacearum F1C1 | 10.1101/2024.09.10.612199 | Bhuyan, S.; Boruah, L.; Jain, M.; Begum, S.; Giri, S. J.; Dutta, L.; Mandal, M.; Ray, S. K. | Ralstonia pseudosolanacearum F1C1 is a soil-borne phytopathogenic bacterium with a broad host range that infects several economically important crops. This study primarily focuses on the infection of this phytopathogen in two such important crop seedlings: tomato and eggplant. The observations of the study reveal a complex set of symptoms that include drooping and blackening of the seedling stem, as well as blackening, chlorosis, and curling of cotyledon leaves. Notably, the symptom of stem softening and translucency is seen primarily in the water-submerged stem regions of the root-inoculated seedlings. Furthermore, the morphology of stem softening and translucency is more frequent in root-inoculated eggplant seedlings, underscoring a difference between tomato and eggplant seedlings regarding the virulence of the bacterium. By investigating these unique pathological phenotypes in the infected seedlings, this study uncovers unique symptoms not previously observed in seedling inoculation experiments. Such findings deepen our understanding of the complex virulence mechanisms of the pathogen. The work also highlights the distinct escape mechanisms exhibited by seedlings, revealing how some of its host plants might resist wilting despite infection, offering new avenues for future research. These findings contribute to the understanding of R. pseudosolanacearum pathogenesis, shedding light on its virulence and host response mechanisms. | 2024-09-13 | |
Morphology of softening and translucency in the stems of tomato and eggplant seedlings due to infection by Ralstonia pseudosolanacearum F1C1 | 10.1101/2024.09.10.612199 | Bhuyan, S.; Boruah, L.; Jain, M.; Begum, S.; Giri, S. J.; Dutta, L.; Mandal, M.; Ray, S. K. | Ralstonia pseudosolanacearum F1C1 is a soil-borne phytopathogenic bacterium with a broad host range that infects several economically important crops. This study primarily focuses on the infection of this phytopathogen in two such important crop seedlings: tomato and eggplant. The observations of the study reveal a complex set of symptoms that include drooping and blackening of the seedling stem, as well as blackening, chlorosis, and curling of cotyledon leaves. Notably, the symptom of stem softening and translucency is seen primarily in the water-submerged stem regions of the root-inoculated seedlings. Furthermore, the morphology of stem softening and translucency is more frequent in root-inoculated eggplant seedlings, underscoring a difference between tomato and eggplant seedlings regarding the virulence of the bacterium. By investigating these unique pathological phenotypes in the infected seedlings, this study uncovers unique symptoms not previously observed in seedling inoculation experiments. Such findings deepen our understanding of the complex virulence mechanisms of the pathogen. The work also highlights the distinct escape mechanisms exhibited by seedlings, revealing how some of its host plants might resist wilting despite infection, offering new avenues for future research. These findings contribute to the understanding of R. pseudosolanacearum pathogenesis, shedding light on its virulence and host response mechanisms. | 2024-09-14 | |
Differentiating wild and domesticated enset (Musaceae) using phytolith analysis | 10.1101/2024.09.09.611979 | Castillo Cobo, C.; Beldados, A.; Ryan, P.; Bond, S.; Vrydaghs, L.; Lulekal Molla, E.; Borrell, J.; Hunt, H.; Fuller, D. Q. | Enset (Ensete ventricosum, Musaceae) is an important economic crop from Ethiopia which accounts for 20% of the staple diet in Ethiopia today. However, its evolutionary history and spread is poorly understood. Archaeology could provide evidence of past use and contribute to our understanding of its early history, but so far, this has not transpired. Cultivated enset is clonally reproduced and seed production rarely occurs, therefore, looking for seed remains is futile and instead archaeobotanical research should focus on microfossils such as phytoliths. Phytoliths have been shown to be diagnostic for the presence of banana (Musa) and are expected to be similarly useful for identifying enset, but we need a better understanding of phytolith production and variability, and the extent to which this may be used to track domestication. The current study provides a fundamental baseline for the identification of Ensete phytoliths through the examination of phytoliths from leaves and other plant parts based on their size and shape. We consider the differentiation of phytoliths across a single plant, based on location in the leaf, the age of the leaf, and different organs of the plant. We also compare phytoliths in the Musaceae Family, and between the enset cultivar and wild samples. | 2024-09-13 | |
ElixirSeeker: A Machine Learning Framework Utilizing Attention-Driven Fusion of Molecular Fingerprints for the Discovery of Anti-Aging Compounds | 10.1101/2024.09.08.611839 | Pan, Y.; Cai, H.; Ye, F.; Xu, W.; Huang, Z.; Zhu, J.; Gong, Y.; Li, Y.; Ezemaduka, A. N.; Gao, S.; Liu, S.; Li, G.; Li, H.; Yang, J.; Ning, J.; Xian, B. | Despite the growing interest in anti-aging drug development, high cost and low success rate pose a significant challenge. We present ElixirSeeker, a new machine-learning framework designed to help speed up the discovery of potential anti-aging compounds by utilizing the attention-driven fusion of molecular fingerprints. Our approach integrates molecular fingerprints generated by different algorithms and utilizes XGBoost to select optimal fingerprint lengths. Subsequently, we assign weights to the molecular fingerprints and employ Kernel Principal Component Analysis (KPCA) to reduce dimensionality, integrating different attention-driven methods. We trained the algorithm using DrugAge database. Our comprehensive analyses demonstrate that 64-bit Attention-ElixirFP maintains high predictive accuracy and F1 score while minimizing computational cost. Using ElixirSeeker to screen external compound databases, we identified a number of promising candidate anti-aging drugs. We tested top 6 hits and found that 4 of these compounds extend the lifespan of Caenorhabditis elegans, including Polyphyllin , Medrysone, Thymoquinone and Medrysone. This study illustrates that attention-driven fusion of fingerprints maximizes the learning of molecular activity features, providing a novel approach for high-throughput machine learning discovery of anti-aging molecules. | 2024-09-13 | |
A scalable approach to absolute quantitation in metabolomics | 10.1101/2024.09.09.609906 | Ferro, L. S.; Wong, A. Y. L.; Howland, J.; Costa, A. S. H.; Pruyne, J. G.; Shah, D.; Lauterbach, J. D.; Hooper, S. B.; Delmar, M. C.; Geremia, J.; Kassis, T.; Kanarek, N.; Campbell, J. M. | Mass spectrometry-based metabolomics allows for the quantitation of metabolite levels in diverse biological samples. The traditional method of converting peak areas to absolute concentrations involves the use of matched heavy isotopologues. However, this approach is laborious and limited to a small number of metabolites. We addressed these limitations by developing PyxisTM, a machine learning-based technology which converts raw mass spectrometry data to absolute concentration measurements without the need for per-analyte standards. Here, we demonstrate Pyxis performance by quantifying metabolome concentration dynamics in murine blood plasma. Pyxis performed equivalently to traditional quantitation workflows used by research institutions, with a fraction of the time needed for analysis. We show that absolute quantitation by Pyxis can be expanded to include concentrations for additional metabolites, without the need to acquire new data. Furthermore, Pyxis allows for absolute quantitation as part of an untargeted metabolomics workflow. By removing the bottleneck of per-analyte standards, Pyxis allows for absolute quantitation in metabolomics that is scalable to large numbers of metabolites. The ability of Pyxis to make concentration-based measurements across the metabolome has the potential to deepen our understanding of diverse metabolic perturbations. | 2024-09-13 | |
Neural representation of vocalization self-monitoring in the bat auditory midbrain | 10.1101/2024.09.12.612784 | Ye, H.; Cui, Z.; Liu, Z.; Qin, X.; Huang, X.; Bai, Y.; Luo, J. | During acoustic interaction, mammals, including humans, not only monitor sounds from external sources but also their own vocalizations, the latter of which is known as vocalization feedback monitoring. Yet, it is unclear whether subcortical auditory regions process vocalization feedback. Here, we established an experimental paradigm that allows recording chronically the single-unit activity of the auditory midbrain (inferior colliculus) in freely vocalizing bats. We report that most collicular neurons represented self-produced biosonar vocalizations distinctively from pure tones and vocalization playbacks. Some neurons showed robust excitatory responses to vocalization feedback yet lacked any excitatory response to pure tones covering the entire frequency range of the vocalizations. Surprisingly, some collicular neurons even reversed the response polarity, from vocalization-induced suppression to vocalization-playback-induced excitation. Moreover, approximately a third of the neurons responded faster to self-produced vocalizations than to both vocalization playbacks and pure tones. These findings show that the midbrain inferior colliculus is involved in vocalization feedback processing, an ability suggested to arise locally in the auditory cortex. | 2024-09-13 | |
LM11a-31 Inhibits p75 Neurotrophin Receptor (p75NTR) Cleavage and is Neuroprotective in a Cell Culture Model of Parkinson's Disease. | 10.1101/2024.09.10.612299 | Pokharel, P. V.; Newchurch, A. M.; Overby, S. C.; Spease, C. A.; Darzi, L. G.; Kraemer, B. R. | The p75 Neurotrophin Receptor (p75NTR) is a multifunctional transmembrane protein that mediates neuronal responses to pathological conditions in specific regions of the nervous system. In many biological contexts, p75NTR signaling is initiated through sequential cleavage of the receptor by - and {gamma}-secretases, which releases receptor fragments for downstream signaling. Our previous work demonstrated that proteolytic processing of p75NTR in this manner is stimulated by oxidative stress in Lund Human Mesencephalic (LUHMES) cells, a dopaminergic neuronal cell line derived from human mesencephalic tissue. Considering the vulnerability of dopaminergic neurons in the ventral mesencephalon to oxidative stress and neurodegeneration associated with Parkinson's disease (PD), we investigated the role of this signaling cascade in neurodegeneration and explored cellular processes that govern oxidative stress-induced p75NTR signaling. In the present study, we provide evidence that oxidative stress induces cleavage of p75NTR by promoting c-Jun N-terminal Kinase (JNK)-dependent internalization of p75NTR from the cell surface. This activation of p75NTR signaling is counteracted by tropomyosin-related kinase (Trk) receptor signaling; however, oxidative stress leads to Trk receptor downregulation, thereby enhancing p75NTR processing. Importantly, we demonstrate that this pathway can be inhibited by LM11a-31, a small molecule modulator of p75NTR, thereby conferring protection against neurodegeneration. Treatment with LM11a-31 significantly reduced p75NTR cleavage and neuronal death associated with oxidative stress. These findings reveal novel mechanisms underlying activation of p75NTR in response to oxidative stress, underscore a key role for p75NTR in dopaminergic neurodegeneration, and highlight p75NTR as a potential therapeutic target for reducing neurodegeneration in PD. | 2024-09-13 | |
Beyond immunity: a transcriptomic landscape of Plasmodium's modulation of mosquito metabolic pathways | 10.1101/2024.09.09.611609 | Garcia-Longoria, L.; Berthomieu, A.; Hellgren, O.; Rivero, A. | The focus of mosquito-Plasmodium interactions has predominantly been centered on mosquito immunity, revealing key mechanisms by which mosquitoes attempt to combat Plasmodium infection. However, recent evidence suggests that beyond immunity, a multitude of mosquito physiological and metabolic pathways play crucial roles in determining whether the parasite completes its development within the mosquito. We review which of these metabolic pathways are potentially modulated by Plasmodium, revealing a fragmented and occasionally contradictory state of knowledge. We then present a comprehensive transcriptomic analysis of Plasmodium-infected and uninfected mosquitoes, examining gene expression of crucial genes across different stages of the parasite's development. These genes range from key enzymes and proteins involved in gut structure and function, to genes involved in egg production and resorption, salivary gland invasion and mosquito behaviour. For this purpose, we use a non-model system consisting of the avian malaria parasite Plasmodium relictum, an invasive parasite threatening bird biodiversity across the world, and its natural vector, the mosquito Culex pipiens. Our results reveal how at each stage of its development within the mosquito, Plasmodium modulates a myriad of mosquito metabolic pathways, in ways that potentially favour its survival and the completion of its life cycle. We discuss whether this constitutes sufficient evidence of parasite-driven manipulation or whether the changes are simply the mosquito's response to the infection, which the parasite may serendipitously exploit to enhance its fitness. Our study extends the comparative transcriptomic analyses of malaria-infected mosquitoes beyond human and rodent parasites, and provides insights into the degree of conservation of metabolic pathways and into the selective pressures exerted by Plasmodium parasites on their vectors. | 2024-09-13 | |
Genome assembly of Firmina major, an endangered savanna tree species endemic to China | 10.1101/2024.09.09.610897 | Yang, J.; Zhang, R.; Ma, Y.; Ma, Y.; Sun, W. | The tree species Firmiana major was once dominant in the savanna vegetation of the arid hot valleys of southwest China, but was considered extinct in the wild in 1998. After eight small populations were relocated by thorough investigations between 2018 and 2020, the species was subsequently recognized as a Plant Species of Extremely Small Populations (PSESP) in China in need of urgent rescue. Moreover, due to severe human disturbance, other species in the tropical woody genus Firmiana are also endangered, and the species in this genus have almost all been listed as second-class National Protected Wild Plants in China. In order to guide future research into the conservation of this group, we present here the high-quality genome assembly of F. major. This is the first genome assembly in the genus Firmiana, and is 1.4 Gb in size. The assembly consists of 1.18 Gb repetitive sequences, 37,673 annotated genes and 31,965 coding genes. | 2024-09-13 | |
START domains generate paralog-specific regulons from a single network architecture | 10.1101/2024.09.09.612080 | Holub, A. S.; Choudury, S. G.; Andrianova, E. P. Y.; Dresden, C. E.; Urquidi Camacho, R.; Jouline, I.; Husbands, A. Y. | Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB (~99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered 'responsive' versus 'non-responsive' by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a new mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence. | 2024-09-13 | |
Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation | 10.1101/2024.09.10.612032 | Zhuang, Q. K.-W.; Bauermeister, K.; Galvez Lopez, J. H.; AlOgayil, N.; Batdorj, E.; Pardo-Manuel de Villena, F.; Taketo, T.; Bourque, G.; Naumova, A. K. | Background. Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs) that represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored. Results. Here, we report a survey of gene, lncRNA and TE expression in four organs from mice with different combinations of gonadal and genetic sex. Data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in liver. In contrast, the X-chromosome dosage alone had modest influence on sex-biased transcription across different organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y chromosome influenced TE, but not gene or lncRNA expression in liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside close (<100 kb) to sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We also tested the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals and found no evidence to support it. Conclusions. Our data show that sex-biased expression of TEs varies among organs with highest numbers of sDETEs found in liver following the trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts. | 2024-09-13 | |
Targets of influenza Human T cell response are mostly conserved in H5N1 | 10.1101/2024.09.09.612060 | Sidney, J.; Kim, A.; de Vries, R. D.; Peters, B.; Meade, P. S.; Krammer, F.; Grifoni, A.; Sette, A. | Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections. | 2024-09-13 | |
How does host age and nutrition affect density regulation of obligate versus facultative bacterial symbionts? Insights from the tsetse fly | 10.1101/2024.09.13.612807 | Whittle, M.; Barreaux, A. M.; Haines, L. R.; Bonsall, M. B.; English, S.; Ponton, F. | The relationships between insect hosts and their symbionts can vary tremendously in the extent to which hosts depend on and control their symbionts. Obligate symbionts that provide micronutrients to their host are often compartmentalised to specialised host organs and depend on their hosts for survival, whereas facultative symbionts retain the ability to survive outside of their hosts. Few studies compare the extent to which a host controls and adjusts the density of obligate and facultative symbionts directly. Here, we used tsetse as a model for teasing apart the relationships between a host (Glossina morsitans morsitans) and obligate (Wigglesworthia glossinidia) and facultative (Sodalis glossinidius) symbionts. We hypothesised that tsetse actively regulate the density of Wigglesworthia according to the host's requirements, depending on their current nutritional state and developmental age. In contrast, we postulated that Sodalis retains some independence from host control, and that the growth of this symbiont is dependent on the conditions of the immediate environment, such as nutrient availability. Using qPCR, we examined how symbiont densities change across host age and the hunger cycle. Additionally, we investigated how host nutrition influences symbiont density, by comparing tsetse that were fed diluted blood (poor nutrition) or blood supplemented with yeast extract (vitamin enriched). We found that the density of Wigglesworthia did not reflect the nutritional status of the host, but was optimised to accommodate long-term host requirements (in terms of nutrient provisioning). In contrast, the density of facultative Sodalis was influenced by the ecological context (i.e. nutrient availability). This suggests that tsetse regulate the abundance of Wigglesworthia to a greater extent than Sodalis. We propose that tsetse exert only partial control over Sodalis growth due to the relatively recent transition of this symbiont to host-associated living. | 2024-09-13 | |
Outside your shell: how temperature shapes genetic variation in two species of congeneric marine snails | 10.1101/2024.09.12.612762 | Wuitchik, D. M.; Fifer, J. E.; Huzar, A. K.; Pechenick, J. A.; Uricchio, L.; Davies, S. W. | Intertidal organisms withstand extreme temperature fluctuations, and their ability to cope with this variation may affect their distributions across the seascape. Genetic variation and local environments likely interact to determine variation in thermal performance across intertidal species ranges, so characterizing the relationship between temperature variation and population structure is key to understanding the biology of marine invertebrates. Here, we use 2bRAD-sequencing to examine population genetic structure in two congeneric intertidal marine gastropods (Crepidula fornicata, C. plana), sampled from locations along a natural temperature gradient on the Northeast shores of the United States. These two species share similar life histories, yet C. plana exhibits a narrower distribution than C. fornicata. Our results demonstrate that both species show patterns of genetic divergence consistent with isolation by distance, though this pattern was only significant in C. fornicata. Both putatively selected and neutral loci displayed significant spatial structuring in C. fornicata; however, only putatively selected loci showed significant clustering in C. plana. When exploring whether temperature differences explained genetic differentiation, we found that 9-12% of genetic differentiation was explained by temperature variation in each species even when controlling for latitude and neutral population structure. Our results suggest that temperature shapes adaptive variation across the seascape in both Crepidula species and encourages further research to differentiate our results from models of neutral evolutionary drift. | 2024-09-13 | |
eDNA sampling systems for salmon ecosystem monitoring | 10.1101/2024.09.11.610878 | Deeg, C. M.; Saunders, R. G.; Tam, C.; Kaukinen, K.; Li, S.; Bass, A. L.; Uu-a-thluk Fisheries, ; Miller, K. M. | Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, the lack of sampling systems enabling high filtration volumes and rapid sample collection in the field have thus far hindered broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the hollow-membrane filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a three day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives. | 2024-09-13 | |
Towards genuine three-dimensional diffusion imaging with physiological motion compensation | 10.1101/2024.09.08.611927 | Wang, Y.; Weng, D.; Zhang, J.; Qian, T.; Liu, W.; Zhou, K.; Wu, Y.; Zhang, B.; Li, Q.; Jing, J.; Zhang, Z. | Purpose: We aim to implement a 3D DWI sequence and show its usage on patients with new ischemic lesions. Materials and Methods: The proposed 3D DWI sequence was implemented by integrating second-order gradient moment nulling (M2) and cardiac motion synchronization (Sync). All data were acquired on a 3T MAGNETOM Prisma scanner (Siemens Healthcare, Erlangen, Germany) using a 64 channel head and neck coil. 21 healthy volunteers underwent 3D DWI scans at 0.9 mm isotropic resolution using four motion compensation methods for comparison: no compensation (M0), M2 only, Sync only and the proposed M2+Sync method. 2D phase variation maps with different motion compensation methods were also acquired for one subject to illustrate the mechanism of the proposed method. A ghost-to-signal ratio (GSR) and blurring index was defined and compared among the four methods with repeated measures ANOVA and Tukey's test. 3D DWI was compared with 2D DWI for ADC quantification. Image quality and ischemic lesion conspicuity were evaluated with 12 patients after endovascular treatment. Results: Whole brain 3D DWI was achieved at 0.9 mm isotropic resolution within 5 minutes using the proposed sequence. M2+Sync achieved the lowest level of GSR and blurring along the slice direction. ADC quantification showed no statistically significant difference between M2+Sync compared to 2D DWI. 3D DWI showed similar image quality, higher lesion conspicuity and counts compared to 2D DWI. Conclusion: Direct 3D DWI can be achieved by the combination of second order gradient moment nulling and cardiac synchronization. | 2024-09-13 |