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10.1101/671024 | DREAM Interrupted: Severing LIN-35-MuvB association in Caenorhabditis elegans impairs DREAM function but not its chromatin localization | The mammalian pocket protein family, which includes the Retinoblastoma protein (pRb) and Rb-like pocket proteins p107 and p130, regulates entry into and exit from the cell cycle by repressing cell cycle gene expression. Although pRb plays a dominant role in mammalian systems, p107 and p130 are the ancestral pocket proteins. The Rb-like pocket proteins interact with the highly conserved 5-subunit MuvB complex and an E2F-DP transcription factor heterodimer, forming the DREAM (for Dp, Rb-like, E2F, and MuvB) complex. DREAM complex assembly on chromatin culminates in repression of target genes mediated by the MuvB subcomplex. Here, we examined how the Rb-like pocket protein contributes to DREAM formation and function by disrupting the interaction between the sole Caenorhabditis elegans pocket protein LIN-35 and the MuvB subunit LIN-52 using CRISPR/Cas9 targeted mutagenesis. A triple alanine substitution of LIN-52s LxCxE motif severed LIN-35-MuvB association and caused classical DREAM mutant phenotypes, including synthetic multiple vulvae, high-temperature arrest, and ectopic expression of germline genes in the soma. However, RNA-seq revealed limited upregulation of DREAM target genes when LIN-35-MuvB association was severed, as compared to gene upregulation following LIN-35 loss. Based on chromatin immunoprecipitation, disrupting LIN-35-MuvB association did not affect the chromatin localization of E2F-DP, LIN-35, or MuvB components. In a previous study we showed that in worms lacking LIN-35, E2F-DP and MuvB chromatin occupancy was reduced genome-wide. With LIN-35 present but unable to associate with MuvB, our present study suggests that the E2F-DP-LIN-35 interaction promotes E2F-DPs chromatin localization, which we hypothesize supports MuvB chromatin occupancy indirectly through DNA. Altogether, this study highlights how the pocket proteins association with MuvB supports DREAM function but is not required for DREAMs chromatin occupancy. | molecular biology |
10.1101/671289 | Agonist-independent Prostaglandin EP3 Receptor signaling is required to prevent insulin hypersecretion and metabolic dysfunction in a non-obese mouse model of insulin resistance | When homozygous for the LeptinOb mutation (Ob), Black-and-Tan Brachyury (BTBR) mice become morbidly obese and severely insulin resistant, and by 10 weeks of age, frankly diabetic. Previous work has shown Prostaglandin EP3 Receptor (EP3) expression and activity is up-regulated in islets from BTBR-Ob mice as compared to lean controls, actively contributing to their beta-cell dysfunction. In this work, we aimed to test the impact of beta-cell-specific EP3 loss on the BTBR-Ob phenotype by crossing Ptger3 floxed mice with the Rat insulin promoter (RIP)-CreHerr driver strain. Instead, germline recombination of the floxed allele in the founder mouse - an event whose prevalence we identified as directly associated with underlying insulin resistance of the background strain - generated a full-body knockout. Full-body EP3 loss provided no diabetes protection to BTBR-Ob mice, but, unexpectedly, significantly worsened BTBR-lean insulin resistance and glucose tolerance. This in vivo phenotype was not associated with changes in beta-cell fractional area or markers of beta-cell replication ex vivo. Instead, EP3-null BTBR-lean islets had essentially uncontrolled insulin hypersecretion. The selective up-regulation of constitutively-active EP3 splice variants in islets from young, lean BTBR mice as compared to C57BL/6J, where no phenotype of EP3 loss has been observed, provides a potential explanation for the hypersecretion phenotype. In support of this, high islet EP3 expression in Balb/c females vs. Balb/c males was fully consistent with their sexually-dimorphic metabolic phenotype after loss of EP3-coupled Gz protein. Taken together, our findings provide a new dimension to the understanding of EP3 as a critical brake on insulin secretion.
New and NoteworthyIslet Prostaglandin EP3 receptor (EP3) signaling is well-known as up-regulated in the pathophysiological conditions of type 2 diabetes, contributing to beta-cell dysfunction. Unexpected findings in mouse models of non-obese insulin sensitivity and resistance provide a new dimension to our understanding of EP3 as a key modulator of insulin secretion. A previously-unknown relationship between mouse insulin resistance and the penetrance of Rat insulin promoter-driven germline floxed allele recombination is critical to consider when creating beta-cell-specific knockouts.
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10.1101/671289 | Prostaglandin EP3 Receptor signaling is required to prevent insulin hypersecretion and metabolic dysfunction in a non-obese mouse model of insulin resistance | When homozygous for the LeptinOb mutation (Ob), Black-and-Tan Brachyury (BTBR) mice become morbidly obese and severely insulin resistant, and by 10 weeks of age, frankly diabetic. Previous work has shown Prostaglandin EP3 Receptor (EP3) expression and activity is up-regulated in islets from BTBR-Ob mice as compared to lean controls, actively contributing to their beta-cell dysfunction. In this work, we aimed to test the impact of beta-cell-specific EP3 loss on the BTBR-Ob phenotype by crossing Ptger3 floxed mice with the Rat insulin promoter (RIP)-CreHerr driver strain. Instead, germline recombination of the floxed allele in the founder mouse - an event whose prevalence we identified as directly associated with underlying insulin resistance of the background strain - generated a full-body knockout. Full-body EP3 loss provided no diabetes protection to BTBR-Ob mice, but, unexpectedly, significantly worsened BTBR-lean insulin resistance and glucose tolerance. This in vivo phenotype was not associated with changes in beta-cell fractional area or markers of beta-cell replication ex vivo. Instead, EP3-null BTBR-lean islets had essentially uncontrolled insulin hypersecretion. The selective up-regulation of constitutively-active EP3 splice variants in islets from young, lean BTBR mice as compared to C57BL/6J, where no phenotype of EP3 loss has been observed, provides a potential explanation for the hypersecretion phenotype. In support of this, high islet EP3 expression in Balb/c females vs. Balb/c males was fully consistent with their sexually-dimorphic metabolic phenotype after loss of EP3-coupled Gz protein. Taken together, our findings provide a new dimension to the understanding of EP3 as a critical brake on insulin secretion.
New and NoteworthyIslet Prostaglandin EP3 receptor (EP3) signaling is well-known as up-regulated in the pathophysiological conditions of type 2 diabetes, contributing to beta-cell dysfunction. Unexpected findings in mouse models of non-obese insulin sensitivity and resistance provide a new dimension to our understanding of EP3 as a key modulator of insulin secretion. A previously-unknown relationship between mouse insulin resistance and the penetrance of Rat insulin promoter-driven germline floxed allele recombination is critical to consider when creating beta-cell-specific knockouts.
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org.highwire.dtl.DTLVardef@15cf1d5org.highwire.dtl.DTLVardef@108f565org.highwire.dtl.DTLVardef@126e479org.highwire.dtl.DTLVardef@61fdf8_HPS_FORMAT_FIGEXP M_FIG C_FIG | physiology |
10.1101/671362 | Curiosity eliminates the exploration-exploitation dilemma | Balancing exploration with exploitation is seen as a mathematically intractable dilemma that all animals face. In this paper, we provide an alternative view of this classic problem that does not depend on exploring to optimize for reward. We argue that the goal of exploration should be pure curiosity, or learning for learnings sake. Through theory and simulations we prove that explore-exploit problems based on this can be solved by a simple rule that yields optimal solutions: when information is more valuable than rewards, be curious, otherwise seek rewards. We show that this rule performs well and robustly under naturalistic constraints. We suggest three criteria can be used to distinguish our approach from other theories. | animal behavior and cognition |
10.1101/671362 | Curiosity eliminates the exploration-exploitation dilemma | Balancing exploration with exploitation is seen as a mathematically intractable dilemma that all animals face. In this paper, we provide an alternative view of this classic problem that does not depend on exploring to optimize for reward. We argue that the goal of exploration should be pure curiosity, or learning for learnings sake. Through theory and simulations we prove that explore-exploit problems based on this can be solved by a simple rule that yields optimal solutions: when information is more valuable than rewards, be curious, otherwise seek rewards. We show that this rule performs well and robustly under naturalistic constraints. We suggest three criteria can be used to distinguish our approach from other theories. | animal behavior and cognition |
10.1101/671362 | Embracing curiosity eliminates the exploration-exploitation dilemma | Balancing exploration with exploitation is seen as a mathematically intractable dilemma that all animals face. In this paper, we provide an alternative view of this classic problem that does not depend on exploring to optimize for reward. We argue that the goal of exploration should be pure curiosity, or learning for learnings sake. Through theory and simulations we prove that explore-exploit problems based on this can be solved by a simple rule that yields optimal solutions: when information is more valuable than rewards, be curious, otherwise seek rewards. We show that this rule performs well and robustly under naturalistic constraints. We suggest three criteria can be used to distinguish our approach from other theories. | animal behavior and cognition |
10.1101/671529 | Histopathological Study Of Different Organs Of Charles Foster Rats Under The Exposure Of Pueraria tuberosa | The present study was undertaken to investigate the safe doses of Pueraria tuberosa water extract (PTWE) on different organs. The OECD guidelines 407 of repeated toxicity was followed with respect to the selection of dose and days for different organs. The selected doses of PTWE were 250, 500, 1000 and 2000 mg/kg b wt for 7, 14, 21 and 28 days. Haematoxylin and eosin staining was used to study the morphological alterations in heart, intestine, testis, adrenal gland and spleen. In the present study, no adverse alterations in cardiac fibers of the heart, size and shapes in crypts and villi of intestine, seminiferous tubules and spermatozoa count in testis, three zones of adrenal gland, and spleen were seen in all treated groups of PTWE. There were no adverse morphological alterations found in described organs. The PTWE are safe at 1000 mg/kg b wt. up to 28 days and 2000 mg/ kg b. wt up to 21 days, respectively. | pharmacology and toxicology |
10.1101/671891 | Modeling and Characterization of Inter-Individual Variability in CD8 T Cell Responses in Mice | To develop vaccines it is mandatory yet challenging to account for inter-individual variability during immune responses. Even in laboratory mice, T cell responses of single individuals exhibit a high heterogeneity that may come from genetic backgrounds, intra-specific processes (e.g. antigen-processing and presentation) and immunization protocols.
To account for inter-individual variability in CD8 T cell responses in mice, we propose a dynamical model coupled to a statistical, nonlinear mixed effects model. Average and individual dynamics during a CD8 T cell response are characterized in different immunization contexts (vaccinia virus and tumor). On one hand, we identify biological processes that generate inter-individual variability (activation rate of naive cells, the mortality rate of effector cells, and dynamics of the immunogen). On the other hand, introducing categorical covariates to analyze two different immunization regimens, we highlight the steps of the response impacted by immunogens (priming, differentiation of naive cells, expansion of effector cells and generation of memory cells). The robustness of the model is assessed by confrontation to new experimental data.
Our approach allows to investigate immune responses in various immunization contexts, when measurements are scarce or missing, and contributes to a better understanding of inter-individual variability in CD8 T cell immune responses. | immunology |
10.1101/672618 | Binned Relative Environmental Change Indicator (BRECI): A tool to communicate the nature of differences between environmental niche model outputs | Niche models are now widely used in many branches of the biological sciences and are often used to contrast the distribution of favourable environments between regions or under changes in environmental conditions such as climate change. Evaluating model performance and selecting optimal models is now accepted as best-practice, and a number of methods are available assist this process. One aspect of ENM application which has not received as much attention is developing methods to communicate the degree and nature of changes between model outputs (typically as raster maps). The method described in this paper, Binned Relative Environmental Change Index (BRECI), seeks to address this shortfall in communicating model results. | ecology |
10.1101/674051 | Easy Kinetics: a novel enzyme kinetic characterization software | Here will be presented the software Easy Kinetics, a publicly available graphical interface that allows rapid evaluation of the main kinetics parameters in an enzyme catalyzed reaction. In contrast to other similar commercial software using algorithms based on non-linear regression models to reach these results, Easy Kinetics is based on a completely different original algorithm, requiring in input the spectrophotometric measurements of {Delta}Abs/min taken twice at only two different substrate concentrations. The results generated show however a significant concordance with those ones obtained with the most common commercial software used for enzyme kinetics characterization, GraphPad Prism 8(C), suggesting that Easy Kinetics can be used for routine tests in enzyme kinetics as an alternative valid software. | biochemistry |
10.1101/674259 | Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma | B-cell non-Hodgkins lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis. | genomics |
10.1101/677393 | Single EGF mutants unravel the mechanism for stabilization of Epidermal Growth Factor Receptor (EGFR) system | The Epidermal Growth Factor Receptor (EGFR) is a membrane-anchored tyrosine kinase that is able to selectively respond to multiple extra-cellular stimuli. Previous studies have indicated that the modularity of this system is affected by ligand-induced differences in the stability of the dimerized receptor in a process known as "Biased signaling". However, this hypothesis has not been explored using single-mutant ligands thus far. Herein, we developed a new approach to identify residues responsible for functional divergence combining the conservation and co-evolution information of ortholog and paralog genes encoding the epidermal growth factor (EGF) ligand. Then, we mutated these residues and assessed the mutants effects on the receptor by employing a combination of molecular dynamics (MD) and biochemical techniques. Although the EGF mutants had comparable binding affinities to the wild type ligand for EGFR, the EGF mutants induced a different phosphorylation and cell growth pattern in multiple cell lines. The MD simulations of the EGF mutants show a long-range effect on the receptor dimer interface. For the first time in this study, a single mutation in EGF is shown to be enough to alter the activation of the pathway at the cellular level. These results also support the theory of biased signaling in the tyrosine kinase receptor system and demonstrate a promising new way to study ligand-receptor interactions. | bioinformatics |
10.1101/677393 | Binding of single-mutant epidermal growth factor (EGF) ligands alter the stability of the EGF receptor dimer and promote growth signaling | The Epidermal Growth Factor Receptor (EGFR) is a membrane-anchored tyrosine kinase that is able to selectively respond to multiple extra-cellular stimuli. Previous studies have indicated that the modularity of this system is affected by ligand-induced differences in the stability of the dimerized receptor in a process known as "Biased signaling". However, this hypothesis has not been explored using single-mutant ligands thus far. Herein, we developed a new approach to identify residues responsible for functional divergence combining the conservation and co-evolution information of ortholog and paralog genes encoding the epidermal growth factor (EGF) ligand. Then, we mutated these residues and assessed the mutants effects on the receptor by employing a combination of molecular dynamics (MD) and biochemical techniques. Although the EGF mutants had comparable binding affinities to the wild type ligand for EGFR, the EGF mutants induced a different phosphorylation and cell growth pattern in multiple cell lines. The MD simulations of the EGF mutants show a long-range effect on the receptor dimer interface. For the first time in this study, a single mutation in EGF is shown to be enough to alter the activation of the pathway at the cellular level. These results also support the theory of biased signaling in the tyrosine kinase receptor system and demonstrate a promising new way to study ligand-receptor interactions. | bioinformatics |
10.1101/677617 | Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory | It has been an established idea in recent years that protein is a physiochemically connected network. Allostery, understood in this new context, is a manifestation of residue communicating between remote sites in this network, and hence a rising interest to identify functionally relevant communication pathways and the frequent communicators within. However, there have been limited computationally trackable general methods to discover proteins allosteric sites in atomistic resolution with good accuracy. In this study, we devised a time-dependent linear response theory (td-LRT) integrating intrinsic protein dynamics and perturbation forces that excite proteins temporary reconfiguration at the non-equilibrium state, to describe atom-specific time responses as the propagating mechanical signals and discover that the most frequent remote communicators can be important allosteric sites, mutation of which could deteriorate the hydride transfer rate in DHFR by 3 orders. The preferred directionality of the signal propagation can be inferred from the asymmetric connection matrix (CM), where the coupling strength between a pair of residues is suggested by their communication score (CS) in the CM, which is found consistent with experimentally characterized nonadditivity of double mutants. Also, the intramolecular communication centers (ICCs), having high CSs, are found evolutionarily conserved, suggesting their biological importance. We also identify spatially clustered top ICCs as the newly found allosteric site in ATG4B. Among 2016 FDA-approved drugs screened to target the site, two interacting with the site most favorably, confirmed by MD simulations, are found to inhibit ATG4B biochemically and be tumor suppressive in colorectal, pancreatic and breast cancer cell lines with an observed additive therapeutic effect when co-used with an active-site inhibitor. | biophysics |
10.1101/678920 | Reproducible microbial community dynamics of two drinking water systems treating similar source waters. | Understanding whether the spatial-temporal dynamics of the drinking water microbiome are reproducible in full-scale drinking water systems is an important step towards devising engineering strategies to manipulate it. Yet, direct comparisons across full-scale drinking water systems are challenging because multiple factors, from source water to treatment process choice and configuration, can be unique to each system. This study compared the spatial-temporal dynamics of the drinking water microbiome in two drinking water treatment plants (DWTPs) with identical sequence of treatment strategies treating source waters from the same river system and with treated drinking water distributed in same large-scale (but independent) distribution system (DWDS) with similar disinfectant residual regiment. Dissimilarities in source water communities were tempered by the pre-disinfection treatments, resulting in highly similar post-filtration microbial communities between the two systems. However, high community turnover due to disinfection resulted in highly dissimilar microbial communities in the finished water between the two systems. Interestingly however, the microbial communities in the two systems increased in similarity during transit through the DWDS despite presence of a disinfectant residual. Overall our study finds that the drinking water microbiome demonstrated reproducible spatial and temporal dynamics within both independent but nearly identical DWTPs and their corresponding DWDSs.
Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY | microbiology |
10.1101/671925 | Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations | Genetic association studies seek to uncover the link between genotype and phenotype, and often utilize inbred reference panels as a replicable source of genetic variation. However, inbred reference panels can differ substantially from wild populations in their genotypic distribution, patterns of linkage-disequilibrium, and nucleotide diversity. As a result, associations discovered using inbred reference panels may not reflect the genetic basis of phenotypic variation in natural populations. To address this problem, we evaluated a mapping population design where dozens to hundreds of inbred lines are outbred for few generations, which we call the Hybrid Swarm. The Hybrid Swarm approach has likely remained underutilized relative to pre-sequenced inbred lines due to the costs of genome-wide genotyping. To reduce sequencing costs and make the Hybrid Swarm approach feasible, we developed a computational pipeline that reconstructs accurate whole genomes from ultra-low-coverage (0.05X) sequence data in Hybrid Swarm populations derived from ancestors with phased haplotypes. We evaluate reconstructions using genetic variation from the Drosophila Genetic Reference Panel as well as variation from neutral simulations. We compared the power and precision of GWAS using the Hybrid Swarm, inbred lines, recombinant inbred lines, and highly outbred populations across a range of allele frequencies, effect sizes, and genetic architectures. Our simulations show that these different mapping panels vary in their power and precision, largely depending on the architecture of the trait. The Hybrid Swam and RILs outperform inbred lines for quantitative traits, but not for monogenic ones. Taken together, our results demonstrate the feasibility of the Hybrid Swarm as a cost-effective method of fine-scale genetic mapping. | genetics |
10.1101/679472 | Artisanal and farmers bread making practices differently shape fungal species diversity in French sourdoughs | Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider diversity of microbial species. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyse French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Their bread making practices were classified in two groups: the farmer- like practices group and the artisanal-like practices group. Surprisingly, the well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species of the closely related Kazachstania genus were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of yeast species. The most remarkable difference was the occurrence of Kazachstania humilis in sourdoughs made with artisanal- like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotyping of these two species in laboratory sourdough mimicking media revealed signatures of domestication for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practices diversity allows the preservation of a higher taxonomic and phenotypic diversity in microbial communities. | ecology |
10.1101/681023 | Estimation of Speciation Times Under the Multispecies Coalescent | MotivationThe coalescent model is now widely accepted as an effective model for incorporating variation in the evolutionary histories of individual genes into methods for phylogenetic inference from genome-scale data. However, because model-based analysis under the coalescent can be computationally expensive for large data sets, a variety of inferential frameworks and corresponding algorithms have been proposed for estimation of species-level phylogenies and the associated parameters, including the speciation times and effective population sizes.
ResultsWe consider the problem of estimating the timing of speciation events along a phylogeny in a coalescent framework. We propose a maximum a posteriori estimator based on composite likelihood (MAPCL) for inferring these speciation times under a model of DNA sequence evolution for which exact site pattern probabilities can be computed. We demonstrate that the MAPCL estimates are statistically consistent and asymptotically normally distributed, and we show how this result can be used to estimate their asymptotic variance. We also provide a more computationally efficient estimator of the asymptotic variance based on the nonparametric bootstrap. We evaluate the performance of our method using simulation and by application to an empirical dataset for gibbons.
Availability and implementationThe method has been implemented in the PAUP* program, freely available at https://paup.phylosolutions.com for Macintosh, Windows, and Linux operating systems.
Contactpeng.650@osu.edu
Supplementary informationSupplementary data are available at Bioinformatics online. | evolutionary biology |
10.1101/682518 | Formation of synthetic RNP granules using engineered phage-coat-protein -RNA complexes | Observations of RNA-protein (RNP) granules within living cells have generated important insights on intracellular processes in recent years. Here, we demonstrate that PP7-coat protein (PCP) and Q{beta}-coat protein (QCP) co-expressed with synthetic long non-coding RNA (slncRNA) encoded with multiple CP binding sites self-assemble into phase-separated synthetic RNP (SRNP) granules within E. coli cells and in vitro. SNRP granules exhibit hallmarks of RNP granule formation including phase separation from a semi-dilute liquid in vitro, and retention of structure after cell lysis. In vivo real-time tracking of SRNP granules reveals that they are found in cell poles of exponentially growing cells, and that their structure exhibits gel-like properties by the slow stochastic insertion and shedding of CP-slncRNA complexes. We propose a transcriptional model that takes into account the cytosolic structure of E. coli (i.e., the cytosol is divided into a biomolecularly dense domain in the nucleoid-dominated region and a dilute liquid domain in the polar regions), and use it to provide a theoretical framework for explaining the increase in intracellular CP-titer as a function slncRNA structure, and the appearance of SRNP granules in non-polar regions of stationary phase cells. Consequently, the SRNP-granule data and resultant model has implications for various bacterial transcriptional and translational processes, and provides an alternative explanation for the super-Poisson kinetics attributed to transcriptional bursts.
Introductory paragraphsynthetic long non-coding RNA molecules encoded with multiple phage coat protein binding sites form phase separated RNP granules when co-expressed with their cognate binding proteins. | biophysics |
10.1101/685537 | Complement C3 and C3aR mediate different aspects of emotional behaviours; relevance to risk for psychiatric disorder | Complement is a key component of the immune system with roles in inflammation and host-defence. Here we reveal novel functions of complement pathways impacting on emotional reactivity of potential relevance to the emerging links between complement and risk for psychiatric disorder. We used mouse models to assess the effects of manipulating components of the complement system on emotionality. Mice lacking the complement C3a Receptor (C3aR-/-) demonstrated a selective increase in unconditioned (innate) anxiety whilst mice deficient in the central complement component C3 (C3-/-) showed a selective increase in conditioned (learned) fear. The dissociable behavioural phenotypes were linked to different signalling mechanisms. Effects on innate anxiety were independent of C3a, the canonical ligand for C3aR, consistent with the existence of an alternative ligand mediating innate anxiety, whereas effects on learned fear were due to loss of iC3b/CR3 signalling. Our findings show that specific elements of the complement system and associated signalling pathways contribute differentially to heightened states of anxiety and fear commonly seen in psychopathology. | neuroscience |
10.1101/685610 | Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases | Hundreds of leucine-rich repeat receptor kinases (LRR-RKs) have evolved to control diverse processes of growth, development, and immunity in plants; the mechanisms that link LRR-RKs to distinct cellular responses are not understood. Here we show that two LRR-RKs, the brassinosteroid hormone receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) and the flagellin receptor FLS2 (FLAGELLIN SENSING 2), regulate downstream glycogen synthase kinase 3 (GSK3) and mitogen-activated protein (MAP) kinases, respectively, through phosphocoding of the BRI1-SUPPRESSOR1 (BSU1) phosphatase. BSU1 was previously identified as a component that inactivates GSK3s in the BRI1 pathway. We found surprisingly that loss of the BSU1 family phosphatases activates effector-triggered immunity (ETI) and impairs flagellin-triggered MAP kinase activation and immunity. The flagellin-activated BOTRYTIS-INDUCED KINASE 1 (BIK1) phosphorylates BSU1 at serine-251. Mutation of serine-251 reduces the ability of BSU1 to mediate flagellin-induced MAP kinase activation and immunity, but not its abilities to suppress ETI and interact with GSK3, which is enhanced through the phosphorylation of BSU1 at serine-764 upon brassinosteroid signaling. These results demonstrate that BSU1 plays an essential role in immunity and transduces brassinosteroid-BRI1 and flagellin-FLS2 signals using different phosphorylation sites. Our study illustrates that phosphocoding in shared downstream components provides signaling specificities for diverse plant receptor kinases. | plant biology |
10.1101/685610 | Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases | Hundreds of leucine-rich repeat receptor kinases (LRR-RKs) have evolved to control diverse processes of growth, development, and immunity in plants; the mechanisms that link LRR-RKs to distinct cellular responses are not understood. Here we show that two LRR-RKs, the brassinosteroid hormone receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) and the flagellin receptor FLS2 (FLAGELLIN SENSING 2), regulate downstream glycogen synthase kinase 3 (GSK3) and mitogen-activated protein (MAP) kinases, respectively, through phosphocoding of the BRI1-SUPPRESSOR1 (BSU1) phosphatase. BSU1 was previously identified as a component that inactivates GSK3s in the BRI1 pathway. We found surprisingly that loss of the BSU1 family phosphatases activates effector-triggered immunity (ETI) and impairs flagellin-triggered MAP kinase activation and immunity. The flagellin-activated BOTRYTIS-INDUCED KINASE 1 (BIK1) phosphorylates BSU1 at serine-251. Mutation of serine-251 reduces the ability of BSU1 to mediate flagellin-induced MAP kinase activation and immunity, but not its abilities to suppress ETI and interact with GSK3, which is enhanced through the phosphorylation of BSU1 at serine-764 upon brassinosteroid signaling. These results demonstrate that BSU1 plays an essential role in immunity and transduces brassinosteroid-BRI1 and flagellin-FLS2 signals using different phosphorylation sites. Our study illustrates that phosphocoding in shared downstream components provides signaling specificities for diverse plant receptor kinases. | plant biology |
10.1101/685743 | The whale shark genome reveals patterns of vertebrate gene family evolution | Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer. | genomics |
10.1101/687137 | CHD4-NURD controls mouse neonate spermatogonia survival | Testis development and sustained germ cell production in adults rely on the establishment and maintenance of spermatogonia stem cells and their proper differentiation into spermatocytes. Chromatin remodeling complexes regulate critical processes during gamete development by restricting or promoting accessibility of DNA repair and gene expression machineries to the chromatin. Here, we investigated the role of CHD4 and CHD3 catalytic subunits of the NURD complex during spermatogenesis. Germ cell-specific deletion of Chd4 early in gametogenesis, but not Chd3, resulted in arrested early gamete development due to failed cell survival of neonate undifferentiated spermatogonia stem cell population. Candidate assessment revealed that CHD4 controls expression of Dmrt1 and its downstream target Plzf, both described as prominent regulators of spermatogonia stem cell maintenance. Our results show the requirement of CHD4 in mammalian gametogenesis pointing to functions in gene expression early in the process. | developmental biology |
10.1101/687137 | Mouse CHD4-NURD is required for spermatogonia survival and normal meiotic progression | Testis development and sustained germ cell production in adults rely on the establishment and maintenance of spermatogonia stem cells and their proper differentiation into spermatocytes. Chromatin remodeling complexes regulate critical processes during gamete development by restricting or promoting accessibility of DNA repair and gene expression machineries to the chromatin. Here, we investigated the role of CHD4 and CHD3 catalytic subunits of the NURD complex during spermatogenesis. Germ cell-specific deletion of Chd4 early in gametogenesis, but not Chd3, resulted in arrested early gamete development due to failed cell survival of neonate undifferentiated spermatogonia stem cell population. Candidate assessment revealed that CHD4 controls expression of Dmrt1 and its downstream target Plzf, both described as prominent regulators of spermatogonia stem cell maintenance. Our results show the requirement of CHD4 in mammalian gametogenesis pointing to functions in gene expression early in the process. | developmental biology |
10.1101/687137 | Mouse CHD4-NURD is required for neonatal spermatogonia survival and normal gonad development | Testis development and sustained germ cell production in adults rely on the establishment and maintenance of spermatogonia stem cells and their proper differentiation into spermatocytes. Chromatin remodeling complexes regulate critical processes during gamete development by restricting or promoting accessibility of DNA repair and gene expression machineries to the chromatin. Here, we investigated the role of CHD4 and CHD3 catalytic subunits of the NURD complex during spermatogenesis. Germ cell-specific deletion of Chd4 early in gametogenesis, but not Chd3, resulted in arrested early gamete development due to failed cell survival of neonate undifferentiated spermatogonia stem cell population. Candidate assessment revealed that CHD4 controls expression of Dmrt1 and its downstream target Plzf, both described as prominent regulators of spermatogonia stem cell maintenance. Our results show the requirement of CHD4 in mammalian gametogenesis pointing to functions in gene expression early in the process. | developmental biology |
10.1101/687061 | MERTK on mononuclear phagocytes regulates T cell antigen recognition at autoimmune and tumor sites | Understanding mechanisms of immune regulation is key to developing immunotherapies for autoimmunity and cancer. We examined the role of mononuclear phagocytes during peripheral T cell regulation in type 1 diabetes and melanoma. MERTK expression and activity in mononuclear phagocytes in the pancreatic islets, promoted islet T cell regulation, resulting in reduced sensitivity of T cell scanning for cognate antigen in pre-diabetic islets. MERTK-dependent regulation led to reduced T cell activation and effector function at the disease site in the islets and prevented rapid progression of type 1 diabetes. In human islets, MERTK-expressing cells were increased in remaining insulin-containing islets of type 1 diabetic patients, suggesting that MERTK protects the islets from autoimmune destruction. MERTK also regulated T cell arrest in melanoma tumors. These data indicate that MERTK signaling in mononuclear phagocytes drives T cell regulation at inflammatory disease sites in peripheral tissues through a mechanism that reduces the sensitivity of scanning for antigen leading to reduced responsiveness to antigen. | immunology |
10.1101/687954 | Label-retention expansion microscopy | Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with super-resolution Stochastic Optical Reconstruction Microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ. | bioengineering |
10.1101/689851 | A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data | High-dimensional data are becoming increasingly common in nearly all areas of science. Developing approaches to analyze these data and understand their meaning is a pressing issue. This is particularly true for single-cell RNA-seq (scRNA-seq), a technique that simultaneously measures the expression of tens of thousands of genes in thousands to millions of single cells. The emerging consensus for analysis workflows significantly reduces the dimensionality of the dataset before performing downstream analysis, such as assignment of cell types. One problem with this approach is that dimensionality reduction can introduce substantial distortion into the data; consider the familiar example of trying to represent the three-dimensional earth as a two-dimensional map. It is currently unclear if such distortion affects analysis of scRNA-seq data. Here, we introduce a straightforward approach to quantifying this distortion by comparing the local neighborhoods of points before and after dimensionality reduction. We found that popular techniques like t-SNE and UMAP introduce substantial distortion even for relatively simple simulated data sets. For scRNA-seq data, we found the distortion in local neighborhoods was often greater than 95% in the representations typically used for downstream analyses. This level of distortion can introduce errors into cell type identification, pseudotime ordering, and other analyses. We found that principal component analysis can generate accurate embeddings, but only when using dimensionalities that are much higher than typically used in scRNA-seq analysis. Our work suggests the need for a new generation of dimensional reduction algorithms that can accurately embed high dimensional data in its true latent dimension. | bioinformatics |
10.1101/689851 | A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data | High-dimensional data are becoming increasingly common in nearly all areas of science. Developing approaches to analyze these data and understand their meaning is a pressing issue. This is particularly true for single-cell RNA-seq (scRNA-seq), a technique that simultaneously measures the expression of tens of thousands of genes in thousands to millions of single cells. The emerging consensus for analysis workflows significantly reduces the dimensionality of the dataset before performing downstream analysis, such as assignment of cell types. One problem with this approach is that dimensionality reduction can introduce substantial distortion into the data; consider the familiar example of trying to represent the three-dimensional earth as a two-dimensional map. It is currently unclear if such distortion affects analysis of scRNA-seq data. Here, we introduce a straightforward approach to quantifying this distortion by comparing the local neighborhoods of points before and after dimensionality reduction. We found that popular techniques like t-SNE and UMAP introduce substantial distortion even for relatively simple simulated data sets. For scRNA-seq data, we found the distortion in local neighborhoods was often greater than 95% in the representations typically used for downstream analyses. This level of distortion can introduce errors into cell type identification, pseudotime ordering, and other analyses. We found that principal component analysis can generate accurate embeddings, but only when using dimensionalities that are much higher than typically used in scRNA-seq analysis. Our work suggests the need for a new generation of dimensional reduction algorithms that can accurately embed high dimensional data in its true latent dimension. | bioinformatics |
10.1101/689737 | Epithelial-Mesenchymal Plasticity is regulated by inflammatory signalling networks coupled to cell morphology. | Morphology dictates how cells sense physical and soluble cues in their environment; thus contributing to fate decisions. The differentiation of epithelial cells into mesenchymal forms, or epithelial-mesenchymal plasticity (EMP), is essential for metazoan development and homeostasis. Here we show that the decision to engage EMP is coupled to cell morphology by cell-cell adhesions by microtubule and nuclear organization (MTNO). Using an integrative omic approach we identify Junctional Adhesion Molecule 3 (JAM3) as a new tumour suppressor in breast cancer patients. JAM3 depletion in epithelial cells alters MTNO and causes differentiation into mesenchymal forms. Soluble TGF{beta} also changes MTNO, and synergizes with JAM3 depletion to promote mesenchymal morphogenesis. Through systematic proteomic analysis we show that changes in MTNO lead to the upregulation of an inflammatory signalling network where YAP/TAZ, FOXO, IKK-NFKB, and JNK pathways are active; but where insulin signalling is suppressed. The actions of the MT-motor Kinesin-1 serve to both change MTNO and promote the upregulation of the core EMP network. Critically, the upregulation of the EMP network predicts the mesenchymal state across cancers.
Graphical Abstract
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org.highwire.dtl.DTLVardef@6ab6d1org.highwire.dtl.DTLVardef@8787borg.highwire.dtl.DTLVardef@1dff5dorg.highwire.dtl.DTLVardef@16856a1_HPS_FORMAT_FIGEXP M_FIG C_FIG | systems biology |
10.1101/690792 | A minimal model of neural computation with dendritic plateau potentials. | AO_SCPLOWBSTRACTC_SCPLOWOver the last two decades, advances in neurobiology have established the essential role of active processes in neural dendrites for almost every aspect of cognition, but how these processes contribute to neural computation remains an open question. We show how two kinds of events within the dendrite, synaptic spikes and localized dendritic plateau potentials, interact on two distinct timescales to give rise to a powerful model of neural computation. In this theoretical model called dendritic plateau computation, a neurons computational function is determined by the compartmentalization of its dendritic tree into functionally independent but mutually coupled segments. We demonstrate the versatility of this mechanism in a simulated navigation experiment, where it allows an individual neuron to reliably detect a specific movement trajectory over hundreds of milliseconds with a high tolerance for timing variability. We conclude by discussing the implications of this model for our understanding of neural computation. | neuroscience |
10.1101/691089 | A Mendelian randomization study of the role of lipoprotein subfractions in coronary artery disease | Recent genetic data can offer important insights into the roles of lipoprotein subfractions and particle sizes in preventing coronary artery disease (CAD), as previous observational studies have often reported conflicting results. In this study, we first used the LD score regression to estimate the genetic correlation of 77 subfraction traits with traditional lipid profile and identified 27 traits that may involve distinct genetic mechanisms. We then used Mendelian randomization (MR) to estimate the causal effect of these traits on the risk of CAD. In univariable MR, the concentration and content of medium high-density lipoprotein (HDL) particles showed a protective effect against coronary artery disease. The effect was not attenuated in multivariable MR that adjusted for traditional lipid profile. The multivariable MR analyses also found that small HDL particles and smaller mean HDL particle diameter may have a protective effect. We identified four genetic markers for HDL particle size and CAD. | genetics |
10.1101/691857 | DNA end-resection in highly accessible chromatin produces a toxic break | The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further.
Despite repetitive attempts to reproduce the data shown in figure 2I, we have failed to obtain convincing evidence that chemical inhibition of Mre11 can improve the fitness of cells exposed to the so-called "halt" breaks. Upon re-analysis of the raw data used to compose figure 2I, we noted inconsistencies in the inclusion of datapoints, for which a satisfactory motivation was not apparent.
In order to reproduce the experiments with the DNA-PK inhibitor, we ordered new batches of this compound, but noticed that the IC50 was significantly lower than that of the earlier batch (as determined in suppl. fig.1). While this might be due to a difference in batches, the IC50 of the newer batches was more comparable to the IC50 of this compound described for other cell lines. This sheds doubts on the quality of the batch used for the experiments shown in our manuscript, and we no longer wish to draw any conclusions based on these experiments.
The authors hope that future experiments can resolve if open chromatin does indeed produce a potentially more toxic DNA break. The authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. | cell biology |
10.1101/690651 | Mechanics of MTOC clustering and spindle positioning in budding yeast Cryptococcus neoformans | The dynamic process of mitotic spindle assembly depends on multitudes of inter-dependent interactions involving kinetochores (KTs), microtubules (MTs), spindle pole bodies (SPBs), and molecular motors. Before forming the mitotic spindle, multiple visible microtubule organizing centers (MTOCs) coalesce into a single focus to serve as a SPB in the pathogenic budding yeast, Cryptococcus neoformans. To explain this unusual phenomenon in the fungal kingdom, we propose a search and capture model, in which cytoplasmic MTs (cMTs) nucleated by MTOCs grow and capture each other to promote MTOC clustering. Our quantitative modeling identifies multiple redundant mechanisms mediated by a combination of cMT-cell cortex interactions and inter-cMT coupling to facilitate MTOC clustering within the physiological time limit as determined by time-lapse live-cell microscopy. Besides, we screen various possible mechanisms by computational modeling and propose optimal conditions that favor proper spindle positioning - a critical determinant for timely chromosome segregation. These analyses also reveal that a combined effect of MT buckling, dynein pull, and cortical push maintains spatiotemporal spindle localization. | biophysics |
10.1101/692251 | Colicin E1 binds to TolC as an open hinge to penetrate the outer-membrane | The double membrane architecture of Gram-negative bacteria forms a barrier that is effectively impermeable to extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM, the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore--an architectural rearrangement from colicin E1s unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plugs the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions. | biophysics |
10.1101/692251 | Colicin E1 opens its hinge to plug TolC | The double membrane architecture of Gram-negative bacteria forms a barrier that is effectively impermeable to extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM, the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore--an architectural rearrangement from colicin E1s unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plugs the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions. | biophysics |
10.1101/692251 | Colicin E1 opens its hinge to plug TolC | The double membrane architecture of Gram-negative bacteria forms a barrier that is effectively impermeable to extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM, the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore--an architectural rearrangement from colicin E1s unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plugs the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions. | biophysics |
10.1101/691444 | Aquatic biodiversity enhances multiple nutritional benefits to humans | Humanity depends on biodiversity for health, well-being and a stable environment. As biodiversity change accelerates, we are still discovering the full range of consequences for human health and well-being. Here, we test the hypothesis -- derived from biodiversity - ecosystem functioning theory -- that species richness and ecological functional diversity allow seafood diets to fulfill multiple nutritional requirements, a condition necessary for human health. We analyzed a newly synthesized dataset of 7245 observations of nutrient and contaminant concentrations in 801 aquatic animal taxa, and found that species with different ecological traits have distinct and complementary micronutrient profiles, but little difference in protein content. The same complementarity mechanisms that generate positive biodiversity effects on ecosystem functioning in terrestrial ecosystems also operate in seafood assemblages, allowing more diverse diets to yield increased nutritional benefits independent of total biomass consumed. Notably, nutritional metrics that capture multiple micronutrients essential for human well-being depend more strongly on biodiversity than common ecological measures of function such as productivity, typically reported for grasslands and forests. Further, we found that increasing species richness did not increase the amount of protein in seafood diets, and also increased concentrations of toxic metal contaminants in the diet. Seafood-derived micronutrients are important for human health and are a pillar of global food and nutrition security. By drawing upon biodiversity-ecosystem functioning theory, we demonstrate that ecological concepts of biodiversity can deepen our understanding of natures benefits to people and unite sustainability goals for biodiversity and human well-being.
Significance statementFood security is not simply about maintaining yields, it is also about the need for a stable supply of nutritionally diverse foods. Obtaining nutritious food is a major challenge facing humanity and diverse aquatic ecosystems can help meet this goal. To test how aquatic biodiversity affects human health, we assembled a new dataset of nutrients, contaminants and ecological traits of 801 aquatic species. We used ecological models to quantify the role of species richness and ecological functional diversity and found that these biodiversity dimensions enhanced seafood micronutrient provisioning by the same mechanisms that link biodiversity to productivity in grasslands, forests and other systems. Our results underscore the need to minimize aquatic biodiversity loss to sustain and improve human well-being. | ecology |
10.1101/695577 | ORP5/8 AND MIB/MICOS LINK ER-MITOCHONDRIA AND INTRAMITOCHONDRIAL CONTACTS FOR NON-VESICULAR TRANSPORT OF PHOSPHATIDYLSERINE | Mitochondria are dynamic organelles essential for cell survival whose structural and functional integrity rely on selective and regulated transport of lipids from/to the endoplasmic reticulum (ER) and across the mitochondrial intermembrane space. As they are not connected by vesicular transport, the exchange of lipids between ER and mitochondria occurs at sites of close organelle apposition called membrane contact sites. However, the mechanisms and proteins involved in these processes are only beginning to emerge. Here, we show that the main physiological localization of the lipid transfer proteins ORP5 and ORP8 is at mitochondria-associated ER membranes (MAMs) subdomains, physically linked to the MIB/MICOS complexes that bridge the two mitochondrial membranes. We also show that ORP5/8 mediate non-vesicular transport of phosphatidylserine (PS) lipids from the ER to mitochondria by cooperating with the MIB/MICOS complexes. Overall our study reveals a novel physical and functional link between ER-mitochondria contacts involved in lipid transfer and intra-mitochondrial membranes contacts maintained by the MIB/MICOS complexes. | cell biology |
10.1101/696252 | From heterogenous morphogenetic fields to homogeneous regions as a step towards understanding complex tissue dynamics | Within developing tissues, cell proliferation, cell motility, and other cell behaviors vary spatially, and this variability gives a complexity to the morphogenesis. Recently, novel formalisms have been developed to quantify tissue deformation and underlying cellular processes. A major challenge for the study of morphogenesis now is to objectively define tissue sub-regions exhibiting different dynamics. Here we propose a method to automatically divide a tissue into regions where the local deformation rate is homogeneous. This was achieved by several steps including image segmentation, clustering, and region boundary smoothing. We illustrate the use of the pipeline using a large dataset obtained during the metamorphosis of the Drosophila pupal notum. We also adapt it to determine regions where the time evolution of the local deformation rate is homogeneous. Finally, we generalize its use to find homogeneous regions for the cellular processes such as cell division, cell rearrangement, or cell size and shape changes. We also illustrate it on wing blade morphogenesis. This pipeline will contribute substantially to the analysis of complex tissue shaping and the biochemical and bio-mechanical regulations driving tissue morphogenesis.
1 Summary statementTissue morphogenesis is driven by multiple mechanisms. This study proposes a methodology to identify regions in the developing tissue, where each of the regions has distinctive cellular dynamics and deformation. | developmental biology |
10.1101/696559 | ReCappable Seq: Comprehensive Determination of Transcription Start Sites derived from all RNA polymerases. | Determination of eukaryotic Transcription Start Sites (TSS) has been based on methods that require the cap structure at the 5 end of transcripts derived from Pol-II RNA polymerase. Consequently, these methods do not reveal TSS derived from the other RNA polymerases which also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq which comprehensively identifies TSS for both Pol-lI and non-Pol-II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5 m7G caps and 5 triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol-II TSS that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSS associated with Pol-III transcripts which have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol-II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and non-coding RNA concurrently and enables the classification of epigenetic profiles associated with Pol-lI and non-Pol-II TSS. | genomics |
10.1101/696831 | Estimates of genetic load suggest frequent purging of deleterious alleles in small populations | It is commonly thought that declining populations will experience negative genetic consequences as a result of increased inbreeding. Here we estimated the average deleteriousness of derived alleles in a range of mammals and found that species with historically small population size and low genetic diversity often have lower genetic load than species with large population sizes. This is likely the result of genetic purging - the more efficient removal of partially deleterious recessive alleles from inbred populations. Our findings suggest that genetic purging occurs over long evolutionary time frames, and therefore rapid population declines are likely to dis-proportionally increase mutational load in species with high diversity, as they carry many deleterious alleles that can reach fixation before genetic purging can remove them. | genomics |
10.1101/696724 | Mapping Transcriptomic Vector Fields of Single Cells | Single-cell RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires dynamical models capable of predicting cell fate and unveiling the governing regulatory mechanisms. Here, we introduce dynamo, an analytical framework that reconciles intrinsic splicing and labeling kinetics to estimate absolute RNA velocities, reconstructs velocity vector fields that predict future cell fates, and finally employs differential geometry analyses to elucidate the underlying regulatory networks. We applied dynamo to a wide range of disparate biological processes including prediction of future states of differentiating hematopoietic stem cell lineages, deconvolution of glucocorticoid responses from orthogonal cell-cycle progression, characterization of regulatory networks driving zebrafish pigmentation, and identification of possible routes of resistance to SARS-CoV-2 infection. Our work thus represents an important step in going from qualitative, metaphorical conceptualizations of differentiation, as exemplified by Waddingtons epigenetic landscape, to quantitative and predictive theories. | systems biology |
10.1101/696294 | Genomic and experimental evidence that alternate transcription initiation of the Anaplastic Lymphoma Kinase (ALK) kinase domain does not predict single agent sensitivity to ALK inhibitors. | Genomic data can facilitate personalized treatment decisions by enabling therapeutic hypotheses in individual patients. Conditional selection, which includes mutual exclusivity, is a signal that has been empirically useful for identifying mutations that may be sensitive to single agent targeted therapies. However, a low mutation frequency can underpower this signal for rare variants and prevent robust conclusions from genomic data. We develop a resampling based method for the direct pairwise comparison of conditional selection between sets of gene pairs. This effectively creates positive control guideposts of mutual exclusivity in known driver genes that normalizes differences in mutation abundance. We applied this method to a transcript variant of anaplastic lymphoma kinase (ALK) in melanoma, termed ALKATI, which has been the subject of a recent controversy in the literature. We reproduced some of the original cell transformation experiments, performed rescue experiments, and analyzed drug response data to revisit the original ALKATI findings. We found that ALKATI is not as mutually exclusive with BRAF or NRAS as BRAF and NRAS genes are with each other. We performed in vitro transformation assays and rescue assays that suggested that alternative transcript initiation in ALK is not likely to be sufficient for cellular transformation or growth and it does not predict single agent therapeutic dependency. Our work strongly disfavors the role of ALKATI as a targetable oncogenic driver that might be sensitive to single agent ALK treatment. The progress of other experimental agents in late-stage melanoma and our experimental and computational re-analysis led us to conclude that further single agent testing of ALK inhibitors in patients with ALKATI should be limited to cases where no other treatment hypotheses can be identified. | bioengineering |
10.1101/692053 | Blood meal analysis of tsetse flies (Glossina pallidipes: Glossinidae) reveals higher host fidelity on wild compared with domestic hosts | Changes in climate and land use can alter risk of transmission of parasites between domestic hosts and wildlife, particularly when mediated by vectors that can travel between populations. Here we focused on tsetse flies (genus Glossina), the cyclical vectors for both Human African Trypanosomiasis (HAT) and Animal African Trypanosomiasis (AAT). The aims of this study were to investigate: 1) the diversity of vertebrate hosts that flies fed on; 2) whether host feeding patterns varied in relation to type of hosts, tsetse feeding behaviour, site or tsetse age and sex; and 3) if there was a relationship between trypanosome detection and host feeding behaviours or host types. Sources of blood meals of Glossina pallidipes were identified by sequencing of the mitochondrial cytochrome b gene and analyzed in relationship with previously determined trypanosome detection in the same flies. In an area dominated by wildlife but with seasonal presence of livestock (Nguruman), 98% of tsetse fed on single wild host species, whereas in an area including a mixture of resident domesticated animals, humans and wildlife (Shimba Hills), 52% of flies fed on more than one host species. Multiple Correspondence Analysis revealed strong correlations between feeding pattern, host type and site but these were resolved along a different dimension than trypanosome status, sex and age of the flies. Our results suggest that individual G. pallidipes in interface areas may show higher feeding success on wild hosts when available but often feed on both wild and domesticated hosts. This illustrates the importance of G. pallidipes as a vector connecting the sylvatic and domestic cycles of African trypanosomes. | evolutionary biology |
10.1101/695049 | Evidence for a deep, distributed and dynamic semantic code in human ventral anterior temporal cortex | How does the human brain encode semantic information about objects? This paper reconciles two seemingly contradictory views. The first proposes that local neural populations independently encode semantic features; the second, that semantic representations arise as a dynamic distributed code that changes radically with stimulus processing. Combining simulations with a well-known neural network model of semantic memory, multivariate pattern classification, and human electrocorticography, we find that both views are partially correct: semantic information is distributed across ventral temporal cortex in a dynamic code that possesses stable feature-like elements in posterior regions but with elements that change rapidly and nonlinearly in anterior regions. This pattern is consistent with the view that anterior temporal lobes serve as a deep cross-modal "hub" in an interactive semantic network, and more generally suggests that tertiary association cortices may adopt dynamic distributed codes difficult to detect with common brain imaging methods. | neuroscience |
10.1101/697334 | Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression | While recent studies have uncovered dedicated neural pathways mediating the positive control of parenting, the regulation of infant-directed aggression and how it relates to adult-adult aggression is poorly understood. Here we show that urocortin-3 (Ucn3)-expressing neurons in the hypothalamic perifornical area (PeFAUcn3) are activated during infant-directed attacks in males and females, but not other behaviors. Functional manipulations of PeFAUcn3 neurons demonstrate the role of this population in the negative control of parenting in both sexes. PeFAUcn3 neurons receive input from areas associated with vomeronasal sensing, stress, and parenting, and send projections to hypothalamic and limbic areas. Optogenetic activation of PeFAUcn3 axon terminals in these regions triggers various aspects of infant-directed agonistic responses, such as neglect, repulsion and aggression. Thus, PeFAUcn3 neurons emerge as a dedicated circuit component controlling infant-directed neglect and aggression, providing a new framework to understand the positive and negative regulation of parenting in health and disease. | neuroscience |
10.1101/698035 | Eye morphogenesis in the blind Mexican cavefish | The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviors during evagination which participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis. | developmental biology |
10.1101/698761 | Mast seeding promotes evolution of scatter-hoarding | Many plant species worldwide are dispersed by scatterhoarding granivores: animals that hide seeds in numerous, small caches for future consumption. Yet, the evolution of scatterhoarding is difficult to explain because undefended caches are at high risk of pilferage. Previous models have attempted to solve this problem by giving cache owners large advantages in cache recovery, by kin selection, or by introducing reciprocal pilferage of "shared" seed resources. However, the role of environmental variability has been so far overlooked in this context. One important form of such variability is masting, which is displayed by many plant species dispersed by scatterhoarders. We use a mathematical model to investigate the influence of masting on the evolution of scatter-hoarding. The model accounts for periodically varying annual seed fall, caching and pilfering behavior, and the demography of scatterhoarders. The parameter values are based mostly on research on European beech (Fagus sylvatica) and yellow-necked mice (Apodemus flavicollis). Starvation of scatterhoarders between mast years decreases the population density that enters masting events, which leads to reduced seed pilferage. Satiation of scatterhoarders during mast events lowers the reproductive cost of caching (i.e. the cost of caching for the future rather than using seeds for current reproduction). These reductions promote the evolution of scatter-hoarding behavior especially when interannual variation in seed fall and the period between masting events are large. | ecology |
10.1101/698605 | Comparative evaluation of full-length isoform quantification from RNA-Seq | Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short. Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control. Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively. | bioinformatics |
10.1101/699389 | Genetic basis of growth, phenology and susceptibility to biotic stressors in maritime pine | Forest ecosystems are increasingly challenged by extreme events, e.g. drought, storms, pest and pathogenic fungi outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e. heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, growth phenology and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), were assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), growth phenology (0.165-0.310) and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021) measured after inoculation under controlled conditions, but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors. | genetics |
10.1101/702050 | Normalization by Valence and Motivational Intensity in the Primary Sensorimotor Cortices (PMd, M1 and S1) | Our brains ability to represent vast amounts of information, such as continuous ranges of reward spanning orders of magnitude, with limited dynamic range neurons, may be possible due to normalization. Recently our group and others have shown that the sensorimotor cortices are sensitive to reward value. Here we ask if psychological affect causes normalization of the sensorimotor cortices by modulating valence and motivational intensity. We had two non-human primate (NHP) subjects (one male bonnet macaque and one female rhesus macaque) make visually cued grip-force movements while simultaneously cueing the level of possible reward if successful, or timeout punishment, if unsuccessful. We recorded simultaneously from 96 electrodes in each the following: caudal somatosensory, rostral motor, and dorsal premotor cortices (cS1, rM1, PMd). We utilized several normalization models for valence and motivational intensity in all three regions. We found three types of divisive normalized relationships between neural activity and the representation of valence and motivation, linear, sigmodal, and hyperbolic. The hyperbolic relationships resemble receptive fields in psychological affect space, where a unit is susceptible to a small range of the valence/motivational space. We found that these cortical regions have both strong valence and motivational intensity representations. | neuroscience |
10.1101/701946 | Reconstructing contact network structure andcross-immunity patterns from multiple infection histories | Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing the concept of infection barcodes. We find that, depending on infection multiplicity and network sampling, infection barcode summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining infection barcodes for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and barcode analysis of infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data.
Author summaryInfectious disease dynamics are constrained both by between-host contacts and pathogen interactions within a host. Furthermore, multiple parasites circulate such that hosts are infected (sometimes simultaneously) by a variety of strains or species. We hypothesise that multiple infection history can inform us about the networks on which parasites are transmitted, but also on within-host interactions such as immunological interference. We developed a simulator for multiple infections on networks. By combining intuitive novel metrics for multiple infection events and established tools from computational data analysis, we show that similarity in infection history between two hosts correlates with their proximity in the contact network. By analysing pathogens co-occurrence patterns within hosts, we also recover immunological interference at the population level. The demonstrated robustness of our results in terms of observability, network clustering, and pathogen diversity opens new perspectives to extract host contact and between-pathogen immunity information from longitudinal cohort data. | ecology |
10.1101/702589 | Dynamic Ins2 gene activity defines β cell maturity states | Heterogeneity within specific cell types is common and increasingly apparent with the advent of single cell transcriptomics. Transcriptional and functional cellular specialization has been described for insulin-secreting {beta} cells of the endocrine pancreas, including so-called extreme {beta} cells exhibiting >2-fold higher insulin gene activity. However, it is not yet clear whether {beta} cell heterogeneity is stable or reflects dynamic cellular states. We investigated the temporal kinetics of endogenous insulin gene activity using live cell imaging, with complementary experiments employing FACS and single cell RNA sequencing, in {beta} cells from Ins2GFP knock-in mice. In vivo staining and FACS analysis of islets from Ins2GFP mice confirmed that at a given moment, [~]25% of {beta} cells exhibited significantly higher activity at the conserved insulin gene Ins2. Live cell imaging captured Ins2 gene activity dynamics in single {beta} cells over time. Autocorrelation analysis indicated that cells displaying fluctuations in Ins2 gene activity most commonly exhibited a frequency of 17 hours. Increased glucose concentrations stimulated more cells to oscillate and resulted in higher average Ins2 gene activity per cell. Single cell RNA sequencing determined that Ins2(GFP)HIGH {beta} cells were enriched for markers of {beta} cell maturity and had reduced expression of anti- oxidant genes. Ins2(GFP)HIGH {beta} cells were also significantly less viable at all glucose concentrations and in the context of ER stress. Collectively, our results demonstrate that the heterogeneity of insulin production, observed in mouse and human {beta} cells, can be accounted for by dynamic states of insulin gene activity. Our observations define a previously uncharacterized form of {beta} cell plasticity. Understanding the dynamics of insulin production has relevance for understanding the pathobiology of diabetes and for regenerative therapy research. | cell biology |
10.1101/700732 | Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy | Genetic mutations lead to the production of mutated proteins from which peptides are presented to T cells as cancer neoantigens. Evidence suggests that T cells that target neoantigens are the main mediators of effective cancer immunotherapies. Although algorithms have been used to predict neoantigens, only a minority are immunogenic. The factors that influence neoantigen immunogenicity are not completely understood. Here, we classified human neoantigen/neopeptide data into three categories based on their TCR-pMHC binding events. We observed a conservative mutant orientation of the anchor residue from immunogenic neoantigens which we termed the "NP" rule. By integrating this rule with an existing prediction algorithm, we found improved performance in neoantigen prioritization. To better understand this rule, we solved several neoantigen/MHC structures. These structures showed that neoantigens that follow this rule not only increase peptide-MHC binding affinity but also create new TCR-binding features. These molecular insights highlight the value of immune-based classification in neoantigen studies and may enable the design of more effective cancer immunotherapies. | cancer biology |
10.1101/702407 | The relative impact of evolving pleiotropy and mutational correlation on trait divergence | Both pleiotropic connectivity and mutational correlations can restrict the decoupling of traits under divergent selection, but it is unknown which is more important in trait evolution. In order to address this question, we create a model that permits within-population variation in both pleiotropic connectivity and mutational correlation, and compare their relative importance to trait evolution. Specifically, we developed an individual-based, stochastic model where mutations can affect whether a locus affects a trait and the extent of mutational correlations in a population. We find that traits can decouple whether there is evolution in pleiotropic connectivity or mutational correlation but when both can evolve then evolution in pleiotropic connectivity is more likely to allow for decoupling to occur. The most common genotype found in this case is characterized by having one locus that maintains connectivity to all traits and another that loses connectivity to the traits under stabilizing selection (subfunctionalization). This genotype is favoured because it allows the subfunctionalized locus to accumulate greater effect size alleles, contributing to increasingly divergent trait values in the traits under divergent selection without changing the trait values of the other traits (genetic modularization). These results provide evidence that partial subfunctionalization of pleiotropic loci may be a common mechanism of trait decoupling under regimes of corridor selection. | evolutionary biology |
10.1101/703918 | Inferring genome-wide correlations of mutation fitness effects between populations | The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these specices, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence. | evolutionary biology |
10.1101/703777 | Analysis of the Human Connectome Data Supports the Notion of a "Common Model of Cognition" for Human and Human-Like Intelligence | The Common Model of Cognition (CMC) is a recently proposed, consensus architecture intended to capture decades of progress in cognitive science on modeling human and human-like intelligence. Because of the broad agreement around it and preliminary mappings of its components to specific brain areas, we hypothesized that the CMC could be a candidate model of the large-scale functional architecture of the human brain. To test this hypothesis, we analyzed functional MRI data from 200 participants and seven different tasks that cover a broad range of cognitive domains. The CMC components were identified with functionally homologous brain regions through canonical fMRI analysis, and their communication pathways were translated into predicted patterns of effective connectivity between regions. The resulting dynamic linear model was implemented and fitted using Dynamic Causal Modeling, and compared against six alternative brain architectures that had been previously proposed in the field of neuroscience (three hierarchical architectures and three hub-and-spoke architectures) using a Bayesian approach. The results show that, in all cases, the CMC vastly outperforms all other architectures, both within each domain and across all tasks. These findings suggest that a common set of architectural principles that could be used for artificial intelligence also underpins human brain function across multiple cognitive domains. | neuroscience |
10.1101/703835 | Comparison of CPU and GPU Bayesian Estimates of Fibre Orientations from Diffusion MRI | BackgroundThe correct estimation of fibre orientations is a crucial step for reconstructing human brain tracts. Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques (bedpostx) is able to estimate several fibre orientations and their diffusion parameters per voxel using Markov Chain Monte Carlo (MCMC) in a whole brain diffusion MRI data, and it is capable of running on GPUs, achieving speed-up of over 100 times compared to CPUs. However, few studies have looked at whether the results from the CPU and GPU algorithms differ. In this study, we compared CPU and GPU bedpostx outputs by running multiple trials of both algorithms on the same whole brain diffusion data and compared each distribution of output using Kolmogorov-Smirnov tests.
ResultsWe show that distributions of fibre fraction parameters and principal diffusion direction angles from bedpostx and bedpostx_gpu display few statistically significant differences in shape and are localized sparsely throughout the whole brain. Average output differences are small in magnitude compared to underlying uncertainty.
ConclusionsDespite small amount of differences in output between CPU and GPU bedpostx algorithms, results are comparable given the difference in operation order and library usage between CPU and GPU bedpostx. | neuroscience |
10.1101/704791 | Adult dentate gyrus neurogenesis: a functional model | In adult dentate gyrus neurogenesis, the link between maturation of newborn neurons and their function, such as behavioral pattern separation, has remained puzzling. By analyzing a theoretical model, we show that the switch from excitation to inhibition of the GABAergic input onto maturing newborn cells is crucial for their proper functional integration. When the GABAergic input is excitatory, cooperativity drives the growth of synapses such that newborn cells become sensitive to stimuli similar to those that activate mature cells. When GABAergic input switches to inhibitory, competition pushes the configuration of synapses onto newborn cells towards stimuli that are different from previously stored ones. This enables the maturing newborn cells to code for concepts that are novel, yet similar to familiar ones. Our theory of newborn cell maturation explains both how adult-born dentate granule cells integrate into the preexisting network and why they promote separation of similar but not distinct patterns. | neuroscience |
10.1101/705350 | The functional connectivity of the human claustrum according to the Human Connectome Project database | The claustrum is an irregular and fine sheet of grey matter in the basolateral telencephalon present in almost all mammals. The claustrum has been the object of several studies using animal models and more recently in human beings using neuroimaging. Believed to be involved in cognition and disease such as fear recognition, suppression of natural urges, multisensory integration, conceptual integration, seizures, multiple sclerosis, and Parkinsons disease. Nevertheless, the function of the claustrum still remains unclear. We present a functional connectivity study of the claustrum in order to identify its main networks. Resting state functional and anatomical MRI data from 100 healthy subjects were analyzed; taken from the Human Connectome Project (HCP, NIH Blueprint: The Human Connectome Project), with 2x2x2 mm3 voxel resolution. Positive functional connectivity was found (p<0.05, FDR corrected) between the claustrum and the insula, anterior cingulate cortex, pre-central and postcentral gyrus, superior temporal gyrus, and subcortical areas. Our findings coincide with the results previously reported in both animal models and studies with humans. Showing the claustrum as a well-connected structure not only structurally but also functionally. Evidencing the claustrum as a node participating in different neural networks. | neuroscience |
10.1101/705491 | Reactive oxygen species prevent lysosome coalescence during PIKfyve inhibition | Lysosomes are terminal, degradative organelles of the endosomal pathway that undergo repeated fusion-fission cycles with themselves, endosomes, phagosomes, and autophagosomes. Lysosome number and size depends on balanced fusion and fission rates. Thus, conditions that favour fusion over fission can reduce lysosome numbers while enlarging their size. Conversely, favouring fission over fusion may cause lysosome fragmentation and increase their numbers. PIKfyve is a phosphoinositide kinase that generates phosphatidylinositol-3,5-bisphosphate to modulate lysosomal functions. PIKfyve inhibition causes an increase in lysosome size and reduction in lysosome number, consistent with lysosome coalescence. This is thought to proceed through reduced lysosome reformation and/or fission after fusion with endosomes or other lysosomes. Previously, we observed that photo-damage during live-cell imaging prevented lysosome coalescence during PIKfyve inhibition. Thus, we postulated that lysosome fusion and/or fission dynamics are affected by reactive oxygen species (ROS). Here, we show that ROS generated by various independent mechanisms all impaired lysosome coalescence during PIKfyve inhibition and accelerated lysosome fragmentation during re-activation. However, depending on the ROS species or mode of production, lysosome dynamics were affected distinctly. H2O2 impaired lysosome motility and reduced lysosome fusion with phagosomes, suggesting that H2O2 reduces lysosome fusogenecity. In comparison, inhibitors of oxidative phosphorylation, glutathione, and thioredoxin that produce superoxide, did not impair lysosome motility but instead promoted clearance of actin puncta on lysosomes formed during PIKfyve inhibition. Additionally, actin depolymerizing agents prevented lysosome coalescence during PIKfyve inhibition. Thus, we discovered that ROS can generally prevent lysosome coalescence during PIKfyve inhibition using distinct mechanisms depending on the type of ROS. | cell biology |
10.1101/706986 | Crystal structure of Sulfolobus solfataricus topoisomerase III reveals a novel carboxyl-terminal zinc finger domain essential for decatenation activity | DNA topoisomerases are essential enzymes for a variety of cellular processes involved in DNA transactions. Mechanistic insights into type IA DNA topoisomerases have come principally from studies on bacterial and eukaryotic enzymes. A structural understanding of type IA topoisomerases in Archaea is lacking. Here, we present a 2.1-angstrom crystal structure of full-length Sulfolobus solfataricus topoisomerase III (Sso topo III), an archaeal member of type IA topoisomerases. The structure shows that Sso topo III adopts a characteristic torus-like architecture consisting of a four-domain core region and a novel carboxyl-terminal zinc finger domain (domain V). Structure-based mutation analyses reveal that a novel zinc-binding motif in domain V is essential for the DNA decatenation activity of Sso topo III. Our data indicate that Sso topo III represents a subclass of Type IA topoisomerases capable of resolving DNA catenates using a domain V-dependent mechanism.
IMPORTANCEType IA topoisomerases are omnipresent in all cellular life forms and serve pivotal roles in cellular processes involved in DNA transactions. While considerable insights have been gained into Type IA topoisomerases from bacteria and eukaryotes, a structural understanding of type IA topoisomerases in Archaea remains elusive. we first determined the crystal structure of full-length Sulfolobus solfataricus topoisomerase III (Sso topo III), an archaeal member of type IA topoisomerases. Our structure provides the first molecular view of this archaeal topoisomerase, which removes negative supercoils and decatenates DNA catenane. Our findings manifest that Sso topo III may serve as an alternative prototype of type IA topoisomerases, whose decatenation mechanism differs from that of known bacterial and eukaryotic topoisomerases III such as Escherichia coli topoisomerase III (EcTOP3). | microbiology |
10.1101/706861 | Lignin-based resistance to Cuscuta campestris parasitism in Heinz resistant tomato cultivars | Cuscuta species (dodders) are agriculturally destructive parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. LIF1 (Lignin Induction Factor 1, an AP2-like transcription factor), SlMYB55, and CuRLR1 (Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR) are identified as crucial factors conferring host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and acts as a negative regulator of LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as a receptor for receiving Cuscuta signals or effectors to regulate lignification-based resistance. In summary, these four regulators control the lignin-based resistance response, preventing C. campestris from parasitizing these resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants.
One-sentence summaryFour key regulators confer lignin accumulation in the tomato stem cortex to block C. campestris host penetration upon infection. | plant biology |
10.1101/707158 | CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps | Spatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer-promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS, a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells, and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome. | bioinformatics |
10.1101/708040 | Apple ripening is controlled by a NAC transcription factor | Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of ripening and associated textural changes are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from [~]800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after three months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein with high similarity to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). To test whether these genes are functionally orthologous, we introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program. | plant biology |
10.1101/706119 | Minor deviations from randomness have huge repercussions on the functional structuring of sequence space | Approaches based on molecular evolution have organized natural proteins into a hierarchy of families, superfamilies, and folds, which are often pictured as islands in a great sea of unrealized and generally non-functional polypeptides. In contrast, approaches based on information theory have substantiated a mostly random scatter of natural proteins in global sequence space. We evaluate these opposing views by analyzing fragments of a given length derived from either a natural dataset or different random models. For this, we compile distances in sequence space between fragments within each dataset and compare the resulting distance distributions between sets. Even for 100-mers, more than 95% of distances can be accounted for by a random sequence model that incorporates the natural amino acid frequency of proteins. When further accounting for the specific residue composition of the respective fragments, which would include biophysical constraints of protein folding, more than 99% of all distances can be modeled. Thus, while the local space surrounding a protein is almost entirely shaped by common descent, the global distribution of proteins in sequence space is close to random, only constrained by divergent evolution through the requirement that all intermediates connecting two forms in evolution must be functional.
Significance StatementWhen generating new proteins by evolution or design, can the entire sequence space be used, or do viable sequences mainly occur only in some areas of this space? As a result of divergent evolution, natural proteins mostly form families that occupy local areas of sequence space, suggesting the latter. Theoretical work however indicates that these local areas are highly diffuse and do not dramatically affect the statistics of sequence distribution, such that natural proteins can be considered to effectively cover global space randomly, though extremely sparsely. By comparing the distance distribution of natural sequences to that of various random models, we find that they are indeed distributed largely randomly, provided that the amino acid composition of natural proteins is respected. | evolutionary biology |
10.1101/710566 | A neuromechanical model of multiple network rhythmic pattern generators for forward locomotion in C. elegans | Multiple mechanisms contribute to the generation, propagation, and coordination of the rhythmic patterns necessary for locomotion in Caenorhabditis elegans. Current experiments have focused on two possibilities: pacemaker neurons and stretch-receptor feedback. Here, we focus on whether it is possible that a chain of multiple network rhythmic pattern generators in the ventral nerve cord also contribute to locomotion. We use a simulation model to search for parameters of the anatomically constrained ventral nerve cord circuit that, when embodied and situated, can drive forward locomotion on agar, in the absence of pacemaker neurons or stretch-receptor feedback. Systematic exploration of the space of possible solutions reveals that there are multiple configurations that result in locomotion that is consistent with certain aspects of the kinematics of worm locomotion on agar. Analysis of the best solutions reveals that gap junctions between different classes of motorneurons in the ventral nerve cord can play key roles in coordinating the multiple rhythmic pattern generators. | neuroscience |
10.1101/709956 | Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients | Compositional multistability is widely observed in multispecies ecological communities. Since differences in community composition often lead to differences in community function, understanding compositional multistability is essential to comprehend the role of biodiversity in maintaining ecosystems. In community assembly studies, it has long been recognized that the order and timing of species migration and extinction influence structure and function of communities. The study of multistability in ecology has focused on the change in dynamical stability across environmental gradients, and was developed mainly for low-dimensional systems. As a result, methodologies for studying the compositional stability of empirical multispecies communities are not well developed. Here, we show that models previously used in ecology can be analyzed from a new perspective - the energy landscape - to unveil compositional stability in observational data. To show that our method can be applicable to real-world ecological communities, we simulated assembly dynamics driven by population level processes, and show that results were mostly robust to different simulation assumptions. Our method reliably captured the change in the overall compositional stability of multispecies communities over environmental change, and indicated a small fraction of community compositions that may be channels for transitions between stable states. When applied to murine gut microbiota, our method showed the presence of two alternative states whose relationship changes with age, and suggested mechanisms by which aging affects the compositional stability of the murine gut microbiota. Our method provides a practical tool to study the compositional stability of communities in a changing world, and will facilitate empirical studies that integrate the concept of multistability from different fields. | ecology |
10.1101/708255 | The Gut Microbiome of Exudivorous Wild and non-Wild Marmosets | Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and non-wild Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was similar across marmosets, Enterobacteriaceae seem to carry out most functional activities in captive host guts. More diverse bacterial taxa seem to perform gut functions in wild marmosets, with Bifidobacterium being important for carbohydrate metabolism. Non-wild marmosets showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for husbandry modifications. | microbiology |
10.1101/708255 | The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity | Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and non-wild Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was similar across marmosets, Enterobacteriaceae seem to carry out most functional activities in captive host guts. More diverse bacterial taxa seem to perform gut functions in wild marmosets, with Bifidobacterium being important for carbohydrate metabolism. Non-wild marmosets showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for husbandry modifications. | microbiology |
10.1101/711200 | Shared genetic underpinnings between genetic generalized epilepsy and background EEG oscillations | ObjectiveParoxysmal epileptiform abnormalities on electroencephalography (EEG) are the hallmark of epilepsies, but it is uncertain to what extent epilepsy and background EEG oscillations share neurobiological underpinnings. Here, we aimed to assess the genetic correlation between epilepsy and background EEG oscillations.
MethodsConfounding factors, including the heterogeneous etiology of epilepsies and medication effects hamper studies on background brain activity in people with epilepsy. To overcome this limitation, we compared genetic data from a GWAS on epilepsy (n=12,803 people with epilepsy and 24,218 controls) with that from a GWAS on background EEG (n=8,425 subjects without epilepsy), in which background EEG oscillation power was quantified in four different frequency bands: alpha, beta, delta and theta. We replicated our findings in an independent epilepsy replication dataset (n=4851 people with epilepsy and 20,428 controls). To assess the genetic overlap between these phenotypes, we performed genetic correlation analyses using linkage disequilibrium score regression, polygenic risk scores and Mendelian randomization analyses.
ResultsOur analyses show strong genetic correlations between genetic generalized epilepsy (GGE) with background EEG oscillations, primarily with the beta frequency band. Furthermore, we show that subjects with higher beta and theta polygenic risk scores have a significantly higher risk of having generalized epilepsy. Mendelian randomization analyses suggest a causal effect of GGE genetic liability on beta oscillations.
SignificanceOur results point to shared biological mechanisms underlying background EEG oscillations and the susceptibility for GGE, opening avenues to investigate the clinical utility of background EEG oscillations in the diagnostic work-up of epilepsy. | genetics |
10.1101/711598 | Implicit visuomotor adaptation remains limited after several days of training | Learning in sensorimotor adaptation tasks has been viewed as an implicit learning phenomenon. The implicit process affords recalibration of existing motor skills so that the system can adjust to changes in the body or environment without relearning from scratch. However, recent findings suggest that the implicit process is heavily constrained, calling into question its utility in motor learning and the theoretical framework of sensorimotor adaptation paradigms. These inferences have been based mainly on results from single bouts of training, where explicit compensation strategies, such as explicitly re-aiming the intended movement direction, contribute a significant proportion of adaptive learning. It is possible, however, that the implicit process supersedes explicit compensation strategies over repeated practice sessions. We tested this by dissociating the contributions of explicit re-aiming strategies and the implicit process over five consecutive days of training. Despite a substantially longer duration of training, the implicit process still plateaued at a value far short of complete learning and, as has been observed in previous studies, was inappropriate for a mirror reversal task. Notably, we find significant between subject differences that call into question traditional interpretation of these group-level results.
Significance StatementIn this set of studies, we find that the implicit process cannot fully account for learning in adaptation tasks, such as the visuomotor rotation and mirror reversal tasks, even following several days of training. In fact, the implicit process can be counterproductive to learning. Most notably, we find significant between subject differences that call into question traditional interpretation of these group-level results. | neuroscience |
10.1101/713420 | Sub-sampling of cues in associative learning | Theories of learning distinguish between elemental and configural stimulus processing depending on whether stimuli are processed independently or as whole configurations. Evidence for elemental processing comes from findings of summation in animals where a compound of two dissimilar stimuli is deemed to be more predictive than each stimulus alone, whereas configural processing is supported by experiments employing similar stimuli in which summation is not found. However, in humans the summation effect is robust and impervious to similarity manipulations. In three experiments in human predictive learning, we show that summation can be obliterated when partially reinforced cues are added to the summands in training and test. This lack of summation only holds when the partially reinforced cues are similar to the reinforced cues (Experiment 1) and seems to depend on participants sampling only the most salient cue in each trial (Experiments 2a and 2b) in a sequential visual search process. Instead of attributing our and others instances of lack of summation to the customary idea of configural processing, we offer a formal sub-sampling rule that might be applied to situations in which the stimuli are hard to parse from each other. | animal behavior and cognition |
10.1101/713420 | Sub-sampling of cues in associative learning | Theories of learning distinguish between elemental and configural stimulus processing depending on whether stimuli are processed independently or as whole configurations. Evidence for elemental processing comes from findings of summation in animals where a compound of two dissimilar stimuli is deemed to be more predictive than each stimulus alone, whereas configural processing is supported by experiments employing similar stimuli in which summation is not found. However, in humans the summation effect is robust and impervious to similarity manipulations. In three experiments in human predictive learning, we show that summation can be obliterated when partially reinforced cues are added to the summands in training and test. This lack of summation only holds when the partially reinforced cues are similar to the reinforced cues (Experiment 1) and seems to depend on participants sampling only the most salient cue in each trial (Experiments 2a and 2b) in a sequential visual search process. Instead of attributing our and others instances of lack of summation to the customary idea of configural processing, we offer a formal sub-sampling rule that might be applied to situations in which the stimuli are hard to parse from each other. | animal behavior and cognition |
10.1101/713420 | Sub-sampling of cues in associative learning | Theories of learning distinguish between elemental and configural stimulus processing depending on whether stimuli are processed independently or as whole configurations. Evidence for elemental processing comes from findings of summation in animals where a compound of two dissimilar stimuli is deemed to be more predictive than each stimulus alone, whereas configural processing is supported by experiments employing similar stimuli in which summation is not found. However, in humans the summation effect is robust and impervious to similarity manipulations. In three experiments in human predictive learning, we show that summation can be obliterated when partially reinforced cues are added to the summands in training and test. This lack of summation only holds when the partially reinforced cues are similar to the reinforced cues (Experiment 1) and seems to depend on participants sampling only the most salient cue in each trial (Experiments 2a and 2b) in a sequential visual search process. Instead of attributing our and others instances of lack of summation to the customary idea of configural processing, we offer a formal sub-sampling rule that might be applied to situations in which the stimuli are hard to parse from each other. | animal behavior and cognition |
10.1101/712836 | Aerobic methoxydotrophy: growth on methoxylated aromatic compounds by Methylobacterium | Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. In addition, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium. We demonstrated growth on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium, but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to M. nodulans, and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation. | microbiology |
10.1101/713081 | Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes | The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma. | evolutionary biology |
10.1101/713081 | Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes | The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma. | evolutionary biology |
10.1101/714295 | Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry using a custom-made database, biomarker assignment, or mathematical classifiers does not differentiate Shigella spp. and Escherichia coli | PurposeShigella spp. and E. coli are closely related and cannot be distinguished using Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF MS to identify and distinguish Shigella spp., E. coli, and its pathotype EIEC were explored.
MethodsA custom-made database was developed, biomarkers were assigned, and classification models using machine learning were designed and evaluated using spectra of 456 Shigella spp., 42 E. coli, and 61 EIEC isolates, obtained by the direct smear method and the ethanol-formic acid extraction method. The isolates were identified using ipaH PCR and phenotypic and serological typing.
ResultsIdentification with a custom-made database resulted in >94% Shigella identified at the genus level and >91% S. sonnei and S. flexneri at the species level, but distinction of S. dysenteriae, S. boydii, and E. coli was poor. Moreover, 10-15% of duplicates rendered discrepant results. With biomarker assignment, 98% S. sonnei isolates were correctly identified, although the S. sonnei biomarkers were not specific as other species, for instance S. boydii and E. coli were also identified as S. sonnei. Discriminating markers for S. dysenteriae, S. boydii, and E. coli were not assigned at all. Classifiers identified Shigella in 96% of isolates correctly, but most E. coli isolates were also assigned to Shigella.
ConclusionNone of the proposed alternative approaches is suitable for use in clinical diagnostics for the identification of Shigella spp., E. coli, and EIEC, reflecting their relatedness and problematic taxonomical classification. We suggest the use of MALDI-TOF MS for the identification of the Shigella spp./E. coli complex, but other tests should be used for distinction. | microbiology |
10.1101/714410 | Better tired than lost: turtle ant trail networks favor coherence over shortest edges | Creating a routing backbone is a fundamental problem in both biology and engineering. The routing backbone of the trail networks of arboreal turtle ants (Cephalotes goniodontus) connects many nests and food sources using trail pheromone deposited by ants as they walk. Unlike species that forage on the ground, the trail networks of arboreal ants are constrained by the vegetation. We examined what objectives the trail networks meet by comparing the observed ant trail networks with networks of random, hypothetical trail networks in the same surrounding vegetation and with trails optimized for four objectives: minimizing path length, minimizing average edge length, minimizing number of nodes, and minimizing opportunities to get lost. The ants trails minimized path length by minimizing the number of nodes traversed rather than choosing short edges. In addition, the ants trails reduced the opportunity for ants to get lost at each node, favoring nodes with 3D configurations most likely to be reinforced by pheromone. Thus, rather than finding the shortest edges, turtle ant trail networks take advantage of natural variation in the environment to favor coherence, keeping the ants together on the trails.
Author SummaryWe investigated the trail networks of arboreal turtle ants in the canopy of the tropical forest, to ask what characterizes the colonys choice of foraging paths within the vegetation. We monitored day to day changes in the junctions and edges of trail networks of colonies in the dry forest of western Mexico. We compared the paths used by the ants to simulated random paths in the surrounding vegetation. We found that the paths of turtle ants prioritize coherence, keeping ants together on the trail, over minimizing the average edge length. The choice of paths reduces the number of junctions in the trail where ants could get lost, and favors junctions with a physical configuration that makes it likely that successive ants will reinforce the same path. Our work suggests that design principles that emphasize keeping information flow constrained to streamlined, coherent trails may be useful in human-designed distributed routing and transport networks or robot swarms. | ecology |
10.1101/707794 | Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel | Mechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. However, by re-engineering the MS channels, chemical signals such as pH change can trigger the activation of some MS channels. This paper elucidate the activation mechanism of an engineered MS channel of large conductance (MscL) at an atomic level through a combination of equilibrium, non-equilibrium, biased, and unbiased molecular dynamics (MD) simulations for the first time. Comparing the wild-type and engineered MscL activation processes at an atomic level suggests that the two systems are likely to be associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are those between the transmembrane (TM) helices 1 and 2 (TM1 and TM2) in engineered MscL channel. In this research, the orientation-based biasing approach for producing and optimizing an open MscL model is a promising way to characterize unknown protein functional states and to research the activation processes in ion channels. String method with swarms of trajectories (SMwST) was used to identify the optimal transition pathway and elucidate the activation mechanism of the engineered MscL. Finally, the free energy profile of engineered MscL associated with the activation process using a novel along-the-path free energy calculation approach is constructed. This work paves the way for a computational framework for the studies aimed at designing pH-triggered channel-functionalized drug delivery liposomes. | biophysics |
10.1101/716365 | Balanced polymorphism at the Pgm-1 locus of the Pompeii worm Alvinella pompejana and its variant adaptability is only governed by two QE mutations at linked sites | The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise and, display specific adaptations to withstand high temperature and hypoxia associated with this highly variable habitat. Previous studies revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with thermal variations where allozymes 90 and 100 exhibited different optimal activities and thermostabilities. The exploration of the mutational landscape of the phosphoglucomutase1 revealed the maintenance of four highly divergent allelic lineages encoding the three most frequent electromorphs over the worms geographic range. This polymorphism is only governed by two linked amino-acid replacements located in exon 3 (E155Q and E190Q). A two-niches model of selection with cold and hot conditions represents the most likely way for the long-term persistence of these isoforms. Using directed mutagenesis, overexpression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Results are coherent with those previously obtained from native proteins and reveal a thermodynamic trade-off between the protein thermostability and catalysis, which is likely to have maintained these functional phenotypes prior to the geographic separation of populations across the Equator, about 1.2 Mya. | evolutionary biology |
10.1101/717249 | Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families | Sequence functional classification has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of living organisms and for biotechnological applications.
ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple probabilistic models whose construction explores evolutionary information in available databases, and a new definition of a representation space where to look at sequences from the point of view of probabilistic models combined together. ProfileView classifies families of proteins for which functions should be discovered or characterised within known groups.
We validate ProfileView on seven classes of widespread proteins, involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterize the functions. Furthermore, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of new biological functions.
ProfileView proves to outperform three functional classification approaches, CUPP, PANTHER, and a recently developed neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter. | bioinformatics |
10.1101/717603 | Assigning metabolic rate measurements to torpor and euthermia in heterothermic endotherms: torpor a new package for R. | Torpor is a state of controlled reduction of metabolic rate (M) in endotherms. Assigning measurements of M to torpor or euthermy can be challenging, especially when the difference between euthermic M and torpid M is small, in species defending a high minimal body temperature in torpor, in thermolabile species, and slightly below the thermoneutral zone (TNZ). Here, we propose a novel method for distinguishing torpor from euthermy. We use the variation in M measured during euthermic rest and torpor at varying ambient temperatures (Ta) to objectively estimate the lower critical temperature (Tlc) of the TNZ and to assign measurements to torpor, euthermic rest or rest within TNZ. In addition, this method allows the prediction of M during euthermic rest and torpor at varying Ta, including resting M within the TNZ. The present method has shown highly satisfactory results using 28 published sets of metabolic data obtained by respirometry on 26 species of mammals. Ultimately, this novel method aims to facilitate analysis of respirometry data in heterothermic endotherms. Finally, the development of the associated R-package (torpor) will enable widespread use of the method amongst biologists.
Summary statementThe presented method and its associated R-package (torpor) enable the assignment of metabolic rate measurements to torpor or euthermy, ultimately improving the standardization of respirometry analyses in heterotherms. | physiology |
10.1101/717603 | Assigning metabolic rate measurements to torpor and euthermy in heterothermic endotherms: 'torpor', a new package for R. | Torpor is a state of controlled reduction of metabolic rate (M) in endotherms. Assigning measurements of M to torpor or euthermy can be challenging, especially when the difference between euthermic M and torpid M is small, in species defending a high minimal body temperature in torpor, in thermolabile species, and slightly below the thermoneutral zone (TNZ). Here, we propose a novel method for distinguishing torpor from euthermy. We use the variation in M measured during euthermic rest and torpor at varying ambient temperatures (Ta) to objectively estimate the lower critical temperature (Tlc) of the TNZ and to assign measurements to torpor, euthermic rest or rest within TNZ. In addition, this method allows the prediction of M during euthermic rest and torpor at varying Ta, including resting M within the TNZ. The present method has shown highly satisfactory results using 28 published sets of metabolic data obtained by respirometry on 26 species of mammals. Ultimately, this novel method aims to facilitate analysis of respirometry data in heterothermic endotherms. Finally, the development of the associated R-package (torpor) will enable widespread use of the method amongst biologists.
Summary statementThe presented method and its associated R-package (torpor) enable the assignment of metabolic rate measurements to torpor or euthermy, ultimately improving the standardization of respirometry analyses in heterotherms. | physiology |
10.1101/710848 | Non-cell autonomous OTX2 transcription factor regulates anxiety-related behaviors in the mouse | The Otx2 homeoprotein transcription factor is expressed in the dopaminergic neurons of the ventral tegmental area, a mesencephalic nucleus involved in the control of complex behaviors through its projections to limbic structures, including the ventral hippocampus, amygdala, nucleus accumbens and medial prefrontal cortex. We find adult mice heterozygous for Otx2 show anxiolysis-like phenotype in light-dark box and elevated plus maze paradigms. However, the number of dopaminergic neurons, the integrity of their axons, their projection patterns in target structures, and the amounts of dopamine and dopamine metabolites in targets structures were not modified. Because OTX2 is expressed by the choroid plexus, secreted into cerebrospinal fluid and transferred to parvalbumin interneurons of the cortex, hippocampus, and amygdala, we investigated if this phenotype could result from the decreased synthesis of OTX2 in the choroid plexus. Indeed, the anxiolysis-like phenotype was partially recapitulated in the Otx2+/AA and scFvOtx2tg/0 choroid-plexus dependent non-cell-autonomous OTX2 loss of function mouse models. Furthermore, the phenotype was reversed by the overexpression of Otx2 specifically in choroid plexus of adult Otx2 heterozygous mice. Taken together, OTX2 synthesis by the choroid plexus followed by its secretion into the cerebrospinal fluid is an important regulator of the anxiety phenotype in the mouse. | neuroscience |
10.1101/719633 | Calcium-permeable AMPA receptors mediate timing-dependent LTP elicited by low repeat coincident pre- and postsynaptic activity at Schaffer collateral-CA1 synapses | High-frequency stimulation induced long-term potentiation (LTP), or low frequency stimulation induced LTD are considered as cellular models of memory formation. Interestingly, spike timing-dependent plasticity (STDP) can induce equally robust timing-dependent LTP (t-LTP) and t-LTD in response to low frequency repeats of coincident action potential (AP) firing in presynaptic and postsynaptic cells. Commonly, STDP paradigms relying on 25-100 repeats of coincident AP firing are used to elicit t-LTP or t-LTD, but the minimum number of repeats required for successful STDP is barely explored. However, systematic investigation of physiologically relevant low repeat STDP paradigms is of utmost importance to explain learning mechanisms in vivo. Here, we examined low repeat STDP at Schaffer collateral-CA1 synapses by pairing one presynaptic AP with either one postsynaptic AP (1:1 t-LTP), or a burst of 4 APs (1:4 t-LTP) and found 3-6 repeats to be sufficient to elicit t-LTP. 6x 1:1 t-LTP required postsynaptic Ca2+ influx via NMDARs and L-type VGCCs and was mediated by increased presynaptic glutamate release. In contrast, 1:4 t-LTP depended on postsynaptic metabotropic GluRs and ryanodine receptor signaling, and was mediated by postsynaptic insertion of AMPA receptors. Unexpectedly, both 6x t-LTP variants were strictly dependent on activation of postsynaptic Ca2+-permeable AMPARs but were differentially regulated by dopamine receptor signaling. Our data show that synaptic changes induced by only 3-6 repeats of mild STDP stimulation occurring in [≤] 10 s can take place on time scales observed also during single trial learning. | neuroscience |
10.1101/719013 | Endocycles support tissue growth and regeneration of the adult Drosophila accessory gland | The Drosophila melanogaster male accessory gland is a functional analog of the mammalian prostate containing two secretory epithelial cell types, termed main and secondary cells. This tissue is responsible for making and secreting seminal fluid proteins and other molecules that contribute to successful reproduction. Here we show that similar to the mammalian prostate, this tissue grows with age and can undergo functional regeneration post-damage. We describe a post-eclosion endocycle required for gland maturation, that is dependent on juvenile hormone signaling. In addition, the differentiated binucleated main cells of the adult accessory gland continue to undergo rare endocycles throughout physiological aging to increase DNA content and cell size. Accessory gland cells remain poised to endocycle and upregulation of signals that promote endocycling and tissue growth are sufficient to trigger dramatic increases in cell ploidy. We provide evidence that the main cells of this tissue remain poised to enter the endocycle to assist in tissue regrowth after damage, providing a novel model for postmitotic regeneration in a binucleate tissue. | developmental biology |
10.1101/720912 | Out of the blue; Phototropins of the leaf vascular bundle sheath mediate the blue light regulation of the leaf hydraulic conductance | The Arabidopsis leaf veins bundle sheath cells (BSCs) - a selective barrier to water and solutes entering the mesophyll - increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light - ineffective in the phot1-5 mutant - acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.
One-Sentence summaryBlue light regulates the leaf hydraulic conductance via the bundle-sheath cells blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs AHA2 H+-pump. | plant biology |
10.1101/720912 | Out of the blue; Phototropins of the leaf vascular bundle sheath mediate the blue light regulation of the leaf hydraulic conductance | The Arabidopsis leaf veins bundle sheath cells (BSCs) - a selective barrier to water and solutes entering the mesophyll - increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light - ineffective in the phot1-5 mutant - acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.
One-Sentence summaryBlue light regulates the leaf hydraulic conductance via the bundle-sheath cells blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs AHA2 H+-pump. | plant biology |
10.1101/720912 | Out of the blue; Phototropins of the leaf vascular bundle sheath mediate the blue light regulation of the leaf hydraulic conductance | The Arabidopsis leaf veins bundle sheath cells (BSCs) - a selective barrier to water and solutes entering the mesophyll - increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light - ineffective in the phot1-5 mutant - acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.
One-Sentence summaryBlue light regulates the leaf hydraulic conductance via the bundle-sheath cells blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs AHA2 H+-pump. | plant biology |
10.1101/720912 | Out of the blue; Phototropins of the leaf vascular bundle sheath mediate the blue light regulation of the leaf hydraulic conductance | The Arabidopsis leaf veins bundle sheath cells (BSCs) - a selective barrier to water and solutes entering the mesophyll - increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light - ineffective in the phot1-5 mutant - acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.
One-Sentence summaryBlue light regulates the leaf hydraulic conductance via the bundle-sheath cells blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs AHA2 H+-pump. | plant biology |
10.1101/721662 | Immune Regulation of Intestinal Stem Cell Proliferation and Differentiation in Drosophila. | Intestinal progenitor cells integrate signals from their niche, and from the gut lumen, to divide and differentiate at a rate that maintains an epithelial barrier to microbial invasion of the host interior. Despite the importance of evolutionarily conserved innate immune defenses to maintain stable host-microbiota relationships, we know little about specific contributions of stem cell immunity to gut homeostasis. We used the Drosophila model to determine the consequences of compromised intestinal stem cell immune activity for epithelial homeostasis. We showed that loss of stem cell immunity greatly impacted growth and renewal in the adult gut. In particular, we noticed that inhibition of stem cell immunity impeded key growth and differentiation events in the progenitor cell compartment leading to a gradual loss of stem cell numbers with age, and an impaired differentiation of mature enteroendocrine cells. Our results highlight the importance of immune signaling in the stem cell population for epithelial function in the adult gut.
HIGHLIGHTSO_LIThe TNFR-like Immune Deficiency (IMD) pathway is active in Drosophila intestinal progenitor cells.
C_LIO_LIInhibition of IMD in progenitors impairs progenitor cell proliferation.
C_LIO_LIBlocking progenitor cell IMD negatively affects generation of mature epithelial cells.
C_LI | immunology |
10.1101/721662 | Immune Regulation of Intestinal Stem Cell Proliferation and Differentiation in Drosophila. | Intestinal progenitor cells integrate signals from their niche, and from the gut lumen, to divide and differentiate at a rate that maintains an epithelial barrier to microbial invasion of the host interior. Despite the importance of evolutionarily conserved innate immune defenses to maintain stable host-microbiota relationships, we know little about specific contributions of stem cell immunity to gut homeostasis. We used the Drosophila model to determine the consequences of compromised intestinal stem cell immune activity for epithelial homeostasis. We showed that loss of stem cell immunity greatly impacted growth and renewal in the adult gut. In particular, we noticed that inhibition of stem cell immunity impeded key growth and differentiation events in the progenitor cell compartment leading to a gradual loss of stem cell numbers with age, and an impaired differentiation of mature enteroendocrine cells. Our results highlight the importance of immune signaling in the stem cell population for epithelial function in the adult gut.
HIGHLIGHTSO_LIThe TNFR-like Immune Deficiency (IMD) pathway is active in Drosophila intestinal progenitor cells.
C_LIO_LIInhibition of IMD in progenitors impairs progenitor cell proliferation.
C_LIO_LIBlocking progenitor cell IMD negatively affects generation of mature epithelial cells.
C_LI | immunology |
10.1101/721761 | Molecular Basis of the Activation and Dissociation of Dimeric PYL2 Receptor in Abscisic Acid Signaling | Phytohormone abscisic acid (ABA) is essential for plant responses to biotic and abiotic stresses. Dimeric receptors are a class of ABA receptors that are important for various ABA responses. While extensive experimental and computational studies have investigated these receptors, it remains not fully understood how ABA leads to their activation and dissociation for interaction with downstream phosphatase. Here, we study the activation and the homodimeric association processes of PYL2 receptor as well as its heterodimeric association with the phosphatase HAB1 using molecular dynamics simulations. Free energy landscapes from ~223 s simulations show that dimerization substantially constrains PYL2 conformational plasticity and stabilizes inactive state, resulting in lower ABA affinity. Also, we establish the thermodynamic model for competitive binding between homodimeric PYL2 association and heterodimeric PYL2-HAB1 association in the absence and presence of ABA. Our results suggest that the binding of ABA destabilizes PYL2 complex and further stabilizes PYL2-HAB1 association, thereby promoting PYL2 dissociation. Overall, this study explains several key aspects on activation of dimeric ABA receptors, which provide new avenues for selective regulation of these receptors. | plant biology |
10.1101/722215 | Grazer behavior can regulate large-scale patterning of community states | Ecosystem patterning can arise from environmental heterogeneity, biological feedbacks that produce multiple persistent ecological states, or their interaction. One source of feed-backs is density-dependent changes in behavior that regulates species interactions. By fitting state-space models to large-scale ([~]500km) surveys on temperate rocky reefs, we find that behavioral feedbacks best explain why kelp and urchin barrens form either reef-wide patches or local mosaics. Best-supported models in California include feedbacks where starvation intensifies grazing across entire reefs create reef-scale, alternatively stable kelp- and urchin-dominated states (32% of reefs). Best-fitting models in New Zealand include the feedback of urchins avoiding dense kelp stands that can increase abrasion and predation risk, which drives a transition from shallower urchin-dominated to deeper kelp-dominated zones, with patchiness at 3-8m depths with intermediate wave stress. Connecting locally-studied processes with region-wide data, we highlight how behavior can explain community patterning and why some systems exhibit community-wide alternative stable states. | ecology |
10.1101/722744 | High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition | The composition of the gut microbiome is impacted by a complex array of factors, from nutrient composition and availability, to physical factors like temperature, pH, and flow rate, as well as interactions among the members of the microbial community. Many of these factors are affected by the host, raising the question of how host genetic variation impacts microbiome composition. Though human studies confirm this type of role for host genetics, its overall importance is still a subject of debate and remains difficult to study. The mouse model, by allowing the strict control of genetics, nutrition, and other environmental factors, has provided an excellent opportunity to extend this work, and the Diversity Outbred (DO) mice in particular present a chance to pinpoint host genetic variants that influence microbiome composition at different levels of generality. Here, we apply 16S rRNA gene sequencing to fecal samples of 247 DO male mice to estimate heritability and perform taxon-specific QTL mapping of microbial relative abundances revealing an increasingly heterogeneous picture of host function and microbial taxa at the host-microbiome interface. We present the first report of significant heritability of phylum Tenericutes in mice, and find novel QTL-spanning genes involved in antibacterial pathways, immune and inflammatory disease, and lipid metabolism. | genetics |
10.1101/707919 | Addressing the Embeddability Problem in Transition Rate Estimation | Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. Here, we discuss an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix. Although the rate matrix itself is built from the empirical transition matrix, it provides an alternative approach for estimating both thermodynamic and kinetic quantities, particularly in diffusive processes. We particularly discuss a fundamental issue with this approach, known as the embeddability problem and offer ways to address this issue. We describe eight different methods to overcome the embeddability problem, including a novel approach developed for this work. The algorithms were tested on data from a one-dimensional toy model to show the workings of these methods and discuss the robustness of each method in terms of its dependence in lag time and trajectory length. | biophysics |