id
stringlengths 14
25
| title
stringlengths 13
378
| abstract
stringlengths 73
8.77k
| category
stringclasses 26
values |
|---|---|---|---|
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 |
10.1101/723205 | Loss of intermediate filament IFB-1 reduces mobility, density and physiological function of mitochondria in C. elegans sensory neurons | Mitochondria and intermediate filament (IF) accumulations often occur during imbalanced axonal transport leading to various types of neurological diseases. It is still poorly understood whether a link between neuronal IFs and mitochondrial mobility exist. In C. elegans, among the 11 cytoplasmic IF family proteins, IFB-1 is of particular interest as it is expressed in a subset of sensory neurons. Depletion of IFB-1 leads to mild dye-filling and significant chemotaxis defects as well as reduced life span. Sensory neuron development is affected and mitochondria transport is slowed down leading to reduced densities of these organelles. Mitochondria tend to cluster in neurons of IFB-1 mutants likely dependent on fission but independent of fusion events. Oxygen consumption and mitochondrial membrane potential is measurably reduced in worms carrying mutations in the ifb-1 gene. Membrane potential also seems to play a role in transport such as FCCP treatment led to increased directional switching of mitochondria. Mitochondria colocalize with IFB-1 in worm neurons and appear in a complex with IFB-1 in pull-down assays. In summary, we propose a model in which neuronal intermediate filaments may serve as critical (transient) anchor points for mitochondria during their long-range transport in neurons for steady and balanced transport.
Abstract Figure
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/723205v3_ufig1.gif" ALT="Figure 1">
View larger version (32K):
org.highwire.dtl.DTLVardef@1c6fc73org.highwire.dtl.DTLVardef@e7fd9aorg.highwire.dtl.DTLVardef@ba9742org.highwire.dtl.DTLVardef@20a9ed_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisVarious neurological diseases are both associated with abnormal accumulations of neuronal intermediate filaments as well as mitochondria. Here, we report a link between these two phenomena employing the model organisms C. elegans. Depletion of neuronal intermediate filament IFB-1 impairs the transport of mitochondria in sensory neurons leading to clustered and accumulated mitochondria affecting neuronal growth and oxygen consumption in nematodes. | cell biology |
10.1101/723056 | The Human Motor Cortex Contributes to Gravity Compensation to Maintain Posture and During Reaching | How the neural motor system recruits muscles to support the arm against gravity is a matter of active debate. It is unknown how the neural motor system compensates for the changing gravity-related joint moments either when holding a steady-state posture or during movement between postural steady states, e.g., during reaching. Here we used single-pulse transcranial magnetic stimulation to compare the roles that the human primary motor cortex plays in the muscle recruitment to compensate for gravity. We hypothesized that the motor cortex contributes to muscle recruitment to both maintain posture and to compensate for changes in gravitational passive joint moments during movement. To test this hypothesis, we used visual targets in virtual reality to instruct five postures and three movements with or against gravity. We then measured the amplitude and gain of motor evoked potentials in multiple muscles of the arm at several phases of the reaching motion and during posture maintenance. Stimulation below the resting motor threshold, calibrated to the biceps muscle, caused motor evoked potentials in all muscles during all postural and reaching tasks. The amplitude of motor evoked potentials was proportional to the motoneuronal excitability measured as muscle activity. The coefficient of proportionality was positively correlated with the postural component of muscle moment during posture and movement. Altogether our results support the hypothesis. The observed contribution of the motor cortex to the recruitment of multiple antagonistic muscles suggests a whole-limb strategy for overcoming passive gravity-related moments with both active muscle moments and muscle co-activation that modulates limb impedance.
New & NoteworthyMaintaining static posture and producing motion appear to be contradictory tasks for the nervous system. In contrast to this seeming dichotomy, our results show that the motorcortical control signals play the same role in both tasks when it is framed in biomechanical terms, i.e., muscle contractions needed to compensate for gravity. | neuroscience |
10.1101/723072 | Humans can navigate complex graph structures acquired during latent learning | Humans appear to represent many forms of knowledge in associative networks whose nodes are multiply connected, including sensory, spatial, and semantic. Recent work has shown that explicitly augmenting artificial agents with such graph-structured representations endows them with more human-like capabilities of compositionality and transfer learning. An open question is how humans acquire these representations. Previously, it has been shown that humans can learn to navigate graph-structured conceptual spaces on the basis of direct experience with trajectories that intentionally draw the network contours (Schapiro et al., 2012;2016), or through direct experience with rewards that covary with the underlying associative distance (Wu et al., 2018). Here, we provide initial evidence that this capability is more general, extending to learning to reason about shortest-path distances across a graph structure acquired across disjoint experiences with randomized edges of the graph - a form of latent learning. In other words, we show that humans can infer graph structures, assembling them from disordered experiences. We further show that the degree to which individuals learn to reason correctly and with reference to the structure of the graph corresponds to their propensity, in a separate task, to use model-based reinforcement learning to achieve rewards. This connection suggests that the correct acquisition of graph-structured relationships is a central ability underlying forward planning and reasoning, and may be a core computation across the many domains in which graph-based reasoning is advantageous. | animal behavior and cognition |
10.1101/722603 | Mitochondrial fission is increased in macrophages during mROS production in response to S. pneumoniae | Immunometabolism and regulation of mitochondrial reactive oxygen species (mROS) are critical determinants of the immune effector phenotype of differentiated macrophages. Mitochondrial function requires dynamic fission and fusion, but whether effector function is associated with altered dynamics during bacterial responses is unknown. We show that macrophage mitochondria undergo fission after 12 h of progressive ingestion of live Streptococcus pneumoniae (pneumococci). Fission is associated with progressive reduction in oxidative phosphorylation but increased mROS generation. Fission is enhanced by mROS production, PI3K{gamma} signaling and by cathepsin B, but not by inflammasome activation or IL-1{beta} generation. Reduced fission following PI3K{gamma} or cathepsin B inhibition is associated with reduced mROS generation and bacterial killing. Fission is associated with Parkin recruitment to mitochondria, but not mitophagy. Fission occurs upstream of apoptosis induction and independently of caspase activation. During macrophage innate responses to live bacteria mitochondria shift from oxidative phosphorylation and ATP generation to mROS production and microbicidal responses with a progressive shift towards mitochondrial fission. | immunology |
10.1101/726117 | An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei | Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential in Trypanosoma brucei. Here we show that the single identifiable T. brucei fucosyltransferase (TbFUT1) is a GDP-Fuc: {beta}-D-galactose -1,2-fucosyltransferase with an apparent preference for a Gal{beta}1,3GlcNAc{beta}1-O-R acceptor motif. Conditional null mutants of TbFUT1 demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion of T. brucei and found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, the TbFUT1 gene was able to complement a Leishmania major mutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids. | microbiology |
10.1101/726166 | Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data | Uncovering the genes governing host-parasite coevolutionary interactions is of importance for disease management. The increasing availability of host and parasite full genome-data allows for cross-species genome-wide association studies based on the genomic data of in-fected hosts and their associated parasite strains sampled from natural populations (i.e. natural co-GWAs). Such studies focus on searching for cross-species allelic associations between pairs of host and parasite SNPs. We aim to quantify the power of natural co-GWAs to pinpoint loci under coevolution with respect to the intrinsic complexities of coevolutionary systems, such as the genetic specificity of the interaction and the temporal allele frequency changes resulting from the interaction. Therefore, we develop the cross-species association (CSA) and the cross-species prevalence (CSP) indices, the latter additionally incorporating genomic data from uninfected hosts. To provide an assessment of the statistical power of these indices, we analytically derive their genome-wide False Discovery Rates (FDR) based on the neutral site-frequency spectrum of the host and the parasite population. Using two coevolutionary models, we investigate under which parameter regimes these indices pin-point the coevolving loci. Under trench warfare dynamics, CSA and CSP are very accurate in pinpointing the loci under coevolution, while under arms race dynamics the power is limited especially for gene-for-gene interactions. Furthermore, we reveal that the combination of both indices across time samples is an indicator for the specificity of the interaction. Our results provide novel insights into the power and biological interpretation of natural cross-species association studies. | evolutionary biology |
10.1101/726752 | Protein yield is tunable by synonymous codon changes of translation initiation sites | Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. To address this problem, we modified up to the first nine codons of messenger RNAs with synonymous substitutions and showed that protein levels can be tuned. These modifications alter the accessibility of translation initiation sites. We also reveal the dynamics between accessibility, gene expression, and turnovers using a coarse-grained simulation. | bioinformatics |
10.1101/726752 | Protein yield is tunable by synonymous codon changes of translation initiation sites | Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. To address this problem, we modified up to the first nine codons of messenger RNAs with synonymous substitutions and showed that protein levels can be tuned. These modifications alter the accessibility of translation initiation sites. We also reveal the dynamics between accessibility, gene expression, and turnovers using a coarse-grained simulation. | bioinformatics |
10.1101/727859 | Epigenetic age is accelerated in schizophrenia with age- and sex-specific effects and associated with polygenic disease risk | BackgroundThe study of biological age acceleration may help identify at-risk individuals and contribute to reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a severe mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a multi-cohort whole blood sample consisting of 1,090 SCZ cases and 1,206 controls, we investigated differential aging using three DNAm clocks (i.e. Hannum, Horvath, Levine). These clocks are highly predictive of chronological age and are known to capture different processes of biological aging.
ResultsWe found that blood-based DNAm aging is significantly altered in SCZ with age- and sex-specific effects that differ between clocks and map to distinct chronological age windows. Most notably, differential phenotypic age (Levine clock) was most pronounced in female SCZ patients in later adulthood compared to matched controls. Female patients with high SCZ polygenic risk scores (PRS) present the highest age acceleration in this age group with +4.30 years (CI: 2.40-6.20, P=1.3E-05). Phenotypic age and SCZ PRS contribute additively to the illness and together explain up to 22.4% of the variance in disease status in this study. This suggests that combining genetic and epigenetic predictors may improve predictions of disease outcomes.
ConclusionsSince increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. These results provide new biological insights into the aging landscape of SCZ with age- and sex-specific effects and warrant further investigations into the potential of DNAm clocks as clinical biomarkers that may help with disease management in schizophrenia. | genomics |
10.1101/725382 | Choice-selective sequences dominate in cortical relative to thalamic inputs to the nucleus accumbens, providing a potential substrate for credit assignment | How are actions linked with subsequent outcomes to guide choices? The nucleus accumbens, which is implicated in this process, receives glutamatergic inputs from the prelimbic cortex and midline regions of the thalamus. However, little is known about whether and how representations differ across these input pathways. By comparing these inputs during a reinforcement learning task in mice, we discovered that prelimbic cortical inputs preferentially represent actions and choices, whereas midline thalamic inputs preferentially represent cues. Choice-selective activity in the prelimbic cortical inputs is organized in sequences that persist beyond the outcome. Through computational modeling, we demonstrate that these sequences can support the neural implementation of reinforcement learning algorithms, both in a circuit model based on synaptic plasticity, and one based on neural dynamics. Finally, we test and confirm predictions of our circuit models by direct manipulation of nucleus accumbens input neurons. Thus, we integrate experiment and modeling to suggest neural solutions for credit assignment. | neuroscience |
10.1101/727867 | scAEspy: a tool for autoencoder-based analysis of single-cell RNA sequencing data | BackgroundSingle-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches.
ResultsAutoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions.
ConclusionsscAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics. | bioinformatics |
10.1101/727867 | Analysis of single-cell RNA sequencing data basedon autoencoders | BackgroundSingle-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches.
ResultsAutoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions.
ConclusionsscAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics. | bioinformatics |
10.1101/728410 | The PRMT7-dependent methylation of shank2 modulates invasion-proliferation switching during breast cancer metastasis | Invasiveness of cancer cells is associated with proliferation inhibition in multiple types of cancers. Here, we identified the pivotal roles of Arginine methyltransferase PRMT7 in promoting invasion and attenuating proliferation of breast cancer cells. PRMT7 exerted its functions through binding to the scaffold protein shank2 to induce the di-methylation of shank2 at R240. Shank2 R240 methylation exposed ANK domain by disrupting its SPN-ANK domain blockade. Moreover, shank2 R240 methylation rendered recruitment of FAK that elicited the FAK auto-phosphorylation, which consequently augmented the shank2-dependent migration and invasion of breast cancer cells. On the other hand, the shank2 R240 methylation impeded proliferation of breast cancer cells by antagonizing the Ras-Raf binding via tethering the mono-ubiquitinated H-Ras. These findings characterize the PRMT7-dependent shank2 methylation as a key player in mediating reciprocal switching between invasion and proliferation, also point to the value of shank2 R240 methylation as a target for tumour metastasis treatment strategies. | cancer biology |
10.1101/728428 | Distinct neurocomputational mechanisms support informational and normative conformity | A change of mind in response to social influence could be driven by informational conformity to increase accuracy, or by normative conformity to comply with social norms such as reciprocity. Disentangling the behavioural, cognitive and neurobiological underpinnings of informational and normative conformity have proven elusive. Here, participants underwent fMRI while performing a perceptual task that involved both advice-taking and advice-giving to human and computer partners. The concurrent inclusion of two different social roles and two different social partners revealed distinct behavioural and neural markers for informational and normative conformity. dACC BOLD response tracked informational conformity towards both human and computer but tracked normative conformity only when interacting with human. A network of brain areas (dmPFC and TPJ) that tracked normative conformity increased their functional coupling with the dACC when interacting with humans. These findings enable differentiating the neural mechanisms by which different types of conformity shape social changes of mind. | neuroscience |
10.1101/729731 | Cell-scale biophysical determinants of cell competition in epithelia | How cells with different genetic makeups compete in tissues is an outstanding question in developmental biology and cancer research. Studies in recent years have revealed that cell competition can either be driven by short-range biochemical signalling or by long-range mechanical stresses in the tissue. To date, cell competition has generally been characterised at the population-scale, leaving the single-cell level mechanisms of competition elusive. Here, we use high time-resolution experimental data to construct a multi-scale agent-based model for epithelial cell competition, and use it to gain a conceptual understanding of the cellular factors that governs competition in cell populations within tissues. We find that a key determinant of mechanical competition is the difference in homeostatic density between winners and losers, while differences in growth rates and tissue organisation do not affect competition end-result. In contrast, the outcome and kinetics of biochemical competition is strongly influenced by local tissue organisation. Indeed, when loser cells are homogenously mixed with winners at the onset of competition, they are eradicated; however, when they are spatially separated, winner and loser cells coexist for long times. These findings suggest distinct biophysical origins for mechanical and biochemical modes of cell competition. | biophysics |
10.1101/730416 | Relating Global and Local Connectome Changes to Dementia and Targeted Gene Expression in Alzheimer's Disease | Networks are present in many aspects of our lives, and networks in neuroscience have recently gained much attention leading to novel representations of brain connectivity. The integration of neuroimaging characteristics and genetics data allows a better understanding of the effects of the genetic variations on brain structural and functional connections. The current work uses whole-brain tractography in a longitudinal setting, and by measuring the brain structural connectivity changes studies the neurodegeneration of Alzheimers disease. This is accomplished by examining the effect of targeted genetic risk factors on the most common local and global brain connectivity measures. Furthermore, we examined the extent to which Clinical Dementia Rating relates to brain connections longitudinally, as well as to gene expression. Here we show that the expression of PLAU gene increases the change over time in betweenness centrality related to the fusiform gyrus. We also show that the betweenness centrality metric impact dementia-related changes in distinct brain regions. Our findings provide insights into the complex longitudinal interplay between genetics and brain characteristics and highlight the role of Alzheimers genetic risk factors in the estimation of regional brain connectivity alterations. | bioinformatics |
10.1101/730648 | Endosomal explosion induced by hypertonicity | Transferring DNA into cells to regulate cell function is a novel research field in recent decades. Chitosan is a gene vector with the properties of low-cost and safe, but high efficient delivery has remained challenging. We developed a strategy termed EEIH for endosomal explosion induced by hypertonicity, in which short-time exposure to hypertonic solutions triggers endosomes destabilization like explosions. EEIH can force chitosan/DNA polyplexes to break through the endosomal barriers to approach the nucleus, which results in boosting the transfection efficiency of chitosan in several cell lines. We demonstrate that EEIH is a significant and practical strategy in chitosan transfection system without sophisticated modification of chitosan. | biophysics |
10.1101/731596 | CrowdGO: machine learning and semantic similarity guided consensus Gene Ontology annotation | BackgroundCharacterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations.
ResultsTo exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the communitys best performing individual methods.
ConclusionCrowdGO offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.
Availability and ImplementationCrowdGO is implemented in Python3, and is freely available from https://gitlab.com/mreijnders/CrowdGO, with a Snakemake workflow and pre-trained models. | bioinformatics |
10.1101/731596 | CrowdGO: machine learning and semantic similarity guided consensus Gene Ontology annotation | BackgroundCharacterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations.
ResultsTo exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the communitys best performing individual methods.
ConclusionCrowdGO offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.
Availability and ImplementationCrowdGO is implemented in Python3, and is freely available from https://gitlab.com/mreijnders/CrowdGO, with a Snakemake workflow and pre-trained models. | bioinformatics |
10.1101/731596 | CrowdGO: machine learning and semantic similarity guided consensus Gene Ontology annotation | BackgroundCharacterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations.
ResultsTo exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the communitys best performing individual methods.
ConclusionCrowdGO offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.
Availability and ImplementationCrowdGO is implemented in Python3, and is freely available from https://gitlab.com/mreijnders/CrowdGO, with a Snakemake workflow and pre-trained models. | bioinformatics |
10.1101/724716 | Sorting motifs target the movement protein of ourmia melon virus to the trans-Golgi network and plasmodesmata | Plants have a highly sophisticated endomembrane system targeted by plant viruses for cell-to-cell movement. The movement protein (MP) of ourmia melon virus (OuMV) is delivered to plasmodesmata (PD) and forms tubules to facilitate cell-to-cell movement. Although several functionally important regions for correct subcellular localization of OuMV MP have been identified, little is known about the pathways OuMV MP hijacks to reach the PD. Here, we demonstrate that OuMV MP localizes to the trans-Golgi network (TGN), but not to the multivesicular body/prevacuolar compartment or Golgi, and carries two putative sorting motifs, a tyrosine (Y) and a dileucine (LL) motif, near its N-terminus. Glycine substitutions in these motifs result in loss of OuMV infectivity in Nicotiana benthamiana and Arabidopsis. Live cell imaging of GFP-labeled sorting motif mutants shows that Y motif mutants fail to localize to the TGN, plasma membrane, and PD. Mutations in the LL motif do not impair plasma membrane targeting of MP but affect its ability to associate with callose deposits at the PD. Taken together, these results suggest that both motifs are indispensable for targeting OuMV MP to PD and for efficient systemic infection but show differences in functionality. Co-immunoprecipitation assays coupled with mass spectrometry identified a series of host factors that could interact with the OuMV MP and link the MP with various pathways, in particular vesicle trafficking and membrane lipids. This study provides new insights into the intracellular targeting of MPs and pathways that plant viruses hijack for cell-to-cell movement. | plant biology |
10.1101/733311 | Transcriptome computational workbench (TCW): analysis of single and comparative transcriptomes | De novo transcriptome sequencing and analysis provides a way for researchers of non-model organisms to explore the differences between various conditions and species. The results are typically not definitive but will lead to new hypotheses to study. Therefore, it is important that the results be reproducible, extensible, queryable, and easily available to all members of the team. Towards this end, the Transcriptome Computational Workbench (TCW) is a software package to perform basic computations for transcriptome analysis (singleTCW) and comparative analysis (multiTCW). It is a Java-based desktop application that uses MySQL for the TCW database. The input to singleTCW is sequence and optional count files; the computations are sequence similarity, gene ontology (GO), open reading frame (ORF), and differential expression (DE). TCW provides support for searching with the super-fast DIAMOND program against UniProt taxonomic databases, though the user can provide other databases to search against. The ORF finder uses hit information, 5th-order Markov models and ORF length. For DE and GO enrichment, TCW interfaces with the R environment and an R script, where R scripts are provided for popular methods. The input to multiTCW is multiple singleTCW databases; the computations are homologous pair assignment, pairwise analysis (e.g. Ka/Ks) from codon-based alignments, clustering (bidirectional best hit, Closure, Best Hit, OrthoMCL, user-supplied), and cluster analysis and annotation. Both singleTCW and multiTCW provide a graphical interface for extensive query and display of the data and results. Example results are presented from two rhizome and one non-rhizome plant, where one of the rhizome plants has replicate count data from four tissues. The supplement describes how to reproduce all tables and figures. The TCW V4 software is freely available at https://github.com/csoderlund/TCW; the package contains the jar files, external software, and demo files. | bioinformatics |
10.1101/732933 | Unfolding and identification of membrane proteins in situ | Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment. | biophysics |
10.1101/732669 | Decoding the sound of hand-object interactions in primary somatosensory cortex | Neurons, even in earliest sensory regions of cortex, are subject to a great deal of contextual influences from both within and across modality connections. Recent work has shown that primary sensory areas can respond to and in some cases discriminate stimuli not of their target modality: for example, primary somatosensory cortex (SI) discriminates visual images of graspable objects. In the present work, we investigated whether SI would discriminate sounds depicting hand-object interactions (e.g. bouncing a ball). In a rapid event-related functional magnetic resonance imaging (fMRI) experiment, participants listened attentively to sounds from three categories: hand-object interactions, and control categories of pure tones and animal vocalizations, while performing a one-back repetition detection task. Multi-voxel pattern analysis revealed significant decoding of different hand-object interactions within SI, but not for either control category. Crucially, in the hand-sensitive voxels defined from an independent tactile localizer, decoding accuracies were significantly higher for hand-object interactions compared to pure tones in left SI. Our findings indicate that simply hearing sounds depicting familiar hand-object interactions elicit different patterns of activity in SI, despite the complete absence of tactile stimulation. These results highlight the rich information that can be transmitted across sensory modalities even to primary sensory areas. | neuroscience |
10.1101/728089 | Genomic insights into the Archaea inhabiting an Australian radioactive legacy site | During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated using shotgun metagenomics. This revealed a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment.
Here, applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs ([≥]50% completeness, [≤]10% redundancy) from 10 different major lineages. They were, mainly, included in four DPANN lineages without standing nomenclature (LFWA-I to IV) and Methanoperedenaceae (ANME-2D).
While most of the new DPANN lineages show reduced genomes with limited central metabolism typical of other DPANN, the orders under the LFWA-III lineage, Ca. Gugararchaeales and Ca. Anstonellales, may constitute distinct orders with a more comprehensive central metabolism and anabolic capabilities within the Micrarchaeota phylum.
The new Methanoperedens spp. MAGs, together with previously published data, suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most Methanoperedens also appears to be a widespread characteristic of the genus for carbon accumulation.
We formally propose 22 new candidate taxa based on data analysed in this manuscript, as well as four missing formal taxa definitions and two new candidate species based on extant data. We present evidence of four new DPANN lineages and six non-conspecific Methanoperedens, while exploring their uniqueness, potential role in elemental cycling, and evolutionary history. | microbiology |
10.1101/720391 | An R Package for Divergence Analysis of Omics Data | Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms. The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. Here we demonstrate how to use the package with data from the Cancer Genome Atlas. | bioinformatics |
10.1101/734012 | Cholesterol recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: the case for TRKB | Cholesterol is an essential constituent of cell membranes. Recently, the discovery of cholesterol recognition amino acid consensus (CRAC) on proteins indicated a putative direct, non-covalent interaction between cholesterol and proteins. In the present study, we evaluated the presence of a CRAC motif and its inverted version (CARC) in the transmembrane region (TMR) of the tyrosine kinase receptor family (RTK) in several species using in silico methods. CRAC motifs were found across all species analyzed, while CARC was found only in vertebrates. The tropomyosin-related kinase B (TRKB), a member of the RTK family, is a core participant in the neuronal plasticity process and exhibits a CARC motif in its TMR. Upon recognition of the conserved CARC motif in the TRKB, we performed molecular dynamics simulations with the mouse TRKB TMR sequence, which indicated that cholesterol interaction with the TRKB CARC motif occurs mainly at the central Y433 residue. Binding assay suggested a bell-shaped effect of cholesterol on BDNF interaction with TRKB receptors. Therefore, CARC/CRAC motifs may have a role in the function of the RTK family TMR. | neuroscience |
10.1101/734012 | Cholesterol recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: the case for TRKB | Cholesterol is an essential constituent of cell membranes. Recently, the discovery of cholesterol recognition amino acid consensus (CRAC) on proteins indicated a putative direct, non-covalent interaction between cholesterol and proteins. In the present study, we evaluated the presence of a CRAC motif and its inverted version (CARC) in the transmembrane region (TMR) of the tyrosine kinase receptor family (RTK) in several species using in silico methods. CRAC motifs were found across all species analyzed, while CARC was found only in vertebrates. The tropomyosin-related kinase B (TRKB), a member of the RTK family, is a core participant in the neuronal plasticity process and exhibits a CARC motif in its TMR. Upon recognition of the conserved CARC motif in the TRKB, we performed molecular dynamics simulations with the mouse TRKB TMR sequence, which indicated that cholesterol interaction with the TRKB CARC motif occurs mainly at the central Y433 residue. Binding assay suggested a bell-shaped effect of cholesterol on BDNF interaction with TRKB receptors. Therefore, CARC/CRAC motifs may have a role in the function of the RTK family TMR. | neuroscience |
10.1101/735183 | Talin-vinculin precomplex drives adhesion maturation by accelerated force transmission and vinculin recruitment | Talin, vinculin, and paxillin are mechanosensitive proteins that are recruited early to integrin-based nascent adhesions (NAs). Using machine learning, traction microscopy, single-particle-tracking, and fluorescence fluctuation analysis, we find that talin, vinculin, and paxillin are recruited in near-synchrony to NAs maturing to focal adhesions. After initial recruitment of all three proteins under minimal load, vinculin accumulates in these NAs at a ~5 fold higher rate than in non-maturing NAs and with faster growth in traction. We identify a domain in talin, R8, which exposes a vinculin-binding-site (VBS) without requiring load. Stabilizing this domain via mutation lowers load-free vinculin binding to talin, impairs maturation of NAs, and reduces the rate of additional vinculin recruitment. Taken together, our data show that talins concurrent localization with vinculin, before engagement with integrins, is essential for NA maturation, which entails traction-mediated unfolding of talin and exposure of additional VBSs triggering further vinculin binding. | cell biology |
10.1101/726588 | Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration | Cell death is a critical process that occurs normally in health and disease. However, its study is limited due to available technologies that only detect very late stages in the process or specific death mechanisms. Here, we report the development of a new fluorescent biosensor called genetically encoded death indicator (GEDI). GEDI specifically detects an intracellular Ca2+ level that cells achieve early in the cell death process and marks a stage at which cells are irreversibly committed to die. The time-resolved nature of GEDI delineates a binary demarcation of cell life and death in real time, reformulating the definition of cell death. We demonstrate that GEDI acutely and accurately reports death of rodent and human neurons in vitro, and show GEDI enables a novel automated imaging platform for single cell detection of neuronal death in vivo in zebrafish larvae. With a quantitative pseudo-ratiometric signal, GEDI facilitates high-throughput analysis of cell death in time lapse imaging analysis, providing the necessary resolution and scale to identify early factors leading to cell death in studies of neurodegeneration. | neuroscience |
10.1101/734038 | THE COSTS AND BENEFITS OF BASAL INFECTION RESISTANCE VS DIVERSE IMMUNE PRIMING RESPONSES IN AN INSECT | In insects, basal pathogen resistance and immune priming can evolve as mutually exclusive strategies, with distinct infection outcomes. However, the evolutionary drivers of such diverse immune functions remain poorly understood. Here, we addressed this key issue by systematically analyzing the differential fitness costs and benefits of priming vs. resistance evolution in Tribolium beetle populations infected with Bacillus thuringiensis. Surprisingly, resistant beetles had increased post-infection reproduction and a longer lifespan under both starving as well as fed conditions, with no other measurable costs. In contrast, priming reduced offspring early survival, development rate and reproduction. Priming did improve post-infection survival of offspring, but this added trans-generational benefit of immune priming might not compensate for its pervasive costs. Resistance was thus consistently more beneficial. Our work represents the first report of experimentally evolved trans-generational priming, and a detailed comparison of the complex fitness consequences of evolved priming vs resistance.
HIGHLIGHTSO_LIDivergent costs and benefits of experimentally evolved immune priming vs resistance
C_LIO_LIIncreased reproduction and lifespan in resistant populations
C_LIO_LINo other hidden costs of resistance
C_LIO_LIIn contrast, reduced juvenile fitness and reproduction in primed populations
C_LIO_LIFirst evidence for experimentally evolved trans-generational immune priming
C_LI | evolutionary biology |
10.1101/733402 | Common breast cancer risk loci predispose to distinct tumor subtypes | BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER), but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.
MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.
ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate <5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at P<0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.
ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction. | genetics |
10.1101/733402 | Common variants in breast cancer risk loci predispose to distinct tumor subtypes | BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER), but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.
MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.
ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate <5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at P<0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.
ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction. | genetics |
10.1101/737890 | Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection | Long intergenic non-coding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as non-coding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated.
Here, we analysed signatures of repressed translation in lincRNA sequences from six eukaryotes. In species under stronger selection, i.e. fission yeast and worm, we detected significantly shorter ORFs than in intronic and non-transcribed control regions, a suboptimal sequence context around start codons for translation initiation, and trinucleotides ("codons") corresponding to less abundant tRNAs than codons in control regions, potentially impeding translation elongation.
We verified that varying tRNA expression levels affect ribosome-binding to lincRNAs by analyzing data from five human cell lines. Notably, for three cell lines, codons in abundant cytoplasmic lincRNAs corresponded to lower expressed tRNAs than control codons, substantiating cell type-specific repression of lincRNA translation in human. Finally, comparing non-coding with peptide-encoding ORFs suggested that codon usage at the start of ORFs to be of particular relevance for ribosome-binding.
The identified sequence signatures may assist distinguishing peptide- from real non-coding lincRNAs in a cell. | genomics |
10.1101/737676 | Priors, population sizes, and power in genome-wide hypothesis tests | Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNA-Seq data, carry a high multiple testing burden. This burden can be overcome by enrolling larger cohorts or alleviated by using prior biological knowledge to favor some hypotheses over others. Here we compare these two methods in terms of their abilities to boost the power of hypothesis testing. We provide a quantitative estimate for progress in cohort sizes, and present a theoretical analysis of the power of oracular hard priors: priors that select a subset of hypotheses for testing, with an oracular guarantee that all true positives are within the tested subset. This theory demonstrates that for GWAS, strong priors that limit testing to 100-1000 genes provide less power than typical annual 20-40% increases in cohort sizes. These theoretical results explain the continued dominance of simple, unbiased univariate hypothesis tests for RNA-Seq studies and GWAS: if a statistical question can be answered by larger cohort sizes, it should be answered by larger cohort sizes rather than by more complicated biased methods involving priors. We suggest that priors are better suited for non-statistical aspects of biology, such as pathway structure and causality, that are not yet easily captured by standard hypothesis tests.
Author summaryBiological experiments often test thousands to millions of hypotheses. Gene-based tests for human RNA-Seq data, for example, involve approximately 20,000 tests; genome-wide association studies (GWAS) involve about 1 million effective tests. A robust approach is to perform individual tests and then apply a Bonferroni correction to account for multiple testing. This approach implies a single-test p-value of 2.5 x 10-6 for RNA-Seq experiments, and a p-value of 5 x 10-8 for GWAS, to control the false-positive rate at a conventional value of 0.05. Many methods have been proposed to alleviate the multiple-testing burden by incorporating a prior probability that boosts the significance for a subset of candidate genes or variants. At the extreme limit, only hypotheses within a candidate set are tested, corresponding to a decreased multiple testing burden. Despite decades of methods development, prior-based tests have not been generally used. Here we compare the power increase possible with a prior with the power increase from a much simpler strategy of increasing a study size. We show that increasing the population size is exponentially more valuable than increasing the strength of prior, even when the true prior is known exactly. Furthermore, even modest yearly increases in actual GWAS cohorts can yield power gains beyond the reach of any reasonable prior. These results provide a rigorous explanation for the continued use of simple, robust methods rather than more sophisticated approaches. They suggest that the value of priors is not in multiple hypothesis testing but rather in non-statistical aspects of interpretation including pathway structure and causality. | genetics |
10.1101/734913 | CXCR4 allows T cell acute lymphoblastic leukemia to escape from JAK1/2 and BCL2 inhibition through CNS infiltration | Targeting the JAK/STAT and BCL2 pathways in patients with relapsed/refractory T cell acute lymphoblastic leukemia (T-ALL) may provide an alternative approach to achieve clinical remissions. Ruxolitinib and venetoclax show a dose-dependent effect on T-ALL individually, but combination treatment reduces survival and proliferation of T-ALL in vitro. Using a xenograft model, the combination treatment fails to improve survival, with death from hind limb paralysis. Despite on-target inhibition by the drugs, histopathology demonstrates increased leukemic infiltration into the central nervous system (CNS) as compared to liver or bone marrow. Liquid chromatography-tandem mass spectroscopy shows that ruxolitinib and venetoclax insufficiently cross into the CNS. The addition of the CXCR4 inhibitor plerixafor with ruxolitinib and venetoclax reduces clinical scores and enhances survival. While combination therapy with ruxolitinib and venetoclax shows promise for treating T-ALL, additional inhibition of the CXCR4-CXCL12 axis may be needed to maximize the possibility of complete remission. | cancer biology |
10.1101/738823 | Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype | The relationship between sequence variation and phenotype is poorly understood. Here we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations in Dihydrofolate Reductase (DHFR). We find that partial loss of DHFR activity causes reversible filamentation despite SOS response indicative of DNA damage, in contrast to thymineless death (TLD) achieved by complete inhibition of DHFR activity by high concentrations of antibiotic Trimethoprim. This phenotype is triggered by a disproportionate drop in intracellular dTTP, which could not be explained by drop in dTMP based on the Michaelis-Menten like in vitro activity curve of Thymidylate Kinase (Tmk), a downstream enzyme that phosphorylates dTMP to dTDP. Instead, we show that a highly cooperative (Hill coefficient 2.5) in vivo activity of Tmk is the cause of suboptimal dTTP levels. dTMP supplementation rescues filamentation and restores in vivo Tmk kinetics to Michaelis-Menten. Overall, this study highlights the important role of cellular environment in sculpting enzymatic kinetics with system level implications for bacterial phenotype. | biophysics |
10.1101/738781 | Environmental and genetic factors cause atypical development of vocalizations in neonatal mice: analyses of neurodevelopmental disorder models using a novel unsupervised machine learning approach | Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a fathers age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offsprings early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders.
One Sentence SummaryAdvanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories. | neuroscience |
10.1101/738781 | Analyses of infant vocal communication in mouse models of autism spectrum disorder using a novel unsupervised machine learning approach | Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a fathers age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offsprings early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders.
One Sentence SummaryAdvanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories. | neuroscience |
10.1101/738781 | Paternal aging affects developmental convergence of vocal behavior in individual mice: machine learning-driven analyses of individuality | Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a fathers age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offsprings early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders.
One Sentence SummaryAdvanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories. | neuroscience |
10.1101/738781 | Advanced paternal age diversifies individual trajectories of vocalization patterns in neonatal mice | Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a fathers age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offsprings early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders.
One Sentence SummaryAdvanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories. | neuroscience |
10.1101/738443 | Decoding the molecular landscape of the developing spatial processing system and production of entorhinal stellate cell-like cells by a direct programming approach. | Classic studies investigating how and when the entorhinal cortex (component of the memory processing system of the brain) develops have been based on traditional thymidine autoradiography and histological techniques. In this study, we take advantage of modern technologies to trace at a high resolution, the cellular complexity of the developing porcine medial entorhinal cortex by using single-cell profiling. The postnatal medial entorhinal cortex comprises 4 interneuron, 3 pyramidal neuron and 2 stellate cell populations which emerge from intermediate progenitor and immature neuron populations. We discover four MGE-derived interneurons and one CGE-derived interneuron population as well as several IN progenitors. We also identify two oligodendrocyte progenitor populations and three populations of oligodendrocytes. We perform a proof-of-concept experiment demonstrating that porcine scRNA-seq data can be used to develop novel protocols for producing human entorhinal cells in-vitro. We identified six transcription factors (RUNX1A1, SOX5, FOXP1, MEF2C, TCF4, EYA2) important in neurodevelopment and differentiation from one RELN+ stellate cell population. Using a lentiviral vector approach, we reprogrammed human induced pluripotent stem cells into stellate cell-like cells which expressed RELN, SATB2, LEF1 and BCL11B. Our findings contribute to the understanding of the formation of the brains cognitive memory and spatial processing system and provides proof-of-concept for the production of entorhinal cells from human pluripotent stem cells in-vitro. | developmental biology |
10.1101/738443 | Decoding the porcine developing spatial processing system and production of human entorhinal stellate cell-like cells by a direct programming approach. | Classic studies investigating how and when the entorhinal cortex (component of the memory processing system of the brain) develops have been based on traditional thymidine autoradiography and histological techniques. In this study, we take advantage of modern technologies to trace at a high resolution, the cellular complexity of the developing porcine medial entorhinal cortex by using single-cell profiling. The postnatal medial entorhinal cortex comprises 4 interneuron, 3 pyramidal neuron and 2 stellate cell populations which emerge from intermediate progenitor and immature neuron populations. We discover four MGE-derived interneurons and one CGE-derived interneuron population as well as several IN progenitors. We also identify two oligodendrocyte progenitor populations and three populations of oligodendrocytes. We perform a proof-of-concept experiment demonstrating that porcine scRNA-seq data can be used to develop novel protocols for producing human entorhinal cells in-vitro. We identified six transcription factors (RUNX1A1, SOX5, FOXP1, MEF2C, TCF4, EYA2) important in neurodevelopment and differentiation from one RELN+ stellate cell population. Using a lentiviral vector approach, we reprogrammed human induced pluripotent stem cells into stellate cell-like cells which expressed RELN, SATB2, LEF1 and BCL11B. Our findings contribute to the understanding of the formation of the brains cognitive memory and spatial processing system and provides proof-of-concept for the production of entorhinal cells from human pluripotent stem cells in-vitro. | developmental biology |
10.1101/742916 | Adaptational lags during periods of environmental change | Effects of climate change can be handled by means of mitigation and adaptation. In the biological sciences, adaptations are solutions which evolved when organisms needed to match an ecological challenge. Based on Adaptive Dynamics theory, a definition is proposed of adapted states and adaptational lags applicable during periods with environmental change of any speed. Adaptation can thus be studied when it emerges from complex eco-evolutionary processes or when targets for adaptation are not defined a priori. The approach is exemplified with a model for delayed germination in an annual plant. Plasticity and maternal effects are often presumed to be adaptive and added to the model to investigate lags in these modes of trait determination. Adaptational lags can change sign and to understand their dynamics, effects of trait space boundaries and characteristics of years with large numbers of recruits had to be considered. Adaptational lags can be crucial elements of adaptive control strategies for managed ecosystems. To demonstrate their practical relevance, examples from pest management show that evolutionary adaptation has been used to infer targets of control. Adaptational lags then serve as measures of the distance to the control target and become integral elements of strategies for adaptive pest population management. | evolutionary biology |
10.1101/742239 | Aquila_stLFR: diploid genome assembly basedstructural variant calling package for stLFRlinked-read | MotivationIdentifying structural variants (SVs) is of critical importance in health and disease, however, detecting them remains a scientific and computing challenge. Several linked-read sequencing technologies, including 10X linked-read, TELL-Seq, and single tube long fragment read (stLFR), have been recently developed as cost-effective approaches to reconstruct multi-megabase haplotypes (phase blocks) from sequence data of a single sample. These technologies provide an optimal sequencing platform to characterize SVs, though few computational algorithms can utilize them. Thus, we developed Aquila_stLFR, an approach that resolves SVs through haplotype-based assembly of stLFR linked-reads.
ResultsAquila_stLFR first partitions LFRs into two haplotype-specific blocks, by taking advantage of the potential phasing ability of the linked-read itself. Each haplotype is then assembled independently, to achieve a complete diploid assembly to finally reconstruct the genome-wide SVs. We benchmarked Aquila_stLFR on a well-studied sample, NA24385, and showed Aquila_stLFR can detect medium to large size (50bp - 10kb) deletions with a high sensitivity and insertions with a high specificity.
AvailabilitySource code and documentation are available on https://github.com/maiziex/Aquila_stLFR.
Contactmaizie.zhou@vanderbilt.edu
Supplementary informationSupplementary data are available at Bioinformatics online. | bioinformatics |
10.1101/743674 | GABA levels in ventral visual cortex decline with age and are associated with neural distinctiveness | Age-related neural dedifferentiation - a decline in the distinctiveness of neural representations in the aging brain-has been associated with age-related declines in cognitive abilities. But why does neural distinctiveness decline with age? Based on prior work in non-human primates and more recent work in humans, we hypothesized that the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) declines with age and is associated with neural dedifferentiation in older adults. To test this hypothesis, we used magnetic resonance spectroscopy (MRS) to measure GABA and functional MRI (fMRI) to measure neural distinctiveness in the ventral visual cortex in a set of older and younger participants. Relative to younger adults, older adults exhibited lower GABA levels and less distinct activation patterns for faces and houses in the ventral visual cortex. Furthermore, individual differences in GABA within older adults positively predicted individual differences in neural distinctiveness. These results provide novel support for the view that age-related reductions of GABA contribute to age-related reductions in neural distinctiveness (i.e., neural dedifferentiation) in the human ventral visual cortex. | neuroscience |
10.1101/744318 | Using target capture to address conservation challenges: population-level tracking of a globally-traded herbal medicine | AO_SCPLOWBSTRACTC_SCPLOWThe promotion of responsible and sustainable trade in biological resources is widely proposed as one solution to mitigate currently high levels of global biodiversity loss. Various molecular identification methods have been proposed as appropriate tools for monitoring global supply chains of commercialized animals and plants. We demonstrate the efficacy of target capture genomic barcoding in identifying and establishing the geographic origin of samples traded as Anacyclus pyrethrum, a medicinal plant assessed as globally vulnerable in the IUCN Red List of Threatened Species. Samples collected from national and international supply chains were identified through target capture sequencing of 443 low-copy nuclear makers and compared to results derived from genome skimming of plastome, standard plastid barcoding regions and ITS. Both target capture and genome skimming provided approximately 3.4 million reads per sample, but target capture largely outperformed standard plant DNA barcodes and entire plastid genome sequences. Despite the difficulty of distinguishing among closely related species and infraspecific taxa of Anacyclus using conventional taxonomic methods, we succeeded in identifying 89 of 110 analysed samples to subspecies level without ambiguity through target capture. Of the remaining samples, we determined that eleven contained plant material from other genera and families and ten were unidentifiable regardless of the method used. Furthermore, we were able to discern the geographical origin of Anacyclus samples collected in Moroccan, Indian and Sri Lankan markets, differentiating between plant materials originally harvested from diverse populations in Algeria and Morocco. With a recent drop in the cost of analysing samples, target capture offers the potential to routinely identify commercialized plant species and determine their geographic origin. It promises to play an important role in monitoring and regulation of plant species in trade, supporting biodiversity conservation efforts, and in ensuring that plant products are unadulterated, contributing to consumer protection. | genomics |
10.1101/745679 | Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies | Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses.
By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying approximately 1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we developed a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a solid foundation for implementing global single-cell proteomics studies across the world. | systems biology |
10.1101/743294 | Wheat inositol pyrophosphate kinase TaVIH2-3B modulates cell-wall composition for drought tolerance in Arabidopsis | BackgroundInositol pyrophosphates (PP-InsPs) are high-energy cellular molecules involved in different signalling and regulatory responses. Two distinct classes of inositol phosphate kinases responsible for the synthesis of PP-InsPs have been identified in Arabidopsis i.e. ITPKinase (inositol 1,3,4 trisphosphate 5/6 kinase) and PP-IP5Kinase (diphosphoinositol pentakisphosphate kinases). Plant PP-IP5Ks are capable of synthesizing InsP8 and were shown to control pathogenic defence and phosphate response signals. However, other roles offered by plant PP-IP5Ks, especially towards abiotic stress, remain poorly understood.
ResultsHere, we characterized two Triticum aestivum L. (hexaploid wheat) PPIP5K homologs, TaVIH1 and TaVIH2, for their physiological functions. We demonstrated that wheat VIH proteins could utilize InsP7 as the substrate to produce InsP8, a process that requires the functional VIH-kinase domains. At the transcriptional level, both TaVIH1 and TaVIH2 are expressed in different wheat tissues, including developing grains, but show selective response to abiotic stresses during drought-mimic experiments. Overexpression of TaVIH2-3B homolog in Arabidopsis conferred tolerance to drought stress and rescued the sensitivity of Atvih2 mutants. RNAseq analysis of TaVIH2-3B transgenic lines of Arabidopsis showed a genome-wide reprogramming with remarkable effects on cell-wall biosynthesis genes with enhanced the accumulation of polysaccharides (arabinogalactan, cellulose and arabinoxylan).
ConclusionsOverall, this work identifies a novel function of VIH proteins, implying their roles in modulating cell-wall homeostasis genes and providing water-deficit stress tolerance. This work suggests that the plant VIH enzymes could be linked to drought tolerance and also opens up investigations to address the roles of plant VIH derived products in generating drought resistant plants. | plant biology |
10.1101/746982 | Meiotic budding yeast assemble bundled triple helices but not ladders | In meiosis, cells undergo two sequential rounds of cell division, termed meiosis I and meiosis II. Textbook models of the meiosis I substage called pachytene show that nuclei have conspicuous 100-nm-wide, ladder-like synaptonemal complexes (SC), which form between homologous chromosomes. It remains unknown if cells have any other large, meiosis-specific nuclear structures. Here we present cryo-ET analysis of frozen-hydrated budding yeast cells before, during, and after pachytene. We found no evidence for the dense ladder-like structures expected of the SC or the ordered chromatin loops expected to project from their sides. Instead, we found large quantities of 12-nm-wide triple-helices that pack into crystalline bundles. These structures are present in meiotic cells, but not in interphase cells, so we call them meiotic triple helices (MTHs). MTHs are enriched in the nucleus but not enriched in the cytoplasm. Bundles of MTHs form at the same time as SCs in wild-type cells and also in mutant cells that are unable to form SCs. These results suggest that in yeast, SCs are not crystalline and that they coexist with large, previously unreported meiotic machines. | cell biology |
10.1101/747527 | Why are children so distractible? Development of attentional capacities and motor control from childhood to adulthood. | Distractibility is the propensity to behaviorally react to irrelevant information. Though children are more distractible the younger they are, the precise contribution of attentional and motor components to distractibility and their developmental trajectories have not been characterized yet. We used a new behavioral paradigm to identify the developmental dynamics of components contributing to distractibility in a large cohort of French participants balanced, between age groups, in gender and socio-economic status (N=352; age: 6-25). Results reveal that each measure of these components, namely voluntary attention, distraction, impulsivity and motor control, present a distinct maturational timeline. In young children, increased distractibility is mostly the result of reduced sustained attention capacities and enhanced distraction, while in teenagers, it is the result of decreased motor control and increased impulsivity. | neuroscience |
10.1101/748301 | The fasciola cinereum subregion of the hippocampus is important for the acquisition of visual contextual memory | The fasciola cinereum (FC) is a subregion of the hippocampus that has received relatively little research attention compared with other hippocampal subregions with respect to anatomical characteristics and functional significance. Here, we show that the FC exhibits clear anatomical borders with CA1. The FC consists of granule cells, but adult neurogenesis was not found. The FC receives inputs from the lateral entorhinal cortex and perirhinal cortex while projecting to the crest of the dentate gyrus (DG). Neurotoxic lesioning of the FC using colchicine impaired the acquisition, but not retrieval, of visual contextual memory in rats. FC lesions also impaired place recognition and object-in-place memory. Place cells in the FC showed robust place fields but fired only transiently in their fields compared with those in CA1. Our findings suggest that the FC may play critical roles in learning a novel environment by facilitating pattern separation in the DG of the hippocampus. | neuroscience |
10.1101/721720 | Motif elucidation in ChIP-seq datasets with a knockout control | Chromatin immunoprecipitation-sequencing (ChIP-seq) is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO--a computational method to automatically optimize motif analyses with knockout controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of knockout controls, which far outperform input controls. It is freely available at https://peako.hoffmanlab.org. | bioinformatics |
10.1101/721720 | Motif elucidation in ChIP-seq datasets with a knockout control | Chromatin immunoprecipitation-sequencing (ChIP-seq) is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO--a computational method to automatically optimize motif analyses with knockout controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of knockout controls, which far outperform input controls. It is freely available at https://peako.hoffmanlab.org. | bioinformatics |
10.1101/748988 | Diversity amongst human cortical pyramidal neurons revealed via their sag currents and frequency preferences | In the human neocortex coherent interlaminar theta oscillations are driven by deep cortical layers, suggesting neurons in these layers exhibit distinct electrophysiological properties. To characterize this potential distinctiveness, we use in vitro whole-cell recordings from cortical layers 2 and 3 (L2&3), layer 3c (L3c) and layer 5 (L5) of the human cortex. Across all layers we observe notable heterogeneity, indicating human cortical pyramidal neurons are an electrophysiologically diverse population. L5 pyramidal cells are the most excitable of these neurons and exhibit the most prominent sag current (abolished by blockade of the hyperpolarization activated cation current, Ih). While subthreshold resonance is more common in L3c and L5, we rarely observe this resonance at frequencies greater than 2Hz. However, the frequency dependent gain of L5 neurons reveals they are most adept at tracking both delta and theta frequency inputs, a unique feature that may indirectly be important for the generation of cortical theta oscillations. | neuroscience |
10.1101/749762 | Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet | Many of genes mediating Known Drug-Disease Association (KDDA) are escaped from experimental detection. Identifying of these genes (hidden genes) is of great significance for understanding disease pathogenesis and guiding drug repurposing. Here, we presented a novel computational tool, called KDDANet, for systematic and accurate uncovering the hidden genes mediating KDDA from the perspective of genome-wide functional gene interaction network. KDDANet demonstrated the competitive performances in both sensitivity and specificity of identifying genes in mediating KDDA in comparison to the existing state-of-the-art methods. Case studies on Alzheimers disease (AD) and obesity uncovered the mechanistic relevance of KDDANet predictions. Furthermore, when applied with multiple types of cancer-omics datasets, KDDANet not only recapitulated known genes mediating KDDAs related to cancer, but also revealed novel candidates that offer new biological insights. Importantly, KDDANet can be used to discover the shared genes mediating multiple KDDAs. KDDANet can be accessed at http://www.kddanet.cn and the code can be freely downloaded at https://github.com/huayu1111/KDDANet. | bioinformatics |
10.1101/749945 | Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments | The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii. | evolutionary biology |
10.1101/749945 | Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments | The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii. | evolutionary biology |
10.1101/749945 | Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments | The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii. | evolutionary biology |
10.1101/751933 | Multi-scale systems genomics analysis predicts pathways, cell types and drug targets involved in normative human cognition variation | An open challenge in human genetics is to better understand the link between genotype variation and the various molecular, cellular, anatomical and physiological systems that it can affect. To address this challenge, we performed genotype-phenotype-systems analysis for accuracy in nine cognitive tasks from the Philadelphia Neurodevelopmental Cohort (3,319 individuals aged 8-21 years). We report a region of genome-wide significance within the 3 end of the FBLN1 gene (p=4.6x10-8), associated with nonverbal reasoning, a heritable form of complex reasoning ability. Integration of published brain-specific omic maps reveals that FBLN1 shows greatest expression in the fetal brain, is a marker of neural progenitor cells, is differentially expressed in schizophrenia and increases genetic risk for bipolar disorder. These findings suggest that nonverbal reasoning and FBLN1 variation warrant further investigation in studies of neurodevelopmental disorders and psychosis. Using genotype-pathway analysis, we identify pathways related to development and to autonomic nervous system dysfunction associated with working memory accuracy. Top-ranking pathway genes include those genetically associated with multiple diseases with working memory deficits, such as schizophrenia and Parkinsons disease, and that are also markers for specific brain cell types. Our findings identify novel molecular players involved in specific cognitive tasks and link variants to genes, pathways, cell types, diseases and drugs. This work advances the "molecules-to-behaviour" view of cognition, and provides a framework for using systems-level organization of data for other biomedical domains. | genomics |
10.1101/751628 | Age-related differences in white matter: Understanding tensor-based results using fixel-based analysis | Aging is associated with widespread alterations in cerebral white matter (WM). Most prior studies of age differences in WM have used diffusion tensor imaging (DTI), but typical DTI metrics (e.g., fractional anisotropy; FA) can reflect multiple neurobiological features, making interpretation challenging. Here, we used fixel-based analysis (FBA) to investigate age-related WM differences observed using DTI in a sample of 45 older and 25 younger healthy adults. Age- related FA differences were widespread but were strongly associated with differences in multifiber complexity (CX), suggesting that they reflected differences in crossing fibers in addition to structural differences in individual fiber segments. FBA also revealed a frontolimbic locus of age-related effects and provided insights into distinct microstructural changes underlying them. Specifically, age differences in fiber density were prominent in fornix, bilateral anterior internal capsule, forceps minor, body of the corpus callosum and corticospinal tract, while age differences in fiber cross section were largest in cingulum bundle and forceps minor. These results provide novel insights into specific structural differences underlying major WM differences associated with aging. | neuroscience |
10.1101/754887 | High photosynthesis rate in the selected wild rice is driven by leaf anatomy mediating high Rubisco activity and electron transport rate | The importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental bases. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice accessions. Fitting A/Ci curves and biochemical analyses showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to leaf nitrogen content, Rubisco activity, and electron transport rate compared to photosynthetically efficient accessions of wild rice Oryza australiensis and Oryza latifolia. The selected wild rice accessions with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, fewer mesophyll cells between two consecutive veins, and higher mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and leaf anatomical features in the rice system itself that could be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.
HighlightDistinct leaf biochemical, photochemical, and developmental features contribute to efficient photosynthesis in the selected wild rice accessions that could potentially be exploited to increase rice leaf photosynthesis. | plant biology |
10.1101/756932 | A signaling axis involving CNOT3, Aurora B and ERK promotes mesendodermal differentiation of ES cells in response to FGF2 and BMP4 | Mesendoderm cells are key intermediate progenitors that form at the early primitive streak (PrS) and give rise to mesoderm and endoderm in the gastrulating embryo. We have identified an interaction between CNOT3 and the cell cycle kinase Aurora B, which requires sequences in the NOT box domain of CNOT3, and regulates MAPK/ERK signalling during mesendoderm differentiation. Aurora B phosphorylates CNOT3 at two sites located close to a nuclear localization signal and promotes localization of CNOT3 to the nuclei of mouse ES cells (ESCs) and metastatic lung cancer cells. ESCs that have both sites mutated give rise to embryoid bodies that are largely devoid of mesoderm and endoderm and are composed mainly of ectoderm. The mutant ESCs are also compromised in their ability to differentiate into mesendoderm in response to FGF2, BMP4 and Wnt3. The double mutation affects interaction of CNOT3 with Aurora B and with ERK and reduces phosphorylation of ERK in response to FGF2, impacting on survival of the differentiated ME cells. Our results identify an adaptor function for CNOT3 that regulates a key pathway in embryogenesis and cancer. | developmental biology |
10.1101/756932 | A signalling axis involving CNOT3, Aurora B and ERK promotes differentiation and survival of mesendodermal progenitor cells | Mesendoderm cells are key intermediate progenitors that form at the early primitive streak (PrS) and give rise to mesoderm and endoderm in the gastrulating embryo. We have identified an interaction between CNOT3 and the cell cycle kinase Aurora B, which requires sequences in the NOT box domain of CNOT3, and regulates MAPK/ERK signalling during mesendoderm differentiation. Aurora B phosphorylates CNOT3 at two sites located close to a nuclear localization signal and promotes localization of CNOT3 to the nuclei of mouse ES cells (ESCs) and metastatic lung cancer cells. ESCs that have both sites mutated give rise to embryoid bodies that are largely devoid of mesoderm and endoderm and are composed mainly of ectoderm. The mutant ESCs are also compromised in their ability to differentiate into mesendoderm in response to FGF2, BMP4 and Wnt3. The double mutation affects interaction of CNOT3 with Aurora B and with ERK and reduces phosphorylation of ERK in response to FGF2, impacting on survival of the differentiated ME cells. Our results identify an adaptor function for CNOT3 that regulates a key pathway in embryogenesis and cancer. | developmental biology |
10.1101/753699 | Contextual extinction of drug-associated discriminative stimuli fails to attenuate drug-vs-food choice in rhesus monkeys | Relapse within the context of a substance use disorder can be triggered by cues that function as discriminative stimuli to signal contingencies of drug availability and promote drug-taking behavior. Extinction procedures can weaken this association between drug-associated cues and drug-taking behavior and may reduce the probability of relapse. This study evaluated a regimen of extinction training on cocaine and heroin self-administration in rhesus monkeys under a drug-vs.-food choice procedure. Behavior was initially maintained under a concurrent schedule of food (1-g food pellets; fixed-ratio 100 schedule) and cocaine injections (0-0.1 mg/kg/injection; fixed-ratio 10) (n=4 males) or heroin injections (0-0.01 mg/kg/injection; fixed-ratio 10) (n=3 females and 1 male) during daily 2-h choice sessions. Subsequently, choice sessions were supplemented by daily 20-h extinction sessions for 14 consecutive days. During extinction sessions, drug-associated discriminative stimuli were presented, but responding produced saline injections. Drug continued to be available during choice sessions. Prior to extinction, both cocaine- and heroin-maintained dose-dependent increases in drug-vs.-food choice. Exposure to 14 extinction sessions failed to significantly decrease drug choice and increase food choice. These preclinical results do not support the effectiveness of extinguishing drug-associated discriminative stimuli as a non-pharmacological treatment strategy for reducing drug choice. | neuroscience |
10.1101/754077 | Reconstruction of plant-pollinator networks from observational data | Empirical measurements of ecological networks such as food webs and mutualistic networks are often rich in structure but also noisy and error-prone, particularly for rare species for which observations are sparse. Focusing on the case of plant-pollinator networks, we here describe a Bayesian statistical technique that allows us to make accurate estimates of network structure and ecological metrics from such noisy observational data. Our method yields not only estimates of these quantities, but also estimates of their statistical errors, paving the way for principled statistical analyses of ecological variables and outcomes. We demonstrate the use of the method with an application to previously published data on plant-pollinator networks in the Seychelles archipelago, calculating estimates of network structure, network nestedness, and other characteristics. | ecology |
10.1101/754762 | Deciphering Legionella effector delivery by Icm/Dot secretion system reveals a new role for c-diGMP signaling | Secretion of bacterial effector proteins into host cells plays a key role in bacterial virulence. Yet, the dynamics of the secretion systems activity remains poorly understood, especially when machineries deal with the export of numerous effectors. We address the question of multi-effector secretion by focusing on the Legionella pneumophila Icm/Dot T4SS that translocates a record number of 300 effectors. We set up a kinetic translocation assay, based on the {beta}-lactamase translocation reporter system combined with the effect of the protonophore CCCP. When used for translocation analysis of Icm/Dot substrates constitutively produced by L. pneumophila, this assay allows a fine monitoring of the secretion activity of the T4SS, independently of the expression control of the effectors. We observed that effectors are translocated with a specific timing, suggesting a control of their docking/translocation by the T4SS. Their delivery is accurately organized to allow effective manipulation of the host cell, as exemplified by the sequential translocation of effectors targeting Rab1, namely SidM/DrrA, LidA, LepB. Remarkably, the timed delivery of effectors does not depend only on their interaction with chaperone proteins but implies cyclic-di-GMP signaling, as the diguanylate cyclase Lpl0780/Lpp0809, contributes to the timing of translocation.
Graphical abstract
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/754762v2_ufig1.gif" ALT="Figure 1">
View larger version (38K):
org.highwire.dtl.DTLVardef@17b7245org.highwire.dtl.DTLVardef@18b2443org.highwire.dtl.DTLVardef@1f9b7ceorg.highwire.dtl.DTLVardef@19275ff_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe dynamics of multi-effector secretion is addressed in the paradigm Legionella Icm/Dot T4SS
C_LIO_LIA kinetic translocation assay allowing a fine monitoring of the T4SS activity is set up
C_LIO_LISpecific secretion patterns consistent with sequential functions in the host are reported
C_LIO_LIT4SS-dependent translocation is promoted by a diguanylate cyclase
C_LIO_LIUnreported control of Type 4 secretion by the second messenger c-di-GMP signaling is revealed
C_LI | microbiology |
10.1101/753293 | Sawfish, Read in Tooth and Saw: rostral teeth as endogenous chemical records of movement and life-history in a critically endangered species | O_LIThe ecology of endangered and rare species can be difficult to study due to their low abundances and legal limits on scientists ability to catch, sample, and track them. This is particularly true of sawfish (family Pristidae) whose numbers have declined precipitously, placing all five species on the IUCN Red List of Threatened Species worldwide. Best known for their distinctive, toothed rostrum, the ecology, movement, and life-history of sawfish is poorly understood.
C_LIO_LISawfish rostral teeth are modified placoid scales, which grow continuously throughout the life of the fish. This continuous growth, combined with their stable calcified makeup, makes sawfish rostral teeth a potential source of temporal records of chemical and isotopic changes through the life of the fish.
C_LIO_LIRostral teeth are often preserved in museums and as curios, potentially providing a source of life-history data to inform conservation actions without the need for field study, or as an important compliment to it. This is the first study to recover temporally explicit chemical data from sawfish rostral teeth.
C_LIO_LIUsing archived samples of largetooth sawfish (Pristis pristis) we show that multiple chemical tracers can be recovered from sawfish rostral teeth, and that these tracers can be used to understand movement across salinity gradients. We further show that sawfish rostral teeth contain repeated structures and indistinct banding which could potentially be used for aging or growth analysis of fish.
C_LI | ecology |
10.1101/753814 | Hybrid incompatibility is stronger in the presence of transposable elements in the Drosophila virilis clade | Mismatches between parental genomes in selfish elements are frequently hypothesized to underlie hybrid dysfunction and drive speciation. However, because the genetic basis of most hybrid incompatibilities is unknown, testing the contribution of selfish elements to reproductive isolation is difficult. Here we evaluated the role of transposable elements (TEs) in hybrid incompatibilities between Drosophila virilis and D. lummei by experimentally comparing hybrid incompatibility in a cross where active TEs are present in D. virilis (TE+) and absent in D. lummei, to a cross where these TEs are absent from both D. virilis (TE-) and D. lummei genotypes. Using genomic data, we confirmed copy number differences in TEs between the D. virilis (TE+) strain and a D. virilis (TE-) strain and D. lummei. We observed F1 postzygotic reproductive isolation specifically in the interspecific cross involving TE+ D. virilis but not in the cross involving TE-D. virilis. A series of backcross experiments, designed to account for alternative models of hybrid incompatibility, showed that expression of this F1 hybrid incompatibility is consistent with the action of TEs rather than other, genic, interactions. A further Y-autosome interaction contributes to additional, sex-specific, inviability in one direction of this cross combination. These experiments demonstrate that TEs can increase reproductive isolation between closely related lineages, thereby adding to the processes that accelerate speciation. | evolutionary biology |
10.1101/758938 | Conformation-dependent influences of hydrophobic amino acids in two in-register parallel β-sheet amyloids, an α-synuclein amyloid and a local structural model of PrPSc | Prions are unconventional pathogens that encode the pathogenic information in conformations of the constituent abnormal isoform of prion protein (PrPSc), independently of nucleotide genome. Therefore, conformational diversity of PrPSc underlies the existence of many prion strains and species barriers of prions, although the conformations still remain undetermined. Interestingly, differences between polymorphic or species-specific residues responsible for the species/strain barriers are often caused by conservative replacements between hydrophobic amino acids. This implies that subtle differences among hydrophobic amino acids are significant for PrPSc structures. Here, we analyzed the influence of different hydrophobic residues on the structures of an in-register parallel {beta}-sheet amyloid of -synuclein (Syn) using molecular dynamics (MD) simulation, and applied the knowledge from the Syn amyloid to modeling local structures of human PrPSc encompassing residues 107-143. We found that mutations equivalent to polymorphisms that cause transmission barriers substantially affect the stabilities; for example, the G127V mutation, which makes the host resistant to various human prion diseases, greatly destabilized the amyloid. Our study demonstrates specifically how and in what structures hydrophobic residues can exert unique effects on in-register parallel {beta}-sheet amyloids and provides insights into the molecular mechanism of the strain diversity of prions and other pathogenic amyloids. | molecular biology |
10.1101/758508 | Lineage-specific control of convergent differentiation by a Forkhead repressor | During convergent differentiation, multiple developmental lineages produce a highly similar or identical cell type. However, few molecular players that drive convergent differentiation are known. Here, we show that the C. elegans Forkhead transcription factor UNC-130 is required in only one of three convergent lineages that produce the same glial cell type. UNC-130 acts transiently as a repressor in progenitors and newly-born terminal cells to allow the proper specification of cells related by lineage rather than by cell type or function. Specification defects correlate with UNC-130:DNA binding, and UNC-130 can be functionally replaced by its human homolog, the neural crest lineage determinant FoxD3. We propose that, in contrast to terminal selectors that activate cell-type specific transcriptional programs in terminally differentiating cells, UNC-130 acts early and specifically in one convergent lineage to produce a cell type that also arises from molecularly distinct progenitors in other lineages. | developmental biology |
10.1101/758581 | Phylogenomic Testing of Root Hypotheses | AO_SCPLOWBSTRACTC_SCPLOWThe determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch - the root branch - of the true species tree, and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesised species tree and its rooting leads us to re-evaluate what phylogenetic signal is directly relevant to LCA inference, and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a-priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative datasets we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust. | evolutionary biology |
10.1101/756304 | NLIMED: Natural Language Interface for ModelEntity Discovery in Biosimulation ModelRepositories | Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends the use of the Resource Description Framework (RDF). This grounding in RDF provides the flexibility to enable searching for entities within models (e.g. variables, equations, or entire models) by utilising the RDF query language SPARQL. However, the rigidity and complexity of the SPARQL syntax and the nature of the tree-like structure of semantic annotations, are challenging for users. Therefore, we propose NLIMED, an interface that converts natural language queries into SPARQL. We use this interface to query and discover model entities from repositories of biosimulation models. NLIMED works with the Physiome Model Repository (PMR) and the BioModels database and potentially other repositories annotated using RDF. Natural language queries are first chunked into phrases and annotated against ontology classes and predicates utilising different natural language processing tools. Then, the ontology classes and predicates are composed as SPARQL and finally ranked using our SPARQL Composer and our indexing system. We demonstrate that NLIMEDs approach for chunking and annotating queries is more effective than the NCBO Annotator for identifying relevant ontology classes in natural language queries. Comparison of NLIMEDs behaviour against historical query records in the PMR shows that it can adapt appropriately to queries associated with well-annotated models. | bioinformatics |
10.1101/752733 | Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species | Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters. | ecology |
10.1101/756536 | The genetic landscape of Ethiopia: diversity, intermixing and the association with culture | The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure in human populations. Using primarily novel genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors upon shaping the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and increased genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic classifications, but indicate pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting how shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, these results identify the most important cultural and geographic proxies for genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians. | genetics |
10.1101/756569 | Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis | B. subtilis is a surface-dwelling bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, mediated by a fast-evolving molecular kin discrimination (KD) system. We here demonstrate that KD-mediated swarm antagonisms in B. subtilis promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer is largely uni-directional and the result of the induction of competence of the recipient strain by the donor strain is linked to a sigW-mediated stress response. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, did not upregulate transformation upon encounter, demonstrating that social interactions can override mechanistic barriers to horizontal gene transfer. KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context. | microbiology |
10.1101/757252 | Protein Design and Variant Prediction Using Autoregressive Generative Models | The ability to design functional sequences and predict effects of variation is central to protein engineering and biotherapeutics. State-of-art computational methods rely on models that leverage evolutionary information but are inadequate for important applications where multiple sequence alignments are not robust. Such applications include the prediction of variant effects of indels, disordered proteins, and the design of proteins such as antibodies due to the highly variable complementarity determining regions. We introduce a deep generative model adapted from natural language processing for prediction and design of diverse functional sequences without the need for alignments. The model performs state-of-art prediction of missense and indel effects and we successfully design and test a diverse 105-nanobody library that shows better expression than a 1000-fold larger synthetic library. Our results demonstrate the power of the alignment-free autoregressive model in generalizing to regions of sequence space traditionally considered beyond the reach of prediction and design. | systems biology |
10.1101/759134 | Integration of brief light flashes varying in intensity and duration by the human circadian system | The melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) are characterised by a delayed off-time following light offset. Here, we exploited this unusual physiologic property to characterise the exquisite sensitivity of the human circadian system to flashed light. In a 34-hour in-laboratory between-subjects design, we examined variable-intensity (3-9500 photopic lux; n=28 participants) full-field flashes at fixed duration (2 ms), and variable-duration (10 s-10 s) full-field flashes at fixed intensity (2000 photopic lux; n=31 participants) delivered using eye masks. We measured the circadian phase shift of the dim-light melatonin onset (DLMO) on the subsequent evening, acute melatonin suppression, objective alertness, and subjective sleepiness during the flash sequence. We find a clear dose-response relationship between flash intensity and the induced circadian phase shift, with an approximate increase of 10 minutes of phase delay for each ten-fold increase in photopic illuminance, but no parametric relationship between flash duration and induced circadian phase shift. | neuroscience |
10.1101/760231 | Mechanisms of distributed working memory in a large-scale network of macaque neocortex | To elucidate the circuit mechanism of persistent neural activity underlying working memory that is distributed across multiple brain regions, we developed an anatomically constrained computational model of large-scale macaque cortex. We found that persistent activity may emerge from inter-areal reverberation, even in a regime where none of the isolated areas is capable of generating persistent activity. The persistent activity pattern along the cortical hierarchy indicates a robust bifurcation in space, characterized by a few association areas near dynamical criticality. A host of spatially distinct attractor states is found, potentially subserving various internal processes. The model yields testable predictions including the idea of counterstream inhibitory bias, and suggests experiments to differentiate local versus distributed mechanisms. Simulated lesion or optogenetic inactivation revealed that distributed activity patterns are resilient while dependent on a structural core. This work provides a theoretical framework for identifying large-scale brain mechanisms and computational principles of distributed cognitive processes. | neuroscience |
10.1101/760892 | Circadian protein regulation in the green lineage II. The clock gene circuit controls a phospho-dawn in Arabidopsis thaliana. | 24-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time-series from Arabidopsis thaliana plants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the phospho-dawn. Members of the SnRK/CDPK family of protein kinases are candidate regulators. A CCA1-over-expressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despite CCA1-over-expression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase / phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating post-translational mechanisms in the transmission of circadian timing information in plants. | systems biology |
10.1101/761551 | IRG1 controls host responses to restrict Mycobacterium tuberculosis infection | Mycobacterium tuberculosis (Mtb), the pathogen causing human tuberculosis, has evolved multiple strategies to successfully prevent clearance by immune cells and to establish dissemination and long-term survival in the host. The modulation of host immunity to maximize pathogen elimination while minimizing inflammation-mediated tissue damage may provide another tool to fight drug-resistant Mtb strains. Metabolic reprogramming of phagocytes can dramatically influence the intracellular colonization by Mtb and the key players involved in this process remain a matter of debate. Here, we demonstrate that aconitate decarboxylase 1 (Acod1; also known as immune-responsive gene 1, IRG1), which converts cis-aconitate into the metabolite itaconate, is a major player in controlling the acute phase of Mtb infection. Exposure of IRG1-deficient mice to a virulent Mtb strain (H37Rv) was lethal, while M. bovis BCG and the H37Ra attenuated Mtb strain induced neither lethality nor severe lung immunopathology. Lungs of IRG1-deficient mice infected by Mtb H37Rv displayed large areas of necrotizing granulomatous inflammation and neutrophil infiltration, accompanied by reduced levels of B and T lymphocytes and increased levels of alveolar and interstitial macrophage populations, compared to their wild type counterparts. Next, we show that IRG1, beyond its recruitment to Mtb-containing vacuoles, restricts Mtb replication and lipid droplets accumulation in phagocytes, hallmarks of a tight interplay between the bacillus and the host. Altogether, IRG1 confines the host response to create a favourable phagocytic environment for Mtb controlled intracellular replication. | immunology |
10.1101/761817 | Stress generation, relaxation and size control in confined tumor growth | Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Stress release experiments show that nonuniform anisotropic elastic stresses can be distributed throughout. The elastic stresses are maintained by structural proteins and adhesive molecules, and can be actively relaxed by a variety of biophysical processes. In this paper, we present a new continuum model to investigate how the growth-induced elastic stresses and active stress relaxation, in conjunction with cell size control feedback machinery, regulate the cell density and stress distributions within growing tumors as well as the tumor sizes in the presence of external physical confinement and gradients of growth-promoting chemical fields. We introduce an adaptive reference map that relates the current position with the reference position but adapts to the current position in the Eulerian frame (lab coordinates) via relaxation. This type of stress relaxation is similar to but simpler than the classical Maxwell model of viscoelasticity in its formulation. By fitting the model to experimental data from two independent studies of tumor spheroid growth and their cell density distributions, treating the tumors as incompressible, neo-Hookean elastic materials, we find that the rates of stress relaxation of tumor tissues can be comparable to volumetric growth rates. Our study provides insight on how the biophysical properties of the tumor and host microenvironment, mechanical feedback control and diffusion-limited differential growth act in concert to regulate spatial patterns of stress and growth. When the tumor is stiffer than the host, our model predicts tumors are more able to change their size and mechanical state autonomously, which may help to explain why increased tumor stiffness is an established hallmark of malignant tumors.
Author summaryThe mechanical state of cells can modulate their growth and division dynamics via mechanotransduction, which affects both the cell size distribution and the tissue size as a whole. Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Besides external confinement and compression on the tumor border, a heterogeneous stress field can be generated inside the tumor by nutrient-driven differential growth. Such growth-induced mechanical stresses can be relaxed by tissue rearrangement, which happens during cell neighbor exchanges, cell divisions, and extracellular matrix renewal. In this study, we have developed a continuum model that describes the above mechanical interactions and the dynamics of tissue rearrangement explicitly. Motivated by published experimental data, we consider mechanotransduction where the local compressive stress slows down cell growth and cell size reduction limits cell division. We have analyzed how external mechanical stimuli and internal processes influence the outcome of cell-and-tissue sizes and spatial patterns of cell density and mechanical stress in growing tumors. | biophysics |
10.1101/761817 | Stress generation, relaxation and size control in confined tumor growth | Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Stress release experiments show that nonuniform anisotropic elastic stresses can be distributed throughout. The elastic stresses are maintained by structural proteins and adhesive molecules, and can be actively relaxed by a variety of biophysical processes. In this paper, we present a new continuum model to investigate how the growth-induced elastic stresses and active stress relaxation, in conjunction with cell size control feedback machinery, regulate the cell density and stress distributions within growing tumors as well as the tumor sizes in the presence of external physical confinement and gradients of growth-promoting chemical fields. We introduce an adaptive reference map that relates the current position with the reference position but adapts to the current position in the Eulerian frame (lab coordinates) via relaxation. This type of stress relaxation is similar to but simpler than the classical Maxwell model of viscoelasticity in its formulation. By fitting the model to experimental data from two independent studies of tumor spheroid growth and their cell density distributions, treating the tumors as incompressible, neo-Hookean elastic materials, we find that the rates of stress relaxation of tumor tissues can be comparable to volumetric growth rates. Our study provides insight on how the biophysical properties of the tumor and host microenvironment, mechanical feedback control and diffusion-limited differential growth act in concert to regulate spatial patterns of stress and growth. When the tumor is stiffer than the host, our model predicts tumors are more able to change their size and mechanical state autonomously, which may help to explain why increased tumor stiffness is an established hallmark of malignant tumors.
Author summaryThe mechanical state of cells can modulate their growth and division dynamics via mechanotransduction, which affects both the cell size distribution and the tissue size as a whole. Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Besides external confinement and compression on the tumor border, a heterogeneous stress field can be generated inside the tumor by nutrient-driven differential growth. Such growth-induced mechanical stresses can be relaxed by tissue rearrangement, which happens during cell neighbor exchanges, cell divisions, and extracellular matrix renewal. In this study, we have developed a continuum model that describes the above mechanical interactions and the dynamics of tissue rearrangement explicitly. Motivated by published experimental data, we consider mechanotransduction where the local compressive stress slows down cell growth and cell size reduction limits cell division. We have analyzed how external mechanical stimuli and internal processes influence the outcome of cell-and-tissue sizes and spatial patterns of cell density and mechanical stress in growing tumors. | biophysics |
10.1101/757989 | Antidepressant drugs act by directly binding to TRKB neurotrophin receptors | It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We discovered that the transmembrane domain of TRKB, the brain-derived neurotrophic factor (BDNF) receptor that promotes neuronal plasticity and antidepressant responses, has a cholesterol-sensing function that mediates synaptic effects of cholesterol. We then found that both typical and fast-acting antidepressants directly bind to TRKB, thereby facilitating synaptic localization of TRKB and its activation by BDNF. Extensive computational approaches including atomistic molecular dynamics simulations revealed a binding site at the transmembrane region of TRKB dimers. Mutation of the TRKB antidepressant-binding motif impaired cellular, behavioral and plasticity-promoting responses to antidepressants in vitro and in vivo. We suggest that binding to TRKB and the allosteric facilitation of BDNF signaling is the common mechanism for antidepressant action, which proposes a framework for how molecular effects of antidepressants are translated into clinical mood recovery. | neuroscience |
10.1101/763318 | LAB-AID (Laboratory Automated Interrogation of Data): an interactive web application for visualization of multi-level data from biological experiments | A key step in understanding the results of biological experiments is visualization of the data. Many laboratory experiments contain a range of measurements that exist within a hierarchy of interdependence. An automated way to visualise and interrogate experimental data would: 1) lead to improved understanding of the results, 2) help to determine which statistical tests should be performed, and 3) easily identify outliers and sources of batch effects. Unfortunately, existing graphing solutions often demand expertise in programming, require considerable effort to import and examine such multi-level data, or are unnecessarily complex for the task at hand. Here we present LAB-AID (Laboratory Automated Interrogation of Data), an interactive tool specifically designed to automatically visualize and query hierarchical data resulting from biological experiments. | bioinformatics |
10.1101/763821 | High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns | Our thoughts arise from coordinated patterns of interactions between brain structures that change with our ongoing experiences. High-order dynamic correlations in neural activity patterns reflect different subgraphs of the brains functional connectome that display homologous lower-level dynamic correlations. We tested the hypothesis that high-level cognition is reflected in high-order dynamic correlations in brain activity patterns. We developed an approach to estimating high-order dynamic correlations in timeseries data, and we applied the approach to neuroimaging data collected as human participants either listened to a ten-minute story or listened to a temporally scrambled version of the story. We trained across-participant pattern classifiers to decode (in held-out data) when in the session each neural activity snapshot was collected. We found that classifiers trained to decode from high-order dynamic correlations yielded the best performance on data collected as participants listened to the (unscrambled) story. By contrast, classifiers trained to decode data from scrambled versions of the story yielded the best performance when they were trained using first-order dynamic correlations or non-correlational activity patterns. We suggest that as our thoughts become more complex, they are reflected in higher-order patterns of dynamic network interactions throughout the brain. | neuroscience |
10.1101/763888 | MRI of Capn15 knockout mice and analysis of Capn15 distribution reveal possible roles in brain development and plasticity | The Small Optic Lobe (SOL) family of calpains are intracellular cysteine proteases that are expressed in the nervous system and play an important role in neuronal development in both Drosophila, where loss of this calpain leads to the eponymous small optic lobes, and in mouse and human, where loss of this calpain leads to eye anomalies. Some human individuals with biallelic variants in CAPN15 also have developmental delay and autism. However, neither the specific effect of the loss of the Capn15 protein on brain development nor the brain regions where this calpain is expressed in the adult is known. Here we show using small animal MRI that mice with the complete loss of Capn15 have smaller brains overall with larger decreases in the thalamus and subregions of the hippocampus. These losses are not seen in Capn15 conditional KO mice where Capn15 is knocked out only in excitatory neurons in the adult. Based on {beta}-galactosidase expression in an insert strain where lacZ is expressed under the control of the Capn15 promoter, we show that Capn15 is expressed in adult mice, particularly in neurons involved in plasticity such as the hippocampus, lateral amygdala and Purkinje neurons, and partially in other non-characterized cell types. The regions of the brain in the adult where Capn15 is expressed do not correspond well to the regions of the brain most affected by the complete knockout suggesting distinct roles of Capn15 in brain development and adult brain function. | neuroscience |
10.1101/756452 | Pulling the strings of cell cycle: a non-coding RNA, CcnA, modulates the master regulators CtrA and GcrA in Caulobacter crescentus | Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time we describe the role of a novel factor named CcnA, a cell cycle regulated ncRNA located at the origin of replication, presumably activated by CtrA and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5 untranslated region (5-UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales. | microbiology |
10.1101/756452 | Pulling the strings of cell cycle: a non-coding RNA, CcnA, modulates the master regulators CtrA and GcrA in Caulobacter crescentus | Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time we describe the role of a novel factor named CcnA, a cell cycle regulated ncRNA located at the origin of replication, presumably activated by CtrA and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5 untranslated region (5-UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales. | microbiology |
10.1101/765578 | Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-species | O_LIStream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and community assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities.
C_LIO_LIWe sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and community composition by quantifing the contribution of each of the four reaches and seven habitats to the overall DNA-species diversity using an additive partition of species diversity analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering led to the co-occurrence of DNA-species using a two-step analysis to find a phylogenetic signal.
C_LIO_LIThe four reaches significantly contributed to DNA-species richness; with the meandering section having the highest contribution. However, we found that habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly communities possibly due to a high species turnover.
C_LIO_LIAmong the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This community structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species.
C_LIO_LIOur study shows the importance of different habitats on the spatial and phylogenetic structure of stonefly community assemblies and sheds light on the habitat-specific diversity that may help improve conservation practices.
C_LI | evolutionary biology |
10.1101/765180 | Single-trial dynamics of competing reach plans in the human motor periphery | Contemporary theories of motor control propose that multiple motor plans compete for selection before the winning command is executed. While most competitions are completed prior to movement onset, movements are often initiated before the competition has been resolved. An example of this is saccadic averaging, wherein the eyes land at an intermediate location between two visual targets. Behavioral and neurophysiological signatures of competing motor commands have been reported for reaching movements, but debate remains about whether such signatures attest to an unresolved competition, arise from averaging across many trials, or reflect a strategy to optimize behavior given task constraints. Here, we recorded electromyographic (EMG) activity from an upper limb muscle while human participants performed a reach analogue of a task that elicits saccadic averaging, freely choosing to reach to one of two identical and suddenly presented visual targets. On each trial, muscle recruitment showed two distinct phases of directionally-tuned activity. In the first wave, time-locked ~100 ms of target presentation, EMG activity was clearly influenced by the non-chosen target, reflecting a competition between two reach commands that was biased in favor of the ultimately chosen target. This resulted in an initial movement direction intermediate between the two targets. In contrast, the second wave of EMG activity, time-locked to voluntary reach onset, was not biased toward the non-chosen target, showing that the competition between targets was resolved by the time of movement initiation. Instead, this second wave of activity was already compensating for the averaging induced by the first wave. Thus, single-trial analysis reveals an evolution in how the non-chosen target differentially influences the first and second wave of EMG activity. Ongoing debates about the interaction between competing reach commands may arise, at least in part, from the use of behavioural tasks that mute the magnitude of the earliest wave of EMG activity.
SIGNIFICANCE STATEMENTContemporary theories of motor control suggest that multiple motor plans compete for selection before the winning command is executed. Evidence for this is found in intermediate reach movements towards two potential target locations, but recent findings have challenged this notion by arguing that they attest to an optimal response strategy. By examining upper limb muscle recruitment during a free-choice reach task, we show early recruitment of a sub-optimal averaged motor command to the two targets that subsequently transitions to a single motor command that compensates for the initially averaged motor command. Thus, recording limb muscle activity permits single-trial resolution of the dynamic influence of the non-chosen target through time | neuroscience |
10.1101/766634 | Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice | Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the NaV1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet Syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency, however putative causal non-coding promoter mutations have been identified. To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. Mice harboring a deletion of the extended evolutionarily-conserved 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and NaV1.1 expression in brain with accompanying electroencephalographic seizures and behavioral deficits. This work identified the 1b region as a critical disease-relevant regulatory element and provides evidence that non-canonical and seemingly redundant promoters can have essential function. | neuroscience |
10.1101/766311 | Representations of complex contexts: A role for hippocampus | The hippocampus plays a critical role in supporting episodic memory, in large part by binding together experiences and items with surrounding contextual information. At present, however, little is known about the roles of different hippocampal subfields in supporting this item-context binding. To address this question, we constructed a task in which items were affiliated with differing types of context - cognitive associations that vary at the local, item level and membership in temporally organized lists that linked items together at a global level. Participants made item recognition judgments while undergoing high-resolution fMRI imaging. We performed voxel pattern similarity analyses to answer the question of how human hippocampal subfields represent retrieved information about cognitive states and the time at which a past event took place. As participants recollected previously presented items, activity patterns in the CA23DG subregion carried information about prior cognitive states associated with these items. We found no evidence to suggest reinstatement of information about temporal context at the level of list membership, but exploratory analyses revealed representations of temporal context at a coarse level in conjunction with representations of cognitive contexts. Results are consistent with characterizations of CA23DG as a critical site for binding together items and contexts in the service of memory retrieval. | neuroscience |
10.1101/767343 | No effect of monetary reward in a visual working memory task | Previous work has shown that humans distribute their visual working memory (VWM) resources flexibly across items: the higher the importance of an item, the better it is remembered. A related, but much less studied question is whether people also have control over the total amount of VWM resource allocated to a task. Here, we approach this question by testing whether increasing monetary incentives results in better overall VWM performance. In three experiments, subjects performed a delayed-estimation task on the Amazon Turk platform. In the first two experiments, four groups of subjects received a bonus payment based on their performance, with the maximum bonus ranging from $0 to $10 between groups. We found no effect of the amount of bonus on intrinsic motivation or on VWM performance in either experiment. In the third experiment, reward was manipulated on a trial-by-trial basis using a within-subjects design. Again, no evidence was found that VWM performance depended on the magnitude of potential reward. These results suggest that encoding quality in visual working memory is insensitive to monetary reward, which has implications for resource-rational theories of VWM. | animal behavior and cognition |
10.1101/767285 | Learning Divisive Normalization in Primary Visual Cortex | Divisive normalization (DN) is a prominent computational building block in the brain that has been proposed as a canonical cortical operation. Numerous experimental studies have verified its importance for capturing nonlinear neural response properties to simple, artificial stimuli, and computational studies suggest that DN is also an important component for processing natural stimuli. However, we lack quantitative models of DN that are directly informed by measurements of spiking responses in the brain and applicable to arbitrary stimuli. Here, we propose a DN model that is applicable to arbitrary input images. We test its ability to predict how neurons in macaque primary visual cortex (V1) respond to natural images, with a focus on nonlinear response properties within the classical receptive field. Our model consists of one layer of subunits followed by learned orientation-specific DN. It outperforms linear-nonlinear and wavelet-based feature representations and makes a significant step towards the performance of state-of-the-art convolutional neural network (CNN) models. Unlike deep CNNs, our compact DN model offers a direct interpretation of the nature of normalization. By inspecting the learned normalization pool of our model, we gained insights into a long-standing question about the tuning properties of DN that update the current textbook description: we found that within the receptive field oriented features were normalized preferentially by features with similar orientation rather than non-specifically as currently assumed.
Author summaryDivisive normalization (DN) is a computational building block throughout sensory processing in the brain. We currently lack an understanding of what role this normalization mechanism plays when processing complex stimuli like natural images. Here, we use modern machine learning methods to build a general DN model that is directly informed by data from primary visual cortex (V1). Contrary to high-predictive deep learning models, our DN-based models parameters offer a straightforward interpretation of the nature of normalization. Within the receptive field, we found that neurons responding strongly to a specific orientation are preferentially normalized by other neurons that are highly active for similar orientations, rather than being normalized by all neurons as it is currently assumed by textbook models. | neuroscience |
10.1101/767772 | An Erwinia amylovora inducible promoter for intragenic improvement of apple fire blight resistance | Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be up-regulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results indicate that pKFDV02 did not keep its promises as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.
Key messagepPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes. | bioengineering |
10.1101/767772 | An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance | Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be up-regulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results indicate that pKFDV02 did not keep its promises as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.
Key messagepPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes. | bioengineering |
10.1101/764340 | Most cancers carry a substantial deleterious load due to Hill-Robertson interference | Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.47) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 40% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage. | evolutionary biology |
10.1101/769752 | More than Two Populations of Microtubules Comprise the Dynamic Mitotic Spindle | The microtubules of the mitotic spindle mediate chromosome alignment to the metaphase plate, then sister chromatid segregation to the spindle poles in anaphase. Previous analyses of spindle microtubule kinetics utilizing fluorescence dissipation after photoactivation described two main populations, a slow and a fast turnover population, and these were ascribed to reflect kinetochore versus non-kinetochore microtubules, respectively. Here, we test this categorization by disrupting kinetochores through depletion of the Ndc80 complex. In the absence of functional kinetochores, microtubule dynamics still exhibit slow and fast turnover populations, though the proportion of each population and the timings of turnover are altered. Importantly, the data obtained following Hec1/Ndc80 depletion suggests other sub-populations, in addition to kinetochore microtubules, contribute to the slow turnover population. Further manipulation of spindle microtubules revealed a complex landscape. Dissection of the dynamics of microtubule populations provides a greater understanding of mitotic spindle kinetics and insight into roles in facilitating chromosome attachment, movement, and segregation during mitosis. | cell biology |