title: Reinstatement of cortical outcome representations during higher-order learning

abstract: Naturalistic learning scenarios are characterized by infrequent experience of external feedback to guide behavior. Higher-order learning mechanisms like second-order conditioning (SOC) may allow stimuli that were never experienced together with reinforcement to acquire motivational value. Despite its explanatory potential for real-world learning, surprisingly little is known about the neural mechanism underlying such associative transfer of value in SOC. Here, we used multivariate cross-session, cross-modality searchlight classification on functional magnetic resonance imaging data obtained from humans during SOC. We show that visual first-order conditioned stimuli (CS) reinstate cortical patterns representing previously paired gustatory outcomes in the lateral orbitofrontal cortex (OFC). During SOC, this OFC region showed increased functional covariation with amygdala, where neural pattern similarity between second-order CS and outcomes increased from early to late stages of SOC. Our data suggest a mechanism by which motivational value is conferred to stimuli that were never paired with reinforcement.


title: Computational hypothesis: How Intra-hepatic functional heterogeneity may influence the cascading progression of free fatty acid-induced non-alcoholic fatty liver disease (NAFLD)

abstract: Non-Alcoholic Fatty Liver Disease (NAFLD) is the most common type of chronic liver disease in developed nations, affecting around 25% of the population. Elucidating the factors causing NAFLD in individual patients to progress in different rates and to different degrees of severity, is a matter of active medical research. Here, we aim to provide evidence that the intra-hepatic heterogeneity of rheological, metabolic and tissue-regenerating capacities plays a central role in disease progression. We developed a generic mathematical model that constitutes the liver as ensemble of small liver units differing in their capacities to metabolize potentially cytotoxic free fatty acids (FFAs) and to repair FFA-induced cell damage. Transition from simple steatosis to more severe forms of NAFLD is described as self-amplifying process of cascading liver failure, which to stop depends essentially on the distribution of functional capacities across the liver. Model simulations provided the following insights: (1) A persistently high plasma level of FFAs is sufficient to drive the liver through different stages of NAFLD; (2) Presence of NAFLD amplifies the deleterious impact of additional tissue-damaging hits; and (3) Coexistence of non-steatotic and highly steatotic regions is indicative for the later occurrence of severe NAFLD stages.

category: systems biology


title: ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low complexity domain

abstract: OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell-specific gene expression programs. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here we report the identification of ATP-binding cassette subfamily F member 1 (ABCF1) as a critical coactivator for OCT4/SOX2. ABCF1 is required for pluripotency gene expression and stem cell self-renewal. ABCF1 binds co-dependent coactivators XPC and DKC1 via its intrinsically disordered region and stimulates transcription by linking SOX2 to the transcription machinery. Furthermore, in response to pathogen infection and DNA damage, ABCF1 binds intracellular DNAs accumulated in cells, concomitant with loss of SOX2 interaction and pluripotency gene transcription. This results in spontaneous differentiation of compromised stem cells and elimination from the self-renewing population. Thus, ABCF1 directly couples pluripotency gene transcription with sensing aberrant DNAs and acts as a checkpoint for self-renewal to safeguard stem cell fidelity and genome integrity.

category: biochemistry


title: ATP-binding cassette protein ABCF1 couples gene transcription with maintenance of genome integrity in embryonic stem cells


title: Fusion protein EWS-FLI1 is incorporated into a protein granule in cells

abstract: Ewing sarcoma is driven by fusion proteins containing a low complexity (LC) domain that is intrinsically disordered and a powerful transcriptional regulator. The most common fusion protein found in Ewing sarcoma, EWS-FLI1, takes its LC domain from the RNA-binding protein EWSR1 (Ewing Sarcoma RNA-binding protein 1) and a DNA-binding domain from the transcription factor FLI1 (Friend Leukemia Virus Integration 1). EWS-FLI1 can bind RNA polymerase II (RNA Pol II) and self-assemble through its low-complexity (LC) domain. The ability of RNA-binding proteins like EWSR1 to self-assemble or phase separate in cells has raised questions about the contribution of this process to EWS-FLI1 activity. We examined EWSR1 and EWS-FLI1 activity in Ewing sarcoma cells by siRNA-mediated knockdown and RNA-seq analysis. More transcripts were affected by the EWSR1 knockdown than expected and these included many EWS-FLI1 regulated genes. We reevaluated physical interactions between EWS-FLI1, EWSR1, and RNA Pol II, and employed a cross-linking based strategy to investigate protein assemblies associated with the proteins. The LC domain of EWS-FLI1 was required for the assemblies observed to form in cells. These results offer new insights into a protein assembly that may enable EWS-FLI1 to bind its wide network of protein partners and contribute to regulation of gene expression in Ewing sarcoma.


title: A novel tolerance index to identify heat tolerance in cultivated and wild barley genotypes

abstract: Thermal stress at the reproductive stage poses a substantial constraint on cereal production worldwide. This study was conducted to assess tolerance to terminal high-temperature stress in 45 wild (Hordeum vulgare ssp. spontaneum) genotypes, 4 cultivars (H. vulgare ssp. vulgare), 98 F3 and 79 BC1F2 families derived from hybridization of the most tolerant wild genotype and a susceptible cultivar  Mona. Results of analysis of variance showed the significant genotypic and high-temperature stress effects on all the traits studied. In contrast to the cultivated genotypes, the wild ones were found less affected by high-temperature stress. The multivariate analysis highlighted the additional high-temperature tolerance components in the tolerant families and wild genotypes. Grain yield strongly correlated (p < 0.01) with stress tolerance, yield stability, and heat tolerance indices. The reduction in the reproduction period caused by high-temperature was much higher in cultivated genotypes than in wild ones. In conclusion, the ingenuous-focused strategies like escape/avoidance are being used primarily to cope with heat stress by cultivars, while adaptive-focused coping strategies such as tolerance are being implemented by wild barley.

category: plant biology


title: Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction

abstract: Heterochromatin spreading, the expansion of gene-silencing structures from DNA-encoded nucleation sites, occurs in distinct settings. Spreading re-establishes gene-poor constitutive heterochromatin every cell cycle, but also invades gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context, i.e. euchromatic, heterochromatic, or different nucleator types, influences the determinants of this process remains poorly understood. By screening a nuclear function gene deletion library in fission yeast using a previously established heterochromatin spreading sensor system, we identified regulators that positively or negatively alter the propensity of a nucleation site to spread heterochromatin. We find that different chromatin contexts are dependent on unique sets of genes for the regulation of heterochromatin spreading. Further, we find that spreading in constitutive heterochromatin requires Clr6 histone deacetylase complexes containing the Fkh2 transcription factor, while the Clr3 deacetylase is globally required for silencing. Fkh2 acts by recruiting Clr6 to nucleation-distal chromatin sites. Our results segregate the pathways that control lateral heterochromatin spreading from those that instruct DNA-directed assembly in nucleation.

category: molecular biology


title: Integrating multimodal data through interpretable heterogeneous ensembles

abstract:
MotivationIntegrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities, but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems.

ResultsWe propose Ensemble Integration (EI) as a novel systematic realization of the late integration approach. EI infers local predictive models from the individual modalities using appropriate algorithms, and uses effective heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data, and mortality due to COVID-19 from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of representative EI predictive models for COVID-19 mortality identified several disease-relevant features, such as laboratory test (BUN and calcium) and vital sign (minimum oxygen saturation) measurements and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

AvailabilityCode and data are available at https://github.com/GauravPandeyLab/ensemble_integration.

Contactgaurav.pandey@mssm.edu

category: bioinformatics


title: RNA secondary structure packages evaluated and improved by high-throughput experiments

abstract: The computer-aided study and design of RNA molecules is increasingly prevalent across a range of disciplines, yet little is known about the accuracy of commonly used structure modeling packages in tasks sensitive to ensemble properties of RNA. Here, we demonstrate that the EternaBench dataset, a set of over 20,000 synthetic RNA constructs designed in iterative cycles on the RNA design platform Eterna, provides incisive discriminative power in evaluating current packages in ensemble-oriented structure prediction tasks. We find that CONTRAfold and RNAsoft, packages with parameters derived through statistical learning, achieve consistently higher accuracy than more widely used packages in their standard settings, which derive parameters primarily from thermodynamic experiments. Motivated by these results, we develop a multitask-learning-based model, EternaFold, which demonstrates improved performance that generalizes to diverse external datasets, including complete mRNAs and viral genomes probed in human cells and synthetic designs modeling mRNA vaccines.

category: biophysics


title: PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix

abstract: TElevated production of collagen-rich extracellular matrix (ECM) is a hallmark of cancer associated fibroblasts (CAFs) and a central driver of cancer aggressiveness. How to target ECM production to oppose cancer is yet unclear, since targeting CAFs has been shown to restrain but also promote cancer progression. Metabolic rewiring is a hallmark of CAFs. Here we find that proline, which is a highly abundant amino acid in collagen proteins, is newly synthesised from glutamine to make tumour collagen in breast cancer xenografts, and that its production is elevated in breast cancer CAFs. PYCR1 is the rate-limiting enzyme for proline synthesis and is highly expressed in the tumour stroma of breast cancer patients and in CAFs. Reducing PYCR1 levels in CAFs is sufficient to reduce tumour collagen production, tumour growth and metastatic spread in vivo and cancer cell proliferation in vitro. PYCR1 and COL1A1 are overexpressed in patients with invasive ductal carcinoma with poor prognosis. Both collagen and glutamine-derived proline synthesis in CAFs are enhanced by increased pyruvate dehydrogenase-derived acetyl-CoA levels, via gene expression regulation through the epigenetic regulator histone acetyl transferase EP300. Altogether, our work unveils unprecedented roles of CAF metabolism to support pro-tumorigenic collagen production. PYCR1 is a recognised cancer cell vulnerability and potential target for therapy, hence, our work provides evidence that targeting PYCR1 in tumours may have the additional benefit of halting the production of pro-tumorigenic ECM.

category: cancer biology


title: Pupil-linked arousal biases evidence accumulation towards desirable percepts during perceptual decision-making

abstract:
People are biased towards seeing outcomes they are motivated to see. The arousal system coordinates the bodys response to motivationally significant events, and is well positioned to regulate motivational effects on sensory perception. However, it remains unclear whether arousal would enhance or reduce motivational biases. Here we measured pupil dilation as a measure of arousal while participants performed a visual categorization task. We used monetary bonuses to motivate participants to see one category over another. Even though the reward-maximizing strategy was to perform the task accurately, participants were more likely to report seeing the motivationally desirable category. Furthermore, higher arousal levels were associated with making motivationally biased responses. Analyses using computational models suggest that arousal enhanced motivational effects by biasing evidence accumulation in favor of motivationally desirable percepts. These results suggest heightened arousal biases people towards what they want to see and away from an objective representation of the environment.

Statement of RelevanceWhen confronted with an event of motivational significance (e.g., an opportunity to earn a huge reward), people often experience a strong arousal response that includes increased sweating, faster heart-rate and larger pupils. Does this arousal response help individuals make more accurate decisions, or does it instead bias and impair decision-making? This work examines the effects of arousal on how people decide what they see when they are motivated to see a particular outcome. We found that heightened arousal, as measured by larger pupils, was associated with a bias in how participants accumulated sensory evidence to make their decisions. As a result, participants became more likely to report seeing an ambiguous visual image as the interpretation they were motivated to see. Our results suggest that arousal biases perceptual judgments towards desirable percepts, and that modulating arousal levels could be a promising approach in reducing motivational biases in decision-making.

category: neuroscience


title: Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit

abstract: Spatially distributed excitation and inhibition collectively shape a visual neurons receptive field (RF) properties. In the direction-selective circuit of the mammalian retina, the role of strong null-direction inhibition of On-Off direction-selective ganglion cells (ON-OFF DSGCs) on their direction selectivity is well-studied. However, how excitatory inputs influence the On-Off DSGCs visual response is underexplored. Here, we report that On-Off DSGCs have a spatially displaced glutamatergic receptive field along their preferred-null motion axis. This displaced receptive field contributes to DSGC null-direction spiking during interrupted motion trajectories. Theoretical analyses indicate that population responses during interrupted motion may help populations of On-Off DSGCs signal the spatial location of moving objects in complex, naturalistic visual environments. Our study highlights that the direction-selective circuit exploits separate sets of mechanisms under different stimulus conditions, and these mechanisms may help encode multiple visual features.


title: Reactivation of single-episode pain patterns in the hippocampus and decision making

abstract:
Aversive and rewarding experiences can exert a strong influence on subsequent behavior. While decisions are often supported by the value of single past episodes, most research has focused on the role of well-learned value associations. Recent studies have begun to investigate the influence of reward-associated episodes, but it is unclear if these results generalize to negative experiences such as pain. To investigate whether and how the value of previous aversive experiences modulates behavior and brain activity, in our experiments female and male human participants experienced episodes of high or low pain in conjunction with incidental, trial-unique neutral pictures. In an incentive-compatible surprise test phase, we found that participants avoided pain-paired objects. In a separate fMRI experiment, at test, participants exhibited significant pain value memory. Neurally, when participants were re-exposed to pain-paired objects, we found no evidence for reactivation of pain-related patterns in pain-responsive regions such as the anterior insula. Critically, however, we found significant reactivation of pain-related patterns of activity in the hippocampus, such that activity significantly discriminated high versus low pain episodes. Further, stronger reactivation in the anterior hippocampus was related to improved pain value memory performance. Our results demonstrate that single incidental aversive experiences can build memories that affect decision making and that this influence may be supported by the hippocampus.

Significance StatementAversive and rewarding experiences can exert a strong influence on our subsequent behavior. While decisions are often supported by single past negative or positive episodes, most research has focused on the role of well-learned value associations. In experiments using aversive heat pain in conjunction with incidental objects, we found that participants choices were biased by the level of pain associated with the objects. Further, when participants saw the objects again, pain-related neural patterns in the hippocampus were re-expressed and this was related to pain value memory performance. These results suggest a mechanism by which even single negative experiences can guide our later decisions.


title: Inferences on a Multidimensional Social Hierarchy Use a Grid-like Code

abstract: Generalizing experiences to guide decision making in novel situations is a hallmark of flexible behavior. It has been hypothesized such flexibility depends on a cognitive map of an environment or task, but directly linking the two has proven elusive. Here, we find that discretely sampled abstract relationships between entities in an unseen two-dimensional (2-D) social hierarchy are reconstructed into a unitary 2-D cognitive map in the hippocampus and entorhinal cortex. We further show that humans utilize a grid-like code in several brain regions, including entorhinal cortex and medial prefrontal cortex, for inferred direct trajectories between entities in the reconstructed abstract space during discrete decisions. Moreover, these neural grid-like codes in the entorhinal cortex are associated with neural decision value computations in the medial prefrontal cortex and temporoparietal junction area during choice. Collectively, these findings show that grid-like codes are used by the human brain to infer novel solutions, even in abstract and discrete problems, and suggest a general mechanism underpinning flexible decision making and generalization.


title: Quantifying Structural Diversity of CNG Trinucleotide Repeats Using Diagrammatic Algorithms

abstract:
Trinucleotide repeat expansion disorders (TREDs) exhibit complex mechanisms of pathogenesis, some of which have been attributed to RNA transcripts of overexpanded CNG repeats, resulting in possibly a gain-of-function. In this paper, we aim to probe the structures of these expanded transcript by analyzing the structural diversity of their conformational ensembles. We used graphs to catalog the structures of an NG-(CNG)16-CN and NG-(CNG)50-CN oligomer and grouped them into sub-ensembles based on their characters and calculated the structural diversity and thermodynamic stability for these ensembles using a previously described graph factorization scheme. Our findings show that the generally assumed structure for CNG repeats--a series of canonical helices connected by two-way junctions and capped with a hairpin loop--may not be the most thermodynamically favorable, and the ensembles are characterized by largely open and less structured conformations. Furthermore, a length-dependence is observed for the behavior of the ensembles diversity as higher-order diagrams are included, suggesting that further studies of CNG repeats are needed at the length scale of TREDs onset to properly understand their structural diversity and how this might relate to their functions.

STATEMENT OF SIGNIFICANCETrinucleotide repeats are DNA satellites that are prone to mutations in the human genome. A family of diverse disorders are associated with an overexpansion of CNG repeats occurring in noncoding regions, and the RNA transcripts of the expanded regions have been implicated as the origin of toxicity. Our understanding of the structures of these expanded RNA transcripts is based on sequences that have limited lengths compared to the scale of the expanded transcripts found in patients. In this paper, we introduce a theoretical method aimed at analyzing the structure and conformational diversity of CNG repeats, which has the potential of overcoming the current length limitations in the studies of trinucleotide repeat sequences.


title: Lynx1 modulates the activity of nAChRs to slow NMJ and muscle fiber degeneration during aging

abstract: The authors have withdrawn their manuscript to revisit some of the data, interpretations and conclusions. Therefore, the authors do not wish this work to be cited as a reference. If you have any questions, please contact the corresponding author.


title: Functional characterization of a "plant-like" HYL1 homolog in the cnidarian Nematostella vectensis indicates a conserved involvement in microRNA biogenesis

abstract:
While the biogenesis of microRNAs (miRNAs) in both animals and plants depends on the RNase III Dicer, its partner proteins are considered distinct for each kingdom. Nevertheless, recent discovery of homologs of Hyponastic Leaves1 (HYL1), a "plant-specific" Dicer partner, in the metazoan phylum Cnidaria, challenges the view that miRNAs evolved convergently in animals and plants. Here we show that the HYL1 homolog Hyl1-like a (Hyl1La) is crucial for development and miRNA biogenesis in the cnidarian model Nematostella vectensis. Inhibition of Hyl1La by morpholinos resulted in metamorphosis arrest in Nematostella embryos and a significant reduction in levels of most miRNAs. Further, meta-analysis of morphants of miRNA biogenesis components, like Dicer1, shows clustering of their miRNA profiles with Hyl1La morphants. Strikingly, immunoprecipitation of Hyl1La followed by quantitative PCR revealed that in contrast to the plant HYL1, Hyl1La interacts only with precursor miRNAs and not with primary miRNAs. This was complemented by an in vitro binding assay of Hyl1La to synthetic precursor miRNA. Altogether, these results suggest that the last common ancestor of animals and plants carried a HYL1 homolog that took essential part in miRNA biogenesis and indicate early emergence of the miRNA system before plants and animals separated.

Impact statementPresence of a functional homolog of HYL1 in Nematostella vectensis, a basal animal model, indicates divergent evolution of miRNA biogenesis pathway in plants and animals from an ancestral miRNA system

category: evolutionary biology


title: An interpretable classification method for predicting drug resistance in M. tuberculosis

abstract:
MotivationPrediction of drug resistance and identification of its mechanisms in bacteria such as Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a challenging problem. Solving this problem requires a transparent, accurate, and flexible predictive model. The methods currently used for this purpose rarely satisfy all of these criteria. On the one hand, approaches based on testing strains against a catalogue of previously identified mutations often yield poor predictive performance; on the other hand, machine learning techniques typically have higher predictive accuracy, but often lack interpretability and may learn patterns that produce accurate predictions for the wrong reasons. Current interpretable methods may either exhibit a lower accuracy or lack the flexibility needed to generalize them to previously unseen data.

ContributionIn this paper we propose a novel technique, inspired by the group testing and Boolean compressed sensing, which yields highly accurate predictions, interpretable results, and is flexible enough to be optimized for various evaluation metrics at the same time.

ResultsWe test the predictive accuracy of our approach on five first-line and seven second-line antibiotics used for treating tuberculosis. We find that it has a higher or comparable accuracy to that of commonly used machine learning models, and is able to identify variants in genes with previously reported association to drug resistance. Our method is intrinsically interpretable, and can be customized for different evaluation metrics. Our implementation is available at github.com/hoomanzabeti/INGOT_DR and can be installed via The Python Package Index (Pypi) under ingotdr. This package is also compatible with most of the tools in the Scikit-learn machine learning library.


title: Transfer learning between preclinical models and human tumors identifies conserved NK cell activation signature in anti-CTLA-4 responsive tumors

abstract:
BackgroundTumor response to therapy is affected by both the cell types and the cell states present in the tumor microenvironment. This is true for many cancer treatments, including notably immune checkpoint inhibitors (ICIs). While it is well-established that ICIs promote T cell activation, their broader impact on other intratumoral immune cells is unclear; this information is needed to identify new mechanisms of action and improve ICI efficacy. Many preclinical studies have begun to use single cell analysis to delineate therapeutic responses in individual immune cell types within tumors. One major limitation to this approach is that therapeutic mechanisms identified in preclinical models have failed to fully translate to human disease, restraining efforts to improve ICI efficacy in bench to bedside research.

MethodWe previously developed a computational transfer learning approach to identify shared biology between independent high-throughput single-cell RNA sequencing (scRNA-seq) datasets. In the present study, we test this frameworks ability to identify conserved and clinically relevant transcriptional changes in complex tumor scRNA-seq data and further expand its application beyond comparison of scRNA-seq datasets into comparison of scRNA-seq datasets with additional data types such as bulk RNA-seq and mass cytometry.

ResultsWe found a conserved signature of NK cell activation in anti-CTLA-4 responsive mice and human tumors. In human melanoma, we found that the NK cell activation signature correlates with longer overall survival and is predictive of anti-CTLA-4 (ipilimumab) response. Additional molecular approaches to confirm the computational findings demonstrated that human NK cells express CTLA-4 and bind anti-CTLA-4 independent of the antibody binding receptor (FcR), and that similar to T cells, CTLA-4 expression by NK cells is modified by cytokine-mediated and target cell-mediated NK cell activation.

ConclusionsThese data demonstrate the ability of our transfer learning approach to identify cell state transitions conserved in preclinical models and human tumors. This approach can be adapted to explore many immuno-oncology questions, enhancing bench to bedside research and enabling better understanding and treatment of disease.

Graphical Abstract

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title: Perceptual gating of a brainstem reflex facilitates speech understanding in humans listeners

abstract: Navigating "cocktail party" situations by enhancing foreground sounds over irrelevant background information is typically considered from a cortico-centric perspective. However, subcortical circuits, such as the medial olivocochlear (MOC) reflex that modulates inner ear activity itself, have ample opportunity to extract salient features from the auditory scene prior to any cortical processing. To understand the contribution of auditory subcortical nuclei and the cochlea, physiological recordings were made along the auditory pathway while listeners differentiated non(sense)-words and words. Both naturally-spoken and intrinsically-noisy, vocoded speech -- filtering that mimics processing by a cochlear implant--significantly activated the MOC reflex, whereas listening to speech-in-background noise revealed instead engagement of midbrain and cortical resources. An auditory periphery model reproduced these speech degradation-specific effects, providing a rationale for goal-directed gating of the MOC reflex to enhance representation of speech features in the auditory nerve. Our data reveals the co-existence of two strategies in the auditory system that may facilitate speech understanding in situations where the speech signal is either intrinsically degraded or masked by extrinsic auditory information.


title: Perceptual gating of a brainstem reflex facilitates speech understanding in human listeners


title: GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data

abstract: Genetic variation in response to the environment is fundamental in the biology of complex traits and diseases, i.e. genotype-by-environment interaction (GxE). However, existing methods are computationally demanding and infeasible to handle biobank-scale data. Here we introduce GxEsum, a method for estimating the phenotypic variance explained by genome-wide GxE based on GWAS summary statistics. Through comprehensive simulations and analysis of UK Biobank with 288,837 individuals, we show that GxEsum can handle a large-scale biobank dataset with controlled type I error rates and unbiased GxE estimates, and its computational efficiency can be hundreds of times higher than existing GxE methods.

category: genetics


title: Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth

abstract:
While Entamoeba histolytica remains a globally important pathogen, it is dramatically understudied. The tractability of E. histolytica has historically been limited, which is largely due to challenging features of its genome. To enable forward genetics, we constructed and validated the first genome-wide E. histolytica RNAi knockdown mutant library. This library allows for Illumina deep sequencing analysis for quantitative identification of mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify gene fragments. We used the library to perform the first RNAi screen in E. histolytica and identified slow growth (SG) mutants. Among genes targeted in SG mutants, many had annotated functions consistent with roles in cellular growth or metabolic pathways. Some targeted genes were annotated as hypothetical or lacked annotated domains, supporting the power of forward genetics in uncovering functional information that cannot be gleaned from databases. While the localization of neither of the proteins targeted in SG1 nor SG2 mutants could be predicted by sequence analysis, we showed experimentally that SG1 localized to the cytoplasm and cell surface, while SG2 localized to the cytoplasm. Overexpression of SG1 led to increased growth, while expression of a truncation mutant did not lead to increased growth, and thus aided in defining functional domains in this protein. Finally, in addition to establishing forward genetics, we uncovered new details of the unusual E. histolytica RNAi pathway. These studies dramatically improve the tractability of E. histolytica and open up the possibility of applying genetics to improve understanding of this important pathogen.

Author SummaryEntamoeba histolytica is a globally important pathogen that is dramatically understudied. One of the major limitations of this organism is its challenging genome. RNAi is the state-of-the-art tool for genetic manipulation in E. histolytica, though the RNAi pathway has several noncanonical features. Here, we harnessed the RNAi pathway to enable RNAi-based forward genetics for the first time in this organism. We validated the RNAi library by performing the first E. histolytica RNAi screen and identified slow growth mutants. We showed that independently-generated mutants also exhibited slow growth phenotypes, and we characterized protein localization and domains for some of the identified slow growth genes. The RNAi library that we constructed enables modern, quantitative Illumina deep sequencing analysis to identify mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify full-length gene fragments inferred from read mapping. Our approach differs from previous approaches for analysis of RNAi screens, and it better represents the actual DNA fragments and their quantities. This study dramatically improves the tractability of this important pathogen. Moreover, the strategies behind this RNAi library, and its analysis, are novel, and can be applied to other organisms.

Author ContributionsA.B. designed and performed the experiments, except fragmentation of gDNA, immunofluorescence, and growth curves with expression of full-length or truncated proteins. R.L.S. performed SG1 and SG2 immunofluorescence experiments. M.C.R. performed growth curves with expression of full-length or truncated proteins. W.H. generated transfectants expressing full-length SG2. C.G.B. fragmented gDNA and processed the fragments to enable subsequent plasmid library construction. T.S.Y.T. and H.W.M. performed Gal/GalNAc lectin immunofluorescence experiments. S.S.H. designed the analysis strategy for Illumina sequencing data, and analyzed all Illumina sequencing data. M.L.S. oversaw the Illumina analysis approach. K.S.R. performed growth curves, conceived of the overall approach and oversaw the design and analysis of the experiments. A.B., S.S.H., and K.S.R. wrote the manuscript.

category: microbiology


title: Neurofunctional basis underlying audiovisual integration of print and speech sound in Chinese children

abstract:
Effortless print-sound integration is essential to reading development, and the superior temporal cortex (STC) is the most critical brain region. However, to date, the conclusion is almost restricted to alphabetic orthographies. To examine the neural basis in non-alphabetic languages and its relationship with reading abilities, we conducted a functional magnetic resonance imaging study in typically developing Chinese children. Two neuroimaging-based indicators of audiovisual processing--additive enhancement (higher activation in the congruent than the average activation of unimodal conditions) and neural integration (different activations between the congruent versus incongruent conditions)--were used to investigate character-sounds (opaque) and pinyin-sounds (transparent) processing. We found additive enhancement in bilateral STCs processing both character and pinyin stimulations. Moreover, the neural integrations in the left STC for the two scripts were strongly correlated. In terms of differentiation, first, areas beyond the STCs showed additive enhancement in processing pinyin-sounds. Second, while the bilateral STCs, left inferior/middle frontal and parietal regions manifested a striking neural integration (incongruent > congruent) for character-sounds, no significant clusters were revealed for pinyin-sounds. Finally, the neural integration in the left middle frontal gyrus for characters was specifically associated with silent reading comprehension proficiency, indicating automatic semantic processing during implicit character-sound integration. In contrast, the neural integration in the left STC for pinyin was specifically associated with oral reading fluency that relies on grapho-phonological mapping. To summarize, this study revealed both script-universal and script-specific neurofunctional substrates of print-sound integration as well as their processing- and region-dependent associations with reading abilities in typical Chinese children.

HighlightsO_LIThe bilateral superior temporal cortices display additive enhancement in processing print-sound information regardless of orthographies.
C_LIO_LIThe location, direction, and strength of the neural audiovisual integration are modulated by orthographic transparency.
C_LIO_LIThe neural integration in the left middle frontal gyrus in processing character-sounds is correlated to reading comprehension.
C_LIO_LIThe neural integration in the left superior temporal gyrus for pinyin is correlated with oral reading fluency.
C_LIO_LIThe neural integrations of character-sounds and pinyin-sounds show spatial overlap and inter-subject correlation in the left superior temporal cortex.
C_LI


title: Comprehensive evaluation of human brain gene expression deconvolution methods

abstract:
Gene expression measurements, similar to DNA methylation and proteomic measurements, are influenced by the cellular composition of the sample analysed. Deconvolution of bulk transcriptome data aims to estimate the cellular composition of a sample from its gene expression data, which in turn can be used to correct for composition differences across samples. Although a multitude of deconvolution methods have been developed, it is unclear whether their performance is consistent across tissues with different complexities of cellular composition. The human brain is unique in its transcriptomic diversity, expressing the highest diversity of alternative splicing isoforms and non-coding RNAs. It comprises a complex mixture of cell-types including transcriptionally similar sub-types of neurons, which undergo gene expression changes in response to neuronal activity. However, a comprehensive assessment of the accuracy of transcriptome deconvolution methods on human brain data is currently lacking.

Here we carry out the first comprehensive comparative evaluation of the accuracy of deconvolution methods for human brain transcriptome data, and assess the tissue-specificity of our key observations by comparison with transcriptome data from human pancreas and heart.

We evaluate 8 transcriptome deconvolution approaches, covering all main classes: 4 partial deconvolution methods, each applied with 9 different cell-type signatures, 2 enrichment methods, and 2 complete deconvolution methods. We test the accuracy of cell-type estimates using in silico mixtures of single-cell RNA-seq data, mixtures of neuronal and glial RNA, as well as nearly 2,000 human brain samples.

Our results bring several important insights into the performance of transcriptome deconvolution: (a) We find that cell-type signature data has a stronger impact on brain deconvolution accuracy than the choice of method. (b) We demonstrate that biological factors influencing brain cell-type signature data (e.g. brain region, in vitro cell culturing), have stronger effects on the deconvolution outcome than technical factors (e.g. RNA sequencing platform). (c) We find that partial deconvolution methods outperform complete deconvolution methods on human brain data. To facilitate wider implementation of correction for cellular composition, we develop a webtool that implements the best performing methods, and is available at https://voineagulab.shinyapps.io/BrainDeconvShiny/ .


title: Complexity analysis of heartbeat-related signals in Brain MRI time series as a potential biomarker for ageing and cognitive performance

abstract: There are multiple magnet resonance imaging (MRI) based approaches to studying the ageing brain. Getting older affects both the structure of the brain and our cognitive capabilities, but there is still no solid evidence on how ageing influences the mechanisms underlying the MRI signal. Here, we apply a zero-spin echoes (ZSEs) weighted MRI sequence which recently was found to be sensitive to wakefulness. We investigated the complexity of the signal time series of this sequence in two age groups; young (18-29 years) and old (over 65 years). While comparing young and old participants, we found qualitative and quantitative evidence that the dynamics of ZSE fluctuations undergo strong changes with age. Finally, we study how differences in complexity of the ZSE signal relate with measures from different cognitive batteries, suggesting that ZSE may reveal cognitive functioning in a new. fashion. The profound sensitivity for dynamic changes shows the potential of ZSE and its underlying physiological mechanism with clinical relevance for all neurovascular diseases.


title: Anipose: a toolkit for robust markerless 3D pose estimation

abstract: AO_SCPLOWBSTRACTC_SCPLOWQuantifying movement is critical for understanding animal behavior. Advances in computer vision now enable markerless tracking from 2D video, but most animals live and move in 3D. Here, we introduce Anipose, a Python toolkit for robust markerless 3D pose estimation. Anipose is built on the popular 2D tracking method DeepLabCut, so users can easily expand their existing experimental setups to obtain accurate 3D tracking. It consists of four components: (1) a 3D calibration module, (2) filters to resolve 2D tracking errors, (3) a triangulation module that integrates temporal and spatial regularization, and (4) a pipeline to structure processing of large numbers of videos. We evaluate Anipose on four datasets: a moving calibration board, fruit flies walking on a treadmill, mice reaching for a pellet, and humans performing various actions. By analyzing 3D leg kinematics tracked with Anipose, we identify a key role for joint rotation in motor control of fly walking. We believe this open-source software and accompanying tutorials (anipose.org) will facilitate the analysis of 3D animal behavior and the biology that underlies it.


title: A miR-124-mediated post-transcriptional mechanism controlling the cell fate switch of astrocytes to induced-neurons

abstract:
miRNA miR-124 has been employed supplementary to neurogenic TFs and other miRNAs to enhance direct neurogenic conversion by suppressing multiple non-neuronal targets. Aim of the study was to investigate whether miR-124 is sufficient to drive direct reprogramming of astrocytes to induced-neurons (iNs) on its own and elucidate its independent mechanism of reprogramming action. Our data show that miR-124 is a potent driver of the reprogramming switch of astrocytes towards an immature neuronal fate, by directly targeting the RNA-binding protein Zfp36l1 implicated in ARE-mediated mRNA decay and subsequently de-repressing Zfp36l1 neurogenic interactome. To this end miR-124 contribution in iNs production largely recapitulates endogenous neurogenesis pathways, being further enhanced upon addition of the neurogenic compound ISX9, which greatly improves both miR-124-induced reprogramming efficiency and iNs functional maturation. Importantly, miR-124 is potent to guide direct conversion of reactive astrocytes to immature iNs of cortical identity in vivo following cortical trauma, confirming its  master reprogramming capacity within the injured cortical microenvironment, while ISX9 supplementation confers a survival advantage to newly produced iNs.

Significance statementDirect reprogramming protocols have employed miR-124 along with other neurogenic factors to support cell fate conversion. Here we have studied the  master reprogramming potential of miR-124 in the direct neurogenic conversion of astrocytes and show that the direct targeting of the abundant in astrocytes RNA binding protein Zfp36l1 is critical in conferring the astrocytic to neurogenic transcriptomic switch, leading to de-repression of Zfp36l1 neurogenic interactome and establishment of immature neuronal identity. Our data uncover a mechanism of miR-124 action during astrocytic reprogramming that recapitulates endogenous neurogenesis pathways, being further reinforced by addition of the neurogenic molecule ISX9 resulting in mature iNs production. Importantly, miR-124 exhibits in vivo reprogramming capacity in a cortical trauma model, further supporting its  master reprogramming potential.


title: Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations

abstract: Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotics mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that whether a drug acts as a bacteriostatic or bactericidal agent has little influence on resistance selection. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strains minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.

category: pharmacology and toxicology


title: R-type voltage-gated Ca2+ channels mediate A-type K+ current regulation of synaptic input in hippocampal dendrites

abstract: The transient K+ current (IA) carried by pore forming Kv4.2 subunits regulates the propagation of synaptic input, dendritic excitability, and synaptic plasticity in CA1 pyramidal neuron dendrites of the hippocampus. We report that the Ca2+ channel subunit Cav2.3 regulates IA in this cell type. We first identified Cav2.3 as a Kv4.2 interacting protein in a proteomic screen and we confirmed Cav2.3-Kv4.2 complex association using multiple techniques. Functionally, Cav2.3 Ca2+-entry increases Kv4.2-mediated whole-cell current due to an increase in Kv4.2 surface expression. Using pharmacology and Cav2.3 knockout mice, Cav2.3 was found to promote whole-cell IA and the increasing gradient of IA in the apical dendrite distal to the neuronal soma. Furthermore, the loss of Cav2.3 function leads to enhancement of synaptic currents and spine Ca2+ influx. These results present Cav2.3 and Kv4.2 as integral constituents of an ion channel complex that impacts synaptic function in the hippocampus.


title: Switchgrass metabolomics reveals striking genotypic and developmental differences in specialized metabolic phenotypes

abstract:
Switchgrass (Panicum virgatum L.) is a bioenergy crop that grows productively on lands not suitable for food production, and is an excellent target for low-pesticide input biomass production. We hypothesize that resistance to insect pests and microbial pathogens is influenced by low molecular weight compounds known as specialized metabolites. We employed untargeted liquid chromatography-mass spectrometry (LC-MS), quantitative gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy to identify differences in switchgrass ecotype metabolomes. This analysis revealed striking differences between upland and lowland switchgrass metabolomes as well as distinct developmental profiles. Terpenoid and polyphenol derived specialized metabolites were identified, including steroidal saponins, di- and sesqui-terpenoids and flavonoids. The saponins are especially abundant in switchgrass extracts and have diverse aglycone cores and sugar moieties. We report seven structurally distinct steroidal saponin classes with unique steroidal cores and glycosylated at one or two positions. Quantitative GC-MS revealed differences in total saponin concentrations in leaf blade, leaf sheath, stem, rhizome and root. The quantitative data also demonstrated that saponin concentrations is higher in roots of lowland than upland ecotype plants, suggesting ecotypic specific biosynthesis and/or biological functions. These results enable future testing of these specialized metabolites on biotic and abiotic stress tolerance and can inform development of low-input bioenergy crops.

One sentence summaryIntegrated mass-spectrometry and nuclear magnetic resonance spectroscopy based metabolomics reveal that switchgrass accumulates structurally diverse terpenoids and phenolics, which vary in abundance and structure in a tissue- and ecotype-specific manner.


title: R7 photoreceptor axon targeting requires matching levels of lost and found expression in R7 and its synaptic partners

abstract: As neural circuits form, growing processes select the correct synaptic partners through interactions between cell surface proteins. The presence of such proteins on two neuronal processes may lead to either adhesion or repulsion; however, the consequences of mismatched expression have rarely been explored. Here we show that the Drosophila CUB-LDL protein Lost and found (Loaf) is required in the UV-sensitive R7 photoreceptor for normal axon targeting only when Loaf is also present in its synaptic partners. Although targeting occurs normally in loaf mutant animals, removing loaf from photoreceptors or expressing it in their postsynaptic neurons Tm5a/b or Dm9 in a loaf mutant causes mistargeting of R7 axons. Loaf localizes primarily to intracellular vesicles including endosomes. We propose that Loaf regulates the trafficking or function of one or more cell surface proteins, and an excess of these proteins on the synaptic partners of R7 prevents the formation of stable connections.

category: developmental biology


title: R7 photoreceptor axon targeting depends on the relative levels of lost and found expression in R7 and its synaptic partners


title: Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection

abstract:
Several molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s).

Software and interactive visualizationhttps://github.com/phoenixding/sdremsc


title: Induction of pancreatic neoplasia in the KRAS/TP53 Oncopig: preliminary report

abstract:
IntroductionFive years survival of pancreatic cancer (PC) remains low. The current murine models may not adequately mimic human PC and can be inadequate for device development. To develop a more accurate large animal model of PC, we induced pancreatic tumors in Oncopigs (transgenic swine expressing KRASG12D and TP53R167H mutants).

MethodsOncopigs (n = 16) were injected via laparotomy with adenovirus expresses Cre recombinase (AdCre) with or without interleukin 8 (IL-8) by either technique 1: into the main pancreatic duct (MPD; via duodenotomy) or by technique 2: into the duct of the isolated pancreatic connecting lobe (CL). Subjects were necropsied after [≤]10 week, followed by histological analysis, cytokine expression analysis, exome sequencing and transcriptome analysis.

ResultsIn a total of 16 OCM subjects, 12 subjects received pancreatic AdCre injection by technique 2 and 9 developed pancreatic tumor (incidence outcome by technique 2: 75%). All of these subjects expired within 2-5 weeks after the tumor induction procedure. All had a similar terminal course: failure to thrive, which was secondary to gastric outlet obstruction, which was secondary to a peripancreatic phlegmon, which was secondary to pancreatitis, which appeared to be secondary to tumor. None of the OCM subjects that underwent a control injection procedure (no AdCre) nor any of the WT littermates that underwent AdCre injection with or without IL-8 developed pancreatitis. Exome and transcriptome analysis of the porcine pancreatic tumors revealed similarity in molecular signatures and pathways with human pancreatic tumors.

ConclusionOncopigs developed pancreatic cancer in a short period of time with similar molecular characteristics like human PC. Further optimization to increase the longevity of this transgenic porcine cancer model will help to investigate the stage-wise progression and therapeutic responses against pancreatic cancer.


title: Patterns of multisensory facilitation distinguish peripersonal from reaching space

abstract: Peripersonal space (PPS) is a multisensory representation of the space near body parts facilitating interactions with the close environment. Studies on non-human and human primates converge in showing that PPS is a body-part-centred representation that guides actions. Because of these characteristics, growing confusion conflates peripersonal and arm-reaching space (ARS), that is the space ones arm can reach. Despite neuroanatomical evidence favors their distinction, no study has contrasted directly their respective extent and behavioral features. Here, in five experiments (N=140) we found that PPS differs from ARS, as evidenced both by participants spatial and temporal performance and its modeling. We mapped PPS and ARS using both their respective gold standard tasks and a novel multisensory facilitation paradigm. Results show that 1) PPS is smaller than ARS; 2) multivariate analyses of spatial patterns of multisensory facilitation predict participants hand locations within ARS; 3) the multisensory facilitation map shifts isomorphically following hand positions, revealing hand-centred coding of PPS, therefore pointing to a functional similarity to the receptive fields of monkeys multisensory neurons. A control experiment further corroborated these results and additionally ruled out the orienting of attention as driving mechanism for the increased multisensory facilitation near the hand. In sharp contrast, ARS mapping results in a larger spatial extent, with undistinguishable patterns across hand positions, cross-validating the conclusion that PPS and ARS are distinct spatial representations. These findings urge for a refinement of theoretical models of PPS, which is relevant to constructs as diverse as self-representation, social interpersonal distance, and motor control.


title: A microRNA Signature of Metastatic Colorectal Cancer

abstract: Although microRNAs (miRNA) are involved in all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood and contradictory results have been published. The aim of this work was to identify miRNAs associated with metastatic progression of colorectal cancer (CRC). Novel and previously published next generation sequencing (NGS) datasets generated from 268 samples with primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues were analyzed. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, utilizing miRNA-tailored quality control and processing, and applying a physiologically meaningful cut-off value (100 reads per million). The results were adjusted for host tissue background expression and samples from the different metastatic sites were independently analyzed. A metastatic signature containing five miRNAs up-regulated at multiple metastatic sites was identified (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p (mir-141-3p), Mir-1307_5p, and Mir-155_5p) along with a number of miRNAs that were differentially expressed at individual metastatic sites. Several of these have previously been implicated in metastasis through involvement in epithelial-to-mesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The identified differentially expressed miRNAs confirm known associations and contribute novel insights into miRNA involvement in the metastatic process. The use of open science practices facilitates reproducibility, and new datasets may easily be added to the publicly available pipeline to continuously improve the knowledge in the field. The identified set of miRNAs provides a reliable starting-point for further research into the role of miRNAs in metastatic progression.


title: A heuristic underlies the search for relief in fruit flies

abstract: Humans rely on multiple systems of sensory information to make decisions. However, strategies that shorten decision-making time by taking into account fewer but more essential elements of information are preferred to strategies involving complex analyses. These "shortcuts to decision" are also termed "heuristics". The identification of heuristic principles in species phylogenetically distant to humans would shed light on the evolutionary origin of speed-accuracy trade-offs and offer the possibility to investigate the brain representations of such trade-offs, urgency, and uncertainty. During experiments on spatial learning, we acknowledged that the search strategies of the invertebrate Drosophila melanogaster, the common fruit fly, resembled a spatial heuristic. Here we show that the fruit fly applies a heuristic termed the "Nearest Neighbour Rule" to avoid bitter taste (a negative stimulation). That is, the fly visits the salient location closest to its current position to hopefully stop the negative stimulation. Only if this strategy proves unsuccessful, the animal uses other learned associations to avoid bitter taste. The acknowledgement of a heuristic in D. melanogaster supports the view that invertebrates can leverage on  economic principles when making choices and that the existence of heuristics in evolution dates to at least 600 million years ago.


title: Lineage and Spatial Mapping of Glioblastoma-associated Immunity

abstract: The diversity of molecular states and cellular plasticity of immune cells in the glioblastoma environment is still poorly understood. Here, we performed scRNA sequencing of the immune compartment and mapped potential cellular interactions leading to an immunosuppressive microenvironment and dysfunction of T cells. Through inferring the dynamic adaptation during T cell activation, we identified three different terminal states with unique transcriptional programs. Modeling of driver genes for terminal T cell fate identified IL-10 signaling alterations in a subpopulation of HAVCR2(+) T cells. To explore in depth cellular interactions, we established an in-silico model by the integration of spatial transcriptomic and scRNA-sequencing, and identified a subset of HMOX1+ myeloid cells defined by IL10 release leading to T cell exhaustion. We found a spatial overlap between HMOX(+) myeloid and HAVCR2(+) T cells, suggesting that myeloid-lymphoid interaction causes immunosuppression present in tumor regions with enriched mesenchymal gene expression. Using human neocortical GBM model, coupled with patient-derived T cells, we confirmed that the functional interaction between myeloid and lymphoid cells, leads to a dysfunctional state of T cells. This IL-10 driven T cell exhaustion was found to be rescued by JAK/STAT inhibition. A comprehensive understanding of the cellular states and plasticity of lymphoid cells in GBM will aid towards successful immunotherapeutic approaches.


title: The timing and impact of psychiatric, cognitive and motor abnormalities in Huntington's disease

abstract:
ObjectiveTo assess the prevalence, timing and functional impact of psychiatric, cognitive and motor abnormalities in Huntingtons disease (HD) gene carriers, we analysed retrospective clinical data from individuals with manifest HD.

MethodsClinical features of HD patients were analysed for 6316 individuals in the European REGISTRY study from 161 sites across 17 countries. Data came from clinical history and the patient-completed Clinical Characteristics Questionnaire that assessed eight symptoms: motor, cognitive, apathy, depression, perseverative/obsessive behavior, irritability, violent/aggressive behavior, and psychosis. Multiple logistic regression was used to analyse relationships between symptoms and functional outcomes.

ResultsThe initial manifestation of HD is increasingly likely to be motor, and less likely to be psychiatric, as age at presentation increases, and is independent of pathogenic CAG repeat length. The Clinical Characteristics Questionnaire captures data on non-motor symptom prevalence that correlate specifically with validated clinical measures. Psychiatric and cognitive symptoms are common in HD gene carriers, with earlier onsets associated with longer CAG repeats. 42.4% of HD patients reported at least one psychiatric or cognitive symptom before motor symptoms, with depression most common. Each non-motor symptom was associated with significantly reduced total functional capacity scores.

ConclusionsPsychiatric and cognitive symptoms are common and functionally debilitating in HD gene carriers. They require recognition and targeting with clinical outcome measures and treatments. However, as it is impossible to distinguish confidently between non-motor symptoms arising from HD and primary psychiatric disorders, particularly in younger pre-manifest patients, non-motor symptoms should not be used to make a clinical diagnosis of HD.


title: Binding of DNA origami to lipids: maximising yield and switching via strand-displacement

abstract: Liposomes are widely used as synthetic analogues of cell membranes and for drug delivery. Lipid-binding DNA nanostructures can modify the shape, porosity and reactivity of liposomes, mediated by cholesterol-modifications. DNA nanostructures can also be designed to switch conformations by DNA strand displacement. However, the optimal conditions to facilitate stable, high-yield DNA-lipid binding while allowing controlled switching by strand-displacement are not known. Here we characterised the effect of cholesterol arrangement, DNA structure, buffer and lipid composition on DNA-lipid binding and strand displacement. We observed that binding was inhibited below pH 4, and above 200 mM NaCl or 40 mM MgCl2, was independent of lipid type, and increased with membrane cholesterol content. For simple motifs, binding yield was slightly higher for double-stranded DNA than single-stranded. For larger DNA origami tiles, 4 - 8 cholesterol modifications were optimal, while edge positions and longer spacers increased yield of lipid-binding. Strand displacement achieved controlled removal of DNA tiles from membranes, but was inhibited by overhang domains, which are used to prevent cholesterol aggregation. These findings provide design guidelines for integrating strand-displacement switching with lipid-binding DNA nanostructures. This paves the way for achieving dynamic control of membrane morphology, enabling broader applications in nanomedicine and biophysics.


title: Estimating abundance and phenology from transect count data with GLMs

abstract: Estimating population abundance is central to population ecology. With increasing concern over declining insect populations, estimating trends in abundance has become even more urgent. At the same time, there is an emerging in interest in quantifying phenological patterns, in part because phenological shifts are one of the most conspicuous signs of climate change. Existing techniques to fit activity curves (and thus both abundance and phenology) to repeated transect counts of insects (a common form of data for these taxa) frequently fail for sparse data, and often require advanced knowledge of statistical computing. These limitations prevent us from understanding both population trends and phenological shifts, especially in the at-risk species for which this understanding is most vital. Here we present a method to fit repeated transect count data with Gaussian curves using linear models, and show how robust abundance and phenological metrics can be obtained using standard regression tools. We then apply this method to eight years of Baltimore checkerspot data using generalized linear models (GLMs). This case study illustrates the ability of our method to fit even years with only a few non-zero survey counts, and identifies a significant negative relationship between population size and annual variation in thermal environment (in growing degree days). We believe our new method provides a key tool to unlock previously-unusable sparse data sets, and may provide a useful middle ground between ad hoc metrics of abundance and phenology and custom-coded mechanistic models.

category: ecology


title: Latent effects of winter warming on Olympia oyster reproduction and larval viability

abstract:
For ectothermic marine invertebrates living in temperate regions, impacts of ocean warming will vary considerably by season. In many species, reproductive and metabolic processes are tightly linked to the seasonal change from winter to spring, yet we know little about how these processes will shift as winters become milder. This study examined latent effects of winter warming on spring reproduction in the Olympia oyster, Ostrea lurida. Adults were collected in autumn from central Puget Sound, WA, USA, and exposed to two winter temperatures (7{degrees}C, 10{degrees}C) in the presence of food limited (5k algal cells/mL) and food abundant (50k algal cells/mL) environments. Following treatments, adults exposed to elevated winter temperature contained larger oocytes regardless of feeding regime, and those also fed abundant food contained more developed sperm. Adults then spawned in common conditions, and larvae were reared through settlement to assess carryover effects of winter conditions on larval viability. Adults previously exposed to elevated winter temperature (10{degrees}C) produced larger larvae, particularly if they were also fed high food levels. More developed gametes and larger larvae suggest that gametogenesis occurred at low levels throughout the winter, possibly resulting in increased maternal provisioning to influence larval size. Interestingly, winter temperature did not impact larval survival, or the timing or magnitude of larval production. In the wild, more developed gametes and larger larvae following milder winters could greatly impact recruitment patterns, possibly benefitting O. lurida populations. In the hatchery setting, larval production and survival is not contingent upon winter conditions, and larval survival does not correlate with oocyte and larval size. Our results suggest that O. lurida reproduction is resilient to winter warming. Furthermore, as global temperature continues to rise, winter conditions should not be overlooked when examining reproductive cycles of O. lurida and other temperate marine invertebrates with similar reproductive cycles.

Highlights of the manuscriptO_LIElevated winter temperature resulted in more developed O. lurida sperm, larger oocytes, and larger larvae.
C_LIO_LIIn experimental settings, O. lurida oocyte and larval size upon release did not predict larval survival, but in the wild where rearing conditions are more challenging, winter warming could benefit wild populations by increasing recruitment.
C_LIO_LIWinter temperature did not affect larval production timing or magnitude, indicating that O. lurida reproductive capacity is relatively resilient to increasing winter temperatures.
C_LI

category: physiology


title: A new approach to evaluate scientific production

abstract: Advances in science and technology depend on the work of research teams and the publication of results through peer-reviewed articles representing a growing socio-economic resource. Current methods to mine the scientific literature regarding a field of interest focus on content, but the workforce credited by authorship remains largely unexplored, and appropriate measures of scientific production are debated. Here, a new bibliometric approach named TeamTree analysis is introduced that visualizes the development and composition of the workforce driving a field. A new citation-independent measure that scales with the H index estimates impact based on publication record, genealogical ties and collaborative connections. This author-centered approach complements existing tools to mine the scientific literature and to evaluate research across disciplines.

category: scientific communication and education


title: TeamTree analysis: a new approach to evaluate scientific production


title: ICOS signaling limits regulatory T cell accumulation and function in visceral adipose tissue

abstract:
A unique population of Foxp3+ regulatory T cells (TR) resides in visceral adipose tissue (VAT) that regulates adipose inflammation and helps preserve insulin sensitivity. The costimulatory molecule ICOS is highly expressed on effector (e)TR that migrate to nonlymphoid tissues, and contributes to their maintenance and function in models of autoimmunity. In this study, we report an unexpected cell-intrinsic role for ICOS expression and downstream PI3K signaling in limiting the abundance, VAT-associated phenotype, and function of TR specifically in VAT. Icos-/- mice and mice expressing a knock-in form of ICOS that cannot activate PI3K had increased VAT-TR abundance and elevated expression of canonical VAT-TR markers. Loss of ICOS signaling facilitated enhanced accumulation of TR to VAT associated with elevated CCR3 expression, and resulted in reduced adipose inflammation and heightened insulin sensitivity in the context of high-fat diet. Thus, we have uncovered a new and surprising molecular pathway that regulates VAT-TR accumulation and function.

SummaryThe authors demonstrate that loss of ICOS-dependent PI3-kinase signaling supports visceral adipose tissue (VAT) TR abundance and function, and this correlates with reduced adipose inflammation and improved insulin sensitivity after high-fat diet. This work highlights a new molecular pathway that regulates VAT-TR accumulation and activity.

category: immunology


title: Physiological noise modeling in fMRI based on the pulsatile component of photoplethysmograph

abstract: The blood oxygenation level-dependent (BOLD) contrast mechanism allows the noninvasive monitoring of changes in deoxyhemoglobin content. As such, it is commonly used in functional magnetic resonance imaging (fMRI) to study brain activity since levels of deoxyhemoglobin are indirectly related to local neuronal activity through neurovascular coupling mechanisms. However, the BOLD signal is severely affected by physiological processes as well as motion. Due to this, several noise correction techniques have been developed to correct for the associated confounds. The present study focuses on cardiac pulsatility fMRI confounds, aiming to refine model-based techniques that utilize the photoplethysmograph (PPG) signal. Specifically, we propose a new technique based on convolution filtering, termed cardiac pulsatility model (CPM) and compare its performance with the cardiac-related RETROICOR (Card-RETROICOR), which is a technique commonly used to model fMRI fluctuations due to cardiac pulsatility. Further, we investigate whether variations in the amplitude of the PPG pulses (PPG-Amp) covary with variations in amplitude of pulse-related fMRI fluctuations, as well as with the systemic low frequency oscillations (SLFOs) component of the fMRI global signal (GS - defined as the mean signal across all gray matter voxels). Capitalizing on 3T fMRI data from the Human Connectome Project, CPM was found to explain a significantly larger fraction of the fMRI signal variance compared to Card-RETROICOR, particularly for subjects with larger heart rate variability during the scan. The amplitude of the fMRI pulse-related fluctuations did not covary with PPG-Amp; however, PPG-Amp explained significant variance in the GS that was not attributed to variations in heart rate or breathing patterns. Our results suggest that the proposed approach can model high-frequency fluctuations due to pulsation as well as low-frequency physiological fluctuations more accurately compared to model-based techniques commonly employed in fMRI studies.


title: Deep Learning Classification of Lipid Droplets in Quantitative Phase Images

abstract:
We report the application of supervised machine learning to the automated classification of lipid droplets in label-free, quantitative-phase images. By comparing various machine learning methods commonly used in biomedical imaging and remote sensing, we found convolutional neural networks to outperform others, both quantitatively and qualitatively. We describe our imaging approach, all implemented machine learning methods, and their performance with respect to computational efficiency, required training resources, and relative method performance measured across multiple metrics. Overall, our results indicate that quantitative-phase imaging coupled to machine learning enables accurate lipid droplet classification in single living cells. As such, the present paradigm presents an excellent alternative of the more common fluorescent and Raman imaging modalities by enabling label-free, ultra-low phototoxicity, and deeper insight into the thermodynamics of metabolism of single cells.

Author SummaryRecently, quantitative-phase imaging (QPI) has demonstrated the ability to elucidate novel parameters of cellular physiology and metabolism without the need for fluorescent staining. Here, we apply label-free, low photo-toxicity QPI to yeast cells in order to identify lipid droplets (LDs), an important organelle with key implications in human health and biofuel development. Because QPI yields low specificity, we explore the use of modern machine learning methods to rapidly identify intracellular LDs with high discriminatory power and accuracy. In recent years, machine learning has demonstrated exceptional abilities to recognize and segment objects in biomedical imaging, remote sensing, and other areas. Trained machine learning classifiers can be combined with QPI within high-throughput analysis pipelines, allowing for efficient and accurate identification and quantification of cellular components. Non-invasive, accurate and high-throughput classification of these organelles will accelerate research and improve our understanding of cellular functions with beneficial applications in biofuels, biomedicine, and more.


title: Motor Protein MYO1C is Critical for Photoreceptor Opsin Trafficking and Vision

abstract: Unconventional myosins linked to deafness are also proposed to play a role in retinal cell physiology. However, their direct role in photoreceptor function remains unclear. We demonstrate that systemic loss of the unconventional myosin MYO1C in mice specifically affected opsin trafficking, leading to loss of visual function. Electroretinogram analysis of Myo1c knockout (Myo1c-KO) mice showed a progressive loss of photoreceptor function. Immunohistochemistry and binding assays demonstrated MYO1C localization to photoreceptor inner and outer segments (OS) and identified a direct interaction of rhodopsin with the MYO1C cargo domain. In Myo1c-KO retinas, rhodopsin mislocalized to rod inner segments (IS) and cell bodies, while cone opsins in OS showed punctate staining. In aged mice, the histological and ultrastructural examination of the phenotype of Myo1c-KO retinas showed progressively shorter photoreceptor OS. These results demonstrate that MYO1C is critical for opsin trafficking to the photoreceptor OS and for normal visual function.

category: cell biology


title: Motor Protein MYO1C is Critical for Photoreceptor Opsin Trafficking and Visual Function


title: Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B.

abstract: Antibiotic resistance is a growing problem, but bacteria can evade antibiotic treatment via tolerance and persistence. Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. Hence, persistence is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. Here, we used the synthetically developed minimal cell Mycoplasma mycoides JCVI-Syn3B to examine essential mechanisms of antibiotic survival. The minimal cell contains only 473 genes, and most genes are essential. Its reduced complexity helps to reveal hidden phenomenon and fundamental biological principles can be explored because of less redundancy and feedback between systems compared to natural cells. We found that Syn3B evolves antibiotic resistance to different types of antibiotics expeditiously. The minimal cell also tolerates and persists against multiple antibiotics. It contains a few already identified persister-related genes, although lacking many systems previously linked to persistence (e.g. toxin-antitoxin systems, ribosome hibernation genes, etc.).

category: synthetic biology


title: Comprehensive characterization of internal and cuticle surface microbiota of laboratory-reared F1 Anopheles albimanus originating from different sites

abstract:
BackgroundResearch on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-collected mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings.

MethodsUsing high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1 progeny of wild-caught adult Anopheles albimanus from four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed.

ResultsResults showed geographical heterogeneity in both F1 larval internal (p=0.001; pseudo-F = 9.53) and cuticle surface (p=0.001; pseudo-F = 8.51) microbiota, and only F1 adult cuticle surface (p=0.001; pseudo-F = 4.5) microbiota, with a more homogenous adult internal microbiota (p=0.12; pseudo-F = 1.6) across collection sites. Overall, ASVs assigned to Leucobacter, Thorsellia, Chryseobacterium and uncharacterized Enterobacteriaceae, dominated F1 larval internal microbiota, while Acidovorax, Paucibacter, and uncharacterized Comamonadaceae, dominated the larval cuticle surface. F1 adults comprised a less diverse microbiota compared to larvae, with ASVs assigned to the genus Asaia dominating both internal and cuticle surface microbiota, and constituting at least 70% of taxa in each microbial niche.

ConclusionsThese results suggest that location-specific heterogeneity in filed mosquito microbiota can be transferred to F1 progeny under normal laboratory conditions, but this may not last beyond the F1 larval stage without adjustments to maintain field-derived microbiota. Our findings provide the first comprehensive characterization of laboratory-colonized F1 An. albimanus progeny from field-derived mothers. This provides a background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.


title: Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs

abstract: Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.

category: biochemistry


title: Ecological differentiation and incipient speciation in the fungal pathogen causing rice blast

abstract: Many invasive fungal species coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. Here, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus (Pyricularia oryzae) covering a broad geographical range. We showed that the four lineages of P. oryzae were found in areas with different prevailing environmental conditions and types of rice grown, indicating niche separation. Pathogenicity tests revealed that specialization to rice subspecies contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong barriers to gene flow between these lineages. Our results demonstrate that the spread of a pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct invasive lineages.


title: Ecological Differentiation Among Globally Distributed Lineages of the Rice Blast Fungus Pyricularia oryzae


title: Neuronal activity in sensory cortex predicts the specificity of learning.

abstract: Learning to avoid dangerous signals while preserving normal responses to safe stimuli is essential for everyday behavior and survival. Fear learning has a high level of inter-subject variability. Following identical experiences, subjects exhibit fear specificities ranging from high (specializing fear to only the dangerous stimulus) to low (generalizing fear to safe stimuli). Pathological fear generalization underlies emotional disorders, such as post-traumatic stress disorder. The neuronal basis of fear specificity remains unknown. Here, we identified the neuronal code that underlies inter-subject variability in fear specificity using longitudinal imaging of neuronal activity before and after differential fear conditioning in the auditory cortex of mice. Neuronal activity prior to, but not after learning predicted the level of specificity following fear conditioning across subjects. Stimulus representation in auditory cortex was reorganized following conditioning. However, the reorganized neuronal activity did not relate to the specificity of learning. These results present a novel neuronal code that determines individual patterns in learning.


title: Sleep and circadian phenotype in people without cone-mediated vision

abstract:
BackgroundLight exposure entrains the circadian clock through the intrinsically photosensitive retinal ganglion cells, which sense light in addition to the cones and rods. In congenital achromatopsia (ACHM; prevalence 1:30-50,000), the cone system is non-functional, resulting in severe light avoidance and photophobia at daytime light levels. How this condition affects circadian and neuroendocrine responses to light is not known.

MethodsIn genetically confirmed ACHM patients (n=7; age 30-72 years; 6 women, 1 male), we examined survey-assessed sleep/circadian phenotype (PSQI, ESS, MEQ, MCTQ), self-reported visual function (NEI-VFQ-25), sensitivity to light (VLSQ-8) and use of spectral filters that modify chronic light exposure. In all but one patient, we measured rest-activity cycles using actigraphy over 3 weeks and measured the melatonin phase angle of entrainment using the dim-light melatonin onset (DLMO).

ResultsACHM patients experience a severely attenuated light-dark cycle due to severe light sensitivity and habitual use of filters to reduce retinal illumination. In aggregate, both MEQ and MCTQ indicated a tendency to late chronotype. We found regular rest-activity patterns in all patients and normal phase angles of entrainment in participants with a measurable DLMO.

ConclusionsOur results reveal that a functional cone system and exposure to daytime light intensities are not necessary for regular behavioural and hormonal entrainment, even when survey-assessed sleep and circadian phenotype indicated a tendency for a late chronotype and sleep problems in our ACHM cohort. Our results can be explained by an adaptation mechanism in circadian photoreception which adjusts to the range of habitual light exposures.


title: FIRM: Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets

abstract: Single-cell RNA-sequencing (scRNA-seq) is being used extensively to measure the mRNA expression of individual cells from deconstructed tissues, organs, and even entire organisms to generate cell atlas references, leading to discoveries of novel cell types and deeper insight into biological trajectories. These massive datasets are usually collected from many samples using different scRNA-seq technology platforms, including the popular SMART-Seq2 (SS2) and 10X platforms. Inherent heterogeneities between platforms, tissues, and other batch effects makes scRNA-seq data difficult to compare and integrate, especially in large-scale cell atlas efforts; yet, accurate integration is essential for gaining deeper insights into cell biology. Through comprehensive data exploration, we found that accurate integration is often hampered by differences in cell-type compositions. Herein we describe FIRM, an algorithm that addresses this problem and achieves efficient and accurate integration of heterogeneous scRNA-seq datasets across multiple tissue types, platforms, and experimental batches. We applied FIRM to numerous large-scale scRNA-seq datasets from mouse, mouse lemur, and human, comparing its performance in dataset integration with other state-of-the-art methods. FIRM-integrated datasets show accurate mixing of shared cell type identities and superior preservation of original structure without overcorrection, generating robust integrated datasets for downstream exploration and analysis. It is also a facile way to transfer cell type labels and annotations from one dataset to another, making it a reliable and versatile tool for scRNA-seq analysis, especially for cell atlas data integration.


title: An Hourglass Circuit Motif Transforms a Motor Program via Subcellularly Localized Muscle Calcium Signaling and Contraction

abstract: Neural control of muscle function is fundamental to animal behavior. Many muscles can generate multiple distinct behaviors. Nonetheless, individual muscle cells are generally regarded as the smallest units of motor control. We report that muscle cells can alter behavior by contracting subcellularly. We previously discovered that noxious tastes reverse the net flow of particles through the C. elegans pharynx, a neuromuscular pump, resulting in spitting. We now show that spitting results from the subcellular contraction of the anterior region of the pm3 muscle cell. Subcellularly localized calcium increases accompany this contraction. Spitting is controlled by an "hourglass" circuit motif: parallel neural pathways converge onto a single motor neuron that differentially controls multiple muscles and the critical subcellular muscle compartment. We conclude that subcellular muscle units enable modulatory motor control and propose that subcellular muscle contraction is a fundamental mechanism by which neurons can reshape behavior.


title: How antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK

abstract: Major facilitator superfamily (MFS) proteins operate via three different mechanisms: uniport, symport, and antiport. Despite extensive investigations, molecular understanding of antiporters is less advanced than other transporters due to the complex coupling between two substrates and the lack of distinct structures. We employ extensive (~300 s) all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial [Formula] antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. Conformational transition only occurs in the presence of substrate, which weakens the electrostatic repulsion and stabilizes the transporter by ~1.5 {+/-} 0.1 kcal/mol. Furthermore, we propose a state-dependent substrate exchange model, in which the relative spacing between the paired basic residues determines whether [Formula] and [Formula] bind simultaneously or sequentially. Overall, this work presents a general working model for the antiport mechanism within MFS family.


title: Temporal evolution and adaptation of SARS-COV 2 codon usage

abstract:
The outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe.

In this study, we compared 134,905 SARS-CoV-2 genomes isolated from all affected countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan, China to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns of SARS-CoV-2 genes encoding the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp). The polyproteins ORF1a and ORF1b were examined separately.

We found that SARS-CoV-2 tends to diverge over time by accumulating mutations on its genome and, specifically, on the sequences encoding proteins N and S. Interestingly, different patterns of codon usage were observed among these genes. Genes S and N tend to use a narrower set of synonymous codons that are better optimized to the human host. Conversely, genes E and M consistently use the broader set of synonymous codons, which does not vary in respect to the reference genome. CAI and SiD time evolutions show a tendency to decrease that emerge for most genes. Forsdyke plots are used to study the nature of mutations and they show a rapid evolutionary divergence of each gene, due to the low values of x-intercepets.

category: genomics


title: Resuscitation of the microbial seed bank alters plant-soil interactions

abstract: While microorganisms are recognized for driving belowground processes that influence the productivity and fitness of plant populations, the vast majority of bacteria and fungi in soil belong to a seed bank consisting of dormant individuals. Still, plant performance may be affected by microbial dormancy through its effects on the activity, abundance, and diversity of soil microorganisms. To test how microbial seed banks influence plant-soil interactions, we purified recombinant resuscitation promoting factor (Rpf), a bacterial protein that terminates dormancy. Then, in a factorially designed experiment, we applied the Rpf to soil containing field mustard (Brassica rapa), an agronomically important plant species. Plant biomass was ~33 % lower in the Rpf treatment compared to plants grown with an unmanipulated microbial seed bank. In addition, Rpf reduced soil respiration, decreased bacterial abundance, and increased fungal abundance. These effects of Rpf on plant performance were accompanied by shifts in bacterial community composition, which may have diluted mutualists or resuscitated pathogens. Our findings suggest that changes in microbial seed banks may influence the magnitude and direction of plant-soil feedbacks in ways that affect above- and below-ground biodiversity and function.


title: Purification of age-distinct insulin secretory granules through antigen restriction

abstract: Endocrine cells employ regulated exocytosis of secretory granules to secrete hormones and neurotransmitters. The competence of secretory granules for exocytosis depends on spatio-temporal variables such as proximity to the plasma membrane and age, with newly-generated granules being preferentially released. Despite recent advances, we still lack a comprehensive view about the molecular composition of insulin granules and how this may change over the lifetime of the organelles. Here we report a strategy for the purification of insulin secretory granules of distinct age from insulinoma INS-1 cells. Tagging the granule-resident protein phogrin with a cleavable CLIP tag, we obtained intact fractions of age-distinct granules for proteomic and lipidomic analyses. We find that the lipid composition changes over time along with the physical properties of the membrane.


title: Analyzing hCov Genome Sequences: Predicting Virulence and Mutation

abstract:
BackgroundCovid-19 pandemic, caused by the SARS-CoV-2 genome sequence of coronavirus, has affected millions of people all over the world and taken thousands of lives. It is of utmost importance that the character of this deadly virus be studied and its nature be analyzed.

MethodsWe present here an analysis pipeline comprising a classification exercise to identify the virulence of the genome sequences and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques.

ResultsWe have classified the SARS-CoV-2 genome sequences with high accuracy and predicted the mutations in the sites of Interest.

ConclusionsIn a nutshell, we have prepared an analysis pipeline for hCov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data.

category: bioinformatics


title: Schizosaccharomyces pombe KAT5 contributes to resection and repair of a DNA double strand break

abstract: Chromatin remodeling is essential for effective repair of a DNA double strand break. KAT5 (S. pombe Mst1, human TIP60) is a MYST family histone acetyltransferase conserved from yeast to humans that coordinates various DNA damage response activities at a DNA double strand break (DSB), including histone remodeling and activation of the DNA damage checkpoint. In S. pombe, mutations in mst1+ causes sensitivity to DNA damaging drugs. Here we show that Mst1 is recruited to DSBs. Mutation of mst1+ disrupts recruitment of repair proteins and delays resection. These defects are partially rescued by deletion of pku70, which has been previously shown to antagonize repair by homologous recombination. These phenotypes of mst1 are similar to pht1-4KR, a non-acetylatable form of histone variant H2A.Z, which has been proposed to affect resection. Our data suggest that Mst1 functions to direct repair of DSBs towards homologous recombination pathways by modulating resection at the double strand break.