title: PMCE: efficient inference of expressive models of cancer evolution with high prognostic power

abstract:
MotivationDriver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive models of cancer evolution. Yet, available methods cannot infer logical formulas connecting events to represent alternative evolutionary routes or convergent evolution.

ResultsWe introduce PMCE, an expressive framework that leverages mutational profiles from crosssectional sequencing data to infer probabilistic graphical models of cancer evolution including arbitrary logical formulas, and which outperforms the state-of-the-art in terms of accuracy and robustness to noise, on simulations.

The application of PMCE to 7866 samples from the TCGA database allows us to identify a highly significant correlation between the predicted evolutionary paths and the overall survival in 7 tumor types, proving that our approach can effectively stratify cancer patients in reliable risk groups.

AvailabilityPMCE is freely available at https://github.com/BIMIB-DISCo/PMCE, in addition to the code to replicate all the analyses presented in the manuscript.

Contactsdaniele.ramazzotti@unimib.it, alex.graudenzi@ibfm.cnr.it.

category: bioinformatics


title: Convergent evolution of primate testis transcriptomes reflects mating strategy

abstract: In independent mammalian lineages where females mate with multiple males (multi-male mating strategies), males have evolved larger testicles relative to those lineages where females mate with fewer males (single-male mating strategies). Here we study published bulk testis transcriptomes from humans, chimpanzees, gorillas and rhesus macaques, as well as mice and rats. Employing a formal model of adaptive evolution, we find that testis transcriptomes have also evolved convergently, reflecting each species mating strategy. Using deconvolution, we infer that testis transcriptome divergence patterns largely reflect convergent shifts in tissue cell type composition. However, we also identify modest amounts of convergent evolution at the cell-autonomous level by analyzing cell-type specific transcriptome data from spermatids and spermatocytes. We further show that in the single-male mating primates, human and gorilla, testis transcriptome profiles are paedomorphic relative to those of multi-male primates, chimpanzee and macaque, suggesting that shifts in timing or rate of testis development could underlie convergent changes in testis mass, histology, and transcriptomes.

category: evolutionary biology


title: A max-margin model for predicting residue-base contacts in protein-RNA interactions

abstract: Protein-RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein-RNA structures, various computational methods have been developed to predict PRIs. However, most of these methods focus on predicting only RNA-binding regions in proteins or only protein-binding motifs in RNA. Methods for predicting entire residue-base contacts in PRIs have not yet achieved sufficient accuracy. Furthermore, some of these methods require the identification of 3D structures or homologous sequences, which are not available for all protein and RNA sequences. Here, we propose a prediction method for predicting residue-base contacts between proteins and RNAs using only sequence information and structural information predicted from sequences. The method can be applied to any protein-RNA pair, even when rich information such as its 3D structure, is not available. In this method, residue-base contact prediction is formalized as an integer programming problem. We predict a residue-base contact map that maximizes a scoring function based on sequence-based features such as k-mers of sequences and the predicted secondary structure. The scoring function is trained using a max-margin framework from known PRIs with 3D structures. To verify our method, we conducted several computational experiments. The results suggest that our method, which is based on only sequence information, is comparable with RNA-binding residue prediction methods based on known binding data.


title: Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system

abstract: Whole-cell biosensors hold potential in a variety of industrial, medical and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system. Here we report on the construction of a range of novel biosensors that are sensitive to acetoacetate, a molecule that plays a number of roles in human health and biology. These biosensors are based on the AtoSC two-component system. An ODE model to describe the action of the AtoSC two-component system was developed and sensitivity analysis of this model used to help inform biosensor design. The final collection of biosensors constructed displayed a range of switching behaviours, at physiologically relevant acetoacetate concentrations and can operate in several Escherichia coli host strains. It is envisaged that these biosensor strains will offer an alternative to currently available commercial strip tests and, in future, may be adopted for more complex in vivo or industrial monitoring applications.

category: synthetic biology


title: Association of NQO1 C609T (Pro187Ser) with risk of Oral Submucous Fibrosis in Eastern Indian population

abstract: Oral submucous fibrosis (OSF) is a debilitating disease mainly attributed to chewing areca nut with a 7.4-13% malignant transformation rate. Present study explores the role of NADPH quinone oxidoreductase 1 (NQO1) C609T (Pro187Ser) polymorphism in susceptibility to OSF among habitual areca nut chewers in an eastern Indian population. Overall, about 18% of the total OSF cases were detected carrying minor TT allele (Ser/Ser) p=0.026. When categorized by age, both CT (Pro/Ser) and TT (Ser/Ser) alleles were significantly higher (p= 0.003 & 0.004 respectively) in cases above 40years of age. NQO1 protein was 42% reduced in buccal tissues of heterozygous (Pro/Ser) carriers, whereas a 70% reduction was observed in TT (Ser/Ser) OSF cases. Our study suggests that the NQO1 C609T polymorphism confers increased risk for OSF in habitual chewers.

category: genetics


title: Fast gene set enrichment analysis

abstract:
Gene set enrichment analysis (GSEA) is an ubiquitously used tool for evaluating pathway enrichment in transcriptional data. Typical experimental design consists in comparing two conditions with several replicates using a differential gene expression test followed by preranked GSEA performed against a collection of hundreds and thousands of pathways. However, the reference implementation of this method cannot accurately estimate small P-values, which significantly limits its sensitivity due to multiple hypotheses correction procedure.

Here we present FGSEA (Fast Gene Set Enrichment Analysis) method that is able to estimate arbitrarily low GSEA P-values with a high accuracy in a matter of minutes or even seconds. To confirm the accuracy of the method, we also developed an exact algorithm for GSEA P-values calculation for integer gene-level statistics. Using the exact algorithm as a reference we show that FGSEA is able to routinely estimate P-values up to 10-100 with a small and predictable estimation error. We systematically evaluate FGSEA on a collection of 605 datasets and show that FGSEA recovers much more statistically significant pathways compared to other implementations.

FGSEA is open source and available as an R package in Bioconductor (http://bioconductor.org/packages/fgsea/) and on GitHub (https://github.com/ctlab/fgsea/).


title: Immunoecology of species with alternative reproductive tactics and strategies

abstract: Alternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecological, developmental, behavioural, life-history, and physiological profile that shifts the balance between reproduction and self-maintenance, one aspect being immunity. Immunoecological work on species with ARTS, which is the topic of this review, is particularly interesting because the alternative morphs make it possible to separate the effects of sex, per se, from other factors that in other species are inextricably linked with sex. We first summarize the evolution, development and maintenance of ARTS. We then review immunoecological hypotheses relevant to species with ARTS, dividing them into physiological, life-history, and ecological hypotheses. In context of these hypotheses, we critically review in detail all immunoecological studies we could find on species with ARTS. Several interesting patterns emerge. Oddly, there is a paucity of studies on insects, despite the many benefits that arise from working with insects: larger sample sizes, simple immune systems, and countless forms of alternative reproductive strategies and tactics. Of all the hypotheses considered, the immunocompetence handicap hypothesis has generated the greatest amount of work, but not necessarily the greatest level of understanding. Unfortunately, it is often used as a general guiding principle rather than a source of explicitly articulated predictions. Other hypotheses are usually considered a posteriori, but it is perhaps time that they take centre stage. Whereas blanket concepts such as "immunocompetence" and "androgens" might useful to develop a rationale, predictions need to be far more explicitly articulated. Integration so far has been a one-way street, with ecologists delving deeper into physiology, seemingly at the cost of ignoring their organisms evolutionary history and ecology. One possible useful framework is to divide ecological and evolutionary factors affecting immunity into those that stimulate the immune system, and those that depress it. Finally, the contributions of genomics to ecology are being increasingly recognized, including in species with ARTS, but we must ensure that evolutionary and ecological hypotheses drive the effort, as there is no grandeur in the strict reductionist view of life.


title: Frameshifts and wild-type protein sequences are always highly similar because the genetic code and genomes were optimized for frameshift tolerance

abstract: Frameshift protein sequences encoded by alternative reading frames of coding genes have been considered meaningless, and frameshift mutations have been considered of little importance for the molecular evolution of coding genes and proteins. However, functional frameshifts have been found widely existing. It was puzzling how a frameshift protein kept its structure and functionality while its amino-acid sequence was changed substantially. Here we show that frame similarities between frameshifts and wild types are higher than random similarities and are defined at the genetic code, gene, and genome levels. In the standard genetic code, frameshift codon substitutions are more conservative than random substitutions. The frameshift tolerability of the standard genetic code ranks in the top 2.0-3.5% of alternative genetic codes, showing that the genetic code is nearly optimal for frameshift tolerance. Furthermore, frameshift-resistant codons (codon pairs) appear more frequently than expected in many genes and certain genomes, showing that the frameshift optimality is reflected not only in the genetic code but more importantly, in its allowance of further optimizing the frameshift tolerance of a particular gene or genome, which shed light on the role of frameshift mutations in molecular and genomic evolution.


title: Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance


title: Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium

abstract:
Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.

Author summaryWe establish a theoretical framework to model 3-locus admixture linkage disequilibrium of an admixed population taking into account the effects of genetic drift, migration and recombination. The theory is used to develop a method for estimating the times of multiple admixtures events. We demonstrate the accuracy of the method on simulated data and we apply it to previously published data from Mexican and Columbian populations to explore the complex history of American populations in the post-Columbian period.


title: Revisiting the effect of red on competition in humans

abstract: Bright red coloration is a signal of male competitive ability in animal species across a range of taxa, including non-human primates. Does the effect of red on competition extend to humans? A landmark study in evolutionary psychology established such an effect through analysis of data for four combat sports at the 2004 Athens Olympics [1]. Here we show that the results do not replicate in an equivalent, independent dataset for the 2008 Beijing Olympics, and that there is substantial variation in the fraction of wins by red across sports in both years. We uncover a number of shortcomings with the research design, analysis, and interpretation underlying the original results. For example, the variation observed in the data may reflect bias towards wins by one color over the other, linked to specific features of the tournament structure for the sports analysed. Reanalysis of the data to address these shortcomings indicates that there is no evidence for an effect of red on the outcomes of Olympic combat sports. Our results refute past claims based on analysis of this system, challenging the related notion that any effect of red in human competition is an evolved response shaped by sexual selection.


title: Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions

abstract:
Part 1Development and calibration of suitably accurate functional assays for BRCA1 RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests of BRCA1 and BRCA2, plus data from the limited number of already classified BRCA1 RING domain missense substitutions, we used logistic regression and related techniques to evaluate three BRCA1 RING domain assays. These were recently described high throughput yeast 2-hybrid and E3 ubiquitin ligase assays, plus a newly developed mammalian 2-hybrid assay. While there were concerns about the accuracy of the yeast 2-hybrid assay and the indirect nature of the ubiquitin ligase assay, the mammalian 2-hybrid assay had excellent correlation with existing missense substitution classifications. After calibration, this assay contributed to classification of one newly reported BRCA1 missense substitution. In principal, the mammalian 2-hybrid assay could be converted to a high-throughput format that would likely retain suitable accuracy.

Part 2How does one achieve clinically applicable classification of the vast majority of all possible sequence variants in disease susceptibility genes? BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid (M2H) assay. Downstream of the M2H laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that about 20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of about 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 47 with concordant computational and functional assay evidence in favor of pathogenicity; these are particularly likely to be classified as Likely Pathogenic once human observational data become available.


title: Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software

abstract:
BackgroundComputational biology provides widely used and powerful software tools for testing and making inferences about biological data. In the face of rapidly increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We are have studied these trade-offs using the results of a large number of independent software benchmarks, and evaluated whether external factors are indicative of accurate software.

MethodWe have extracted accuracy and speed ranks from independent benchmarks of different bioinformatic software tools, and evaluated whether the speed, author reputation, journal impact, recency and developer efforts are indicative of accuracy.

ResultsWe found that software speed, author reputation, journal impact, number of citations and age are all unreliable predictors of software accuracy. This is unfortunate because citations, author and journal reputation are frequently cited reasons for selecting software tools. However, GitHub-derived records and high version numbers show that the accurate bioinformatic software tools are generally the product of many improvements over time, often from multiple developers.

DiscussionWe also find that the field of bioinformatics has a large excess of slow and inaccurate software tools, and this is consistent across many sub-disciplines. Meanwhile, there are few tools that are middle-of-road in terms of accuracy and speed trade-offs. We hypothesise that a form of publication-bias influences the publication and development of bioinformatic software. In other words, software that is intermediate in terms of both speed and accuracy may be difficult to publish - possibly due to author, editor and reviewer practices. This leaves an unfortunate hole in the literature as the ideal tools may fall into this gap. For example, high accuracy tools are not always useful if years of CPU time are required, while high speed is not useful if the results are also inaccurate.


title: Correcting Chimeric Crosstalk in Single Cell RNA-seq Experiments

abstract: As part of the process of preparing sequencing libraries that include unique molecular identifiers (UMIs) such as many single cell RNA-seq (scRNA-seq) libraries, a diverse template must be amplified. During amplification, spurious chimeric molecules can be formed between molecules originating in different cells. While several computational and experimental strategies have been suggested to mitigate the impact of chimeric molecules, suitable approaches for scRNA-seq experiments do not exist. We demonstrate that chimeras become increasingly problematic as samples are sequenced deeply and propose both supervised and unsupervised computational solutions. These solutions are validated in the context of a deeply sequenced species mixing experiment, and, orthogonally, using replicate PCR amplifications of the same scRNA-seq library. Our code is publicly available at https://github.com/asncd/schimera.


title: The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

abstract:
Predicting a multicellular organisms phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.

This work updates the first biorXiv version, February 2017, https://doi.org/10.1101/105437, with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.

category: plant biology


title: Aperiodic neural activity is a better predictor of schizophrenia than neural oscillations

abstract:
Diagnosis and symptom severity in schizophrenia is associated with irregularities across neural oscillatory frequency bands, including theta, alpha, beta, and gamma. However, electroencephalographic signals consist of both periodic and aperiodic background activity, characterized by the (1/f) slope of the power spectrum. We compared traditional band-limited periodic oscillatory activity to aperiodic activity, in schizophrenia participants and healthy controls, during an attention task. Classification analysis revealed that the change in slope of the power spectrum better predicted group status than traditional oscillatory power. It even outperformed the predictions made using participants own behavioral performance. Additionally, the differences in slope were highly consistent as they were observed across all electrodes. In sum, the aperiodic slope appears to be a more accurate, consistent, and robust metric to differentiate schizophrenic patients from healthy controls.

Significance statementUnderstanding the neurobiological origins of schizophrenia and identifying reliable and consistent biomarkers are of critical importance in improving treatment of that disease. Numerous studies have reported disruptions to neural oscillations in schizophrenia patients. This has, in part, led to schizophrenia being characterized as a disease of disrupted neural coordination, reflected by changes in frequency band power. We report however that changes in aperiodic background noise (i.e., spectral slope) can also predict clinical status. Unlike band-limited power though, the aperiodic slope predicts status better than participants own behavioral performance. Furthermore, it is a consistent predictor across all electrodes. Alterations in aperiodic noise are consistent with well-established inhibitory neuron dysfunctions associated with schizophrenia, allowing for a direct link between noninvasive EEG and chronic, widespread, neurobiological deficits.

category: neuroscience


title: Population Temporal Structure Supplements The Rate Code During Sensorimotor Transformations

abstract:
Sensorimotor transformations are mediated by premotor brain networks where individual neurons represent sensory, cognitive, and movement-related information. Such multiplexing poses a conundrum - how does a decoder know precisely when to initiate a movement if its inputs are active at times when a movement is not desired (e.g., in response to sensory stimulation)? Here, we propose a novel hypothesis: movement is triggered not only by an increase in firing rate, but critically by a reliable temporal pattern in the population response. Laminar recordings in the superior colliculus (SC), a midbrain region that plays an essential role in orienting eye movements, indicate that the temporal structure across neurons is a factor governing movement initiation. Specifically, using a measure that captures the fidelity of the population code - here called temporal stability - we show that the temporal structure fluctuates during the visual response but becomes increasingly stable during the movement command, even when the mean population activity is similar between the two epochs. Analyses of pseudo-populations in SC and cortical frontal eye fields (FEF) corroborated this model. We also used spatiotemporally patterned microstimulation to causally test the contribution of population temporal stability to movement initiation and found that stable stimulation patterns were more likely to evoke a movement, even when other features of the patterns such as mean pulse rates and population state subspaces were matched. Finally, a spiking neuron model was able to discriminate between stable and unstable input patterns, providing a putative biophysical mechanism for decoding temporal structure. These findings offer an alternative perspective on the relationship between movement preparation and generation by situating the correlates of movement initiation in the temporal features of activity in shared neural substrates. They also suggest a need to look beyond the instantaneous rate code at the single neuron or population level and consider the effects of short-term population history on neuronal communication and behaviour.

SummarySensorimotor transformations are mediated by premotor brain networks where individual neurons represent sensory, cognitive, and movement-related information. Such multiplexing poses a conundrum - how does a decoder know precisely when to initiate a movement if its inputs are active at times when a movement is not desired (e.g., in response to sensory stimulation)? Here, we propose a novel hypothesis: movement is triggered not only by an increase in firing rate, but critically by a reliable temporal pattern in the population response. Laminar recordings in the macaque superior colliculus (SC), a midbrain hub of orienting control, and pseudo-population analyses in SC and cortical frontal eye fields (FEF) corroborated this hypothesis. Importantly, we used spatiotemporally patterned microstimulation to causally verify the importance of temporal structure and demonstrate its role in gating movement initiation. We also offer a spiking neuron model with dendritic integration as a putative mechanism to decode this temporal information. These findings offer new insights into the long-standing debate on movement generation and highlight the importance of short-term population history in neuronal communication and behavior.


title: Sexual dimorphism and plasticity in wing shape in three Diptera

abstract:
The ability of powered flight in insects facilitated their great evolutionary success allowing them to occupy various ecological niches. Beyond this primary task, wings are often involved in various premating behaviors, such as the generation of courtship songs and the initiation of mating in flight. These specific functions imply special adaptations of wing morphology, as well as sex-specific wing morphologies. Although wing morphology has been extensively studied in Drosophila melanogaster, a comprehensive understa nding of sexual wing shape dimorphisms and developmental plasticity is missing for other Diptera. Therefore, we raised flies of the three Diptera species Drosophila melanogaster, Ceratitis capitata and Musca domestica at different environmental conditions and applied geometric morphometrics to analyze wing shape. Our data showed extensive interspecific differences in wing shape, as well as a clear sexual wing shape dimorphism in all three species. We revealed an impact of different rearing temperatures wing shape in all three species, which was mostly explained by plasticity in wing size in D. melanogaster. Rearing densities had significant effects on allometric wing shape in D. melanogaster, while no obvious effects were observed for the other two species. Additionally, we do not find evidence for sex-specific response to different rearing conditions in all three species. We determined species-specific and common trends in shape alterations, and we hypothesize developmental and functional implications of our data.

Contribution to the Field StatementThe size and shape of organisms and organs must be tightly controlled during development to ensure proper functionality. However, morphological traits vary considerably in nature contributing to phenotypic diversity. Such variation can be the result of evolutionary adaptations as well as plasticity for example as reaction to changing environmental conditions during development. It is therefore a major aim in Biology to unravel the processes that control differences in adult morphology. Insect wings are excellent models to study how organ size and shape evolves because they facilitate basic tasks such as mating and feeding. Accordingly, a tremendous variety of wings sizes and shapes evolved in nature. Additionally, plasticity in wing morphology in response to different rearing conditions has been observed in many insects contributing to phenotypic diversity. In this work we applied Geometric Morphometrics to study wing shape in the three Diptera species: the Mediterranean fruit fly Ceratitis capitata, the Vinegar fly Drosophila melanogaster and the housefly Musca domestica. Flies were raised in different temperature and density regimes that allowed us to study the effects of these environmental factors on wing shape. Additionally, in accordance with different mating behaviors of these flies, we observed a clear sexual shape dimorphism in all three species. Since the three studied species represent serious pests and disease vectors, our findings may contribute to existing and future monitoring efforts.

category: zoology


title: Laser-free super-resolution microscopy

abstract: We report that high-density single-molecule super-resolution microscopy can be achieved with a conventional epifluorescence microscope setup and a Mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM), is an extension of single molecule localisation microscopy (SMLM) techniques and allows single molecules to be switched on and off (a phenomenon termed as "blinking"), detected and localised. The use of a short burst of deep blue excitation (350-380 nm) can be further used to reactivate the blinking, once the blinking process has slowed or stopped. A resolution of 90 nm is achieved on test specimens (mouse and amphibian meiotic chromosomes). Finally, we demonstrate that STED and LFSM can be performed on the same biological sample using a simple commercial mounting medium. It is hoped that this type of correlative imaging will provide a basis for a further enhanced resolution.

category: biophysics


title: The Effects of Central Nervous System Stimulants on Drosophila melanogaster Reproduction

abstract: Stimulant drugs are used everyday by people around the world. The effect stimulants have on developing human fetuses is widely unknown. The fruit fly Drosophila melanogaster has become a valuable system to model the complex effects and properties of drugs in mammals. In this study, Drosophila is used to analyze the effects of stimulant exposure on reproduction to determine if stimulants cause a significant decrease in the number of offspring produced by parent generations. Caffeine, nicotine, and pseudoephedrine hydrochloride were found to significantly decrease the number of offspring in experimental populations. Further experimentation is necessary to understand the mechanisms underlying these results.

category: developmental biology


title: Proteins with prion-like domains can form viscoelastic condensates that enable membrane remodeling and endocytosis

abstract: Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, S. cerevisiae. These puncta have the hallmarks of biomolecular condensates and enable membrane remodeling to drive actin-independent endocytosis. The puncta, which we refer to as endocytic condensates, form and dissolve reversibly in response to changes in temperature and solution conditions. The condensates are organized around dynamic protein-protein interaction networks, which involve interactions among PLDs with high glutamine contents. The endocytic coat protein Sla1 is at the hub of the protein-protein interaction network. Using active rheology, we indirectly characterized the material properties of endocytic condensates. These experiments show that endocytic condensates are viscoelastic materials and allow us to estimate the interfacial tension between endocytic condensates and their surroundings. We then adapt the physics of contact mechanics, specifically the contact theory of Hertz, to develop a quantitative framework for describing how interfacial tensions among condensates, the membrane, and the cytosol can deform the plasma membrane to enable actin independent endocytosis.

category: cell biology


title: Intestine-to-neuronal signaling alters risk-taking behaviors in food-deprived Caenorhabditis elegans

abstract:
Animals integrate changes in external and internal environments to generate behavior. While neural circuits detecting external cues have been mapped, less is known about how internal states like hunger are integrated into behavioral outputs. We use the nematode C. elegans to decode how changes in internal nutritional status affects chemosensory behaviors. We show that acute food deprivation leads to a reversible decline in repellent, but not attractant, sensitivity. This behavioral change requires two conserved transcription factors MML-1 (Mondo A) and HLH-30 (TFEB), both of which translocate from the intestinal nuclei to the cytoplasm upon food deprivation. Next, we identify insulin-like peptides INS-23 and INS-31 as candidate ligands relaying food-status signals from the intestine to other tissues. Furthermore, we show that ASI chemosensory neurons use the DAF-2 insulin receptor, PI-3 Kinase, and the mTOR complex to integrate these intestine-released peptides. Together, our study shows how internal food status signals are integrated by transcription factors and intestine-neuron signaling to generate flexible behaviors.

Author SummaryWe have all experienced behavioral changes when we are hungry - the pang in our stomach can cause us to behave erratically. In particular, hungry animals, including humans, are known to pursue behaviors that involve higher risk compared to when they are well-fed. Here we explore the molecular details of this behavior in the invertebrate animal model C. elegans. This behavior, termed sensory integration, shows that C. elegans display reduced copper sensitivity when hungry. Copper is toxic and repellant to C. elegans; reduced avoidance indicates that these animals use riskier food search behaviors when they are hungry. Luckily, like us, this behavioral change is reversible upon re-feeding. This hunger-induced behavioral change is not due to increased attraction to food or depletion of fat stores, but rather insulin signaling between the intestine and specific neurons. We use genetic tools, microscopy, and behavioral tests to determine that this risky behavior involves sensation of "lack of food" in the intestine, release of signaling molecules, and engagement with sensory neurons. Our work highlights new and potentially evolutionarily conserved ways in which intestinal cells and neurons communicate leading to largescale behavioral change, providing further support for the importance of the gut-brain-axis.


title: Distinct C4 Sub-Types and C3 Bundle Sheath Isolation In The Paniceae Grasses

abstract: In C4 plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4 acid decarboxylases being used to release CO2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4 species into three biochemical sub-types. However, more recently the notion that C4 species mix and match C4 acid decarboxylases has increased in popularity and, as a consequence, the validity of specific biochemical sub-types has been questioned. Using five species from the grass tribe Paniceae, we show that, while in some species transcripts encoding multiple C4 acid decarboxylases accumulate, in others, transcript abundance and enzyme activity is almost entirely from one decarboxylase. In addition, the development of a bundle sheath isolation procedure for a close C3 species in the Paniceae enables the preliminary exploration of C4 sub-type evolution.


title: The effects of an 8-week mindful eating intervention on anticipatory reward responses in striatum and midbrain

abstract:
Obesity is a highly prevalent disease, usually resulting from chronic overeating. Accumulating evidence suggests that increased neural responses during the anticipation of high-calorie food play an important role in overeating. A promising method for counteracting enhanced food anticipation in overeating might be mindfulness-based interventions (MBIs). However, the neural mechanisms by which MBIs can affect food reward anticipation are unclear. In this randomized, actively controlled study, the primary objective was to investigate the effect of an 8-week mindful eating intervention on reward anticipation. On the neural level, we hypothesized that mindful eating would decrease striatal reward anticipation responses. Additionally, responses in the midbrain - from which the reward pathways originate - were explored. Using functional magnetic resonance imaging (fMRI), we tested 58 healthy participants with a wide body mass index range (BMI: 19-35 kg/m2), motivated to change their eating behavior. During scanning they performed an incentive delay task, measuring neural reward anticipation responses to caloric and monetary cues before and after 8 weeks of mindful eating or educational cooking (active control). Compared with the educational cooking intervention, mindful eating affected neural reward anticipation responses, with relatively reduced caloric versus monetary reward responses. This effect was, however, not seen in the striatum, but only in the midbrain. The secondary objective was to assess temporary and long-lasting (one year follow-up) intervention effects on self-reported eating behavior and anthropometric measures (BMI, waist circumference, waist-to-hip-ratio (WHR)). We did not observe effects of the mindful eating intervention on eating behavior. Instead, the control intervention showed temporary beneficial effects on BMI, waist circumference, and diet quality, but not on WHR or self-reported eating behavior, as well as long-lasting increases in knowledge about healthy eating. These results suggest that an 8-week mindful eating intervention may have decreased the relative salience of food cues by affecting midbrain but not striatal reward responses. However, these exploratory results should be verified in confirmatory research.

The primary and secondary objectives of the study were registered in the Dutch Trial Register (NTR): NL4923 (NTR5025).


title: Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs

abstract:
Transcriptional bursting involves genes rapidly switching between active and inactive states. Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is unknown how acetylated chromatin is dynamically targeted and regulated by chromatin remodelers such as PBAF. Thus, we sought to understand how PBAF targets acetylated chromatin using live-cell single molecule fluorescence microscopy. Our work reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAFs bromodomains impairs targeting, stable engagement and persistent binding on chromatin in hubs. Interestingly, PBAF has a higher probability to stably engage chromatin inside hubs indicating that hubs contain a unique nucleosomal scaffold compared to global chromatin. Dual color imaging of PBAF in hubs near H3.3 or HP1 reveals that PBAF targets both euchromatic and heterochromatic regions with distinct genome binding kinetics that mimic chromatin stability. Removal of PBAFs bromodomains stabilizes H3.3 and HP1 binding within chromatin indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data, suggests that PBAF differentially and dynamically engages a variety of chromatin structures involved in both activation and repression of transcription via bromodomains. Furthermore, PBAFs binding stability on chromatin may reflect the chromatin remodeling potential of different bound chromatin states.

Statement of SignificanceTranscriptional bursting involves a gene rapidly switching between transcriptionally active and inactive states. To regulate transcriptional bursting, chromatin must interchange between euchromatin and heterochromatin to permit or restrict access of transcription factors including RNA Polymerase II to enhancer and gene promoters. However, little is known regarding how chromatin remodelers dynamically read a rapidly changing 4D epigenome. We used live-cell single molecule imaging to characterize the spatiotemporal chromatin binding dynamics of PBAF, a chromatin remodeler that accesses both euchromatin and heterochromatin to regulate transcription. PBAF cycles on and off chromatin hubs in select nuclear regions where it distinctly engages euchromatin and heterochromatin via bromodomains in its BAF180 subunit. Our study provides the framework to understand how the 4D epigenome is regulated.


title: cytoNet: Spatiotemporal Network Analysis of Cell Communities

abstract:
We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNets capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin 4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.

Availability and ImplementationQutubLab.org/how | cytoNet contact: cytoNetProject@gmail.com Brain Initiative Alliance Toolmaker cytoNet site: https://www.braininitiative.org/toolmakers/resources/cytonet/

Author / Lay SummarycytoNet provides an online tool to rapidly characterize relationships between objects within images and video frames. To study complex tissue, cell and subcellular topologies, cytoNet integrates vision science with the mathematical technique of graph theory. This allows the method to simultaneously identify environmental effects on single cells and on network topology. cytoNet has versatile use across neuroscience, stem cell biology and regenerative medicine. cytoNet applications described in this study include: (1) characterizing how sensing pain alters neural circuit activity, (2) quantifying how vascular cells respond to neurotrophic stimuli overexpressed in the brain after injury or exercise, (3) delineating features of fat tissue that may confer resistance to obesity and (4) uncovering structure-function relationships of human stem cells as they transform into neurons.

category: bioengineering


title: Plant genetic effects on microbial hubs impact fitness across field trials

abstract: Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTUs. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.


title: MARS-Net: Deep learning-based segmentation pipeline for profiling cellular morphodynamics from multiple types of live cell microscopy

abstract: Quantitative studies of cellular morphodynamics rely on extracting leading-edge velocity time-series based on accurate cell segmentation from live cell imaging. However, live cell imaging has numerous challenging issues about accurate edge localization. Here, we develop a deep learning-based pipeline, termed MARS-Net (Multiple-microscopy- type-based Accurate and Robust Segmentation Network), that utilizes transfer learning and the datasets from multiple types of microscopy to localize cell edges with high accuracy, allowing quantitative profiling of cellular morphodynamics. For effective training with the datasets from multiple types of live cell microscopy, we integrated the pretrained VGG-19 encoder with U-Net decoder and added dropout layers. Using this structure, we were able to train one neural network model that can accurately segment various live cell movies from phase contrast, spinning disk confocal, and total internal reflection fluorescence microscopes. Intriguingly, MARS-Net produced more accurate edge localization than the neural network models trained with single microscopy type datasets, whereas the standard U-Net could not increase the overall accuracy. We expect that MARS-Net can accelerate the studies of cellular morphodynamics by providing accurate segmentation of challenging live cell images.


title: Histone deacetylase inhibition reduces deleterious cytokine release induced by ingenol stimulation

abstract:
IntroductionLatency reversal agents (LRAs), such as protein kinase C (PKC) agonists, constitute a promising strategy for exposing and eliminating the HIV-1 latent reservoir. PKC agonists activate NF-{kappa}B and, in turn, induce deleterious pro-inflammatory cytokine production. Adjuvant pharmacological agents, such as ruxolitinib, a JAK inhibitor, and rapamycin, an mTOR inhibitor, have previously been combined with LRAs to reduce deleterious pro-inflammatory cytokine secretion without inhibiting HIV-1 viral reactivation in vitro. Histone deacetylase inhibitors (HDACi) are known to dampen pro-inflammatory cytokine secretion in the context of other diseases and can synergize with other LRAs to bring dormant proviruses out of latency. In this study we investigated whether a broad panel of epigenetic modifiers, including HDACi, could effectively dampen PKC-induced pro-inflammatory cytokine secretion during latency reversal.

MethodsWe screened an epigenetic modifier library to identify compounds that reduced intracellular IL-6 production induced by the PKC agonist Ingenol-3,20-dibenzoate. We further tested the most promising epigenetic inhibitor class, HDACi, for their ability to reduce a broad panel of pro-inflammatory cytokines and reactivate latent HIV-1 ex vivo.

ResultsWe identified nine epigenetic modulators that reduced PKC-induced intracellular IL-6. In cells from aviremic individuals living with HIV-1, the HDAC1-3 inhibitor, suberohydroxamic acid (SBHA), reduced secretion of pro-inflammatory cytokines TNF-, IL-5, IL-2r, and IL-17 but did not significantly reactivate latent HIV-1 when used in combination with Ingenol-3,20-dibenzoate.

ConclusionThe addition of SBHA to Ingenol-3,20-dibenzoate reduces deleterious cytokine production during latency reversal but does not induce significant viral reactivation in aviremic donor PBMCs. The ability of SBHA to reduce PKC-induced pro-inflammatory cytokines when used in combination with Ingenol-3,20-dibenzoate suggests that SBHA can be used to reduced PKC induced pro-inflammatory cytokines but not to achieve latency reversal in the context of HIV-1.

category: microbiology


title: Plasma amyloid β levels are driven by genetic variants near APOE, BACE1, APP, PSEN2: A genome-wide association study in over 12,000 non-demented participants

abstract:
INTRODUCTIONThere is increasing interest in plasma A{beta} as an endophenotype and biomarker of Alzheimers disease (AD). Identifying the genetic determinants of plasma A{beta} levels may elucidate important processes that determine plasma A{beta} measures.

METHODSWe included 12,369 non-demented participants derived from eight population-based studies. Imputed genetic data and plasma A{beta}1-40, A{beta}1-42 levels and A{beta}1-42/A{beta}1-40 ratio were used to perform genome-wide association studies, gene-based and pathway analyses. Significant variants and genes were followed-up for the association with PET A{beta} deposition and AD risk.

RESULTSSingle-variant analysis identified associations across APOE for A{beta}1-42 and A{beta}1-42/A{beta}1-40 ratio, and BACE1 for A{beta}1-40. Gene-based analysis of A{beta}1-40 additionally identified associations for APP, PSEN2, CCK and ZNF397. There was suggestive interaction between a BACE1 variant and APOE{varepsilon}4 on brain A{beta} deposition.

DISCUSSIONIdentification of variants near/in known major A{beta}-processing genes strengthens the relevance of plasma-A{beta} levels both as an endophenotype and a biomarker of AD.


title: Measuring nonapoptotic caspase activity with a transgenic reporter in mice

abstract:
The protease caspase-3 is a key mediator of apoptotic programmed cell death. But weak or transient caspase activity can contribute to neuronal differentiation, axonal pathfinding, and synaptic long-term depression. Despite the importance of sublethal, or nonapoptotic, caspase activity in neurodevelopment and neural plasticity, there has been no simple method for mapping and quantifying nonapoptotic caspase activity in rodent brains. We therefore generated a transgenic mouse expressing a highly sensitive and specific fluorescent reporter of caspase activity, with peak signal localized to the nucleus. As a proof of concept, we first obtained evidence that nonapoptotic caspase activity influences neurophysiology in an amygdalar circuit. Then focusing on the amygdala, we were able to quantify a sex-specific persistent elevation in caspase activity in females after restraint stress. This simple in vivo caspase activity reporter will facilitate systems-level studies of apoptotic and nonapoptotic phenomena in behavioral and pathological models.

Significance StatementCaspase-3 is an enzyme that can cause cell death when highly active but can also perform important cellular functions, such as maturation and structural changes, when only weakly or transiently active. Despite the importance of this nonlethal type of caspase activity, there is no straightforward method to measure it in live rodents. We therefore developed mice that have a fluorescent reporter that is sensitive enough to detect nonlethal caspase activity. Surprisingly, we found that weak caspase activity influences the synchrony of neuronal firing across different brain regions. We also observed increased caspase activity in female mice after severe stress. This simple, live-animal caspase activity reporter can subserve multiple applications in behavior and pathology research.


title: Improved management facilitates return of an iconic fish species

abstract:
Species declines and losses of biota are often associated with shifting baselines in perceived historical abundances, and/or neglect or abandonment of recovery actions aimed at ecological restoration. Such declines are frequently accompanied by contractions in the geographical distribution of the species, with associated negative ecological impacts and diminishing socio-economic benefits. Here we show using citizen science and other data that after 50-60 years of near total absence, the iconic top predator and highly migratory species bluefin tuna, Thunnus thynnus, returned by the hundreds if not thousands in waters near Denmark, Norway and Sweden during August-October 2015-2017. The re-utilisation of this former habitat is part of a geographically more widespread expansion of the summer foraging area to the northern part of the northeast Atlantic Ocean, encompassing waters from east Greenland to west Sweden. The remarkable return to the Skagerrak, Kattegat and North Sea has been facilitated by improved fishery management for bluefin tuna and its prey. Bluefin tuna biomass in the northeast Atlantic and Mediterranean has been increasing since a recovery plan was implemented in the late 2000s, and biomasses of two key prey species (herring, Clupea harengus; mackerel, Scomber scombrus) recovered during the late 1980s-1990s. The reappearance of bluefin tuna in the Skagerrak-Kattegat and other waters of northern Europe, despite a recent history of mismanagement and illegal fishing in the northeast Atlantic and Mediterranean which led to a critical population decline, offers hope that other marine ecological recoveries are possible under improved management of fisheries and ecosystems.

One Sentence SummaryImproved management promotes the return of an ocean icon to northern Europe.

Significance StatementCommercial fisheries are often perceived being in a state of decline and collapse, putting food and economic security at risk. Such declines are frequently accompanied by contractions in stock distribution, negative ecological impacts and diminishing socio-economic benefits. Here we present an example based on one of the worlds most valuable and iconic fish species, bluefin tuna, which demonstrates that effective management of both bluefin tuna and its prey has been a key factor leading to a remarkable reoccupation of formerly lost habitat. This reappearance, following decades of absence, occurred despite the bluefin tuna stock having had a recent, long history of unsustainable and illegal exploitation. Marine ecological recovery actions can be successful, even in situations which may initially appear intractable.

category: ecology


title: Early urinary candidate biomarkers and clinical outcomes of intervention in a rat model of experimental autoimmune encephalomyelitis

abstract: Multiple sclerosis is a chronic autoimmune demyelinating disease of the central nervous system and is difficult to diagnose in early stages. Without homeostatic control, urine was reported to have the ability to accumulate early changes in the body. We expect that urinary proteome can reflect early changes in the nervous system. In this study, the early urinary proteome changes in a most employed multiple sclerosis rat model (experimental autoimmune encephalomyelitis (EAE)) were analyzed to explore early urinary candidate biomarkers, and early treatment of methylprednisolone were used to evaluate the therapeutic effect. Compare with controls, twenty-five urinary proteins were altered at day 7 when there were no clinical symptoms and no obvious histological changes. Among them, twenty-three have human homologs and fourteen were reported to be differently expressed in the serum/cerebrospinal fluid/brain tissues of multiple sclerosis patients or animal models. Functional analysis showed that the dysregulated proteins were associated with asparagine degradation, neuroinflammation and lipid metabolism. After the early treatment of methylprednisolone, the incidence of encephalomyelitis in the intervention group was only 1/13. This study demonstrates that urine may be a good source of biomarkers for the early detection of multiple sclerosis and early treatment can significantly delay disease progression. These findings may provide important information for early diagnosis and intervention of multiple sclerosis in the future.

category: biochemistry


title: Majority of choice-related variability in perceptual decisions is present in early sensory cortex

abstract: While performing challenging perceptual tasks such as detecting a barely visible target, our perceptual reports vary across presentations of identical stimuli. This perceptual variability is presumably caused by neural variability in our brains. How much of the neural variability that correlates with the perceptual variability is present in the primary visual cortex (V1), the first cortical processing stage of visual information? To address this question, we recorded neural population responses from V1 using voltage-sensitive dye imaging while monkeys performed a challenging reaction-time visual detection task. We found that V1 population responses in the period leading to the decision correspond more closely to the monkeys report than to the visual stimulus. These results, together with a simple computational model that allows one to quantify the captured choice-related variability, suggest that most of this variability is present in V1 as additive noise, and that areas downstream to V1 contain relatively little independent choice-related variability.


title: Removing unwanted variation between samples in Hi-C experiments

abstract: Hi-C data is commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from different individuals, and that properties of this unwanted variation changes across the contact map. We present BNBC, a method for normalization and batch correction of Hi-C data and show that it substantially improves comparisons across samples, including in a QTL analysis as well as differential enrichment across cell types.

category: genomics


title: A bacterial GW-effector directly targets Arabidopsis Argonaute 1 to suppress PAMP-triggered immunity and cause disease

abstract: Pseudomonas syringae (P. syringae) type-III effectors were previously found to suppress the Arabidopsis microRNA (miRNA) pathway through unknown mechanisms. Here, we first show that the P. syringae HopT1-1 effector promotes pathogenicity by suppressing the Arabidopsis Argonaute 1 (AGO1)-dependent miRNA pathway. We further demonstrate that HopT1-1 physically interacts with Arabidopsis AGO1 through conserved glycine/tryptophan (GW) motifs. Importantly, this AGO-binding platform was found to be essential for the ability of HopT1-1 to suppress both miRNA activity and PAMP-Triggered Immunity (PTI). These results therefore indicate that the RNA silencing suppression activity of HopT1-1 is intimately coupled to its virulence function. Overall, these findings provide the first evidence that a bacterial effector has evolved to directly target an AGO protein to suppress PTI and cause disease.


title: Differential and defective expression of Koala Retrovirus indicate complexity of host and virus evolution

abstract: Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously thought to be either virus free or to have only exogenous variants of KoRV with low rates of KoRV induced disease. In contrast, animals in the northern part of their range universally have both endogenous and exogenous KoRV with very high rates of KoRV induced disease such as lymphoma. This paper uses a combination of sequencing technologies, Illumina RNA sequencing of "southern" (south Australian) and "northern" (SE QLD) koalas and CRISPR enrichment and nanopore sequencing of DNA of "southern" (South Australian and Victorian animals) to retrieve full length loci and intregration sites of KoRV variants. We demonstrate that koalas that tested negative to the KoRV pol gene qPCR, used to detect replication competent KoRV, are not in fact KoRV free but harbour defective, presumably endogenous, "RecKoRV" variants that are not fixed between animals. This indicates that these populations have historically been exposed to KoRV and raises questions as to whether these variants have arisen by chance or whether they provide a protective effect from the infectious forms of KoRV. This latter explanation would offer the intriguing prospect of being able to monitor and selectively breed for disease resistance to protect the wild koala population from KoRV induced disease.


title: Experimental evidence of non-classical brain functions

abstract:
Exploring unknown quantum systems is an experimental challenge. Recent proposals exploring quantum gravity have suggested circumventing this problem by considering the unknown system as a mediator between two known systems. If such a mediation can locally generate entanglement in the known systems, then the mediator must be non-classical.

The same approach may be applicable to other systems, in particular the brain, where speculations about quantum operations in consciousness and cognition have a long history. Translated to the brain, the mediator is then an unknown brain function. For the quantum systems, we could use proton spins of bulk water, which most likely interfere with the any brain function. Entanglement in these spins can be witnessed with multiple quantum coherence (MQC). We based our witness protocol on zero quantum coherence (ZQC) whereby potential signals from local properties were minimised.

For short repetitive periods, we found ZQC signals in large parts of the brain, whereby the temporal appearance resembled heartbeat-evoked potentials (HEPs). Similar to HEPs, we also found that the ZQC signal depended on conscious awareness. Consciousness-related signals have, to our knowledge, not yet been reported in NMR. Remarkably, we could exclude local properties as contrast mechanism because (a) the ZQC signals had no correlates known in conventional MRI, and (b) the ZQC signals only appeared if the local properties of the magnetisation, which are complementary to non-local properties, were reduced. Our findings suggest that we may have witnessed entanglement mediated by consciousness-related brain functions. Those brain functions must then operate non-classically, which would mean that consciousness is non-classical.


title: A GenoChemetic strategy  for derivatization of the violacein natural product scaffold

abstract: Natural products and their analogues are often challenging to synthesise due to their complex scaffolds and embedded functional groups. Solely relying on engineering the biosynthesis of natural products may lead to limited compound diversity. Integrating synthetic biology with synthetic chemistry allows rapid access to much more diverse portfolios of xenobiotic compounds which may accelerate the discovery of new therapeutics. As a proof-of-concept, by supplementing an Escherichia coli strain expressing the violacein biosynthesis pathway with 5-bromo-tryptophan in vitro or tryptophan 7-halogenase RebH in vivo, 6 halogenated analogues of violacein or deoxyviolacein were generated, demonstrating promiscuity of the violacein biosynthesis pathway. Furthermore, 20 new derivatives were generated from 5-brominated violacein analogues via Suzuki-Miyaura cross-coupling reaction directly using the crude extract without prior purification. Herein, we demonstrate a flexible and rapid approach to access diverse chemical space that can be applied to a wide range of natural product scaffolds.


title: Proof of concept continuous event logging in living cells

abstract: Cells must detect and respond to molecular events such as the presence or absence of specific small molecules. To accomplish this, cells have evolved methods to measure the presence and concentration of these small molecules in their environment and enact changes in gene expression or behavior. However, cells dont usually change their DNA in response to such outside stimuli. In this work, we have engineered a genetic circuit that can enact specific and controlled genetic changes in response to changing small molecule concentrations. Known DNA sequences can be repeatedly integrated into a genomic array such that their identity and order encodes information about past small molecule concentrations that the cell has experienced. To accomplish this, we use catalytically inactive CRISPR-Cas9 (dCas9) to bind to and block attachment sites for the integrase Bxb1. Therefore, through the co-expression of dCas9 and guide RNA, Bxb1 can be directed to integrate one of two engineered plasmids, which correspond to two orthogonal small molecule inducers that can be recorded with this system. We identified the optimal location of guide RNA binding to the Bxb1 attP integrase attachment site, and characterized the detection limits of the system by measuring the minimal small molecule concentration and shortest induction time necessary to produce measurable differences in array composition as read out by Oxford Nanopore long read sequencing technology.


title: Modeling Dynamic Transcriptional Circuits with CRISPRi

abstract: Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) promises to reproduce the functions of traditional synthetic transcriptional circuits, but with better orthogonality, programmability, and extensibility. However, CRISPRi lacks obvious cooperativity-a feature classically considered critical for several classic gene regulatory circuits. We use a simple dynamical model of CRISPRi to show that it can be used to build repressilators, toggle switches, and incoherent feed-forward loops. We also show that the function some of these circuits are expected to be sensitive to several key parameters, and we provide specifications for those parameters. Our modeling reveals key engineering requirements and considerations for the construction of dynamic CRISPRi circuits, and provides a roadmap for building those circuits.


title: Scanning along a compressed timeline of the future

abstract: Several authors have suggested a deep symmetry between the psychological processes that underlie our ability to remember the past and make predictions about the future. The judgment of recency (JOR) task measures temporal order judgments for the past by presenting pairs of probe stimuli; participants choose the probe that was presented more recently. We performed a short-term relative JOR task and introduced a novel judgment of imminence (JOI) task to study temporal order judgments for the future. In the JOR task, participants were presented with a sequence of stimuli and asked to choose which of two probe stimuli was presented closer to the present. In the JOI task, participants were trained on a probabilistic sequence. After training, the sequence was interrupted with probe stimuli. Participants were asked to choose which of two probe stimuli was expected to be presented closer to the present. Replicating prior work on JOR, we found that RT results supported a backward self-terminating search model operating on a temporally-organized representation of the past. We also showed that RT distributions are consistent with this model and that the temporally-organized representation is compressed. Critically, results for the JOI task probing expectations of the future were mirror-symmetric to results from memory, suggesting a forward self-terminating search model operating on a temporally-organized representation of the future.

category: animal behavior and cognition


title: Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer

abstract: Acquired resistance to carboplatin is a major obstacle to the cure of ovarian cancer, but its molecular underpinnings are still poorly understood and often inconsistent between in vitro modeling studies. Using sequential treatment cycles, multiple clones derived from a single ovarian cancer cell reached similar levels of resistance. The resistant clones showed significant transcriptional heterogeneity, with shared repression of cell cycle processes and induction of IFN response signaling, and subsequent pharmacological inhibition of the JAK/STAT pathway led to a general increase in carboplatin sensitivity. Gene-expression based virtual synchronization of 26,772 single cells from 2 treatment steps and 4 resistant clones was used to evaluate the activity of Hallmark gene sets in proliferative (P) and quiescent (Q) phases. Two behaviors were associated with resistance: 1) broad repression in the P phase observed in all clones in early resistant steps and 2) prevalent induction in Q phase observed in the late treatment step of one clone. Furthermore, the induction of IFN response in P phase or Wnt-signaling in Q phase were observed in distinct resistant clones. These observations suggest a model of resistance hysteresis, where functional alterations of the P and Q phase states affect the dynamics of the successive transitions between drug exposure and recovery, and prompts for a precise monitoring of single-cell states to develop more effective schedules for, or combination of, chemotherapy treatments.

category: cancer biology


title: System drift and speciation

abstract: Even if a species phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways cause a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organisms internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size (Ne). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne generations. This model also naturally predicts Haldanes rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.


title: The effectiveness of glass beads for plating cell cultures

abstract: Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this, the exact impact of its parameters on colony growth has not been extensively studied. A common protocol involves the shaking of glass beads within a petri dish containing solid growth media. We investigated the effects of multiple parameters in this protocol - the number of beads, the shape of movement, and the number of movements. Standard suspensions of Escherichia coli were spread while varying these parameters to assess their impact on colony growth. Results were assessed by a variety of metrics - the number of colonies, the mean distance between closest colonies, and the variability and uniformity of their spatial distribution. Finally, we devised a mathematical model of shifting billiard to explain the heterogeneities in the observed spatial patterns. Exploring the parameters that affect the most fundamental techniques in microbiology allows us to better understand their function, giving us the ability to precisely control their outputs for our exact needs.


title: Iron oxidation by a fused cytochrome-porin common to diverse iron-oxidizing bacteria

abstract:
Iron (Fe) oxidation is one of Earths major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron-oxidizers. The genomes of many, diverse iron-oxidizers encode a homolog to an outer-membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron-oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 {+/-} 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. Sequence analysis and modeling reveal the entire Cyc2 family share a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. Based on structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron-oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.

ImportanceIron is practically ubiquitous across Earths environments, central to both life and geochemical processes, which depend heavily on the redox state of iron. Although iron oxidation, or "rusting," can occur abiotically at near neutral pH, we find neutrophilic iron-oxidizing bacteria (FeOB) are widespread, including in aquifers, sediments, hydrothermal vents, pipes, and water treatment systems. FeOB produce highly reactive Fe(III) oxyhydroxides that bind a variety of nutrients and toxins, thus these microbes are likely a controlling force in iron and other biogeochemical cycles. There has been mounting evidence that Cyc2 functions as an iron oxidase in neutrophiles, but definitive proof of its function has long eluded us. This work provides conclusive biochemical evidence of iron oxidation by Cyc2 from neutrophiles. Cyc2 is common to a wide variety of iron-oxidizers, including acidophilic and phototrophic iron-oxidizers, suggesting that this fused cytochrome-porin structure is especially well-adapted for iron oxidation.


title: Novel Integrative Modeling of Molecules and Morphology Pinpoints Caninae Evolution across Timescales

abstract: Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.


title: Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales


title: Dynamic Flux Balance Analysis Models in SBML

abstract: Computational models in systems biology and systems medicine are typically simulated using a single formalism such as ordinary differential equations (ODE). However, more complex models require the coupling of multiple formalisms since different biological phenomena are better described by different methods. For example, metabolism in steady state is often modeled using flux-balance analysis (FBA) whereas dynamic changes of model components are better described via ODEs. The coupling of FBA and ODE modeling formalisms results in dynamic FBA models. A major challenge is how to describe such hybrid models that couple multiple formalisms in a standardized way so that they can be exchanged between tools and simulated consistently in a reproducible manner. This paper presents a scheme for encoding and implementation of dynamic FBA models in the Systems Biology Markup Language (SBML), thereby enabling the exchange of multi-framework computational models between software tools. We demonstrate the feasibility of the approach using various example models and show that different tools are able to simulate the hybrid models and agree on the results. As part of this work, two independent implementations of a multi-framework simulation method for dynamic FBA have been developed supporting such models: iBioSim and sbmiutils.

category: bioinformatics


title: Seidr: Efficient Calculation of Robust Ensemble Gene Networks

abstract:
Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few usable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seithr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks.

Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms.

Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.


title: High-throughput microcolony growth analysis from suboptimal low-magnification micrographs

abstract:
New technological advances have enabled high-throughput phenotyping at the single-cell level, yet analyzing the large amount of data generated by high throughput phenotyping experiments automatically and accurately is a considerable challenge. Here we introduce Processing Images Easily (PIE), software that automatically tracks growth of microbial colonies in low-magnification brightfield images by combining adaptive object-center recognition with gradient-based object-outline recognition. PIE recognizes colony outlines very robustly and accurately across a wide range of image brightnesses, focal depths, and organisms. Beyond accurate colony recognition, PIE is designed to easily integrate with complex experiments, allowing colony tracking across multiple experimental phases and classification based on fluorescence intensity. We show that PIE can be used to accurately measure the growth rates of large numbers (>90,000) of bacterial or yeast microcolonies in a single-time-lapse experiment, allowing calculation of population-wide growth properties. Finally, PIE is able to track individual colonies across multiple experimental phases, measuring both growth and fluorescence properties of the microcolonies.

Author SummaryHigh-throughput microscopy has enabled automated collection of large amounts of growth and gene-expression data in microbes. Computational methods that can precisely recognize and track organisms in images are essential to performing measurements at scale using automated microscopy. We have developed PIE, software that automatically recognizes microbial colonies in microscopy images, tracks them in imaging time-series, and performs measurements of growth and, potentially, gene expression. PIE is highly effective on low-resolution images, outperforming current state-of-the-art approaches in both speed and accuracy, and works well in microbes of varying shapes and sizes. In addition, PIE allows tracking microcolonies across arbitrary sequences of experimental phases, each collecting data in different modalities. We show that PIE allows measurement of growth and fluorescence properties in tens of thousands of microbial colonies in a single experiment, and that in turn the scale of these measurements can lead to important insights about interindividual differences in growth and stress response. PIE is available as a Python package (https://doi.org/10.5281/zenodo.4987127) with documentation currently at https://pie-image.readthedocs.io/; users can also run analysis on individual images or time-series without the need to install PIE by using our web application, currently available at http://pie.hpc.nyu.edu/.


title: Visual and auditory brain areas share a representational structure that supports emotion perception

abstract: Emotionally expressive music and dance occur together across the world. This may be because features shared across the senses are represented the same way even in different sensory brain areas, putting music and movement in directly comparable terms. These shared representations may arise from a general need to identify environmentally relevant combinations of sensory features, particularly those that communicate emotion. To test the hypothesis that visual and auditory brain areas share a representational structure, we created music and animation stimuli with crossmodally matched features expressing a range of emotions. Participants confirmed that each emotion corresponded to a set of features shared across music and movement. A subset of participants viewed both music and animation during brain scanning, revealing that representations in auditory and visual brain areas were similar to one another. This shared representation captured not only simple stimulus features, but also combinations of features associated with emotion judgments. The posterior superior temporal cortex represented both music and movement using this same structure, suggesting supramodal abstraction of sensory content. Further exploratory analysis revealed that early visual cortex used this shared representational structure even when stimuli were presented auditorily. We propose that crossmodally shared representations support mutually reinforcing dynamics across auditory and visual brain areas, facilitating crossmodal comparison. These shared representations may help explain why emotions are so readily perceived and why some dynamic emotional expressions can generalize across cultural contexts.


title: Bayesian model comparison for rare variant association studies

abstract: Whole genome sequencing studies applied to large populations or biobanks with extensive phenotyping raise new analytic challenges. The need to consider many variants at a locus or group of genes simultaneously and the potential to study many correlated phenotypes with shared genetic architecture provide opportunities for discovery and inference that are not addressed by the traditional one variant, one phenotype association study. Here, we introduce a Bayesian model comparison approach that we refer to as MRP (Multiple Rare-variants and Phenotypes) for rare-variant association studies that considers correlation, scale, and direction of genetic effects across a group of genetic variants, phenotypes, and studies. The approach requires only summary statistic data. To demonstrate the efficacy of MRP, we apply our method to exome sequencing data (N = 184,698) across 2,019 traits from the UK Biobank, aggregating signals in genes. MRP demonstrates an ability to recover previously-verified signals such as associations between PCSK9 and LDL cholesterol levels. We additionally find MRP effective in conducting meta-analyses in exome data. Notable non-biomarker findings include associations between MC1R and red hair color and skin color, IL17RA and monocyte count, IQGAP2 and mean platelet volume, and JAK2 and platelet count and crit (mass). Finally, we apply MRP in a multi-phenotype setting; after clustering the 35 biomarker phenotypes based on genetic correlation estimates into four clusters, we find that joint analysis of these phenotypes results in substantial power gains for gene-trait associations, such as in TNFRSF13B in one of the clusters containing diabetes and lipid-related traits. Overall, we show that the MRP model comparison approach is able to improve upon useful features from widely-used meta-analysis approaches for rare variant association analyses and prioritize protective modifiers of disease risk.


title: Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration

abstract: NK cell responses depend on the balance of signals from inhibitory and activating receptors. However, how the integration of antagonistic signals occurs upon NK cell-target cell interaction is not fully understood. Here, we provide evidence that NK cell inhibition via the inhibitory receptor Ly49A is dependent on its relative colocalization at the nanometer scale with the activating receptor NKG2D upon immune synapse (IS) formation. NKG2D and Ly49A signal integration and colocalization was studied using NKG2D-GFP and Ly49A-RFP-expressing primary NK cells, forming ISs with NIH3T3 target cells, with or without expression of single chain trimer (SCT) H2-Dd and an extended form of SCT H2-Dd-CD4 MHC-I molecules. Nanoscale colocalization was assessed by Forster resonance energy transfer (FRET) between NKG2D-GFP and Ly49A-RFP and measured for each synapse. In the presence of their respective cognate ligands, NKG2D and Ly49A colocalize at a nanometer scale leading to NK cell inhibition. However, increasing the size of the Ly49A ligand reduced the nanoscale colocalization with NKG2D consequently impairing Ly49A-mediated inhibition. Thus, our data shows NK cell signal integration is critically dependent on the dimensions of NK cell ligand-receptor pairs by affecting their relative nanometer-scale colocalization at the IS. Together, our results suggest the balance of NK cell signals, and NK cell responses, are determined by the relative nanoscale colocalization of activating and inhibitory receptors in the immune synapse.

category: immunology


title: Genie: An interactive real-time simulation for teaching genetic drift

abstract: Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is specially challenging. Here we present Genie, a browser-based educational tool that facilitates demonstration of concepts such as genetic drift, population isolation, gene flow, and genetic mutation. Because it does not need to be downloaded and installed, Genie can scale to large groups of students and is useful for both in-person and online instruction. Genie was used to teach genetic drift to Evolution students at Arizona State University during Spring 2016 and Spring 2017. The effectiveness of Genie to teach key genetic drift concepts and misconceptions was assessed with the Genetic Drift Inventory developed by Price et al. (2014). Overall, Genie performed comparably to that of traditional static methods across all evaluated classes. We have empirically demonstrated that Genie can be successfully integrated with traditional instruction to reduce misconceptions about genetic drift.

category: scientific communication and education


title: The effect of mutational robustness on the evolvability of multicellular organisms

abstract: Canalization involves mutational robustness, the lack of phenotypic change as a result of genetic mutations. Given the large divergence in phenotype across species, understanding the relationship between high robustness and evolvability has been of interest to both theorists and experimentalists. Although canalization was originally proposed in the context of multicellular organisms, the effect of multicellularity on evolvability has not been considered by theoreticians. We address this issue using a Boolean population model with explicit representation of an environment in which multicellular individuals with explicit genotype and phenotype evolve. Robustness is described by a single real number between zero and one. We find that high robustness is favored in constant environments, and lower robustness is favored after environmental change. Multicellularity severely constrains robustness: peak evolvability occurs at an absolute level of robustness of about 0.99 compared with values of about 0.5 in a classical neutral network model. Multicellularity results in a sharp peak of evolvability in which the maximum is set by the fact that the fixation of adaptive mutations becomes more improbable as robustness decreases. When robustness is put under genetic control, robustness levels leading to maximum evolvability are selected for, but maximal relative fitness appears to require recombination.

category: evolutionary biology


title: The importance of semantic network brain regions in integrating prior knowledge with an ongoing dialogue

abstract: To understand a dialogue we need to know the specific topics that are being discussed. This enables us to integrate our knowledge of what was said previously, in order to interpret the current dialogue. Here, we selectively manipulated knowledge about the narrative content of dialogues between two people, presented in short videos. The videos were clips taken from television situation comedies and the speech in the first-half of the clip could either be presented normally (high context) or spectrally rotated in order to render it unintelligible (low context). Knowledge of the preceding narrative boosted memory for the following dialogues as well as increased the inter-subject semantic similarity of recalled descriptions of the dialogues. Sharing knowledge of the preceding narrative across participants had two effects on fMRI markers of neural processing: (1) it strengthened temporal inter-subject correlations in regions including the left angular (AG) and inferior frontal gyri (IFG), and (2) it increased spatial inter-subject pattern similarity in the bilateral anterior temporal lobes (ATL). We argue that these brain regions, which are known to be involved in semantic processing, support the activation and integration of prior knowledge, which helps people to better understand and remember dialogues as they unfold.


title: Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis

abstract: Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which shows unprecedented number of splice variants in testis. Further, Pirmy transcript variants act as templates for several piRNAs. We identified ten differentially expressed autosome-encoded sperm proteins in mutant mice. Pirmy transcript variants have homology to 5/3UTRs of these deregulated autosomal genes. Thus, subfertility in Y-deleted mice appears to be a polygenic phenomenon that is partially regulated epistatically by the Y-chromosome. Our study provides novel insights into possible role of MSY-derived ncRNAs in male fertility and reproduction. Finally, sperm phenotypes from the Y-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of Y-derived ncRNAs in male sterility and speciation.


title: Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey systems

abstract: Many world fisheries display a declining mean trophic level of catches. This "fishing down the food web" is often attributed to reduced densities of high-trophic-level species. We show here that the fishing down pattern can actually emerge from the adaptive harvesting of a predator-prey community, where changes in fishing patterns are driven by the relative profitabilities of the harvested species. The shift from a predator- to a prey-focused fishing pattern can yield abrupt changes in the system, strongly impacting species densities. Such regime shifts occur when the predator species is highly valuable relative to the prey, and when the top-down control on the prey is strong. Moreover, we find that when the two species are jointly harvested, high adaptation speeds can reduce the resilience of fisheries. Our results therefore suggest that flexibility in harvesting strategies will not necessarily benefit fisheries but may actually harm their sustainability.