title: Genetic architecture and genomic prediction accuracy of apple quantitative traits across environments

abstract: Implementation of genomic tools is desirable to increase the efficiency of apple breeding. The apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic prediction accuracy, and studying genotype by environment interactions (GxE). Here we show contrasting genetic architecture and genomic prediction accuracies for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic prediction accuracies of 0.18-0.88 were estimated using single-environment univariate, single-environment multivariate, multi-environment univariate, and multi-environment multivariate models. The GxE accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.


title: A comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia

abstract: Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here we apply different analytical methodologies to the same dataset to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made de novo genome assemblies for the focal species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.

category: genomics


title: GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates

abstract: Biomedical entity normalization unifies the language across biomedical experiments and studies, and further enables us to obtain a holistic view of life sciences. Current approaches mainly study the normalization of more standardized entities such as diseases and drugs, while disregarding the more ambiguous but crucial entities such as pathways, functions and cell types, hindering their real-world applications. To achieve biomedical entity normalization on these under-explored entities, we first introduce an expert-curated dataset OBO-syn encompassing 70 different types of entities and 2 million curated entity-synonym pairs. To utilize the unique graph structure in this dataset, we propose GraphPrompt, a promptbased learning approach that creates prompt templates according to the graphs. Graph-Prompt obtained 41.0% and 29.9% improvement on zero-shot and few-shot settings respectively, indicating the effectiveness of these graph-based prompt templates. We envision that our method GraphPrompt and OBO-syn dataset can be broadly applied to graph-based NLP tasks, and serve as the basis for analyzing diverse and accumulating biomedical data.

category: bioinformatics


title: Graph Transformer for drug response prediction

abstract:
BackgroundPrevious models have shown that learning drug features from their graph representation is more efficient than learning from their strings or numeric representations. Furthermore, integrating multi-omics data of cell lines increases the performance of drug response prediction. However, these models showed drawbacks in extracting drug features from graph representation and incorporating redundancy information from multi-omics data. This paper proposes a deep learning model, GraTransDRP, to better drug representation and reduce information redundancy. First, the Graph transformer was utilized to extract the drug representation more efficiently. Next, Convolutional neural networks were used to learn the mutation, meth, and transcriptomics features. However, the dimension of transcriptomics features is up to 17737. Therefore, KernelPCA was applied to transcriptomics features to reduce the dimension and transform them into a dense presentation before putting them through the CNN model. Finally, drug and omics features were combined to predict a response value by a fully connected network. Experimental results show that our model outperforms some state-of-the-art methods, including GraphDRP, GraOmicDRP.

Availability of data and materialshttps://github.com/chuducthang77/GraTransDRP.


title: ACTIN Anchors the Highly Oligomeric DRP1 at Mitochondria-Sarcoplasmic Reticulum Contact Sites in Adult Murine Heart: Its Functional Implication

abstract:
RationaleMitochondrial fission and fusion are relatively infrequent in adult cardiomyocytes compared to another cell types1-3. This is surprising considering that proteins involved in mitochondrial dynamics are highly expressed in the heart. It has been previously reported that dynamin-related protein 1 (DRP1) has a critical role in mitochondrial fitness and cardiac protection1, 4. Cardiac DRP1 ablation in the adult heart evokes a progressive dilated cardiac myopathy and lethal heart failure1. Nevertheless, the conditional cardiac-specific DRP1 knock-out animals present a significantly longer survival rate compared with global DRP1 KO models1, 4, 5. We have described before the great importance for cardiac physiology of the strategic positioning of mitochondrial proteins in the cardiac tissue6, 7. Therefore, we hypothesize that DRP1 plays a regulatory role in cardiac physiology and mitochondrial fitness by preferentially accumulating at mitochondria and junctional sarcoplasmic reticulum (jSR) contact sites, where the high Ca2+ microdomain is formed during excitation-contraction (EC) coupling.

ObjectiveThis study aims to determine whether mitochondria-associated DRP1 is preferentially accumulated in the mitochondria and jSR contact sites, the mechanism responsible for such a biased distribution, and its functional implication.

Methods and ResultsUsing high-resolution imaging approaches, we found that mitochondria-associated DRP1 in cardiomyocytes was localized in the discrete regions where T-tubule, jSR, and mitochondria are adjacent to each other. Western blot results showed that mitochondria-bound DRP1 was restricted to the mitochondria-associated membranes (MAM), with undetectable levels in purified mitochondria. Furthermore, in comparison to the cytosolic DRP1, the membrane-bound DRP1 in SR and MAM fractions formed high molecular weight oligomers demosntratd by 2D blue native technique. In both electrically paced adult cardiomyocytes and Langendorff-perfused beating hearts, the oscillatory Ca2+ pulses preserved MAM-associated DRP1 accumulation. Interestingly, similar to DRP1, all mitochondria-bound {beta}-ACTIN only exists in MAM and not in the purified mitochondria.

Additionally, co-immunoprecipitation pulls down both DRP1 and {beta}-ACTIN together. Inhibition of {beta}-ACTIN polymerization with Cytochalasin D disrupts the tight association between DRP1 and {beta}-ACTIN. In cardiac-specific DRP1 knock-out mouse after 6 weeks of tamoxifen induction (DRP1icKo), the cardiomyocytes show disarray of sarcomere, a decrease of cardiac contraction, loss of mitochondrial membrane potential, significantly decreased spare respiratory capacity, and frequent occurrence of early after contraction (EAC), suggesting the heart is susceptible to arrhythmias and heart failure. Despite of this phenotype, DRP1icKo animals have longer life span than other DRP1 KO models. Strikingly, DRP1 levels are only modestly decreased in the MAM when compared with the rest of the cellular fractions. These preserved levels were accompanied by the preservation of the mitochondrial pool in the MAM fraction obtained from the DRP1icKO hearts.

ConclusionsThe results show that in adult cardiomyocytes, mitochondria bound DRP1 clusters in high molecular weight protein complexes at MAM. This clustering is fortified by EC coupling mediated Ca2+ transients and requires its interaction with {beta}-ACTIN. Together with the better preserved DRP1 levels in the DRP1icKO model in the MAM, we conclude that DRP1 is anchored at the mitochondria-SR interface through {beta}-ACTIN and positions itself to play a fundamental role in regulating mitochondrial quality control in the working heart.

category: physiology


title: Students Attitudes Surrounding STEM: A Social Cognitive Career Theory Instrument for High School

abstract: To meet the demand of the growing science and health sectors in the United States, there is a critical necessity to engage more people in science, technology, engineering, and math (STEM). To broaden participation in STEM, we must understand the factors that shape perspectives and beliefs around career selection. Good measurement of these factors is crucial to quantify how effectively educational interventions impact student attitudes towards STEM. Adolescents are particularly suited for quantifying intervention efficacy because students build their identities during these formative years and make important career choices. To better quantify intervention efficacy at the high school level, we developed an instrument entitled Student Attitudes Surrounding STEM (SASS), which builds upon the social cognitive career theory (SCCT) framework for understanding career selection. Questionnaire responses were collected from 932 high school students, and split into samples of 400 for exploratory factor analysis and 532 for confirmatory factor analysis. The questions clustered into six factors: self-efficacy experience, self-efficacy academic, outcome expectations, interests, negative perceptions of scientists, and career awareness. The SASS exhibited adequate construct validity as determined by fit indices and theoretical considerations. Furthermore, the instrument demonstrated criterion validity, internal consistency, and test-retest reliability. This tool represents a novel integration of three latent variables into SCCT, negative perceptions of scientists, career awareness, and an experience factor for self-efficacy.

category: scientific communication and education


title: Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans

abstract:
Sexual dimorphism occurs where different sexes of the same species display differences in characteristics not limited to reproduction. For the nematode Caenorhabditis elegans, in which the complete neuroanatomy has been solved for both hermaphrodites and males, sexually dimorphic features have been observed both in terms of the number of neurons and in synaptic connectivity. In addition, male behaviours, such as food-leaving to prioritise searching for mates, have been attributed to neuropeptides released from sex-shared or sex-specific neurons.

In this study, we show that the lury-1 neuropeptide gene shows a sexually dimorphic expression pattern; being expressed in pharyngeal neurons in both sexes but displaying additional expression in tail neurons only in the male. We also show that lury-1 mutant animals show sex differences in feeding behaviours, with pharyngeal pumping elevated in hermaphrodites but reduced in males. LURY-1 also modulates male mating efficiency, influencing motor events during contact with a hermaphrodite. Our findings indicate sex-specific roles of this peptide in feeding and reproduction in C. elegans, providing further insight into neuromodulatory control of sexually dimorphic behaviours.

category: neuroscience


title: Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization.

abstract:
Prosocial behavior, in particular helping others in need, occurs preferentially in response to the perceived distress of ones own group members, or ingroup. The development of neural mechanisms underlying social selectivity towards ingroup members are not well established. Here, we used a rat helping behavior test to explore the development and neural basis of ingroup bias for prosocial behavior in adolescent rats. We previously found that adult rats selectively help others from their own social group, and that this selectivity is associated with activation in reward and motivation circuits. Surprisingly, we found that adolescent rats helped both ingroup and outgroup members, evidence suggesting that ingroup bias emerges in adulthood. Analysis of brain-wide neural activity, indexed by expression of the early-immediate gene c-Fos, revealed increased activity for ingroup members across a broad set of regions, which was congruent for adults and adolescents. However, adolescents showed reduced hippocampal and insular activity, and increased orbitofrontal cortex activity compared to adults. Adolescent rats who did not help trapped others also demonstrated increased amygdala connectivity. Together, these findings demonstrate that biases for group-dependent prosocial behavior develop with age in rats and suggest that specific brain regions contribute to this prosocial selectivity, overall pointing to possible targets for the functional modulation of ingroup bias.

One Sentence SummaryProsocial selectivity increases with age in parallel with hippocampal and insular activation, providing insight into the neural classification of group membership.


title: Synapse-associated astrocyte mitochondria stabilize motor circuits to prevent excitotoxicity

abstract: Early stages of the devastating neurodegenerative disease amyotrophic lateral sclerosis (ALS) are characterized by motor neuron hyperexcitability. During this phase, peri-synaptic astrocytes are neuroprotective. When reactive, loss of wild-type astrocyte functions results in excitotoxicity. How astrocytes stabilize motor circuit function in early-stage ALS is poorly understood. Here, we used Drosophila motor neurons to define the role of astrocyte-motor neuron metabolic coupling in a model of ALS: astrocyte knockdown of the ALS-causing gene tbph/TARDBP. In wild-type, astrocyte mitochondria were dynamically trafficked towards active motor dendrites/synapses to meet local metabolic demand. Knockdown of tbph in astrocytes resulted in motor neuron hyperexcitability, reminiscent of early-stage ALS, which was met with a compensatory accumulation of astrocyte mitochondria near motor dendrites/synapses. Finally, we blocked mitochondria-synapse association in tbph knockdown animals and observed locomotor deficits and synapse loss. Thus, synapse-associated astrocyte mitochondria stabilize motor circuits to prevent the transition from hyperexcitability to excitotoxicity.


title: Panzootic chytrid fungus exploits diverse amphibian host environments through plastic infection strategies

abstract: While many pathogens are limited to a single host, others can jump from host to host, which likely contributes to the emergence of infectious diseases. Despite this threat to biodiversity, traits associated with overcoming eco-evolutionary barriers to achieve host niche expansions are not well understood. Here, we examined the case of Batrachochytrium dendrobatidis (Bd), a multi-host pathogen that infects the skin of hundreds of amphibian species worldwide. To uncover functional machinery driving multi-host invasion, we analyzed Bd transcriptomic landscapes across 14 amphibian hosts and inferred the origin and evolutionary history of pathogenic genes under a phylogenetic framework comprising 12 other early-divergent zoosporic fungi. Our results not only revealed a conserved basal genetic machinery, but also highlighted the ability of Bd to display plastic infection strategies when challenged under suboptimal host environments. We found that genes related to amphibian skin exploitation have arisen mainly via gene duplications. We argue that plastic gene expression can drive variation in Bd lifecycles with different mode and tempo of development. Our findings support the idea that host skin environments exert contrasting selective pressures, such that gene expression plasticity constitutes one of the evolutionary keys leading to the success of this panzootic multi-host pathogen.

category: evolutionary biology


title: PhyloHerb: A phylogenomic pipeline for processing genome skimming data for plants

abstract:
O_LIPremise of the study: The application of high throughput sequencing, especially to herbarium specimens, is greatly accelerating biodiversity research. Among various techniques, low coverage Illumina sequencing of total genomic DNA (genome skimming) can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb -- a bioinformatic pipeline to efficiently and effectively assemble phylogenomic datasets derived from genome skimming.
C_LIO_LIMethods and Results: PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences using BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, data partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.
C_LIO_LIConclusions: Using published data from Clusiaceae, we demonstrated that PhyloHerb can accurately identify genes using highly fragmented assemblies derived from sequencing older herbarium specimens. Our approach is effective at all taxonomic depths and is scalable to thousands of species.
C_LI


title: Compositional forecasting of Chinook Salmon Evolutionarily Significant Units in bycatch for Pacific Hake fisheries

abstract: Bycatch impacts on non-target species present significant management problems in diverse fisheries throughout the world. Despite successful efforts to minimize bycatch in US West Coast Pacific Hake fisheries, these impacts remain a concern, particularly for sensitive populations of Chinook Salmon. NOAA Fisheries needed predictive models to estimate proportions of Chinook Salmon Evolutionarily Significant Units (ESUs) expected in bycatch. We used genetic mixture analysis to estimate ESU proportions from at-sea bycatch between 2008 and 2015. Using latitude as a predictor and applying jackknife cross validation, we found Dirichlet regression more accurately estimated abundant ESUs, whereas multinomial logistic regression performed better with rare ESUs. This targeted, ESU-specific approach showed the spatial distribution of sensitive stocks in bycatch and supported NOAAs obligations to forecast impacts on listed ESUs. The overarching goal of this continuing work is to maximize sustainable harvest while protecting threatened and endangered Chinook Salmon ESUs.

category: genetics


title: Can we use anti-predator behavior theory to predict wildlife responses to high-speed vehicles?

abstract: Animals seem to rely on antipredator behavior to avoid vehicle collisions. There is an extensive body of antipredator behavior theory that have been used to predict the distance/time animals should escape from predators. These models have also been used to guide empirical research on escape behavior from vehicles. However, little is known as to whether antipredator behavior models are appropriate to apply to an approaching high-speed vehicle. We addressed this gap by (a) providing an overview of the main hypothesis and predictions of different antipredator behavior models via a literature review, (b) exploring whether these models can generate quantitative predictions on escape distance when parameterized with empirical data from the literature, and (c) evaluating their sensitivity to vehicle approach speed via a simulation approach where we assessed model performance based on changes in effect size with variations in the slope of the flight initiation distance (FID) vs. approach speed relationship. We used literature on birds for goals (b) and (c). We considered the following eight models: the economic escape model, Blumsteins economic escape model, the optimal escape model, the perceptual limit hypothesis, the visual cue model, the flush early and avoid the rush (FEAR) hypothesis, the looming stimulus hypothesis, and the Bayesian model of escape behavior. We were able to generate quantitative predictions about escape distances with the last five models. However, we were only able to assess sensitivity to vehicle approach speed for the last three models. The FEAR hypothesis is most sensitive to high-speed vehicles when the species follows the spatial (FID remains constant as speed increases) and the temporal margin of safety (FID increases with an increase in speed) rules of escape. The looming stimulus effect hypothesis reached small to intermediate levels of sensitivity to high-speed vehicles when a species follows the delayed margin of safety (FID decreases with an increase in speed). The Bayesian optimal escape model reached intermediate levels of sensitivity to approach speed across all escape rules (spatial, temporal, delayed margins of safety) but only for larger (> 1 kg) species, but was not sensitive to speed for smaller species. Overall, no single antipredator behavior model could characterize all different types of escape responses relative to vehicle approach speed but some models showed some levels of sensitivity for certain rules of escape. We derive some applied applications of our finding by suggesting the estimation of critical vehicle approach speeds for managing populations that are especially susceptible to road mortality. Overall, we recommend that new escape behavior models specifically tailored to high- speeds vehicles should be developed to better predict quantitatively the responses of animals to an increase in the frequency of cars, airplanes, drones, etc. they will be facing in the next decade.

category: animal behavior and cognition


title: Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes

abstract: DNA methylation analysis by sequencing is becoming increasingly popular, yielding methylomes at single-base pair resolution. It has tremendous potential for cell-type heterogeneity analysis with intrinsic read-level information. Although diverse deconvolution methods were developed to infer cell-type composition based on bulk sequencing-based methylomes, the systematic evaluation has not been performed yet. Here, we thoroughly benchmark six previously published methods: Bayesian epiallele detection (BED), DXM, PRISM, csmFinder+coMethy, ClubCpG and MethylPurify, together with two array-based methods, MeDeCom and Houseman, as a comparison group. Sequencing-based deconvolution methods consist of two main steps, informative region selection and cell-type composition estimation, thus each was individually assessed. With these sophisticated evaluation, we demonstrate the method achieving the highest performance in different types of samples. We found that cell-type deconvolution performance is influenced by different factors depending on the number of cell types within the mixture. Finally, we propose a best-practice deconvolution strategy for sequencing data and limitations which need to be handled.


title: HiC-GNN: A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks

abstract:
Chromosome conformation capture (3C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3C that allows for genome wide quantification of chromosome interaction. From such interaction data, it is possible to infer the three-dimensional (3D) structure of the underlying chromosome. In this paper, we use a node embedding algorithm and a graph neural network to predict the 3D coordinates of each genomic loci from the corresponding Hi-C contact data. Unlike other chromosome structure prediction methods, our method can generalize a single model across Hi-C resolutions, multiple restriction enzymes, and multiple cell populations while maintaining reconstruction accuracy. We derive these results using three separate Hi-C data sets from the GM12878, GM06990, and K562 cell lines. We also compare the reconstruction accuracy of our method to four other existing methods and show that our method yields superior performance. Our algorithm outperforms the state-of-the-art methods in the accuracy of prediction and introduces a novel method for 3D structure prediction from Hi-C data.

Author SummaryWe developed a novel method, HiC-GNN, for predicting the three-dimensional structures of chromosomes from Hi-C data. HiC-GNN is unique from other methods for chromosome structure prediction in that it learns in an eager setting rather than a lazy setting. Thus, the models learned by HiC-GNN can be generalized to unseen data. To the authors knowledge, this generalizing capability is not present in any existing methods. We show that this generalization is robust to input resolution, restriction enzyme, and contact sparsity. We also show that our method outperforms existing methods using both generalized and non-generalized models. Moreover, we also show that our method is more robust to contact variance than the compared methods.

AvailabilityAll our source codes and data are available at https://github.com/OluwadareLab/HiC-GNN, and is made available as a containerized application that can be run on any platform.


title: HARLEY: A Semi-Automated detection of foci in fluorescence images of yeast

abstract: Quantification of cellular structures in fluorescence microscopy data is a key means of understanding cellular function. Unfortunately, numerous cellular structures present unique challenges in their ability to be unbiasedly and accurately detected and quantified. In our studies on stress granules in yeast, users displayed a striking variation of up to 3.7-fold in foci calls and were only able to replicate their results with 62-78% correlation, when requantifying the same images. To facilitate consistent results we developed HARLEY (Human Augmented Recognition of LLPS Ensembles in Yeast), a customizable software for detection and quantification of stress granules in S.cerevisiae. After a brief model training on ~20 cells the detection of foci is fully automated and based on closed loops in intensity contours, constrained only by the a-priori known size of the features of interest. Since no shape is implied, this method is not limited to round features, as is often the case with other algorithms. Candidate features are annotated with a set of geometrical and intensity-based properties to train a kernel Support Vector Machine to recognize features of interest. The trained classifier is then used to create consistent results across datasets. HARLEY is aimed at users without technical expertise, allows for batch processing and is freely available, which should be of broad interest to users focused on analysis of microscopy data in yeast.


title: Using a Champion-Oriented Mindset to Overcome the Challenges of Graduate School

abstract: Despite efforts to increase diversity, a glaring underrepresentation of minorities (URM) persists in the fields of science, technology, engineering, and mathematics (STEM). Graduate school can be a stressful step in the STEM pipeline, especially for students previously unaware of the structure and challenges of post-graduate education. To promote successful minority participation in STEM and prepare prospective students for the impending challenges of graduate school, we developed a workshop based on the mentoring and fostering of a champion-oriented mindset entitled, "The Trials and Tribulations of Graduate School: How Do You Make an Impact?". We administered the workshop to a cohort of university undergraduates and conducted pre- and post-workshop surveys to measure students perceived need for instruction on specific workshop topics. The results suggest that the workshop was well received by the students and provided information that they considered helpful to help navigate the graduate school process.


title: The Importance of Mentors and How to Handle More Than One Mentor

abstract:
IntroductionWorking with multiple mentors is a critical way for students to expand their network, gain opportunities, and better prepare for future scholastic or professional ventures. However, students from underrepresented groups (UR) are less likely to be mentored or have access to mentors, particularly in science, technology, engineering, and mathematics (STEM) fields. We developed and implemented a workshop, to provide the necessary foundation for students to be better prepared for establishing future mentorships throughout graduate and professional school.

MethodsFaculty well-versed in the area of effective mentorship from multiple universities developed and delivered a 1.5-hour workshop to address the roles of a mentor, especially when it comes to UR students, and how students may effectively work with multiple mentors. This workshop was delivered to a group of students from the HBCU Winston Salem State University, and a pre/post-Likert scale-based survey was administered.

ResultsWe analyzed the raw data with nonparametric tests for comparison within paired samples. Wilcoxon matched-pairs and signed-rank tests showed statistically significant growth in student self-ratings related to the workshop learning objectives.

ConclusionsThe "How to Handle More than One Mentor to Achieve Excellence" workshop was well received as a component of pre-graduate and pre-professional training. Incorporating workshops like this may increase student preparedness around developing and cultivating healthy mentorship relationships throughout STEM training.

EDUCATIONAL OBJECTIVESBy the end of this workshop, learners will be able to:

O_LIDescribe the role of mentors in developing the next generation of trainees.
C_LIO_LIDescribe current research on mentorship among underrepresented populations.
C_LIO_LIApply skills on effective communication needed in the development of successful mentorship relationships.
C_LIO_LIWork with multiple mentors at one time while maintaining solid professional and personal relationships.
C_LI


title: Striatal compartmentalization and clustering of different subtypes of astrocytes is altered in the zQ175 Huntington's disease mouse model

abstract: Huntingtons disease (HD) is a devastating neurodegenerative disease that primarily affects the striatum, a brain region that controls movement and some forms of cognition. Dysfunction and loss of medium spiny neurons of the striatum is accompanied by astrogliosis (increased astrocyte density and pathology). For decades, astrocytes were considered a homogeneous cell type, but recent transcriptomic analyses revealed astrocytes are a heterogeneous population classified into multiple subtypes depending on the expression of different gene markers. Here, we studied whether three different striatal astrocyte subtypes expressing glutamine synthetase (GS), glial fibrillary acidic protein (GFAP), or S100 calcium-binding protein B (S100B) are differentially altered in HD. We conducted a comparative immunofluorescence analysis in the striatum of WT and the heterozygous zQ175 HD mouse model and found that the expression and abundance of GFAP+ and S100B+ astrocytes increased in zQ175 mice, while GS+ astrocytes showed no alteration. We then explored whether there was a differential spatial distribution of any of these subtypes within the striatum. We developed a systematic brain compartmentalization approach and found that while GS+ and S100B+ astrocytes were more homogeneously distributed throughout the striatum in zQ175 mice, GFAP+ astrocytes preferentially accumulated in the dorsomedial and dorsolateral striatum, which are regions associated with goal-directed and habitual behaviors. Additionally, GFAP+ astrocytes in zQ175 mice showed increased clustering, a parameter that indicates increased proximity and that is associated with localized inflammation and/or neurodegeneration. Our data suggest a differential susceptibility in both increased density and striatal compartmentalization of different subtypes of astrocytes in zQ175. These results highlight new potential implications for our understanding of astrocyte pathology in HD.


title: The developing kidney actively negotiates geometric packing conflicts to avoid defects

abstract:
The physiological functions of several organs rely on branched tubular networks, but little is known about conflicts in development between building enough tubules for adequate function and geometric constraints imposed by organ size. We show that the mouse embryonic kidney epithelium negotiates a physical packing conflict between tubule tip duplication and limited area at the organ surface. Imaging, computational, and soft material modeling of tubule  families identifies six geometric packing phases, including two defective ones. Experiments in kidney explants show that a retrograde tension on tubule families is necessary and sufficient for them to avoid defects by switching to a vertical orientation that increases packing density. These results reveal developmental contingencies in response to physical limitations, and create a framework for classifying kidney defects.

One-Sentence SummaryEpithelial branching in the kidney causes a geometric packing conflict that is resolved through internally generated tensions

category: developmental biology


title: Chaperones drive in vitro evolution of uracil glycosylase towards misfolded states

abstract: Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time-scale and is driven by the given bait. Here, we used directed in vitro evolution of a random library of Uracil glycosylase (eUNG) displayed on yeast surface to select for binding to chaperones GroEL, DnaK+DnaJ+ATP (DnaKJ) or E.coli cell extract (CE). Using binding to the eUNG inhibitor Ugi as probe for native foldedess, the CE selected population was further divided to Ugi binders (+U) (native) or non-binders (-U). We found that GroEL, DnaKJ and CE-U select and enrich for mutations causing eUNG to misfold, with the three being enriched in mutations in buried and conserved positions, with a tendency to increase positive charge. Still, each selection, as well as CE+U and natural evolution of eUNG has its own trajectory. While GroEL and CE-U selected for mutants highly sensitive to protease cleavage, DnaKJ selected for partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. CE+U selected for more neutral mutations than natural evolution. In a more general context, our results show that GroEL has a higher tendency to purge promiscuous misfolded protein mutants from the system, while DnaKJ binds mutants misfolding-prone species that are, upon chaperone release, more likely to natively refold. CE-U shares some of the properties of GroEL and DnaKJ selected populations, while harboring also unique properties, explained by the existence of additional chaperones in CE, such as Tig, HtpG and ClpB.


title: In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states


title: Experimental and in silico Alphafold2 derived structures of the SNX-RGS proteins suggest a new class of lipid transfer protein

abstract: Recent advances in protein structure prediction using machine learning such as AlphaFold2 and RosettaFold presage a revolution in structural biology. Genome-wide predictions of protein structures are providing unprecedented insights into their architecture and intradomain interactions, and applications have already progressed towards assessing protein complex formation. Here we present detailed analyses of the sorting nexin proteins that contain regulator of G-protein signalling domains (SNX-RGS proteins), providing a key example of the ability of AlphaFold2 to reveal novel structures with previously unsuspected biological functions. These large proteins are conserved in most eukaryotes and are known to associate with lipid droplets (LDs) and sites of LD-membrane contacts, with key roles in regulating lipid metabolism. They possess five domains, including an N-terminal transmembrane domain that anchors them to the endoplasmic reticulum, an RGS domain, a lipid interacting phox homology (PX) domain and two additional domains named the PXA and PXC domains of unknown structure and function. Here we report the crystal structure of the RGS domain of sorting nexin 25 (SNX25) and show that the AlphaFold2 prediction closely matches the experimental structure. Analysing the full-length SNX-RGS proteins across multiple homologues and species we find that the distant PXA and PXC domains in fact fold into a single unique structure that notably features a large and conserved hydrophobic pocket. The nature of this pocket strongly suggests a role in lipid or fatty acid binding, and we propose that these molecules represent a new class of conserved lipid transfer proteins.

category: biochemistry


title: Structural predictions of the SNX-RGS proteins suggest they belong to a new class of lipid transfer proteins


title: The Effect of Oblique Image Acquisition on the Accuracy of Quantitative Susceptibility Mapping and a Robust Tilt Correction Method

abstract:
PurposeQuantitative susceptibility mapping (QSM) is increasingly used for clinical research where oblique image acquisition is commonplace but its effects on QSM accuracy are not well understood.

Theory and MethodsThe QSM processing pipeline involves defining the unit magnetic dipole kernel, which requires knowledge of the direction of the main magnetic field [Formula] with respect to the acquired image volume axes. The direction of [Formula] is dependent upon the axis and angle of rotation in oblique acquisition. Using both a numerical brain phantom and in-vivo acquisitions, we analysed the effects of oblique acquisition on magnetic susceptibility maps. We compared three tilt correction schemes at each step in the QSM pipeline: phase unwrapping, background field removal and susceptibility calculation, using the root-mean-squared error and QSM-tuned structural similarity index (XSIM).

ResultsRotation of wrapped phase images gave severe artefacts. Background field removal with projection onto dipole fields gave the most accurate susceptibilities when the field map was first rotated into alignment with [Formula]. LBV and VSHARP background field removal methods gave accurate results without tilt correction. For susceptibility calculation, thresholded k-space division, iterative Tikhonov regularisation and weighted linear total variation regularisation all performed most accurately when local field maps were rotated into alignment with [Formula] before susceptibility calculation.

ConclusionFor accurate QSM, oblique acquisition must be taken into account. Rotation of images into alignment with [Formula] should be carried out after phase unwrapping and before background field removal. We provide open-source tilt-correction code to incorporate easily into existing pipelines: https://github.com/o-snow/QSM_TiltCorrection.git.

category: bioengineering


title: Pathogenic potential prediction for novel fungal DNA based on a curated fungi-hosts data collection

abstract:
BackgroundEmerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remains comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone.

ResultsWe present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats.

ConclusionsThe neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1,400 genomes with host and pathogenicity metadata supports training of machine learning models and sequence comparison, not limited to the pathogen detection task.

AvailabilityThe data, models and code are hosted at https://zenodo.org/record/5846345, https://zenodo.org/record/5711877, and https://gitlab.com/dacs-hpi/deepac.


title: Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection


title: ChiMera: An easy to use pipeline for Bacterial Genome Based Metabolic Network Reconstruction, Evaluation and Visualization

abstract:
Several genome scale metabolic reconstruction tools have been developed in the last decades. They have helped to construct many metabolic models, which have contributed to a variety of fields, e.g., genetic engineering, drug discovery, prediction of phenotypes, and other model-driven discoveries. However, the use of these programs requires a higher level of bioinformatic skills, and most of them are not scalable for multiple genomes. Moreover, the functionalities required to build models are generally scattered through multiple tools, requiring knowledge of their utilization.

Here, we present ChiMera, which combines the most efficient tools in model reconstruction, prediction, and visualization. ChiMera uses CarveMe top-down approach based on genomic evidence to prune a global model with a high level of curation, generating a draft genome able to produce growth predictions using flux balance analysis for gram-positive and gram-negative bacteria. ChiMera also contains two modules of visualization implemented, predefined and universal. The first generates maps for the most important pathways, e.g., core-metabolism, fatty acid oxidation and biosynthesis, nucleotides and amino acids biosynthesis, glycolysis, and others. The second module produces a genome-wide metabolic map, which can be used to harvest KEGG pathway information for each compound in the model. A module of gene essentiality and knockout is also present. Overall, ChiMera combines model creation, gap-filling, FBA and metabolic visualization to create a simulation ready genome-scale model, helping genetic engineering projects, prediction of phenotypes, and other model-driven discoveries in a friendly manner.


title: Integration of Diverse Transcriptomics Datasets using Random Forest to Predict Universal Functional Pathways in Tfr Cells

abstract:
MotivationT follicular regulatory (Tfr) cells are a specialized cell subset that controls humoral immunity. Despite a number of individual transcriptomic studies on these cells, core functional pathways have been difficult to uncover due to the substantial transcriptional overlap of these cells with other effector cell types, as well as transcriptional changes occurring due to disease settings. Developing a core transcriptional module for Tfr cells that integrates multiple cell type comparisons as well as diverse disease settings will allow a more accurate prediction of functional pathways. Researchers studying allergic reactions, immune responses to vaccines, autoimmunity and cancer could use this gene set to better understand the roles of Tfr cells in controlling disease progression.

Additional cell types beyond Tfr cells that have similar features of transcriptomic complexity within diverse disease settings may also be studied using similar approaches. High-throughput sequencing technologies allow the generation of large datasets that require specific tools to best interpret the data. The development of a core transcriptional module for Tfr cells will allow investigators to determine if Tfr cells may have functional roles within their biological systems with little knowledge of Tfr biology. With this work, we have addressed the need of core gene modules to define specific subsets of immune cells.

ResultsWe introduce an integrated "core Tfr cell gene module" that can be incorporated into GSEA analysis using various input sizes. The integrated core Tfr gene module was built using transcriptomic studies in Tfr cells from several different tissues, disease settings, and cell type comparisons. Random forest was used to integrate the transcriptomic studies to generate the core gene module. A GSEA gene set was formulated from the integrated core Tfr gene module for incorporation into end-user friendly GSEA. The gene sets are presented along with random genes taken from the GTEX data set and are presented as GMT files. The user can upload the gene set to the GSEA website or any gene set tool which takes GMT files. We also present the full results of the model including p-values calculated by random forest. This provides users with more flexibility in choosing a p-value cutoff that is most appropriate for the experimental setting.

AvailabilityThe core Tfr gene sets are freely available at: https://github.com/alosdiallo/TFR_Model. We have also included all of the code and data used in developing these gene sets. The code and results are released under an MIT license.

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain

abstract: Class I WW domains mediate protein interactions by binding short linear PPxY motifs. They occur predominantly as tandem repeats, and their target proteins often contain multiple PPxY motifs, but the interplay of WW/peptide interactions is not always intuitive. WW domain-containing oxidoreductase (WWOX) protein harbors two WW domains: unstable WW1 capable of PPxY binding, and well-folded but mutated WW2 that cannot bind such motifs. WW2 is considered to act as a WW1 chaperone, but the underlying mechanism remains to be revealed. Here we combine NMR, ITC and structural modeling to elucidate the role of both WW domains in WWOX binding to single and double motif peptides derived from its substrate ErbB4. Using NMR we identified an interaction surface between the two domains that supports a WWOX conformation that is compatible with peptide substrate binding. ITC and NMR measurements reveal that while binding affinity to a single motif is marginally increased in the presence of WW2, affinity to a dual motif peptide increases tenfold, and that WW2 can directly bind double motif-peptides using its canonical binding site. Finally, differential binding of peptides in a mutagenesis study is consistent with a parallel orientation binding to the WW1-WW2 tandem domain, agreeing with structural models of the interaction. Our results reveal the complex nature of tandem WW domain organization and substrate binding, highlighting the contribution of WWOX WW2 to both stability and binding. This opens the way to assess how evolution can utilize the multivariate nature of binding to fine-tune interactions for specific biological functions.

category: biophysics


title: Continuum Theory for Planar Cell Polarity

abstract: Planar Cell Polarity (PCP), characterized by asymmetric localization of proteins at the cell membrane within the epithelial plane, plays essential roles in embryonic development and physiological functions. The significance of PCP can be appreciated by the outcomes of its failure in the form of defects in neural tube formation, tracheal malfunctions, organ shape misregulation, hair follicle misalignment etc. Extensive experimental works on PCP in fruit fly Drosophila melanogaster have classified the proteins involved in PCP into a  core module, acting locally by inter-cellular protein interactions, and a  global module, responsible for the alignment of cell polarities with that of the tissue axis. Despite the involvement of different molecular players the asymmetric localization of the proteins of the two modules on cell membrane primarily involves inter-cellular dimer formations. We have developed a continuum model of the localization of PCP proteins on the cell membrane and its regulation via intra- and inter-cellular protein-protein interactions. We have identified the conditions for the asymmetric protein localization, or PCP establishment, for uniform and graded protein expression levels in the tissue. We have found that in the absence of any tissue level expression gradient polarized state of the tissue does not arise. However, in the presence of tissue-level expression gradients of proteins the polarized state remains stable. We have also looked at the influence of the loss of PCP proteins from a select region of the tissue on the polarization of the cells outside of that region. This continuum theory of planar cell polarity can be coupled with active-matter hydrodynamics to study cell flows and their regulation by genetic machinery.


title: Thymosin β4 preserves vascular smooth muscle phenotype in atherosclerosis via regulation of Low Density Lipoprotein Related Protein 1 (LRP1)

abstract:
ObjectiveAtherosclerosis is a progressive, degenerative vascular disease and a leading cause of morbidity and mortality. In response to endothelial damage, platelet derived growth factor (PDGF)-BB induced phenotypic modulation of medial smooth muscle cells (VSMCs) promotes atherosclerotic lesion formation and destabilisation of the vessel wall. VSMC sensitivity to PDGF-BB is determined by endocytosis of Low density lipoprotein receptor related protein 1 (LRP1)-PDGFR{beta} complexes to balance receptor recycling with lysosomal degradation. Consequently, LRP1 is implicated in various arterial diseases. Having identified T{beta}4 as a regulator of LRP1-mediated endocytosis to protect against aortic aneurysm, we sought to determine whether T{beta}4 may additionally function to protect against atherosclerosis, by regulating LRP1-mediated growth factor signalling.

Approach and ResultsBy single cell transcriptomic analysis, Tmsb4x, encoding T{beta}4, strongly correlated with contractile gene expression and was significantly down-regulated in cells that adopted a modulated phenotype in atherosclerosis. We assessed susceptibility to atherosclerosis of global T{beta}4 knockout mice using the ApoE-/- hypercholesterolaemia model. Inflammation, elastin integrity, VSMC phenotype and signalling were analysed in the aortic root and descending aorta. T{beta}4KO; ApoE-/- mice develop larger atherosclerotic plaques than control mice, with medial layer degeneration characterised by accelerated VSMC phenotypic modulation. Defects in T{beta}4KO; ApoE-/- mice phenocopied those in VSMC-specific LRP1 nulls and, moreover, were underpinned by hyperactivated LRP1-PDGFR{beta} signalling.

ConclusionsWe identify an atheroprotective role for endogenous T{beta}4 in maintaining differentiated VSMC phenotype via LRP1-mediated PDGFR{beta} signalling.

category: pathology


title: Potassium effects on NCC are attenuated during inhibition of Cullin E3-ubiquitin ligases

abstract: The thiazide sensitive sodium-chloride co-transporter (NCC) plays a vital role in maintaining sodium (Na+) and potassium (K+) homeostasis. NCC activity is modulated by the with-no-lysine kinases 1 and 4 (WNK1 and WNK4), the abundance of which are controlled by the RING-type E3 ligase Cullin 3 (Cul3) and its substrate adapter Kelch-like protein 3. Dietary K+ intake has an inverse correlation with NCC activity, but the mechanism underlying this phenomenon remains to be fully elucidated. Here, we investigated the involvement of other members of the Cullin family in mediating K+ effects on NCC phosphorylation (active form) and abundance. In kidneys from mice fed diets varying in K+ content, there were negative correlations between NCC (phosphorylated and total) and active (neddylated) forms of Cullins (Cul1, 3, 4 and 5). High dietary K+ effects on phosphorylated NCC were attenuated in Cul3 mutant mice (CUL3-Het/{Delta}9). Short-term (30 min) and long-term (24 h) alterations in the extracellular K+ concentration did not affect Cullin neddylation levels in ex vivo renal tubules. Short-term, the ability of high extracellular K+ to decrease NCC phosphorylation was preserved in the presence of MLN4924 (pan Cullin inhibitor), but the response to low extracellular K+ was absent. Long-term, MLN4924 attenuated the effects of high extracellular K+ on NCC phosphorylation and responses to low extracellular K+ were absent. Our data suggest that in addition to Cul3, other Cullins are involved in mediating the effects of K+ on NCC phosphorylation and abundance.


title: Homeostatic active zone remodeling consolidates memories in the Drosophila mushroom body

abstract:
Establishing a detailed understanding of how the distinct forms of synaptic plasticity spatio-temporally engage into the initial storage and subsequent consolidation of memories remains a fundamental challenge of neuroscience. In addition to the better understood postsynaptic plasticity, different forms of presynaptic plasticity are widely expressed in mammalian brains and apparently operate along Hebbian or homeostatic rules. Their behavioral relevance remains enigmatic, however. Lately, acute upregulation of active zone (AZ) scaffold protein BRP and release factor Unc13A via specific axonal transport factors were shown to mediate stable expression of presynaptic homeostatic plasticity (PHP) at Drosophila neuromuscular junctions (NMJs).

We here demonstrate that AZ scaling processes are specifically needed for stable expression of both, NMJ PHP as well as aversive olfactory mid-term memory within intrinsic neurons of the Drosophila mushroom body (MB). We first demonstrate that AZ upscaling via BRP is specifically needed for expression but not induction of NMJ homeostatic plasticity, thus establishing a direct temporal plasticity sequence of molecularly distinct AZ remodeling steps. Notably, when we reduced BRP and associated transport factors in MB intrinsic neurons, short-term memory persisted but robust deficits in stable memory expression for a few hours after conditioning were observed. In contrast, AZ release site protein RIM-BP affecting PHP induction was additionally needed for successful formation of short-term memory.

Taken together, our data establish a specific role of homeostatic presynaptic long-term plasticity for memory consolidation. Such homeostatic refinement processes might well be needed to successfully integrate and display synaptic engrams constituting intermediary term memories.


title: Microglial MorphOMICs unravel region- and sex-dependent morphological phenotypes from postnatal development to degeneration

abstract: Microglia contribute to tissue homeostasis in physiological conditions with environmental cues influencing their ever-changing morphology. Strategies to identify these changes usually involve user-selected morphometric features, which, however, have proved ineffective in establishing a spectrum of context-dependent morphological phenotypes. Here, we have developed MorphOMICs, a topological data analysis approach to overcome feature-selection-based biases and biological variability. We extracted a spatially heterogeneous and sexually-dimorphic morphological phenotype for seven adult brain regions, with ovariectomized females forming their own distinct cluster. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration models, 5xFAD and CK-p25. Females show an earlier morphological shift in the immediately-affected brain regions. Finally, we demonstrate that both the primary- and the short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs maps microglial morphology into a spectrum of cue-dependent phenotypes in a minimally-biased and semi-automatic way.


title: Oligodendrocytes are a lifelong source of nuclear and ribosomal material for neurons in the mouse brain

abstract:
Nuclear and ribosomal components define cell identity and function by regulating chromatin dynamics, gene expression, and protein turnover. Here we report that in the mouse central nervous system (CNS) under normal conditions, neurons accumulate nuclear and ribosomal material of oligodendrocyte (OL) origin. We show that neuronal accumulation of OL-derived nuclear and ribosomal material is brain area-specific, and in the cortex and hippocampal dentate gyrus gradually propagates during postnatal brain maturation. We further demonstrate that OL-to-neuron material transfer persists throughout adulthood and responds to neuroinflammation. We found that satellite OL of the gray matter form internuclear contacts with receiving neurons in the mouse brain. Similar close internuclear associations between satellite OL and neurons are present in the adult human cortex. Our findings provide the first evidence of wide-spread dynamic and selective OL-to-neuron nuclear and ribosomal material transfer in the mouse CNS and indicate that satellite OL serve as powerful mediators of neuronal function. Equivalent processes may occur in the human CNS and cause neurological disorders when dysregulated.

One Sentence SummaryNeurons receive OL-derived nuclear and ribosomal material


title: Social-vocal brain networks in a non-human primate

abstract:
During social interactions, individuals influence each other to coordinate their actions. Vocal communication is an exceptionally efficient way to exert such influence. Where and how social interactions are dynamically modulated in the brain is unknown. We used functional ultrasound imaging in marmoset monkeys - a highly vocal species - to investigate the dynamics of medial social brain areas in vocal perception, production, and audio-vocal interaction. We found that the activity of a distributed network of subcortical and cortical regions distinguishes calls associated with different social contexts. This same brain network showed different dynamics during externally and internally driven vocalizations. These findings suggest the existence of a social-vocal brain network in medial cortical and subcortical areas that is fundamental in social communication.

One Sentence SummaryA network of medial subcortical and cortical brain areas gate social communication in primates.


title: Mapping Consistent, Reproducible, and Transcriptionally Relevant Connectome Hubs of the Human Brain

abstract: Human brain connectomes include sets of densely connected regions, known as connectome hubs, which play a vital role in understanding global brain communication, cognitive processing, and brain disorders. However, the consistency and reproducibility of functional connectome hubs anatomical localization have not been established to date and the genetic signatures underlying robust connectome hubs remain unknown. Here, we conduct the first worldwide, harmonized meta-connectomic analysis by pooling resting-state functional MRI data of 5,212 healthy young adults across 61 independent cohorts. We identify highly consistent and reproducible functional connectome hubs in heteromodal and unimodal regions both across cohorts and across individuals. These connectome hubs show heterogeneous connectivity profiles and are critical for both intra- and inter-network communications. Using post-mortem gene expression data, we show that these connectome hubs have a spatiotemporally distinctive transcriptomic pattern dominated by genes involved in the neuropeptide signaling pathway, neurodevelopmental processes, and metabolic processes. These results highlight the robustness of macroscopic connectome hubs and their potential cellular and molecular underpinnings.


title: Mapping Consistent, Reproducible, and Transcriptionally Relevant Functional Connectome Hubs of the Human Brain


title: Convergent Cerebrospinal Fluid Proteomes and Metabolic Ontologies in Humans and Animal Models of Rett Syndrome

abstract: MECP2 loss-of-function mutations cause Rett syndrome, a disorder that results from a disrupted brain transcriptome. How these transcriptional defects are decoded into a disease proteome remains unknown. We studied the proteome in Rett syndrome cerebrospinal fluid (CSF) across vertebrates. We identified a consensus proteome and ontological categories shared across Rett syndrome cerebrospinal fluid (CSF) from three species, including humans. Rett CSF proteomes enriched proteins annotated to HDL lipoproteins, complement, mitochondria, citrate/pyruvate metabolism, as well as synapse compartments. We used these prioritized and shared ontologies to select analytes for orthogonal quantification. These studies independently validated our proteome and ontologies. Ontologically selected CSF hits had genotypic discriminatory capacity as determined by Receiver Operating Characteristic (ROC) analysis and distinguished Rett from a related neurodevelopmental disorder, CDKL5 deficiency disorder. We propose that Mecp2 mutant CSF proteomes and ontologies inform novel putative mechanisms and biomarkers of disease. We suggest that Rett syndrome is a metabolic disorder impacting synapse function.


title: An atlas of the developing Tribolium castaneum	 brain reveals conserved anatomy and divergent timing to Drosophila melanogaster

abstract: Insect brains are formed by conserved sets of neural lineages whose fibres form cohesive bundles with characteristic projection patterns. Within the brain neuropil these bundles establish a system of fascicles constituting the macrocircuitry of the brain. The overall architecture of the neuropils and the macrocircuitry appear to be conserved. However, variation is observed e.g., in size and shape and timing of development. Unfortunately, the developmental and genetic basis of this variation is poorly understood although the rise of new genetically tractable model organisms such as the red flour beetle Tribolium castaneum allows the possibility to gain mechanistic insights. To facilitate such work, we present an atlas of the developing brain of T. castaneum, covering the first larval instar, the prepupal stage and the adult, by combining wholemount immunohistochemical labelling of fibre bundles (acetylated tubulin) and neuropils (synapsin) with digital 3D reconstruction using the TrakEM2 software package. Upon comparing this anatomical dataset with the published work in D. melanogaster, we confirm an overall high degree of conservation. Fibre tracts and neuropil fascicles, which can be visualized by global neuronal antibodies like anti-acetylated tubulin in all invertebrate brains, create a rich anatomical framework to which individual neurons or other regions of interest can be referred to. The framework of a largely conserved pattern allowed us to describe differences between the two species with respect to parameters such as timing of neuron proliferation and maturation. These features likely reflect adaptive changes in developmental timing that govern the change from larval to adult brain.


title: Efficient targeting of NY-ESO-1 tumor antigen to human cDC1s by lymphotactin results in cross-presentation and antigen-specific T cell expansion

abstract: Type 1 conventional dendritic cells (cDC1s) are characterized by their ability to induce potent CD8+ T cell responses. In efforts to generate novel vaccination strategies, notably against cancer, human cDC1s emerge as an ideal target to deliver antigens. cDC1s uniquely express XCR1, a seven transmembrane G protein-coupled receptor (GPCR). Due to its restricted expression and endocytic nature, XCR1 represents an attractive receptor to mediate antigen-delivery to human cDC1s. To explore tumor antigen delivery to human cDC1s, we used an engineered version of XCR1-binding lymphotactin (XCL1), XCL1(CC3). Site-specific sortase-mediated transpeptidation was performed to conjugate XCL1(CC3) to an analog of the HLA-A*02:01 epitope of the cancer testis antigen New York Esophageal Squamous Cell Carcinoma-1 (NY-ESO-1). While poor epitope solubility prevented isolation of stable XCL1-antigen conjugates, incorporation of a single polyethylene glycol (PEG) chain upstream of the epitope-containing peptide enabled generation of soluble XCL1(CC3)-antigen fusion constructs. Binding and chemotactic characteristics of the XCL1-antigen conjugate, as well as its ability to induce antigen-specific CD8+ T cell activation by cDC1s, was assessed. PEGylated XCL1(CC3)-antigen conjugates retained binding to XCR1, and induced cDC1 chemoattraction in vitro. The model epitope was efficiently cross-presented by human cDC1s to activate NY-ESO-1-specific CD8+ T cells. Importantly, vaccine activity was increased by targeting XCR1 at the surface of cDC1s. Our results present a novel strategy for the generation of targeted vaccines fused to insoluble antigens. Moreover, our data emphasize the potential of targeting XCR1 at the surface of primary human cDC1s to induce potent CD8+ T cell responses.

category: immunology


title: Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes

abstract:
The sulfur-containing amino acid cysteine is abundant in the environment including in freshwater lakes. Biological degradation of cysteine can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments, including freshwater lakes. Here, we investigated the ecological significance of cysteine in oxic freshwater lake environments, using model systems of isolated cultures, controlled growth experiments, and multi-omics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. In total, we identified 29 isolates that produced H2S and belonged to the phylum proteobacteria Bacteroidetes, Proteobacteria and Actinobacteria. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized 3 freshwater isolates using whole-genome sequencing, and quantitatively tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophila, Stenotrophomonas bentonitica (Gammaproteobacteria) and Chryseobacterium piscium (Bacteroidetes). We observed a decrease in cysteine and increase in H2S, and identified genes involved in cysteine degradation in all 3 genomes. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a five-year time series of metagenomic data from the same isolation source at Lake Mendota and identified their presence throughout the time series. Overall, our study shows that sulfur-containing amino acids can drive microbial H2S production in oxic environments. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from degradation of organosulfur compounds.

ImportanceHydrogen sulfide (H2S), a naturally occurring gas with biological origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments such as sediments, or the bottom layers of lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for the biological production of H2S such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we found that multiple bacteria originating from a freshwater lake can not only produce H2S, but do so in oxic conditions. Overall, our study highlights the ecological importance of oxic H2S production in natural ecosystems, and necessitates a change in our outlook of sulfur biogeochemistry.

category: microbiology


title: Babesia duncani as a model organism to study the development, virulence and drug susceptibility of intraerythrocytic parasites in vitro and in vivo

abstract:
Hematozoa are a subclass of protozoan parasites that invade and develop within vertebrate red blood cells to cause the pathological symptoms associated with diseases of both medical and veterinary importance such as malaria and babesiosis. A major limitation in the study of the most prominent hematozoa, Plasmodium spp, the causative agents of malaria, is the lack of a broadly accessible mouse model to evaluate parasite infection in vivo as is the case for P. falciparum or altogether the lack of an in vitro culture and mouse models as is the case for P. vivax, P. malariae and P. ovale. Similarly, no in vitro culture system exists for Babesia microti, the predominant agent of human babesiosis. In this study, we show that human red blood cells infected with the human pathogen Babesia duncani continuously propagated in culture, as well as merozoites purified from parasite cultures, can cause lethal infection in immunocompetent C3H/HeJ mice. Furthermore, highly reproducible parasitemia and survival outcomes were established using specific parasite loads and different mouse genetic backgrounds. Using the combined in culture-in mouse (ICIM) model of B. duncani infection, we demonstrate that current recommended combination therapies for the treatment of human babesiosis, while synergistic in cell culture, have weak potency in vitro and failed to clear infection or prevent death in mice. Interestingly, using the ICIM model, we identified two new endochin-like quinolone prodrugs, ELQ-331 and ELQ-468, that alone or in combination with atovaquone are highly efficacious against B. duncani and B. microti. The novelty, ease of use and scalability of the B. duncani ICIM dual model make it an ideal system to study intraerythrocytic parasitism by protozoa, unravel the molecular mechanisms underlying parasite virulence and pathogenesis, and accelerate the development of innovative therapeutic strategies that could be translated to unculturable parasites and important pathogens for which an animal model is lacking.

Author SummaryUse of model organisms is vital to the understanding of virulence and pathogenesis of a large number of human and animal pathogens. In case of hematozoan parasites that invade and develop within vertebrate erythrocytes, the studies are challenging because of the dearth of small animal model systems and the lack of continuous parasite growth in in vitro culture conditions. Here, we report a small animal model of lethal infection of Babesia duncani, one of the causative agents of human babesiosis. We show that in vitro cultured parasites and as well as parasites propagated in vivo can establish highly reproducible parasitemia which is dependent on the parasite load and also defined by different mouse genetic backgrounds. We further use this combined in culture-in mouse (ICIM) model of B. duncani infection to demonstrate the anti-babesial efficacy of two novel endochin like quinoline compounds. We propose that this ICIM dual model of B. duncani is an ideal system to get insights into protozoan intraerythrocytic parasitism, virulence, pathogenesis, and therapeutics and will open the vista to other important pathogens which are unculturable or lack an animal model.


title: Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome

abstract:
DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. We show that overall, DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

One-Sentence SummaryDNA methylation patterns are associated with ecological changes and virus-host dynamics in the marine microbiome.


title: Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling

abstract: The proper trafficking of eukaryotic proteins is essential to cellular function. Genetic, environmental, and other stresses can induce protein mistargeting, and in turn threaten cellular protein homeostasis. Current methods for measuring protein mistargeting are difficult to translate to living cells, and thus the role of cellular signaling networks in stress-dependent protein mistargeting processes, such as ER pre-emptive quality control (ER pQC), are difficult to parse. Herein, we use genetically encoded peroxidases to characterize protein import into the endoplasmic reticulum (ER). We show that the ERHRP/cytAPEX pair provides good selectivity and sensitivity for identifying protein mistargeting, using the known ER pQC substrate transthyretin (TTR). Although ERHRP labeling induces formation of detergent-resistant TTR aggregates, this is minimized by using low ERHRP expression, without loss of labeling efficiency. cytAPEX labeling recovers TTR that is mistargeted as a consequence of Sec61 inhibition or ER stress-induced ER pQC. Furthermore, we demonstrate that stress-free activation of the ER stress-associated transcription factor ATF6 recapitulates the TTR import deficiency of ER pQC. Hence, proximity labeling is an effective strategy for characterizing factors that influence ER protein import in living cells.

category: molecular biology


title: Nanoscale structural organization and stoichiometry of the budding yeast kinetochore

abstract: Proper chromosome segregation is crucial for cell division. In eukaryotes, this is achieved by the kinetochore, an evolutionarily conserved multi-protein complex that physically links the DNA to spindle microtubules, and takes an active role in monitoring and correcting erroneous spindle-chromosome attachments. Our mechanistic understanding of these functions, and how they ensure an error-free outcome of mitosis, is still limited, partly because we lack a comprehensive understanding of the kinetochore structure in the cell. In this study, we use single molecule localization microscopy to visualize individual kinetochore complexes in situ in budding yeast. For all major kinetochore proteins, we measured abundance and position within the metaphase kinetochore. Based on this comprehensive dataset, we propose a quantitative model of the budding yeast kinetochore. While confirming many aspects of previous reports based on bulk imaging of kinetochores, our results present a somewhat different but unifying model of the inner kinetochore. We find that the centromere-specialized histone Cse4 is present in more than two copies per kinetochore along with its binding partner Mif2.

category: cell biology


title: Reemployment of Kupffer's vesicle cells into axial and paraxial mesoderm via transdifferentiation

abstract: Kupffers vesicle (KV) in the teleost embryo is a fluid-filled vesicle surrounded by a layer of epithelial cells with rotating primary cilia. KV transiently acts as the left-right organizer but degenerates after the establishment of left-right asymmetric gene expression. Previous labelling experiments indicated that descendants of KV-epithelial cells are incorporated into mesodermal tissues after KV collapses (KV-collapse) in zebrafish embryos. However, the overall picture of their differentiation potency had been unclear due to the lack of suitable genetic tools and molecular analyses. In the present study, we established a novel zebrafish transgenic line with a promoter of charon, in which all KV-epithelial cells and their descendants are specifically labelled until the larval stage. We found that KV-epithelial cells underwent epithelial-mesenchymal transition upon KV-collapse and infiltrate into adjacent mesodermal progenitors, the presomitic mesoderm and chordoneural hinge. Once incorporated, the descendants of KV-epithelial cells expressed distinct mesodermal differentiation markers and contributed to the mature populations such as the axial muscles and notochordal sheath through normal developmental process. These results indicate that fully differentiated KV-epithelial cells possess unique plasticity in that they are reemployed into mesodermal lineages through transdifferentiation after they complete their initial role in KV.


title: Retinoid-X Receptor Agonists Increase Thyroid Hormone Competence in Lower Jaw Remodeling of Pre-Metamorphic Xenopus laevis tadpoles

abstract: Thyroid hormone (TH) signaling plays critical roles during vertebrate development, including regulation of skeletal and cartilage growth. TH acts through its receptors (TRs), nuclear hormone receptors (NRs) that heterodimerize with Retinoid-X receptors (RXRs), to regulate gene expression. A defining difference between NR signaling during development compared to in adult tissues, is competence, the ability of the organism to respond to an endocrine signal. Amphibian metamorphosis, especially in Xenopus laevis, the African clawed frog, is a well-established in vivo model for studying the mechanisms of TH action during development. Previously, weve used one-week post-fertilization X. laevis tadpoles, which are only partially competent to TH, to show that in the tail, which is naturally refractive to exogenous T3 at this stage, RXR agonists increase TH competence, and that RXR antagonism inhibits the TH response. Here, we focused on the jaw that undergoes dramatic TH-mediated remodeling during metamorphosis in order to support new feeding and breathing styles. We used a battery of approaches in one-week-old tadpoles, including quantitative morphology, differential gene expression and whole mount cell proliferation assays, to show that both pharmacologic (bexarotene) and environmental (tributyltin) RXR agonists potentiated TH-induced responses but were inactive in the absence of TH; and the RXR antagonist UVI 3003 inhibited TH action. At this young age, the lower jaw has not developed to the point that T3-induced changes produce an adult-like jaw morphology, and we found that increasing TH competence with RXR agonists did not give us a more natural-metamorphic phenotype, even though Bex and TBT significantly potentiated cellular proliferation and the TH induction of runx2, a transcription factor critical for developing cartilage and bone. Prominent targets of RXR-mediated TH potentiation were members of the matrix metalloprotease family, suggesting that RXR potentiation may emphasize pathways responsible for rapid changes during development.


title: A single-cell transcriptome atlas of human early embryogenesis

abstract: The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4- to 6-week human embryos when essentially all organs are just laid out. Based on over 100,000 single-cell transcriptomes, we generated a comprehensive atlas of 333 cell types that belong to 18 developmental systems, and identified hundreds of cell type specific markers as well as dynamic gene changes. Combined with data of other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.


title: Socioeconomics drive population change in the world's largest carnivores

abstract: Land-use1,2 and climate change3-5 have been linked to wildlife population declines, but the role of socioeconomic factors in driving declines, and promoting population recoveries, remains relatively unexplored despite its likely importance. Here, we evaluate a comprehensive array of potential drivers of population changes observed in some of the worlds most charismatic species - large mammalian carnivores. Our results reveal a strong role of human socioeconomic development, which we find has a greater impact on population change than habitat loss and climate change. Increases in socioeconomic development are linked to sharp population declines but, importantly, once development is high, carnivore populations have the potential to recover. These links between human development and wildlife population health highlight the challenges ahead to achieve the different UN Sustainable development goals.

category: ecology


title: Remote sensing reveals multi-decadal losses of tree cover in California driven by increasing fire disturbance and climate stress

abstract:
Forests provide natural climate solutions for sequestering carbon and mitigating climate change yet are threatened by increasing temperatures and disturbance. Accurate information on vegetation dynamics is lacking in some regions with forest carbon offset programs and dense forests like California. To address this, we combined remote sensing observations with geospatial databases to develop annual maps of vegetation cover (tree, shrub, herbaceous) and disturbance type (fires, harvest, and forest die-off) in California at 30 m resolution from 1985 to 2021. California lost 3783 km2 of its tree cover area (5.5% relative to initial cover). Early gains in tree cover area were more than offset by fire-driven declines, resulting in greater shrub and herbaceous cover area. Fires and tree cover area loss occurred where temperatures were high or increasing, whereas tree cover gain occurred in cooler areas. Disturbance and warming are threatening the integrity of Californias forests and its carbon offsets program.

TeaserClimate and disturbance-driven tree cover loss challenges the viability of forests as natural climate solutions in California


title: Genetic assimilation of ancestral plasticity during parallel adaptation

abstract: Phenotypic plasticity in ancestral populations is hypothesised to facilitate adaptation, but evidence supporting its contribution is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel genetic and phenotypic adaptive changes has not been explored. The most general finding is that nearly all ancestral gene expression plasticity is reversed following adaptation, but this is usually examined transcriptome-wide rather than focused on the genes directly involved in adaptation. We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared to ancestral, zinc-sensitive plants. Our experiments show that reinforcement of ancestral plasticity plays an influential role in the evolution of plasticity in derived populations and, surprisingly, one third of constitutive differences between ecotypes are the result of genetic assimilation of ancestral plasticity. Ancestral plasticity also increases the chance that genes are recruited repeatedly during adaptation. However, despite a high degree of convergence in gene expression levels between independently adapted lineages, genes with ancestral plasticity are as likely to have similar expression levels in adapted populations as genes without. Overall, these results demonstrate that ancestral plasticity does play an important role in adaptive parallel evolution, particularly via genetic assimilation across evolutionary replicates.


title: Australia as a global sink for the genetic diversity of avian influenza A virus

abstract:
Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.

Author SummaryA result of the ever-growing poultry industry is a dramatic global increase in the incidence of high pathogenicity avian influenza virus outbreaks. In contrast, wild birds are believed to be the main reservoir for low pathogenic avian influenza A virus. Due to intensive research and surveillance of AIV in waterfowl in the Northern Hemisphere, we have a better understanding of AIV ecology and evolution in that region compared to the Southern Hemisphere, which are characterised by different patterns of avian migration and ecological conditions. We analysed 333 unique AIV genomes collected from wild birds in Australia to understand how Australia fits into global AIV dynamics and how viruses are maintained and dispersed within the continent of Australia. We show that the Southern Hemisphere experiences differing evolutionary dynamics to those seen in Northern Hemisphere with Australia representing a global sink for AIV.


title: The evolution of ovary-specific gene expression in Hawaiian Drosophilidae

abstract: 1With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. However, our results provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the Drosophila ovary.


title: Identifying evolutionary divergence in gene expression across species and organs: a case-study using Hawaiian Drosophila


title: Mitochondrial DNA metabolism is coupled with 20S proteasome function via regulation of deoxyribonucleotide homeostasis in Saccharomyces cerevisiae

abstract: The synthesis of mitochondrial DNA (mtDNA) is not coupled with cell cycle. Previous studies have shown that the size of deoxyribonucleoside triphosphate (dNTP) pools plays an important role in regulating mtDNA replication and amplification. In yeast, dNTPs are synthesized by the cytosolic ribonucleotide reductase (RNR). It is currently poorly understood as to how RNR activity is regulated in non-dividing or quiescent cells to finely tune mtDNA metabolism to cope with different metabolic states. Here, we show that defect in the 20S proteasome drastically destabilizes mtDNA. The mtDNA instability phenotype in 20S proteasome mutants is suppressed by overexpression of RNR3 or by the deletion of SML1, encoding a minor catalytic subunit and an intrinsic inhibitor of RNR respectively. We found that Sml1 is stabilized in the 20S proteasomal mutants, suggesting that 20S affects mtDNA stability by stabilizing Sml1. Interestingly, defect in the regulatory 19S proteasomal function has only subtle effect on mtDNA stability, supporting a role of the 20S proteasome in dNTP homeostasis independent of 19S. Finally, we found that when cells are transitioned from glycolytic to oxidative growth, Sml1 level is reduced in a 20S-dependent manner. In summary, our study establishes a link between cellular proteostasis and mtDNA metabolism through the regulation of dNTP homeostasis. We propose that increased degradation of Sml1 by the 20S proteasome under respiratory conditions provides a mechanism to stimulate dNTP synthesis and promote mtDNA amplification.


title: The FORCE panel: An all-in-one SNP marker set for confirming investigative genetic genealogy leads and for general forensic applications

abstract: The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5,422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3,931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing [~]20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of [~]99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict 1st to 5th degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5,000 SNP panel for forensic applications.


title: Potential effects of life history on demographic genetic structure in stage-structured plant populations

abstract: Standing genetic variation, or genetic diversity, is a source of adaptive evolution, and is crucial for long-term population persistence under environmental changes. One empirical method to predict the temporal dynamics of standing genetic variation in age- or stage-structured populations is to compare genetic diversity and composition among age/stage classes. The resultant within-population genetic structure, sometimes referred to as demographic genetic structure, has been regarded as a proxy of potential genetic changes that accompany sequential generation turnover. However, especially in stage-structured plant populations, individuals in more juvenile stages do not necessarily represent future populations, as they might die, stop growing, or retrogress over the course of life history. How demographic genetic structure is subjected to life history and whether it is a good proxy of temporal genetic dynamics had remained unclear. Here, we developed a matrix model which well describes temporal dynamics of expected heterozygosity, a common proxy of genetic diversity, for a neutral locus in stage-structured populations under equilibrium assumption. Based on the model, two indices of demographic genetic structure were formulated: relative ratio of expected heterozygosity and genetic differentiation among stage classes. We found that the two indices were largely determined by stable stage distribution and population size, and that they did not show clear correlations with the change rate of genetic diversity, indicating that inferring future genetic diversity from demographic genetic structure conventionally is misleading. Our study facilitates reliable interpretation on empirical demographic genetic data.


title: The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

abstract: Three-dimensional (3D) chromatin organization maps help to dissect cell type-specific gene regulatory programs. Furthermore, 3D chromatin maps have contributed to elucidating the pathogenesis of complex genetic diseases by connecting distal regulatory regions and genetic risk variants to their respective target genes. To understand the cell type-specific regulatory architecture of diabetes risk, we generated transcriptomic and 3D epigenomic profiles of human pancreatic acinar, alpha, and beta cells using single-cell RNA-seq, single-cell ATAC-seq, and high-resolution Hi-C of sorted cells. Comparisons of these profiles revealed differential A/B (open/closed) chromatin compartmentalization, chromatin looping, and transcriptional factor mediated control of cell type-specific gene regulatory programs. We identified a total of 4,750 putative causal-variant-target-gene pairs at 194 type 2 diabetes GWAS signals using pancreatic 3D chromatin maps. We found that the connections between candidate causal variants and their putative target effector genes are cell-type stratified and emphasize previously underappreciated roles for alpha and acinar cells in diabetes pathogenesis.


title: Mutation, selection, and the prevalence of the C. elegans mortal germline phenotype

abstract: C. elegans strains with the heat-sensitive mortal germline (Mrt) phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans tolerance. Mrt is transgenerationally-heritable, and proximately under epigenetic control. Previous studies have suggested that Mrt presents a relatively large mutational target, and that Mrt is not uncommon in natural populations of C. elegans. The Mrt phenotype is not monolithic. Some strains exhibit a strong Mrt phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the Mrt phenotype, and (2) quantify the frequency of Mrt in a collection of 95 wild isolates. Over the course of ~16,000 meioses, we detected one mutation to a strong Mrt phenotype, resulting in a point estimate of the mutation rate UMrt{approx} 6x10-5/genome/generation. We detected no mutations to a weak Mrt phenotype. 6/95 wild isolates have a strong Mrt phenotype, and although quantification of the weak Mrt phenotype is inexact, the weak Mrt phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong Mrt phenotype [Formula], similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak Mrt variants in nature combined with the low mutation rate suggests that Mrt may be maintained by balancing selection.