title: The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

abstract:
Despite extensive studies on the curve-shaped bacterium Vibrio cholerae, the causative agent of the diarrheal disease cholera, its virulence-associated regulatory two-component signal transduction system VarS/VarA is not well understood. This pathway, which mainly signals through the downstream protein CsrA, is highly conserved among gamma-proteobacteria, indicating there is likely a broader function of this system beyond virulence regulation. In this study, we investigated the VarA-CsrA signaling pathway and discovered a previously unrecognized link to the shape of the bacterium. We observed that varA-deficient V. cholerae cells showed an abnormal spherical morphology during late-stage growth. Through peptidoglycan (PG) composition analyses, we discovered that these mutant bacteria contained an increased content of disaccharide dipeptides and reduced peptide crosslinks, consistent with the atypical cellular shape. The spherical shape correlated with the CsrA-dependent overproduction of aspartate ammonia lyase (AspA) in varA mutant cells, which likely depleted the cellular aspartate pool; therefore, the synthesis of the PG precursor amino acid meso-diaminopimelic acid was impaired. Importantly, this phenotype, and the overall cell rounding, could be prevented by means of cell wall recycling. Collectively, our data provide new insights into how V. cholerae use the VarA-CsrA signaling system to adjust its morphology upon unidentified external cues in its environment.

Significance StatementResponsible for the diarrheal disease cholera, the bacterium Vibrio cholerae tightly regulates its virulence program according to external stimuli. Here, we discovered that a sensing-response mechanism involved in the regulation of virulence also controls bacterial shape. We show that V. cholerae lacking this system lose their normal comma shape and become spherical due to an abnormal cell wall composition caused by metabolic changes that reduce available cell wall building blocks. Our study therefore sheds new light on how V. cholerae modulates its morphology based on environmental changes.


title: MurA escape mutations uncouple peptidoglycan biosynthesis from PrkA signaling

abstract:
Gram-positive bacteria are protected by a thick mesh of peptidoglycan (PG) completely engulfing their cells. This PG network is the main component of the bacterial cell wall, it provides rigidity and acts as foundation for the attachment of other surface molecules. Biosynthesis of PG consumes a high amount of cellular resources and therefore requires careful adjustments to environmental conditions.

An important switch in the control of PG biosynthesis of Listeria monocytogenes, a Gram-positive pathogen with a high infection fatality rate, is the serine/threonine protein kinase PrkA. A key substrate of this kinase is the small cytosolic protein ReoM. We have shown previously that ReoM phosphorylation regulates PG formation through control of MurA stability. MurA catalyzes the first step in PG biosynthesis and the current model suggests that phosphorylated ReoM prevents MurA degradation by the ClpCP protease. In contrast, conditions leading to ReoM dephosphorylation stimulate MurA degradation. How ReoM controls degradation of MurA and potential other substrates is not understood. Also, the individual contribution of the [~]20 other known PrkA targets to PG biosynthesis regulation is unknown.

We here present murA mutants which escape proteolytic degradation. The release of MurA from ClpCP-dependent proteolysis was able to constitutively activate PG biosynthesis and further enhances the intrinsic cephalosporin resistance of L. monocytogenes. This activation required the RodA3/PBP B3 transglycosylase/transpeptidase pair as additional effectors of the PrkA signaling route. One murA escape mutation not only fully rescued an otherwise non-viable prkA mutant during growth in batch culture and inside macrophages but also overcompensated cephalosporin hypersensitivity. Our data collectively indicate that the main purpose of PrkA-mediated signaling in L. monocytogenes is control of MurA stability during extra- and intracellular growth. These findings have important implications for the understanding of PG biosynthesis regulation and {beta}-lactam resistance of L. monocytogenes and related Gram-positive bacteria.

Author SummaryPeptidoglycan (PG) is the main component of the bacterial cell wall and many of the PG synthesizing enzymes are antibiotic targets. We previously have discovered a new signaling route controlling PG production in the human pathogen Listeria monocytogenes. This route also determines the intrinsic resistance of L. monocytogenes against cephalosporins, a group of {beta}-lactam antibiotics. Signaling involves PrkA, a membrane-embedded protein kinase, that is activated during cell wall stress to phosphorylate its target ReoM. Depending on its phosphorylation, ReoM activates or inactivates PG production by controlling the proteolytic stability of MurA, which catalyzes the first step in PG biosynthesis. MurA degradation depends on the ClpCP protease and we here have isolated murA mutations that escape this degradation. Using these mutants, we could show that regulation of PG biosynthesis through control of MurA stability is the primary purpose of PrkA-mediated signaling in L. monocytogenes. Further experiments identified the transglycosylase RodA and the transpeptidase PBP B3 as additional effectors of PrkA signaling. Our results suggest that both proteins act together to translate the signals received by PrkA into intensification of PG biosynthesis. These findings shed new light on the regulation of PG biosynthesis in Gram-positive bacteria with intrinsic {beta}-lactam resistance.

category: microbiology


title: Bma-LAD-2, an intestinal cell adhesion protein, as a potential therapeutic target for lymphatic filariasis

abstract:
Lymphatic filariasis (LF) is a debilitating disease that afflicts over 70 million people worldwide. It is caused by the parasitic nematodes Wuchereria bancrofti, Brugia malayi, and Brugia timori. While efforts to eliminate LF have seen substantial success, complete eradication will likely require more time and resources than predicted. Identifying new drug and vaccine targets in adult filariae could help elimination efforts.

This studys aim was to evaluate intestinal proteins in adult Brugia malayi worms as possible therapeutic targets. Using siRNA, we successfully inhibited transcripts of four candidate genes: Bma-Serpin, Bma-ShTK, Bma-Reprolysin, and Bma-LAD-2. Of those, Bma-LAD-2, an immunoglobulin superfamily cell adhesion molecule (IgSF CAM), was determined to be essential for adult worm survival. We observed a 70.42% knockdown in Bma-LAD-2 transcript levels 1 day post-siRNA incubation and an 87.02% reduction in protein expression 2 days post-siRNA incubation. This inhibition of Bma-LAD-2 expression resulted in an 80% decrease in worm motility over 6 days, a 93.43% reduction in microfilaria release (Mf) by day 6 post-siRNA incubation, and a significant decrease in MTT reduction. Transmission electron microscopy revealed the loss of microvilli and unraveling of mitochondrial cristae in the intestinal epithelium of Bma-LAD-2 siRNA-treated worms. Strikingly, Bma-LAD-2 siRNA-treated worms exhibited an almost complete loss of pseudocoelomic fluid, suggesting that loss of these tight junctions led to the leakage and subsequent loss of the worms structural integrity. Luciferase immunoprecipitation system assay demonstrated that serum from 30 patients with LF did not have detectable IgE antibodies against Bma-LAD-2, indicating that LF exposure does not result in IgE sensitization to this antigen.

These results indicate that Bma-LAD-2 is an essential protein for adult Brugia malayi and may be an effective drug or vaccine target. In addition, these findings further validate the strategy of targeting the worm intestine to prevent and treat helminthic infections.

Author SummaryBrugia malayi is a parasitic nematode that can cause lymphatic filariasis, a debilitating disease prevalent in tropical and subtropical countries. Significant progress has been made towards eliminating the disease. However, complete eradication may require new therapeutics such as drugs or a vaccine that kill adult filariae. In this study, we identified an immunoglobulin superfamily cell adhesion molecule (Bma-LAD-2) as a potential drug and vaccine candidate. When we knocked down Bma-LAD-2 expression, we observed a decrease in worm motility, fecundity, and metabolism. We also visualized the loss of microvilli, destruction of the mitochondria in the intestinal epithelium, and loss of pseudocoelomic fluid contents after Bma-LAD-2 siRNA treatment. Finally, we demonstrated that serum from filaria-infected patients does not contain preexisting IgE to Bma-LAD-2, which indicates that this antigen would likely be safe to administer as a vaccine in endemic populations.


title: Robust maintenance of cell surface tension in mitosis by RhoA-driven myosin II mechanoresponse

abstract: As cells enter mitosis, cell cortex contraction generates surface tension to establish a geometry feasible for division in a physically confined environment. Cell surface tension rises in prophase and continues to stay constant during metaphase to support mitosis. How the cell surface tension is maintained throughout mitosis is not well explored. We show that the cell surface tension is actively maintained by a mechanosensitive RhoA pathway at the cell cortex during mitosis. Mechanical activation of RhoA leads to non-muscle myosin IIB (NMIIB) stabilization and mechanosensitive accumulation at the cell cortex via Rho kinase (ROCK) regulation of the NMIIB head domain. Interestingly, when the NMIIB tail domain regulation is perturbed, the NMIIB has reduced ability to generate tension but could still support mitotic cells to withstand compressive stress by undergoing mechanosensitive accumulation at the cell cortex. Thus, mechanical RhoA activation drives NMIIB mechanoresponse via its head domain regulation to maintain cell surface tension during mitosis.

category: cell biology


title: Lipid chaperone LBP-8 coordinates with nuclear factors to promote longevity in Caenorhabditis elegans

abstract: Eukaryotic cells are composed of a variety of organelles. Their coordination plays crucial roles in cellular homeostasis and organism longevity and is mediated by proteins with the ability to transport between different organelles. In Caenorhabditis elegans, LBP-8 is a pro-longevity lipid chaperone that can localize to both lysosomes and the nucleus. Here we profiled LBP-8s binding partners using immunoprecipitation and mass spectrometry. From the 45 identified candidates, we discovered four nuclear factors that are required for the LBP-8-induced longevity. Among them, RPC-2, an RNA Polymerase III core subunit, is also necessary for the nuclear localization of LBP-8. Moreover, we have screened nuclear transport machinery components, and revealed the requirement of the nuclear import, not export, for the LBP-8 longevity effects. Together, these results suggest that the lipid chaperone LBP-8 relies on specific nuclear factors to retain in the nucleus and regulate longevity.


title: PAEP and cilia gene splicing changes in endometrial glands during the implantation window in women with recurrent pregnancy loss

abstract: Endometrial glands are essential for fertility, consisting of ciliated and secretory cells that facilitate a suitable uterine environment for embryo implantation. This study sought to determine whether an endometrial gland specific transcriptome and splicing profile are altered in women with recurrent pregnancy loss. Our data provide a comprehensive catalogue of cilia and PAEP gene isoforms and relative exon usage in endometrial glands. We report a previously unannotated endometrial gland cilia transcript GALNT11 and its susceptibility to exon skipping. Key endometrial receptivity gene transcripts are also reported to change in endometrial glands of women with recurrent pregnancy loss. The endometrial gland cilia and PAEP targets identified in this study could be used to identify a perturbed endometrium, isolate causes of recurrent pregnancy loss and develop targeted therapies in personalised medicine.

category: developmental biology


title: Evolutionary transition from a single RNA replicator to a multiple replicator network

abstract: In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we performed long-term evolution experiments using an RNA that replicates by a self-encoded RNA replicase. The RNA diversified into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuated and gradually stabilized. The final population, comprising five RNA lineages, forms a replicator network with diverse interactions, including cooperation to help the replication of all other members. These results support the capability of molecular replicators to spontaneously develop complexity through Darwinian evolution, a critical step for the emergence of life.

category: evolutionary biology


title: Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

abstract:
Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.

Significance statementUnderstanding the genetic basis of important phenotypes is a central goal of genetics. However, the highly polygenic architectures of complex traits inferred by large-scale genome-wide association studies (GWAS) in humans stand in contrast to the results of quantitative trait locus (QTL) mapping studies in model organisms. Here, we use a barcoding approach to conduct QTL mapping in budding yeast at a scale two orders of magnitude larger than the previous state of the art. The resulting increase in power reveals the polygenic nature of complex traits in yeast, and offers insight into widespread patterns of pleiotropy and epistasis. Our data and analysis methods offer opportunities for future work in systems biology, and have implications for large-scale GWAS in human populations.

category: genetics


title: Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution

abstract: Cryptosporidiosis is a major global health problem and a primary cause of diarrhoea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic C. hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes (GIPVs), including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a coevolutionary arms race with the host. Lastly, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, may be driving evolution of more virulent C. hominis variants.

category: genomics


title: Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution


title: RBBP4 modulates gene activity through acetylation and methylation of histone H3 lysine 27

abstract: RBBP4 is a core subunit of polycomb repressive complex 2 (PRC2) and HDAC1/2-containing complexes, which are responsible for histone H3 lysine 27 (H3K27) methylation and deacetylation respectively. However, the mechanisms by which RBBP4 modulates the functions of these complexes remain largely unknown. We generated viable mouse embryonic stem cell lines with RBBP4 mutations that disturbed methylation and acetylation of H3K27 on target chromatin and found that RBBP4 is required for PRC2 assembly and H3K27me3 establishment on target chromatin. Moreover, in the absence of EED and SUZ12, RBBP4 maintained chromatin binding on PRC2 loci, suggesting that the pre-existence of RBBP4 on nucleosomes serves to recruit PRC2 to restore H3K27me3 on newly synthesized histones. As such, disruption of RBBP4 function led to dramatic changes in transcriptional profiles. In spite of the PRC2 association, we found that transcriptional changes were more closely tied to the deregulation of H3K27ac rather than H3K27me3 where increased levels of H3K27ac were found on numerous cis-regulatory elements, especially putative enhancers. These data suggest that RBBP4 controls acetylation levels by adjusting the activity of HDAC complexes. As histone methylation and acetylation have been implicated in cancer and neural disease, RBBP4 could serve as a potential target for disease treatment.


title: The genome of the endangered Macadamia jansenii displays little diversity but represents an 1 important genetic resource for plant breeding

abstract: Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.


title: Methylothon: a versatile course-based high school research experience in microbiology and bioinformatics-- with pink bacteria

abstract: Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here we present an overview of the modules learning goals, describe course resources (available for public use on http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from Spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees, and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.

category: scientific communication and education


title: Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

abstract:
Infections due to carbapenem-resistant Enterobacteriaceae have recently emerged as one of the most urgent threats to hospitalized patients within the United States and Europe. By far the most common etiological agent of these infections is Klebsiella pneumoniae, frequently manifesting in hospital-acquired pneumonia with a mortality rate of [~]50% even with antimicrobial intervention. We performed transcriptomic analysis of data collected from in vitro characterization of both laboratory and clinical isolates revealed shifts in expression of multiple master metabolic regulators across isolate types. Metabolism has been previously shown to be an effective target for antibacterial therapy, and GENREs have provided a powerful means to accelerate identification of potential targets in silico. Combining these techniques with the transcriptome meta-analysis, we generated context-specific models of metabolism utilizing a well-curated GENRE of K. pneumoniae (iYL1228) to identify novel therapeutic targets. Functional metabolic analyses revealed that both composition and metabolic activity of clinical isolate-associated context-specific models significantly differs from laboratory isolate-associated models of the bacterium. Additionally, we identified increased consumption of L-valine in clinical isolate-specific growth simulations. Importantly, valine has been shown to augment macrophage phagocytosis, and this result could be indicative of an immunosuppressive strategy Klebsiella pneumoniae evolved for survival during infection. These findings warrant future studies for potential efficacy of valine transaminase inhibition as a target against K. pneumoniae infection.

ImportanceIncidences of infection by Klebsiella pneumoniae have grown in frequency to become the leading agents of CRE infection among hospitalized patients in the United States and Europe. Transcriptomic meta-analysis of data collected from both laboratory and clinical isolates indicated significant shifts in expression of key transcription factors related to metabolism. Metabolic network reconstructions have previously proven effective for quickly identifying potential targets in silico, therefore we combined these approaches by integrating the transcriptomic data from each isolate type into a well-curated GENRE of K. pneumoniae to predict emergent metabolic patterns. Leveraging this systems-biology approach we found discordant patterns of active metabolism between clinical and laboratory isolates, with a striking difference in L-valine catabolism. Exogenous valine is known to increase macrophage phagocytosis, and our results may support immunomodulatory activity in K. pneumoniae evolved to avoid host clearance.


title: Osteoblast-osteoclast co-cultures: a systematic review and map of available literature

abstract:
Drug research with animal models is expensive, time-consuming and translation to clinical trials is often poor, resulting in a desire to replace, reduce, and refine the use of animal models. One approach to replace and reduce the use of animal models in research is using in vitro cell-culture models.

To study bone physiology, bone diseases and drugs, many studies have been published using osteoblast-osteoclast co-cultures. The use of osteoblast-osteoclast co-cultures is usually not clearly mentioned in the title and abstract, making it difficult to identify these studies without a systematic search and thorough review. As a result, researchers are all developing their own methods from the ground up, leading to conceptually similar studies with many methodological differences and, as a direct consequence, incomparable results.

The aim of this study was to systematically review existing osteoblast-osteoclast co-culture studies published up to 6 January 2020, and to give an overview of their methods, predetermined outcome measures (formation and resorption, and ALP and TRAP quantification as surrogate markers for formation and resorption, respectively), and other useful parameters for analysis. Information regarding these outcome measures was extracted and collected in a database, and each study was further evaluated on whether both the osteoblasts and osteoclasts were analyzed using relevant outcome measures. From these studies, additional details on methods, cells and culture conditions were extracted into a second database to allow searching on more characteristics.

The two databases presented in this publication provide an unprecedented amount of information on cells, culture conditions and analytical techniques for using and studying osteoblast-osteoclast cocultures. They allow researchers to identify publications relevant to their specific needs and allow easy validation and comparison with existing literature. Finally, we provide the information and tools necessary for others to use, manipulate and expand the databases for their needs.


title: Metallothionein-2A protect Cardiomyocytes from Ischemia/ Reperfusion through inhibiting p38

abstract: The resumption of coronary artery blood supply is often accompanied by myocardial ischemia/reperfusion (I/R) injury after the occurrence of myocardial infarction, shock, cardiac surgery and other events. Metallothionein-2A (MT2A) has the functions of scavenging free radicals, anti-oxidative stress, anti-apoptosis, anti-autophagy, promoting vascular growth. The activation of p38 MAPK pathway can induce cardiomyocyte apoptosis in H9c2 cardiomyocytes during I/R, thereby aggravating the myocardial I/R injury. However, it is not clear that the effect of MT2A on p38 in cardiomyocytes under I/R. A simulated I/R model was used. Our objective was to investigate the protective effect of MT2A on I/R-caused mortality in H9c2 cardiomyocytes through its influence on p38, as well as the relationships among these processes. The results indicate that both endogenously overexpressed MT2A and exogenously added MT2A can inhibit the active expression of p38 during I/R. Based on these results, I/R induces apoptosis and p-p38 in cardiomyocytes. MT2A can inhibit the active expression of p38. MT2A protects cardiomyocytes from I/R injury, and that p38 is one of the molecules of MT2A against I/R injury in cardiomyocytes.


title: The efficacy of a ketogenic diet in preclinical models of IDH wild-type and IDH mutant glioma

abstract: Infiltrative gliomas are the most common neoplasms arising in the brain, and remain largely incurable despite decades of research. A subset of these gliomas contains mutations in isocitrate dehydrogenase 1 (IDH1) or, less commonly, IDH2 (together called "IDHmut"). These mutations alter cellular biochemistry, and IDHmut gliomas are generally less aggressive than IDH wild-type (IDHwt) gliomas. Some preclinical studies and clinical trials have suggested that a ketogenic diet (KD), characterized by low-carbohydrate and high-fat content, may be beneficial in slowing glioma progression. However, not all studies have shown promising results, and to date, no study has addressed whether IDHmut gliomas might be more sensitive to KD. The aim of the current study was to compare the effects of KD in preclinical models of IDHwt versus IDHmut gliomas. In vitro, simulating KD by treatment with the ketone body {beta}-hydroxybutyrate had no effect on the proliferation of patient-derived IDHwt or IDHmut glioma cells. Likewise, a cycling KD, wherein mice alternated between KD and a standard diet (SD), had no effect on the in vivo growth of patient-derived IDHwt or IDHmut gliomas, even though the cycling KD did result in persistently elevated circulating ketones. Furthermore, KD conferred no survival benefit in mice engrafted with Sleeping-Beauty transposase-engineered IDHmut glioma. These data suggest that neither IDHwt nor IDHmut gliomas are particularly responsive to KD.

category: cancer biology


title: Single-nucleus transcriptomic analyses reveal microglial activation underlying cerebellar degeneration in Ataxia Telangiectasia

abstract: While ATM loss-of-function has long been identified as the genetic cause of Ataxia Telangiectasia (AT), how this genetic mutation leads to selective and progressive cerebellar degeneration of Purkinje and granule cells remains unknown. We performed single-nucleus RNA-sequencing of the human cerebellum and prefrontal cortex from individuals with AT and matched unaffected controls to identify AT-associated transcriptomic changes in a cell-type- and brain-region-specific manner. We provide the largest single-nucleus transcriptomic atlas of the adult human cerebellum to-date (126,356 nuclei), identify upregulation of apoptotic and ER stress pathways in Purkinje and granule neurons, and uncover strong downregulation of calcium ion homeostasis genes in Purkinje neurons. Our analysis reveals prominent inflammation of microglia in AT cerebellum with transcriptional signatures similar to aging and neurodegenerative microglia, and suggests that microglia activation precedes Purkinje and granule neuron death in disease progression. Our data implicates a novel role of microglial activation underlying cerebellar degeneration in AT.

category: neuroscience


title: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression

abstract: Allele-specific expression (ASE) is a phenomenon where one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final allelic composition of a genes product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific gene regulation, but how they contribute to this crosstalk remains understudied. Here, we explored how allelic genotype, parent-of-origin, tissue type, sex, and dietary fat simultaneously influence ASE biases in a F1 reciprocal cross mouse model. Male and female mice from a F1 reciprocal cross of the LG/J and SM/J strains were fed a high fat or low fat diet. We harnessed strain-specific variants to distinguish between two classes of ASE: parent-of-origin dependent (unequal expression based on an alleles parental origin) and sequence dependent (unequal expression based on an alleles nucleotide identity). We present a comprehensive map of ASE patterns in 2,853 genes across three metabolically-relevant tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue type and environmental context. They vary across metabolic tissues, between males and females, and in response to dietary fat levels. Surprisingly, we found 45 genes with inconsistent ASE biases that switched direction across tissues and/or contexts (e.g. SM/J biased in one cohort, LG/J biased in another). We also integrated ASE and QTL data from populations at various degrees of intercrossing the LG/J and SM/J strains. ASE genes in these tissues are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes for functional validation. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific gene regulation, which is an essential step towards deciphering the genotype to phenotype map.


title: Resurgent Na+ currents promote ultrafast spiking in projection neurons that drive fine motor control

abstract: The underlying mechanisms that promote precise spiking in upper motor neurons controlling fine motor skills are not well understood. Here we report that projection neurons in the adult zebra finch song nucleus RA display: 1) robust high-frequency firing, 2) ultra-short half-width spike waveforms, 3) superfast Na+ current inactivation kinetics and 4) large resurgent Na+ currents (INaR). These spiking properties closely resemble those of specialized pyramidal neurons in mammalian motor cortex and are well suited for precise temporal coding. They emerge during the critical period for vocal learning in males but not females, coinciding with a complete switch of modulatory Na+ channel subunit expression from Nav{beta}3 to Nav{beta}4. Dynamic clamping and dialysis of Nav{beta}4s C-terminal peptide into juvenile RA neurons provide evidence that this subunit, and its associated INaR, promote neuronal excitability. We propose that Nav{beta}4 underpins INaR that facilitates precise, prolonged, and reliable high-frequency firing in upper motor neurons.


title: Auditory word comprehension is less incremental in isolated words

abstract: Speech input is often understood to trigger rapid and automatic activation of successively higher-level representations for comprehension of words. Here we show evidence from magnetoencephalography that incremental processing of speech input is limited when words are heard in isolation as compared to continuous speech. This suggests a less unified and automatic process than is often assumed. We present evidence that neural effects of phoneme-by-phoneme lexical uncertainty, quantified by cohort entropy, occur in connected speech but not isolated words. In contrast, we find robust effects of phoneme probability, quantified by phoneme surprisal, during perception of both connected speech and isolated words. This dissociation rules out models of word recognition in which phoneme surprisal and cohort entropy are common indicators of a uniform process, even though these closely related information-theoretic measures both arise from the probability distribution of wordforms consistent with the input. We propose that phoneme surprisal effects reflect automatic access of a lower level of representation of the auditory input (e.g., wordforms) while cohort entropy effects are task-sensitive, driven by a competition process or a higher-level representation that is engaged late (or not at all) during the processing of single words.


title: A neural hub that coordinates learned and innate courtship behaviors

abstract: Holistic behaviors often require the coordination of innate and learned movements. The neural circuits that enable such coordination remain unknown. Here we identify a midbrain cell group (A11) that enables male zebra finches to coordinate their learned songs with various innate behaviors, including female-directed calling, orientation and pursuit. Anatomical mapping reveals that A11 is at the center of a complex network including the song premotor nucleus HVC as well as brainstem regions crucial to innate calling and locomotion. Notably, lesioning A11 terminals in HVC blocked female-directed singing, but did not interfere with female-directed calling, orientation or pursuit. In contrast, lesioning A11 cell bodies abolished all female-directed courtship behaviors. However, males with either type of lesion still produced songs when in social isolation. Lastly, monitoring A11 terminals in HVC showed that during courtship A11 inputs to the song premotor cortex signal the transition from innate to learned vocalizations. These results show how a brain region important to reproduction in both birds and mammals coordinates learned vocalizations with innate, ancestral courtship behaviors.


title: The Cortical Spectrum: a robust structural continuum in primate cerebral cortex revealed by histological staining and magnetic resonance imaging

abstract: High-level characterizations of the primate cerebral cortex sit between two extremes: on one end the cortical mantle is seen as a mosaic of structurally and functionally unique areas, and on the other it is seen as a uniform six-layered structure in which functional differences are defined solely by extrinsic connections. Neither of these extremes captures the crucial neuroanatomical finding: that the cortex exhibits systematic gradations in architectonic structure. These gradations have been shown to predict cortico-cortical connectivity, which in turn suggests powerful ways to ground connectomics in anatomical structure, and by extension cortical function. A challenge to more widespread use of this concept is the labor-intensive and invasive nature of histological staining, which is the primary means of recognizing anatomical gradations. Here we show that a novel computational analysis technique can be used to derive a coarse-grained picture of cortical variation. For each of 78 cortical areas spanning the entire cortical mantle of the rhesus macaque, we created a high dimensional set of anatomical features derived from captured images of cortical tissue stained for myelin and SMI-32. The method involved semi-automated de-noising of images, and enabled comparison of brain areas without hand-labeling of features such as layer boundaries. We applied nonmetric multidimensional scaling (NMDS) to the dataset to visualize similarity among cortical areas. This analysis shows a systematic variation between weakly laminated (limbic) cortices and sharply laminated (eulaminate) cortices. We call this smooth continuum the  cortical spectrum. We also show that this spectrum is visible within subsystems of the cortex: the occipital, parietal, temporal, motor, prefrontal, and insular cortices. We compared the NMDS-derived spectrum with a spectrum produced using T1- and T2-weighted magnetic resonance imaging (MRI) data derived from macaque, and found close agreement of the two coarse-graining methods. This evidence suggests that T1/T2 data, routinely obtained in human MRI studies, can be used as an effective proxy for data derived from high-resolution histological methods. More generally, this approach shows that the cortical spectrum is robust to the specific method used to compare cortical areas, and is therefore a powerful tool to understand the principles of organization of the primate cortex.


title: Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

abstract: PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

category: bioinformatics


title: Pseudomonas aeruginosa synthesizes the autoinducers of its oxylipin-dependent quorum sensing system extracellularly

abstract:
The oxylipin-dependent quorum sensing system (ODS) of Pseudomonas aeruginosa relies on the production and sensing of two oxylipin autoinducers, 10S-hydroxy-(8E)-octadecenoic acid (10-HOME) and 7S,10S dihydroxy-(8E)-octadecenoic acid (7,10-DiHOME). Here, and contrary to the prevailing notion that bacterial autoinducers are synthesized intracellularly, we show that 10-HOME and 7,10-DiHOME biosynthesis occurs extracellularly, and this requires the secretion of the oxylipin synthases. We implemented a genetic screen of P. aeruginosa strain PAO1, which identified fourteen genes required for the synthesis of oxylipins. Among the identified genes, four encoded components of the ODS system and the other ten were part of the Xcp type II secretion system (T2SS). We created a deletion mutant of xcpQ, which encodes the outer membrane component of Xcp, and found it recapitulated the impaired functionality of the transposon mutants. Upon further examination, the lack of ODS function was demonstrated to be caused by the blocking of the DS enzymes secretion. Notably, the xcpQ mutant activated the ODS system when exposed to 10-HOME and 7,10-DiHOME, indicating that the sensing component of this quorum sensing system remains fully functional. In contrast with the detrimental effect previously described for T2SS in biofilm formation, here we observed that T2SS was required for robust in vitro and in vivo biofilm formation in an ODS dependent manner. To the best of our knowledge, this study is the first to find QS autoinducers that are synthetized in the extracellular space and provides new evidence for the role of the T2SS for biofilm formation in P. aeruginosa.

IMPORTANCEWe previously showed that the ODS quorum sensing system of P. aeruginosa produces and responds to oxylipins derived from host oleic acid by enhancing biofilm formation and virulence. Herein, we developed a genetic screen strategy to explore the molecular basis for oxylipins synthesis and detection. Unexpectedly, we found that the ODS autoinducer synthases cross the outer membrane using the Xcp Type 2 secretion system of P. aeruginosa and thus, the biosynthesis of oxylipins occur extracellularly. Biofilm formation, which was thought to be impaired as result of Xcp activity, was found to be enhanced as result of ODS activation. This is a unique QS system strategy and reveals a new way by which P. aeruginosa interacts with the host environment.


title: Identification of a stereotypic molecular arrangement of glycine receptors at native spinal cord synapses

abstract: Precise quantitative information about the molecular architecture of synapses is essential to understanding the functional specificity and downstream signaling processes at specific populations of synapses. Glycine receptors (GlyRs) are the primary fast inhibitory neurotransmitter receptors in the spinal cord and brainstem. These inhibitory glycinergic networks crucially regulate motor and sensory processes. Thus far the nanoscale organization of GlyRs underlying the different network specificities has not been defined. Here, we have quantitatively characterized the molecular arrangement and ultra-structure of glycinergic synapses in spinal cord tissue using quantitative super-resolution correlative light and electron microscopy (SR-CLEM). We show that endogenous GlyRs exhibit equal receptor-scaffold occupancy and constant packing densities of about 2000 GlyRs m-2 at synapses across the spinal cord and throughout adulthood, even though ventral horn synapses have twice the total copy numbers, larger postsynaptic domains and more convoluted morphologies than dorsal horn synapses. We demonstrate that this stereotypic molecular arrangement is maintained at glycinergic synapses in the oscillator mouse model of the neuromotor disease hyperekplexia despite a decrease in synapse size, indicating that the molecular organization of GlyRs is preserved in this hypomorph. We thus conclude that the morphology and size of inhibitory postsynaptic specializations rather than differences in GlyR packing determine the postsynaptic strength of glycinergic neurotransmission in motor and sensory spinal cord networks.

category: molecular biology


title: Identification of a stereotypic molecular arrangement of endogenous glycine receptors at spinal cord synapses


title: Characterization of apicomplexan amino acid transporters (ApiATs) in the malaria parasite Plasmodium falciparum

abstract:
During the symptomatic human blood phase, malaria parasites replicate within red blood cells. Parasite proliferation relies on the uptake of nutrients, such as amino acids, from the host cell and the blood plasma, requiring transport across multiple membranes. Amino acids are delivered to the parasite through the parasite surrounding vacuolar compartment by specialized nutrient-permeable channels of the erythrocyte membrane and the parasitophorous vacuole membrane (PVM). However, further transport of amino acid across the parasite plasma membrane (PPM) is currently not well characterized. In this study, we focused on a family of Apicomplexan amino acid transporters (ApiATs) that comprises five members in Plasmodium falciparum. First, we localized four of the PfApiATs at the PPM using endogenous GFP-tagging. Next, we applied reverse genetic approaches to probe into their essentiality during asexual replication and gametocytogenesis. Upon inducible knockdown and targeted gene disruption a reduced asexual parasite proliferation was detected for PfApiAT2 and PfApiAT4. Functional inactivation of individual PfApiATs targeted in this study had no effect on gametocyte development. Our data suggest that individual PfApiATs are partially redundant during asexual in vitro proliferation and fully redundant during gametocytogenesis of P. falciparum parasites.

IMPORTANCEMalaria parasites live and multiply inside cells. To facilitate their extremely fast intracellular proliferation they hijack and transform their host cells. This also requires the active uptake of nutrients, such as amino acids, from the host cell and the surrounding environment through various membranes that are the consequence of the parasites intracellular lifestyle. In this manuscript we focus on a family of putative amino acid transporters termed ApiAT. We show expression and localization of four transporters in the parasite plasma membrane of Plasmodium falciparum-infected erythrocytes that represent one interface of the pathogen to its host cell. We probed into the impact of functional inactivation of individual transporters on parasite growth in asexual and sexual blood stages of P. falciparum and reveal that only two of them show a modest but significant reduction in parasite proliferation but no impact on gametocytogenesis pointing towards redundancy within this transporter family.


title: Increasing triacylglycerides and lipid storage by unsaturated lipids protects renal proximal tubules

abstract: In diabetic patients, dyslipidemia frequently contributes to organ damage such as diabetic kidney disease (DKD). DKD is associated with excessive renal deposition of triacylglycerol (TAG) in lipid droplets (LD). Yet, it is unclear whether LDs play a protective or damaging role and how this might be influenced by dietary patterns. By using a diabetes mouse model, we find here that high fat diet enriched in the unsaturated oleic acid (OA) caused more lipid storage in LDs in renal proximal tubular cells (PTC) but less tubular damage than a corresponding butter diet with the saturated palmitic acid (PA). Mechanistically, we identify endoplasmic reticulum (ER) stress as the main cause of PA-induced PTC injury. ER stress is caused by elevated cellular levels of saturated TAG precursors and to higher membrane order in the ER. The resulting cell death is preceded by a transcriptional rewiring of phospholipid metabolism. Simultaneous addition of OA rescues the cytotoxic effects by normalizing membrane order and by increasing the total TAG amount. The latter also stimulates the formation of LDs that in turn can release unsaturated lipids upon demand by lipolysis. Our study thus clarifies mechanisms underlying PA-induced cell stress in PTCs and emphasizes the importance of olive oil for the prevention of DKD.


title: Increasing triacylglycerol formation and lipid storage by unsaturated lipids protects renal proximal tubules in diabetes


title: Myosin-1b interacts with UNC45A and controls intestinal epithelial morphogenesis

abstract:
Vesicle trafficking and the establishment of apico-basal polarity are essential processes in epithelium morphogenesis. Myosin-1b, an actin-motor able to bind membranes, regulates membrane shaping and vesicle trafficking. Here, we investigate Myosin-1b function in gut morphogenesis and congenital disorders using cell line and zebrafish larvae as well as patient biopsies. In a 3D Caco-2 cyst model, lumen formation is impaired in absence of Myosin-1b. In zebrafish, both Morpholino knock-down and genetic mutation of myo1b result in intestinal bulb epithelium folding defects associated with vesicle accumulation, reminiscent of a villous atrophy phenotype. We show that Myosin-1b interacts with the chaperone UNC45A, genetic deletion of which also results in gut folding defects in zebrafish. Loss of function mutations in UNC45A have been reported in complex hereditary syndromes, notably exhibiting intestinal disorders associated with villous atrophy. In UNC45A-depleted cells and in patient biopsies, Myosin-1b protein level is strikingly decreased. The appearance of Myosin-1b aggregates upon proteasome inhibition in cells points at a degradation mechanism of misfolded Myosin-1b in the absence of its chaperone. In conclusion, Myosin-1b plays an unexpected role in the development of the intestinal epithelium folds or villi downstream UNC45A, establishing its role in the gut defects reported in UNC45A patients.

Summary statementMyosin-1b is important for intestinal epithelium folding during zebrafish development and participates in the villous atrophy clinical manifestation downstream UNC45A loss of function.


title: The genetic and social contributions to sex differences in lifespan in Drosophila serrata

abstract: Sex differences in lifespan remain an intriguing puzzle for evolutionary biologists. A possible explanation for lower lifespan in males is the unconditional expression of recessive deleterious alleles in heterogametic X chromosomes in males (the unguarded X hypothesis). Empirical evidence, however, has yielded controversial results that can be attributed to differences in both genetic and social background. Here, we test the unguarded X hypothesis in Drosophila serrata using a factorial design to quantify the effects of genotype, sex, social environment, and their interactions on phenotypic variation for lifespan. Using an experimental approach, we manipulated two inbred laboratory genotypes and their reciprocal F1s, while controlling for different levels of density and mating status to account for any potential social effects. Our results also show subtle but significant genotype dependent effects for both density and mating, but ultimately find the unguarded X hypothesis insufficient to fully explain sexual dimorphism in D. serrata lifespan.


title: APOK3, a pollen killer antidote in Arabidopsis thaliana

abstract: According to the principles of heredity, each parental allele of hybrids equally participates in the progeny. At some loci, however, it happens that one allele is favored to the expense of the other. Gamete killers are genetic systems where one allele (the killer) triggers the death of the gametes carrying the other (killed) allele. They have been found in many organisms, and are of major interest to understand mechanisms of evolution and speciation. Gamete killers are particularly prevalent in plants, where they can compromise crop breeding. Here, we deciphered a pollen killer in Arabidopsis thaliana by exploiting natural variation, de novo genomic sequencing and mutants, and analyzing segregations in crosses. We found that the killer allele carries an antidote gene flanked by two elements mandatory for the killing activity. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. This gene appeared in the species by association of domains recruited from other genes, and it recently underwent duplications within a highly variable locus, particularly in the killer genotypes. Exploring the species diversity, we identified sequence polymorphisms correlated with the antidote activity.


title: Visualizing the Costs and Benefits of Correcting P-Values for Multiple Hypothesis Testing in Omics Data

abstract: The multiple hypothesis testing problem is inherent in high-throughput quantitative genomic, transcriptomic, proteomic, and other "omic" screens. The correction of p-values for multiple testing is a critical element of quantitative omic data analysis, yet many researchers are unfamiliar with the sensitivity costs and false discovery rate (FDR) benefits of p-value correction. We developed models of quantitative omic experiments, modeled the costs and benefits of p-value correction, and visualized the results with color-coded volcano plots. We developed an R Shiny web application for further exploration of these models which we call the Simulator of P-value Multiple Hypothesis Correction (SIMPLYCORRECT). We modeled experiments in which no analytes were truly differential between the control and test group (all null hypotheses true), all analytes were differential, or a mixture of differential and non-differential analytes were present. We corrected p-values using the Benjamini-Hochberg (BH), Bonferroni, and permutation FDR methods and compared the costs and benefits of each. By manipulating variables in the models, we demonstrated that increasing sample size or decreasing variability can reduce or eliminate the sensitivity cost of p-value correction and that permutation FDR correction can yield more hits than BH-adjusted and even unadjusted p-values in strongly differential data. SIMPLYCORRECT can serve as a tool in education and research to show how p-value adjustment and various parameters affect the results of quantitative omics experiments.


title: APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms

abstract: Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide-spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified database search algorithms with guaranteed control on the false discovery rate (FDR) and guaranteed increase in the identified peptides. To fill in this gap, we propose a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatible with all database search algorithms. Notably, under a target FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex protein standard shows that APIR outpowers individual database search algorithms and guarantees the FDR control. Real data studies show that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. Note that the APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis, e.g., differential gene expression analysis on RNA sequencing data.


title: Plotgardener: Cultivating precise multi-panel figures in R

abstract:
The R programming language is one of the most widely used programming languages for transforming raw genomic data sets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure and tools developed by the Bioconductor project. However, existing plotting packages rely on relative positioning and sizing of plots, which is often sufficient for exploratory analysis but is poorly suited for the creation of publication-quality multi-panel images inherent to scientific manuscript preparation. We present plotgardener, a coordinate-based genomic data visualization package that offers a new paradigm for multi-plot figure generation in R. Plotgardener allows precise, programmatic control over the placement, aesthetics, and arrangements of plots while maximizing user experience through fast and memory-efficient data access, support for a wide variety of data and file types, and tight integration with the Bioconductor environment. Plotgardener also allows precise placement and sizing of ggplot2 plots, making it an invaluable tool for R users and data scientists from virtually any discipline.

AvailabilityPackage: https://bioconductor.org/packages/plotgardener

Code: https://github.com/PhanstielLab/plotgardener

Documentation: https://phanstiellab.github.io/plotgardener/


title: Weight Pulling: A Novel Mouse Model of Human Progressive Resistance Exercise

abstract: This study describes a mouse model of progressive resistance exercise that utilizes a full-body/multi-joint exercise (weight pulling) along with a training protocol that mimics a traditional human paradigm (3 training sessions per week, [~]8-12 repetitions per set, 2 minutes of rest between sets, [~]2 maximal-intensity sets per session, last set taken to failure, and a progressive increase in loading that is based on the individuals performance). We demonstrate that weight pulling can induce an increase in the mass of numerous muscles throughout the body. The relative increase in muscle mass is similar to what has been observed in human studies, and it is associated with the same type of long-term adaptations that occur in humans (e.g., fiber hypertrophy, myonuclear accretion, and in some instances a fast-to-slow transition in Type II fiber composition). Moreover, we demonstrate that weight pulling can induce the same type of acute responses that are thought to drive these long-term adaptations (e.g., the activation of signaling through mTORC1 and the induction of protein synthesis at 1 hr post-exercise). Collectively, the results of this study indicate that weight pulling can serve as a highly translatable mouse model of progressive resistance exercise.

category: physiology


title: Spatio-temporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy

abstract: Beginning in the first trimester, fetally derived extravillous trophoblasts (EVTs) invade the uterus and remodel its spiral arteries, transforming them into large, dilated blood vessels that lack smooth muscle and are partially lined with EVTs instead of vascular endothelium. Several mechanisms have been proposed to explain how EVTs coordinate with decidual cells to promote a tissue microenvironment conducive to spiral artery remodeling (SAR). However, it remains a matter of debate which immune and stromal cell types participate in these interactions, how this process evolves with respect to gestational age, and which anatomic routes are the predominate path of EVT invasion in humans. To elucidate this complex interplay, we used multiplexed ion beam imaging by time of flight with a 37-plex antibody panel to build the first spatio-temporal atlas of the human maternal-fetal interface in the first half of pregnancy at single-cell resolution. We analyzed ~500,000 cells and 588 spiral arteries within intact decidua from 66 patients between 6-20 weeks of gestation. Using custom machine learning algorithms for cell segmentation and classification, we evaluated the spatial distributions and phenotype of 20 maternal and five EVT populations with respect to gestational age and SAR. Gestational age substantially influenced the frequency of most maternal immune and stromal cells, with tolerogenic subsets expressing CD206, CD163, TIM-3, Galectin-9, and IDO-1 preferentially enriched at later time points. In contrast, SAR progression, and not gestational age, preferentially correlated with local invasion of EVTs. Lastly, by comparing spatial co-occurrence and phenotype of decidual interstitial, perivascular and intravascular EVTs with respect to SAR progression, we developed a statistical model suggesting an intravasation mechanism as the predominant route of EVT invasion in superficial decidua. Taken together, these results support a coordinated model of decidualization in which increasing gestational age drives a transition in maternal decidua towards a tolerogenic niche conducive to locally regulated, EVT-dependent SAR.

category: systems biology


title: Spectral Separation of Evoked and Background Cortical Activity - Application to Short Latency Median Nerve Evoked Potentials

abstract:
BackgroundSpectral analysis of repeatedly evoked potentials (EPs) is challenging since recordings contain a superposition of evoked signals and background activity. We developed a novel approach, N-interval Fourier Transform Analysis (N-FTA), which allows for reliable separation and accurate assessment of evoked and background spectral components. We applied this approach to spectral analysis of median nerve short latency EPs for identifying spectral bands of clinical relevance.

MethodsWe performed right median nerve stimulation in two volunteers at 2.46 Hz and 3.95 Hz stimulation rate (600 and 1000 repetitions respectively). We applied N-FTA for splitting the periodically repeated evoked components from irregular background activity and investigated spectral components in the low, medium and high frequency (LF-, MF-, HF-) bands. We present a signal processing approach, which allows for accurately extracting diagnostically relevant features (signal morphology, latency and amplitude) using an 18 Hz to 240 Hz bandwidth.

ResultsIn the LF-band < 10 Hz, evoked-to-background ratio (EBR) was below -15 dB due to the high level near DC background activity (1/f-activity, eye blinks,{theta} -band). Highest EBR was near -5 dB and obtained at a few tens of Hz. Relatively broad continuous segments of evoked activity were detected in the MF band. These frequencies of a few hundred Hz were linked to the signal segment between the N20 and P25 peaks in the time domain. High frequency oscillations (HFOs) near 600 Hz were approximately -25 dB below the background level and near the limit of the sensitivity of N-FTA. By subtracting stimulation artifacts and applying zero-phase filters it was possible to extract diagnostically relevant short latency EP features (signal morphology, latency and amplitude) only from the MF-band with a similar accuracy as a routinely used broad-band setting. HFOs displayed amplitudes of a few tenths of {micro}V.

SummaryN-FTA allows for accurate, simultaneous spectral analysis of evoked and background activity in individual trials. The approach allowed for identifying target frequency bands of high evoked activity and for tailoring signal processing such, that morphology and latency can be obtained at a significantly reduced bandwidth. This should allow for development of more robust and faster recording techniques in the near future.


title: The Temporal Pattern of Spiking Activity of a Thalamic Neuron are Related to the Amplitude of the Cortical Local Field Potential

abstract:
Neuron activity in the sensory cortices mainly depends on feedforward thalamic inputs. High-frequency activity of a thalamic input can be temporally integrated by a neuron in the sensory cortex and is likely to induce larger depolarization. However, feedforward inhibition (FFI) and depression of excitatory synaptic transmission in thalamocortical pathways attenuate depolarization induced by the latter part of high-frequency spiking activity and the temporal summation may not be effective. The spiking activity of a thalamic neuron in a specific temporal pattern may circumvent FFI and depression of excitatory synapses. The present study determined the relationship between the temporal pattern of spiking activity of a single thalamic neuron and the degree of cortical activation as well as that between the firing rate of spiking activity of a single thalamic neuron and the degree of cortical activation. Spiking activity of a thalamic neuron was recorded extracellularly from the lateral geniculate nucleus (LGN) in male Long-Evans rats. Degree of cortical activation was assessed by simultaneous recording of local field potential (LFP) from the visual cortex. A specific temporal pattern appearing in three consecutive spikes of an LGN neuron induced larger cortical LFP modulation than high-frequency spiking activity during a short period. These findings indicate that spiking activity of thalamic inputs is integrated by a synaptic mechanism sensitive to an input temporal pattern.

Significance StatementSensory cortical activity depends on thalamic inputs. Despite the importance of thalamocortical transmission, how spiking activity of thalamic inputs is integrated by cortical neurons remains unclear. Feedforward inhibition and synaptic depression of excitatory transmission may not allow simple temporal summation of membrane potential induced by consecutive spiking activity of a thalamic neuron. A specific temporal pattern appearing in three consecutive spikes of a thalamic neuron induced larger cortical local field potential modulation than high-frequency spiking activity during a short period. The findings indicate the importance of the temporal pattern of spiking activity of a single thalamic neuron on cortical activation.


title: A flow-based latent state generative model of neural population responses to natural images

abstract: We present a joint deep neural system identification model for two major sources of neural variability: stimulus-driven and stimulus-conditioned fluctuations. To this end, we combine (1) state-of-the-art deep networks for stimulus-driven activity and (2) a flexible, normalizing flow-based generative model to capture the stimulus-conditioned variability including noise correlations. This allows us to train the model end-to-end without the need for sophisticated probabilistic approximations associated with many latent state models for stimulus-conditioned fluctuations. We train the model on the responses of thousands of neurons from multiple areas of the mouse visual cortex to natural images. We show that our model outperforms previous state-of-the-art models in predicting the distribution of neural population responses to novel stimuli, including shared stimulus-conditioned variability. Furthermore, it successfully learns known latent factors of the population responses that are related to behavioral variables such as pupil dilation, and other factors that vary systematically with brain area or retinotopic location. Overall, our model accurately accounts for two critical sources of neural variability while avoiding several complexities associated with many existing latent state models. It thus provides a useful tool for uncovering the interplay between different factors that contribute to variability in neural activity.


title: Strong and specific connections between retinal axon mosaics and midbrain neurons revealed by large scale paired recordings

abstract:
The superior colliculus (SC) is a midbrain structure that plays important roles in visually guided behaviors. Neurons in the SC receive afferent inputs from retinal ganglion cells (RGC), the output cells of the retina, but how SC neurons integrate RGC activity in vivo is unknown. SC neurons might be driven by strong but sparse retinal inputs, thereby reliably transmitting specific retinal functional channels. Alternatively, SC neurons could sum numerous but weak inputs, thereby extracting new features by combining a diversity of retinal signals. Here, we discovered that high-density electrodes simultaneously capture the activity and the location of large populations of retinal axons and their postsynaptic SC target neurons, permitting us to investigate the retinocollicular circuit on a structural and functional level in vivo. We show that RGC axons in the mouse are organized in mosaics that provide a single cell precise representation of the retina as input to SC. This isomorphic mapping between retina and SC builds the scaffold for highly specific wiring in the retinocollicular circuit which we show is characterized by strong connections and limited functional convergence, established in log-normally distributed connection strength. Because our novel method of large-scale paired recordings is broadly applicable for investigating functional connectivity across brain regions, we were also able to identify retinal inputs to the avian optic tectum of the zebra finch. We found common wiring rules in mammals and birds that provide a precise and reliable representation of the visual world encoded in RGCs to neurons in retinorecipient areas.

HIGHLIGHTSO_LIHigh-density electrodes capture the activity of afferent axons and target neurons in vivo
C_LIO_LIRetinal ganglion cells axons are organized in mosaics
C_LIO_LISingle cell precise isomorphism between dendritic and axonal RGC mosaics
C_LIO_LIMidbrain neurons are driven by sparse but strong retinal inputs
C_LIO_LIFunctional wiring of the retinotectal circuit is similar in mammals and birds
C_LI


title: Prediction and action in cortical pain processing

abstract:
Predicting that a stimulus is painful facilitates action to avoid harm. But how distinct are the neural processes underlying the prediction of upcoming painful events, and those taking action to avoid or prevent them? In this fMRI experiment, we addressed this by investigating brain activity as a function of current and predicted painful or nonpainful thermal stimulation, and the ability of voluntary action to affect the duration of the upcoming stimulation. Participants (n = 30) performed a task which involved the administration of a painful or nonpainful stimulus (S1), which predicted an immediately subsequent very painful or nonpainful stimulus (S2). On action-effective trials, pressing a response button within a specified time window during S1 reduced the duration of the upcoming stimulation in S2. On action-ineffective trials, pressing the button had no effect on upcoming stimulation. Predicted pain increased activation in regions including anterior cingulate cortex (ACC), midcingulate cortex (MCC), and insula; however, activation in ACC and MCC depended on whether a meaningful action was performed, with MCC activation showing a direct relationship with motor output. Region-of-interest analyses revealed that insulas responses for predicted pain were also modulated by potential action consequences, especially in the left hemisphere, albeit without a direct relationship with motor output. Taken together, these findings suggest that cortical pain processing is not specifically tied to the sensory stimulus, but instead depends on the consequences of that stimulus for sensorimotor control of behavior.

Significance statementDuring acute pain, the processing of an acute sensory event likely occurs in parallel with predictive processing about its relevance for current and upcoming voluntary behavior. Here, we temporally separated the functional processes underlying current and predicted pain and found that activation in regions typically implicated in acute pain is modulated both by the noxious nature of upcoming events and by the possibility to affect those events via voluntary action (a button press). Our findings suggest that cortical pain processing is not specifically tied to the sensory stimulus, but instead is processed in "consequence-level" terms based on what the stimulus implies for sensorimotor control of behavior.


title: Myelination deficits in the auditory brainstem of a mouse model of Fragile X Syndrome, a possible mechanism for auditory phenotypes

abstract: 1Auditory symptoms are one of the most frequent sensory issues described in people with Fragile X Syndrome (FXS), the most common genetic form of intellectual disability. However, the mechanisms that lead to these symptoms are under explored. In this study, we examined whether alterations in myelination in auditory brainstem circuitry contribute to auditory impairments in FXS mice. Specifically, we studied myelinated fibers that terminate in the Calyx of Held, which encode temporally precise sound arrival time, and are some of the most heavily myelinated axons in the brain. We measured anatomical myelination characteristics using coherent anti-stokes Raman spectroscopy (CARS) and electron microscopy (EM) in a FXS mouse model in the medial nucleus of the trapezoid body (MNTB) where the Calyx of Held synapses. We measured number of mature oligodendrocytes (OL) and oligodendrocyte precursor cells (OPCs) to determine if changes in myelination were due to changes in the number of myelinating or immature glial cells. The two microscopy techniques (EM and CARS) showed a decrease in fiber diameter in FXS mice. Additionally, EM results indicated reductions in myelin thickness and axon diameter, and an increase in g-ratio, a measure of structural and functional myelination. Lastly, we showed an increase in both OL and OPCs in MNTB sections of FXS mice suggesting that the myelination phenotype is not due to an overall decrease in number of myelinating OLs. This is the first study to show that a potential myelination mechanism can explain alterations seen in FXS at the level of the auditory brainstem.


title: Cortical dopamine reduces the impact of motivational biases governing automated behaviour

abstract: Motivations shape our behaviour: the promise of reward invigorates, while in the face of punishment, we hold back. Abnormalities of motivational processing are implicated in clinical disorders characterised by excessive habits and loss of top-down control, notably substance and behavioural addictions. Striatal and frontal dopamine have been hypothesised to play complementary roles in the respective generation and control of these motivational biases. However, while dopaminergic interventions have indeed been found to modulate motivational biases, these previous pharmacological studies used regionally non-selective pharmacological agents. Here, we tested the hypothesis that frontal dopamine controls the balance between Pavlovian, bias-driven automated responding and instrumentally learned action values. Specifically, we examined whether selective enhancement of cortical dopamine either (i) enables adaptive suppression of Pavlovian control when biases are maladaptive; or (ii) non-specifically modulates the degree of bias-driven automated responding. Healthy individuals (n=35) received the catechol-o-methyltransferase (COMT) inhibitor tolcapone in a randomized, double-blind, placebo-controlled cross-over design, and completed a motivational Go NoGo task known to elicit motivational biases. In support of hypothesis (ii), tolcapone globally decreased motivational bias. Specifically, tolcapone improved performance on trials where the bias was unhelpful, but impaired performance in bias-congruent conditions. These results indicate a non-selective role for cortical dopamine in the regulation of motivational processes underpinning top-down control over automated behaviour. The findings have direct relevance to understanding neurobiological mechanisms underpinning addiction and obsessive-compulsive disorders, as well as highlighting a potential trans-diagnostic novel mechanism to address such symptoms.


title: Vestibular CCK neurons drive motion-induced malaise

abstract: Passive motion can induce kinetosis (motion sickness, MS) in susceptible individuals. MS is an evolutionary conserved mechanism caused by mismatches between motion-related sensory information and past visual and motion memory, triggering a malaise accompanied by hypolocomotion, hypothermia, hypophagia and aversion to novel foods presented coincidentally. Vestibular nuclei (VN) are critical for the processing of movement input, and motion-induced activation of VN neurons recapitulates MS-related signs. However, the genetic identity of VN neurons mediating MS-related autonomic and aversive responses remains unknown. Here, we identify a glutamatergic vestibular circuitry necessary to elicit MS-related behavioral responses, defining a central role of cholecystokinin (CCK)- expressing glutamatergic VN neurons in vestibular-induced malaise. Moreover, we show that CCK VN inputs onto the parabrachial nucleus activate Calca-expressing neurons and are sufficient to establish hypothermia and aversion to novel food. Together, we provide novel insight into the neurobiological regulation of MS, unravelling key genetically defined neural substrates for kinetosis.


title: Durable Immunity to Ricin Toxin Elicited by a Thermostable, Lyophilized Subunit Vaccine

abstract:
The development of vaccines against biothreat toxins like ricin (RT) is considered an integral component of the United States national security efforts. RiVax(R) is a thermostable, lyophilized RT subunit vaccine adsorbed to aluminum salt adjuvant intended for use by military personnel and first responders. Phase 1 studies indicated that RiVax is safe and immunogenic, while a three dose, intramuscular vaccination regimen in non-human primates elicited protection against lethal dose RT challenge by aerosol. Here we investigated, in a mouse model, the durability of RiVax-induced antibody responses and corresponding immunity to lethal dose RT challenge. Groups of mice were subcutaneously administered 3 or 1 g of RiVax on days 0 and 21 and challenged with 10 x LD50 RT by injection at six different intervals over the course of twelve months. Serum antibody titers and epitope-specific competition assays were determined prior to each challenge. We report that the two-dose, 3 g regimen conferred near complete protection against RT challenge on day 35 and complete protection thereafter (challenge days 65, 95, 125, 245, and 365). The two-dose, 3 g regimen was superior to the 1 g regimen as revealed by slight differences in survival and morbidity scores (e.g., hypoglycemia, weight loss) on challenge days 35 and 365. In separate experiments, a single 3 g RiVax vaccination proved only marginally effective at eliciting protective immunity to RT, underscoring the necessity of a prime-boost regimen to achieve full and long-lasting protection against RT.

IMPORTANCERicin toxin (RT) is a notorious biothreat, as exposure to even trace amounts via injection or inhalation can induce organ failure and death within a matter of hours. In this study, we advance the preclinical testing of a candidate RT vaccine known as RiVax(R). RiVax is a recombinant non-toxic derivative of RTs enzymatic subunit that has been evaluated for safety in Phase I clinical trials and efficacy in a variety of animal models. We demonstrate that two doses of RiVax is sufficient to protect mice from lethal dose RT challenge for up to one year. We describe kinetics and other immune parameters of the antibody response to RiVax and discuss how these immune factors may translate to humans.

category: immunology


title: A HYPOMETABOLIC DEFENSE STRATEGY AGAINST PLASMODIUM INFECTION

abstract: Hypoglycemia is a clinical hallmark of severe malaria, the often-lethal presentation of Plasmodium falciparum infection of humans. Here we report that mice reduce blood glucose levels in response to Plasmodium infection via a coordinated response whereby labile heme, an alarmin produced via hemolysis, induces anorexia and represses hepatic glucose production (HGP). While protective against unfettered immune-mediated inflammation, organ damage and anemia, when sustained over time heme-driven repression of HGP can progress towards hypoglycemia, compromising host energy expenditure and thermoregulation. This hypometabolic state arrests the development of asexual stages of Plasmodium spp., which undergo pyknosis and develop mitochondrial dysfunction. In response, Plasmodium activates a transcriptional program reducing its virulence and inducing sexual differentiation towards the production of transmissible gametocytes. We infer that malaria-associated hypoglycemia represents a trade-off of an evolutionarily conserved defense strategy restricting Plasmodium spp. from accessing host-derived glucose and balancing parasite virulence and transmission.


title: Re-evaluating the role of nucleosomal bivalency in early development

abstract: Nucleosomes, composed of DNA and histone proteins, represent the fundamental repeating unit of the eukaryotic genome1; posttranslational modifications of these histone proteins influence the activity of the associated genomic regions to regulate cell identity2-4. Traditionally, trimethylation of histone 3-lysine 4 (H3K4me3) is associated with transcriptional initiation5-10, whereas trimethylation of H3K27 (H3K27me3) is considered transcriptionally repressive11-15. The apparent juxtaposition of these opposing marks, termed "bivalent domains"16-18, was proposed to specifically demarcate of small set transcriptionally-poised lineage-commitment genes that resolve to one constituent modification through differentiation, thereby determining transcriptional status19-22. Since then, many thousands of studies have canonized the bivalency model as a chromatin hallmark of development in many cell types. However, these conclusions are largely based on chromatin immunoprecipitations (ChIP) with significant methodological problems hampering their interpretation. Absent direct quantitative measurements, it has been difficult to evaluate the strength of the bivalency model. Here, we present reICeChIP, a calibrated sequential ChIP method to quantitatively measure H3K4me3/H3K27me3 bivalency genome-wide, addressing the limitations of prior measurements. With reICeChIP, we profile bivalency through the differentiation paradigm that first established this model16,18: from naive mouse embryonic stem cells (mESCs) into neuronal progenitor cells (NPCs). Our results cast doubt on every aspect of the bivalency model; in this context, we find that bivalency is widespread, does not resolve with differentiation, and is neither sensitive nor specific for identifying poised developmental genes or gene expression status more broadly. Our findings caution against interpreting bivalent domains as specific markers of developmentally poised genes.


title: In their sister's footsteps: Taxonomic divergence obscures substantial functional overlap among the metabolically diverse symbiotic gut communities of adult and larval turtle ants

abstract: Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. While the composition of gut symbiont communities shifts with host development in holometabolous insects, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through genomic and metagenomic screenings and targeted in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts from the Enterobacteriales, Lactobacillales and Rhizobiales orders, with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant fibers common in turtle ant diets, and energy-generating fermentation. Additionally, several members of the specialized turtle ant adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers and other carbohydrates. Symbionts from both life stages have the genomic capacity to recycle nitrogen, synthesize amino acids and B-vitamins, and perform several key aspects of sulfur metabolism. We also document, for the first time in ants, an adult-associated Campylobacterales symbiont with an apparent capacity to anaerobically oxidize sulfide, reduce nitrate, and fix carbon dioxide. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae appear as an important component of turtle ant colony digestion and nutrition. In addition, the conserved nature of the digestive, energy-generating, and nutritive capacities among adult-enriched symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 46 million years of residency.


title: Effective population size for culturally evolving traits

abstract:
Population size has long been considered an important driver of cultural diversity and complexity. Results from population genetics, however, demonstrate that in populations with complex demographic structure or mode of inheritance, it is not the census population size, N, but the effective size of a population, Ne, that determines important evolutionary parameters. Here, we examine the concept of effective population size for traits that evolve culturally, through processes of innovation and social learning. We use mathematical and computational modeling approaches to investigate how cultural Ne and levels of diversity depend on (1) the way traits are learned, (2) population connectedness, and (3) social network structure. We show that one-to-many and frequency-dependent transmission can temporally or permanently lower effective population size compared to census numbers. We caution that migration and cultural exchange can have counter-intuitive effects on Ne. Network density in random networks leaves Ne unchanged, scale-free networks tend to decrease and small-world networks tend to increase Ne compared to census numbers. For one-to-many transmission and different network structures, effective size and cultural diversity are closely associated. For connectedness, however, even small amounts of migration and cultural exchange result in high diversity independently of Ne. Our results highlight the importance of carefully defining effective population size for cultural systems and show that inferring Ne requires detailed knowledge about underlying cultural and demographic processes.

AUTHOR SUMMARYHuman populations show immense cultural diversity and researchers have regarded population size as an important driver of cultural variation and complexity. Our approach is based on cultural evolutionary theory which applies ideas about evolution to understand how cultural traits change over time. We employ insights from population genetics about the "effective" size of a population (i.e. the size that matters for important evolutionary outcomes) to understand how and when larger populations can be expected to be more culturally diverse. Specifically, we provide a formal derivation for cultural effective population size and use mathematical and computational models to study how effective size and cultural diversity depend on (1) the way culture is transmitted, (2) levels of migration and cultural exchange, as well as (3) social network structure. Our results highlight the importance of effective sizes for cultural evolution and provide heuristics for empirical researchers to decide when census numbers could be used as proxies for the theoretically relevant effective numbers and when they should not.


title: Parallel evolution of urban-rural clines

abstract: Urbanization is the dominant trend of global land use change. The replicated nature of environmental change associated with urbanization should drive parallel evolution, yet insight into the repeatability of evolutionary processes in urban areas has been limited by a lack of multi-city studies. Here we leverage community science data on coat color in >60,000 eastern gray squirrels (Sciurus carolinensis) across 43 North American cities to test for parallel clines in melanism, a genetically based trait associated with thermoregulation and crypsis. We show the prevalence of melanism was positively associated with urbanization as measured by impervious cover. Urban-rural clines in melanism were strongest in the largest cities with extensive forest cover and weakest or absent in cities with warmer winter temperatures, where thermal selection likely limits the prevalence of melanism. Our results suggest that novel traits can evolve in a highly repeatable manner among urban areas, modified by factors intrinsic to individual cities, including their size, land cover, and climate.


title: Parallel evolution of urban-rural clines in melanism in a widespread mammal


title: blupADC: An R package and shiny toolkit for comprehensive genetic data analysis in animal and plant breeding

abstract:
SummaryGenetic analysis is a systematic and complex procedure in animal and plant breeding. With fast development of high-throughput genotyping techniques and algorithms, animal and plant breeding has entered into a genomic era. However, there is a lack of software, which can be used to process comprehensive genetic analyses, in the routine animal and plant breeding program. To make the whole genetic analysis in animal and plant breeding straightforward, we developed a powerful, robust and fast R package that includes genomic data format conversion, genomic data quality control and genotype imputation, breed composition analysis, pedigree tracing, analysis and visualization, pedigree-based and genomic-based relationship matrix construction, and genomic evaluation. In addition, to simplify the application of this package, we also developed a shiny toolkit for users.

Availability and implementationblupADC is developed primarily in R with core functions written in C++. The development version is maintained at https://github.com/TXiang-lab/blupADC.

Supplementary informationSupplementary data are available online


title: Comparing Heritability Estimators under Alternative Structures of Linkage Disequilibrium

abstract: SNP heritability of a trait is the proportion of its variance explained by the additive effects of the genome-wide single nucleotide polymorphisms (SNPs). The existing approaches to estimate SNP heritability can be broadly classified into two categories. One set of approaches model the SNP effects as fixed effects and the other treats the SNP effects as random effects. These methods make certain assumptions about the dependency among individuals (familial relationship) as well as the dependency among markers (linkage disequilibrium, LD) to provide consistent estimates of SNP heritability as the number of individuals increases. While various approaches have been proposed to account for such dependencies, it remains unclear which estimates reported in the literature are more robust against various model mis-specifications. Here we investigate the impact of different structures of LD and familial relatedness on heritability estimation. We show that the performance of different methods for heritability estimation depends heavily on the structure of the underlying pattern of LD and the degree of relatedness among sampled individuals. However, contrary to the claim in the current literature, we did not find significant differences in the performance of these fixed-SNP-effects and random-SNP-effects approaches. Moreover, we established the equivalence between the two method-of-moments estimators, one from each of these two lines of approaches.


title: Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs.

abstract: The application of single-cell RNA sequencing (scRNAseq) for the evaluation of chemicals, drugs, and food contaminants presents the opportunity to consider cellular heterogeneity in pharmacological and toxicological responses. Current differential gene expression analysis (DGEA) methods focus primarily on two group comparisons, not multi-group dose-response study designs used in safety assessments. To benchmark DGEA methods for dose-response scRNAseq experiments, we proposed a multiplicity corrected Bayesian testing approach and compare it against 8 other methods including two frequentist fit-for-purpose tests using simulated and experimental data. Our Bayesian test method outperformed all other tests for a broad range of accuracy metrics including control of false positive error rates. Most notable, the fit-for-purpose and standard multiple group DGEA methods were superior to the two group scRNAseq methods for dose-response study designs. Collectively, our benchmarking of DGEA methods demonstrates the importance in considering study design when determining the most appropriate test methods.


title: OpenMonkeyChallenge: Dataset and Benchmark Challenges for Pose Tracking of Non-human Primates

abstract: The ability to automatically track non-human primates as they move through the world is important for several subfields in biology and biomedicine. Inspired by the recent success of computer vision models enabled by benchmark challenges (e.g., object detection), we propose a new benchmark challenge called OpenMonkeyChallenge that facilitates collective community efforts through an annual competition to build generalizable non- human primate pose tracking models. To host the benchmark challenge, we provide a new public dataset consisting of 111,529 annotated (17 body landmarks) photographs of non-human primates in naturalistic contexts obtained from various sources including the internet, three National Primate Research Centers, and the Minnesota Zoo. Such annotated datasets will be used for the training and testing datasets to develop generalizable models with standardized evaluation metrics. We demonstrate the effectiveness of our dataset quantitatively by comparing it with existing datasets based on seven state-of-the-art pose tracking models.

category: animal behavior and cognition


title: Modular multilevel TMS device with wide output range and ultrabrief pulse capability for sound reduction

abstract:
ObjectiveThis article presents a novel transcranial magnetic stimulation (TMS) pulse generator with a wide range of pulse shape, amplitude, and width.

ApproachBased on a modular multilevel TMS (MM-TMS) topology we had proposed previously, we realized the first such device operating at full TMS energy levels. It consists of ten cascaded H-bridge modules, each implemented with insulated-gate bipolar transistors, enabling both novel high-amplitude ultrabrief pulses as well as pulses with conventional amplitude and duration. The MM-TMS device can output pulses including up to 21 voltage levels with a step size of up to 1100 V, allowing relatively flexible generation of various pulse waveforms and sequences. The circuit further allows charging the energy storage capacitor on each of the ten cascaded modules with a conventional TMS power supply.

Main resultsThe MM-TMS device can output peak coil voltages and currents of 11 kV and 10 kA, respectively, enabling suprathreshold ultrabrief pulses (> 8.25 s active electric field phase). Further, the MM-TMS device can generate a wide range of near-rectangular monophasic and biphasic pulses, as well as more complex staircase-approximated sinusoidal, polyphasic, and amplitude-modulated pulses. At matched estimated stimulation strength, briefer pulses emit less sound, which could enable quieter TMS. Finally, the MM-TMS device can instantaneously increase or decrease the amplitude from one pulse to the next in discrete steps by adding or removing modules in series, which enables rapid pulse sequences and paired-pulse protocols with variable pulse shapes and amplitudes.

SignificanceThe MM-TMS device allows unprecedented control of the pulse characteristics which could enable novel protocols and quieter pulses.

category: bioengineering


title: Mechanical and possible auxetic properties of human Achilles tendon during in vitro testing to failure

abstract: The Achilles tendon is the strongest tendon in the human body, but the basis of its high tensile strength has not been elucidated in detail. Here we have loaded healthy, human, Achilles tendons to failure in an anatomically authentic fashion while studying the local three-dimensional deformation and strains in real time, with very high precision, using digital image correlation (DIC). These studies identified a remarkable degree of anisotropic, medio-lateral auxetic behavior, with Poissons ratios not exceeding minus 1 in any part of the tendon at any time; under certain loads, discrete areas within the tendon had a Poissons ratio below minus 6. Early in the loading cycle, the proximal region of the tendon accumulated high lateral strains while longitudinal strains remained low. This behavior shielded the mid-substance of the tendon, its weakest part, from high longitudinal strains until immediately before rupture. These new insights are of great relevance to understanding the material basis of tendon injuries, designing improved prosthetic replacements, and developing regenerative strategies.