bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche
Authors: Carr Erin C. , Barton Quin , Grambo Sarah , Sullivan Mitchell , Renfro Cecile M. , Kuo Alan , Pangilinan Jasmyn , Lipzen Anna , Keymanesh Keykhosrow , Savage Emily , Barry Kerrie , Grigoriev Igor V. , Riekhof Wayne R. , Harris Steven D. 
Published: December 2021

AbstractBlack yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeasts from the genusExophialathat were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been namedExophiala viscosa (i.e., E. viscosaJF 03-3 Goopyand E. viscosaJF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niches within the biological soil crust consortium. Our results reveal thatE. viscosais capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excrete melanin that can potentially provide UV resistance to the biological soil crust community. Besides the identification of a novel species within the genusExophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.
FcγRIIB regulates (auto)antibody responses by limiting marginal zone B cell activation
Authors: Barlev Ashley N. , Malkiel Susan , Dorjée Annemarie L. , Suurmond Jolien , Diamond Betty 
Published: December 2021

AbstractFcγRIIB is an inhibitory receptor expressed throughout B cell development. Diminished expression or function is associated with lupus in mice and humans, in particular through an effect on autoantibody production and plasma cell differentiation. Here, we analysed the effect of B cell-intrinsic FcγRIIB expression on B cell activation and plasma cell differentiation.Loss of FcγRIIB on B cells (Fcgr2b cKO mice) led to a spontaneous increase in autoantibody titers. This increase was most striking for IgG3, suggestive of increased extrafollicular responses. Marginal zone (MZ) and IgG3+ B cells had the highest expression of FcγRIIB and the increase in serum IgG3 was linked to increased MZ B cell signaling and activation in the absence of FcγRIIB. Likewise, human circulating MZ-like B cells had the highest expression of FcγRIIB, and their activation was most strongly inhibited by engaging FcγRIIB. Finally, marked increases in IgG3+ plasma cells and B cells were observed during extrafollicular plasma cell responses with both T-dependent and T-independent antigens in Fcgr2b cKO mice. The increased IgG3 response following immunization of Fcgr2b cKO mice was lost in MZ-deficient Notch2/Fcgr2b cKO mice.Thus, we present a model where high FcγRIIB expression in MZ B cells prevents their hyperactivation and ensuing autoimmunity.Graphical abstract
Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer
Authors: Lykoskoufis Nikolaos M. R. , Planet Evarist , Ongen Halit , Trono Didier , Dermitzakis Emmanouil T. 
Published: December 2021

ABSTRACTTransposable elements (TEs) are interspersed repeats that contribute to more than half of the human genome, and TE-embedded regulatory sequences are increasingly recognized as major components of the human regulome. Perturbations of this system can contribute to tumorigenesis, but the impact of TEs on gene expression in cancer cells remains to be fully assessed. Here, we analyzed 275 normal colon and 276 colorectal cancer (CRC) samples from the SYSCOL colorectal cancer cohort and discovered 10,111 and 5,152 TE expression quantitative trait loci (eQTLs) in normal and tumor tissues, respectively. Amongst the latter, 376 were exclusive to CRC, likely driven by changes in methylation patterns. We identified that transcription factors are more enriched in tumor-specific TE-eQTLs than shared TE-eQTLs, indicating that TEs are more specifically regulated in tumor than normal. Using Bayesian Networks to assess the causal relationship between eQTL variants, TEs and genes, we identified that 1,758 TEs are mediators of genetic effect, altering the expression of 1,626 nearby genes significantly more in tumor compared to normal, of which 51 are cancer driver genes. We show that tumor-specific TE-eQTLs trigger the driver capability of TEs subsequently impacting expression of nearby genes. Collectively, our results highlight a global profile of a new class of cancer drivers, thereby enhancing our understanding of tumorigenesis and providing potential new candidate mechanisms for therapeutic target development.
Human IAPP is a contributor to painful diabetic peripheral neuropathy
Authors: Albariqi Mohammed M. H. , Versteeg Sabine , Brakkee Elisabeth M. , Coert J. Henk , Elenbaas Barend O. W. , Prado Judith , Hack C. Erik , Höppener Jo W. M. , Eijkelkamp Niels 
Published: December 2021

AbstractPeripheral neuropathy is a frequent complication of type 2 diabetes mellitus (T2DM). We investigated whether human islet amyloid polypeptide (hIAPP), which forms pathogenic aggregates that damage pancreatic islet β-cells in T2DM, is involved in T2DM-associated peripheral neuropathy.In vitro, hIAPP incubation with sensory neurons reduced neurite outgrowth and increased levels of mitochondrial reactive oxygen species. Transgenic hIAPP mice that have elevated plasma hIAPP levels without hyperglycemia developed peripheral neuropathy as evidenced by pain-associated behavior and reduced intra-epidermal nerve fiber (IENF) density. Similarly, hIAPP Ob/Ob mice that have hyperglycaemia in combination with elevated plasma hIAPP levels had signs of neuropathy, although more aggravated.In wild-type mice, intraplantar and intravenous hIAPP injections induced long-lasting allodynia and decreased IENF density. Non-aggregating murine IAPP, mutated hIAPP (Pramlintide), or hIAPP with pharmacologically inhibited aggregation did not induce these effects. T2DM patients had reduced IENF density and more hIAPP oligomers in the skin compared to non-T2DM controls. Thus, we provide evidence that hIAPP aggregation is neurotoxic and mediates peripheral neuropathy in mice. The increased abundance of hIAPP aggregates in the skin of T2DM patients supports the notion that hIAPP is a potential contributor to T2DM neuropathy in humans.Graphic abstract
Inactivation mechanism and efficacy of grape seed extract for Human Norovirus surrogate
Authors: Oh Chamteut , Chowdhury Ratul , Samineni Laxmicharan , Shisler Joanna L , Kumar Manish , Nguyen Thanh H. 
Published: December 2021

AbstractProper disinfection of harvested food and water is critical to minimize infectious disease. Grape seed extract (GSE), a commonly used health supplement, is a mixture of plant-derived polyphenols. Polyphenols possess anti-microbial and -fungal properties, but anti-viral effects are not well-known. Here we show that GSE outperformed chemical disinfectants (e.g., free chlorine and peracetic acids) in inactivating Tulane virus, a human norovirus surrogate. GSE induced virus aggregation, an event that correlated with a decrease in virus titers. This aggregation and disinfection was not reversible. Molecular docking simulations indicate that polyphenols potentially formed hydrogen bonds and strong hydrophobic interactions with specific residues in viral capsid proteins. Together, these data suggest that polyphenols physically associate with viral capsid proteins to aggregate viruses as a means to inhibit virus entry into the host cell. Plant-based polyphenols like GSE are an attractive alternative to chemical disinfectants to remove infectious viruses from water or food.ImportanceHuman noroviruses are major food- and water-borne pathogens, causing approximately 20% of all cases of acute gastroenteritis cases in developing and developed countries. Proper sanitation or disinfection are critical strategies to minimize human norovirus-caused disease until a reliable vaccine is created. Grape seed extract (GSE) is a mixture of plant-derived polyphenols that is used as a health supplement. Polyphenols are known for antimicrobial, antifungal, and antibiofilm activities, but antiviral effects are not well-known. In studies here, plant-derived polyphenols outperformed chemical disinfectants (e.g., free chlorine and peracetic acids) in inactivating Tulane virus, a human norovirus surrogate. Based on data from additional molecular assays and molecular docking simulations, the current model is that the polyphenols in GSE bind to the Tulane virus capsid, an event that triggers virion aggregation. It is thought that this aggregation prevents Tulane virus from entering host cells.
Multiplexed high-throughput immune cell imaging reveals molecular health-associated phenotypes
Authors: Severin Yannik , Hale Benjamin D. , Mena Julien , Goslings David , Frey Beat M. , Snijder Berend 
Published: December 2021

SummaryPhenotypic plasticity is essential to the immune system, yet the factors that shape it are not fully understood. Here, we comprehensively analyze immune cell phenotypes including morphology across human cohorts by single-round multiplexed immunofluorescence, automated microscopy, and deep learning. Using the uncertainty of convolutional neural networks to cluster the phenotypes of 8 distinct immune cell subsets, we find that the resulting maps are influenced by donor age, gender, and blood pressure, revealing distinct polarization and activation-associated phenotypes across immune cell classes. We further associate T-cell morphology to transcriptional state based on their joint donor variability, and validate an inflammation-associated polarized T-cell morphology, and an age-associated loss of mitochondria in CD4+T-cells. Taken together, we show that immune cell phenotypes reflect both molecular and personal health information, opening new perspectives into the deep immune phenotyping of individual people in health and disease.
Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo
Authors: Schubert Michael , Hong Christy , Jilderda Laura J. , Rueda Marta Requesens , Tijhuis Andréa E. , Simon Judith E. , Bakker Petra L. , Cooper Jon L. , Damaskou Aristi , Wardenaar René , Bakker Bjorn , Gupta Sahil , van den Brink Anouk , Ruiz Lorena Andrade , Koster Miriam H. , Youssef Sameh A. , Luinenburg Danielle , Strong Alex , Engleitner Thomas , Ponstingl Hannes , de Haan Gerald , de Bruin Alain , Rad Roland , Nijman Hans W. , Medema René H. , van Vugt Marcel A.T.M. , de Bruyn Marco , Spierings Diana C.J. , Colomé-Tatché Maria , Vassiliou George S. , Foijer Floris 
Published: December 2021

AbstractChromosomal instability is a hallmark of cancer, but also an instigator of aneuploidy-induced stress, reducing cellular fitness. To better understand how cells with CIN adjust to aneuploidy and adopt a malignant fate in vivo, we performed a genome-wide mutagenesis screen in mice. We find that specifically aneuploid tumors inactivate Stat1 signaling in combination with increased Myc activity. By contrast, loss of p53 is common, but not enriched in CIN tumors. Validation in another tissue type confirmed that CIN promotes immune cell infiltration, which is alleviated by Stat1 loss combined with Myc activation, but not with p53 inactivation, or Myc activation alone. Importantly, we find that this mechanism is preserved in human aneuploid cancers. We conclude that aneuploid cancers inactivate Stat1 signaling to circumvent immune surveillance.
Permissive aggregative group formation favors coexistence in yeast
Authors: Belpaire Tom E. R. , Pešek Jiří , Lories Bram , Verstrepen Kevin J. , Steenackers Hans P. , Ramon Herman , Smeets Bart 
Published: December 2021

ABSTRACTIn Saccharomyces cerevisiae, the FLO1 gene encodes flocculins that lead to formation of multicellular flocs, that offer protection to the constituent cells. Flo1p was found to preferentially bind to fellow cooperators compared to defectors lacking FLO1 expression, resulting in enrichment of cooperators within the flocs. Given this dual function in cooperation and kin recognition, FLO1 has been termed a ‘green beard gene’. Because of the heterophilic nature of Flo1p binding however, we hypothesize that kin recognition is permissive and depends on the relative stability of FLO1+/flo1− versus FLO1+/FLO1+ bonds, which itself can be dependent on environmental conditions and intrinsic cell properties. We combine single cell measurements of adhesion strengths, individual cell-based simulations of cluster formation and evolution, and in vitro flocculation experiments to study the impact of relative bond stability on defector exclusion as well as benefit and stability of cooperation. We hereto vary the relative bond stability by changing the shear flow rate and the inherent bond strength. We identify a marked trade-off between both aspects of the green beard mechanism, with reduced relative bond stability leading to increased kin recognition, but at the expense of decreased cluster sizes and benefit of cooperation. Most notably, we show that the selection of FLO1 cooperators is negative-frequency dependent, which we directly attribute to the permissive character of the Flo1p bond. Taking into account the costs associated to FLO1 expression, this asymmetric selection results in a broad range of ecological conditions where coexistence between cooperators and defectors is stable. Although the kin recognition aspect of the FLO1 ‘green beard gene’ is thus limited and condition dependent, the negative-frequency dependency of selection can conserve the diversity of flocculent and non-flocculent phenotypes ensuring flexibility towards variable selective pressures.
Pectin self-assembly and its disruption by water: Insights into plant cell wall mechanics
Authors: John Jacob , Ray Debes , Aswal Vinod K. , Deshpande Abhijit P. , Varughese Susy 
Published: December 2021

AbstractPlant cell walls undergo multiple cycles of dehydration and rehydration during their life. Calcium crosslinked low methoxy pectin is a major constituent of plant cell walls. Understanding the dehydration-rehydration behavior of pectin gels may shed light on the water transport and mechanics of plant cells. In this work, we report the contributions of microstructure to the mechanics of pectin-Ca gels subjected to different extents of dehydration and subsequent rehydration. This is investigated using a pectin gel composition that forms ‘egg-box bundles’, a characteristic feature of the microstructure of low methoxy pectin-Ca gels. Large Amplitude Oscillatory Shear (LAOS) rheology along with Small Angle Neutron Scattering and Near Infrared (NIR) spectroscopy on pectin gels are used to elucidate the mechanical and microstructural changes during dehydration-rehydration cycles. As the extent of dehydration increase, the reswelling ability, strain-stiffening behavior and the yield strain decreases. These effects are more prominent at faster rates of dehydration and are not completely reversible upon rehydration to the initial undried state. Microstructural changes due to the aggregation of egg-box bundles and single chains and the associated changes in the water configurations lead to these irreversible changes.
Energy expenditure deficits drive obesity in a mouse model of Alström syndrome
Authors: Stephenson Erin J , Kinney Clint E , Statyton Amanda S , Han Joan C 
Published: December 2021

AbstractAlström syndrome (AS) is a rare multi-system disorder for which early-onset childhood obesity is a cardinal feature. Like humans with AS, animal models withAlms1loss-of-function mutations develop obesity, supporting the notion that ALMS1/Alms1 is required for the regulatory control of energy balance across species. This study aimed to determine which component(s) of energy balance are reliant on Alms1. Here, we performed comprehensive energy balance phenotypingAlms1tvrm102mice at both eight- and eighteen-weeks-of-age. We found that adiposity gains occurred early and rapidly inAlms1tvrm102male mice but much later in females. Rapid increases in body fat in males was due to a marked reduction in energy expenditure (EE) during early life and not due to any genotype-specific increases in energy intake under chow conditions. Energy intake did increase in a genotype-specific manner when mice were provided a high-fat-diet, exacerbating the effects of reduced EE on obesity progression. The EE deficit observed in maleAlms1tvrm102mice did not persist as mice aged, suggesting loss of Alms1 either causes a developmental delay in the mechanisms controlling early life EE, or that activation of compensatory mechanisms occurs after obesity is established. Future studies will determine how ALMS1/Alms1 modulates EE and how sex moderates this process.
A Spatial Transcriptomics Study of the Brain-Electrode Interface in Rat Motor Cortex
Authors: Whitsitt Quentin A. , Patel Bella , Hunt Brad , Purcell Erin K. 
Published: December 2021

AbstractThe study of the foreign body reaction to implanted electrodes in the brain is an important area of research for the future development of neuroprostheses and experimental electrophysiology. After electrode implantation in the brain, microglial activation, reactive astrogliosis, and neuronal cell death create an environment immediately surrounding the electrode that is significantly altered from its homeostatic state. To uncover physiological changes potentially affecting device function and longevity, spatial transcriptomics was implemented in this preliminary study to identify changes in gene expression driven by electrode implantation. This RNA-sequencing technique (10x Genomics, Visium) uses spatially coded, RNA-binding oligonucleotides on a microscope slide to spatially identify each sequencing read. For these experiments, sections of rat motor cortex implanted with Michigan-style silicon electrodes were mounted on the Visium slide for processing. Each tissue section was labeled for neurons and astrocytes using immunohistochemistry to provide a spatial reference for mapping each sequencing read relative to the device tract. Results from rat motor cortex at 24 hours, 1 week, and 6 weeks post implantation showed up to 5811 differentially expressed genes between implanted and non-implanted tissue sections. Many of these genes are related to biological mechanisms previously reported in studies of the foreign body response to implanted electrodes, while others are novel to this study. These results will provide a foundation for future work to both improve and measure the effects of gene expression on the long-term stability of recordings from implanted electrodes in the brain. Ongoing work will expand on these initial observations as we gain a better understanding of the dynamic, molecular changes taking place in the brain in response to electrode implantation.
Mechanical stretch regulates macropinocytosis in Hydra vulgaris
Authors: Skokan Taylor D. , Hobmayer Bert , McKinley Kara L. , Vale Ronald D. 
Published: December 2021

AbstractCells rely on a diverse array of engulfment processes to sense, exploit, and adapt to their environments. Macropinocytosis is a versatile example of such a process, allowing for the indiscriminate and rapid uptake of large volumes of fluid and membrane. Much of the molecular machinery essential for macropinocytosis has been well established. However, most of these studies relied on tissue culture models, leaving the regulation of this process within the context of organs and organisms unresolved. Here, we report that large-scale macropinocytosis occurs in the outer epithelial layer of the cnidarian Hydra vulgaris. Exploiting Hydra’s relatively simple body plan, we developed approaches to visualize macropinocytosis over extended periods of time in living tissue, revealing constitutive engulfment across the entire body axis. Using pharmacological perturbations, we establish a role for stretch-activated channels, including Piezo, and downstream calcium influx in inhibiting this process. Finally, we show that the direct application of planar stretch leads to calcium influx and a corresponding inhibition of macropinocytosis. Together, our approaches provide a platform for the mechanistic dissection of constitutive macropinocytosis in physiological contexts and reveal a role for macropinocytosis in responding to membrane tension.
Genome-wide association study and multi-trait analysis of opioid use disorder identifies novel associations in 639,709 individuals of European and African ancestry
Authors: Deak Joseph D. , Zhou Hang , Galimberti Marco , Levey Daniel , Wendt Frank R. , Sanchez-Roige Sandra , Hatoum Alexander , Johnson Emma C. , Nunez Yaira Z. , Demontis Ditte , Børglum Anders D. , Rajagopal Veera M. , Jennings Mariela V. , Kember Rachel L. , Justice Amy C. , Edenberg Howard J. , Agrawal Arpana , Polimanti Renato , Kranzler Henry R. , Gelernter Joel 
Published: December 2021

AbstractBackgroundDespite the large toll of opioid use disorder (OUD), genome-wide association studies (GWAS) of OUD to date have yielded few susceptibility loci.MethodsWe performed a large-scale GWAS of OUD in individuals of European (EUR) and African (AFR) ancestry, optimizing genetic informativeness by performing MTAG (Multi-trait analysis of GWAS) with genetically correlated substance use disorders (SUDs). Meta-analysis included seven cohorts: the Million Veteran Program (MVP), Psychiatric Genomics Consortium (PGC), iPSYCH, FinnGen, Partners Biobank, BioVU, and Yale-Penn 3, resulting in a total N=639,709 (Ncases=20,858) across ancestries. OUD cases were defined as having lifetime OUD diagnosis, and controls as anyone not known to meet OUD criteria. We estimated SNP-heritability (h2SNP) and genetic correlations (rg). Based on genetic correlation, we performed MTAG on OUD, alcohol use disorder (AUD), and cannabis use disorder (CanUD).ResultsThe EUR meta-analysis identified three genome-wide significant (GWS; p≤5×10−8) lead SNPs—one at FURIN (rs11372849; p=9.54×10−10) and two OPRM1 variants (rs1799971, p=4.92×10−09 ; rs79704991, p=1.37×10−08; r2=0.02). Rs1799971 (p=4.91×10−08) and another OPRM1 variant (rs9478500; p=1.95×10−8; r2=0.03) were identified in the cross-ancestry meta-analysis. Estimated h2SNP was 12.75%, with strong rg with CanUD (rg =0.82; p=1.14×10−47) and AUD (rg=0.77; p=6.36×10−78). The OUD-MTAG resulted in 18 GWS loci, some of which map to genes or gene regions that have previously been associated with psychiatric or addiction phenotypes.ConclusionsWe identified multiple OUD variant associations at OPRM1, single variant associations with FURIN, and 18 GWS associations in the OUD-MTAG. OUD is likely influenced by both OUD-specific loci and loci shared across SUDs.