bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling
Authors: Bisht Kanchan , Okojie Kenneth A. , Sharma Kaushik , Lentferink Dennis H. , Sun Yu-Yo , Chen Hong-Ru , Uweru Joseph O. , Amancherla Saipranusha , Calcuttawala Zainab , Campos-Salazar Antony Brayan , Corliss Bruce , Jabbour Lara , Benderoth Jordan , Friestad Bria , Mills William A. , Isakson Brant E. , Tremblay Marie-Ève , Kuan Chia-Yi , Eyo Ukpong B. 
Published: August 2021

AbstractMicroglia are brain-resident immune cells with a repertoire of functions in the developing, mature and pathological brain. Their wide-ranging roles in physiology include the clearance of cellular debris, elimination of excess synapses, regulation of neuronal activity and contributions to blood vessel development. Despite these known roles for microglia, the extent of their interactions with the vasculature and potential regulation of vascular physiology has been insufficiently explored. Here, using in vivo acute and longitudinal two-photon imaging in transgenic mice combined with electron microscopy, fixed tissue immunohistochemistry, pharmacological treatments and laser speckle imaging, we document the steady-state interactions between ramified CX3CR1+ myeloid cell somata and capillaries in the brain. We first confirm that these myeloid cells are bona fide microglia by molecular, morphological and ultrastructural approaches. Then we give a detailed spatio-temporal characterization of these capillary-associated microglia (CAMs) comparing and contrasting them with parenchymal microglia (PCMs) in their static, dynamic and chronic morphological activities including during microglial depletion and repopulation. Molecularly, we identify microglial-specific purinergic P2RY12 receptors as a receptor regulating CAM interactions under the control of released purines from pannexin 1 (PANX1) channels. Furthermore, to elucidate roles for microglia in vascular structure and function, we eliminated microglia and showed that this triggered capillary dilation, blood flow increase, and impaired vasodilative responses. We find that P2RY12−/− and PANX1−/− mice recapitulate these vascular impairments suggesting purines released through PANX1 channels play important roles in activating microglial P2RY12 receptors to regulate neurovascular structure and function.
ZeBox: A novel non-intrusive continuous-use technology to trap and kill airborne microbes
Authors: Phadke Kruttika S. , Madival Deepak G. , Venkataraman Janani , Kundu Debosmita , Ramanujan K. S. , Holla Nisha , Arakeri Jaywant , Tomar Gaurav , Datta Santanu , Ghatak Arindam 
Published: August 2021

AbstractPreventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called “ZeBox” that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface’s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5-9 log reduction) and >90% efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.
Shisa7 phosphorylation regulates GABAergic transmission and neurodevelopmental behaviors
Authors: Wu Kunwei , Shepard Ryan David , Castellano David , Tian Qingjun , Dong Lijin , Lu Wei 
Published: August 2021

AbstractGABA-A receptors (GABAARs) are crucial for development and regulation of the central nervous system. Altered GABAergic signaling is hypothesized to be involved in the pathophysiology of neurodevelopmental disorders. Nevertheless, how aberrant cellular and molecular mechanisms affect GABAARs in these diseases remain elusive. Recently, we identified Shisa7 as a GABAAR auxiliary subunit that modulates GABAAR trafficking, kinetics, and pharmacology, and discovered a phosphorylation site in Shisa7 (S405) critical for extrasynaptic α5-GABAAR trafficking and tonic inhibition. However, the role of S405 phosphorylation in the regulation of synaptic inhibition, plasticity, and behavior remains unknown. Here, we found that expression of a phospho-null mutant (Shisa7 S405A) in heterologous cells and neurons diminishes α2-GABAAR trafficking. Subsequently, we generate a Shisa7 S405A knock-in (KI) mouse line that displays reduced surface expression of GABAARs in hippocampal neurons. Importantly, both synaptic and tonic inhibition are decreased in KI mice. Moreover, chemically induced inhibitory long-term potentiation is impaired, highlighting a critical role of Shisa7 S405 in GABAergic plasticity. Lastly, KI mice exhibit enhanced locomotor activity and grooming associated with neurodevelopmental disorders. Collectively, our study reveals a phosphorylation site critical for Shisa7-dependent trafficking of synaptic and extrasynaptic GABAARs which contributes to behavioral endophenotypes displayed in neurodevelopmental disorders.
Burning for grassland pollination: recently burned patches promote plant flowering and insect pollinators
Authors: da Silva Goldas Camila , Podgaiski Luciana Regina , da Silva Carolina Veronese Corrêa , de Souza Mendonça Milton 
Published: August 2021

AbstractGrasslands are historically and evolutionarily associated with disturbances, such as fire, that drive biodiversity assembly patterns and biotic interactions. Disturbance suppression in fire- prone ecosystems usually leads to a decline in forb diversity and flowering due to biomass accumulation, which could jeopardize pollinator diversity. In this study, we investigated patterns and drivers of plant flowering and flower insect visitor communities in a chronosequence of patches from different time-since-fire categories in Southern Brazilian grasslands. Old-burnt patches (more than 2 years since fire) had taller vegetation, more biomass and grass cover than intermediate (about 1 year after fire) and freshly-burnt patches (less than 6 months since fire), which had increased bare soil cover. Forb flower abundance was much higher in freshly-burnt patches, directly predicted by the degree of habitat openness. Pollinator insects were then benefited by floral resource aggregation in freshly-burnt patches, increasing in abundance (bees and butterflies) and species richness (bees). Beetle communities were positively influenced by vegetation height. Furthermore, plant species flowering and bee species composition varied between freshly and old-burnt grasslands, with indicator species found for all recovery stages but mainly freshly-burnt patches. Altogether, these results indicate the importance of maintaining freshly-burnt patches in the grassland landscape: it helps to sustain flower diversity, pollination services, and flowering plant reproduction. Our findings support the idea that a mosaic of grasslands from different times-since- fire should be considered for grassland conservation.
Uncertainty quantification in subject-specific estimation of local vessel mechanical properties
Authors: Rego Bruno V. , Weiss Dar , Bersi Matthew R. , Humphrey Jay D. 
Published: August 2021

AbstractQuantitative estimation of local mechanical properties remains critically important in the ongoing effort to elucidate how blood vessels establish, maintain, or lose mechanical homeostasis. Recent advances based on panoramic digital image correlation (pDIC) have made high-fidelity 3D reconstructions of small-animal (e.g., murine) vessels possible when imaged in a variety of quasi-statically loaded configurations. While we have previously developed and validated inverse modeling approaches to translate pDIC-measured surface deformations into biomechanical metrics of interest, our workflow did not heretofore include a methodology to quantify uncertainties associated with local point estimates of mechanical properties. This limitation has compromised our ability to infer biomechanical properties on a subject-specific basis, such as whether stiffness differs significantly between multiple material locations on the same vessel or whether stiffness differs significantly between multiple vessels at a corresponding material location. In the present study, we have integrated a novel uncertainty quantification and propagation pipeline within our inverse modeling approach, relying on empirical and analytic Bayesian techniques. To demonstrate the approach, we present illustrative results for the ascending thoracic aorta from three mouse models, quantifying uncertainties in constitutive model parameters as well as circumferential and axial tangent stiffness. Our extended workflow not only allows parameter uncertainties to be systematically reported, but also facilitates both subject-specific and group-level statistical analyses of the mechanics of the vessel wall.
Myofiber injury induces capillary disruption and regeneration of disorganized microvascular networks
Authors: Jacobsen Nicole L. , Norton Charles E. , Shaw Rebecca L. , Cornelison DDW , Segal Steven S. 
Published: August 2021

AbstractMyofibers regenerate following injury, however the microvasculature must also recover to restore skeletal muscle function. We aimed to define the nature of microvascular damage and repair during skeletal muscle injury and regeneration induced by BaCl2. To test the hypothesis that microvascular disruption occurred secondary to myofiber injury in mice, isolated microvessels were exposed to BaCl2 or the myotoxin was injected into the gluteus maximus (GM) muscle. In isolated microvessels, BaCl2 depolarized smooth muscle cells and endothelial cells while increasing [Ca2+]i, but did not elicit cell death. At 1 day post injury (dpi) of the GM, capillary fragmentation coincided with myofiber degeneration while arteriolar and venular networks remained intact; neutrophil depletion before injury did not prevent capillary damage. Perfused capillary networks reformed by 5 dpi in association with more terminal arterioles and were dilated through 10 dpi; with no change in microvascular area or branch point number in regenerating networks, fewer capillaries aligned with myofibers and capillary networks were no longer organized into microvascular units. By 21 dpi, capillary orientation and organization had nearly recovered to that in uninjured GM. We conclude that following their disruption secondary to myofiber damage, capillaries regenerate as disorganized networks that remodel while regenerated myofibers mature.
Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes
Authors: Venzon Mericien , Das Ritika , Luciano Daniel J. , Burnett Julia , Park Hyun Shin , Devlin Joseph Cooper , Kool Eric T. , Belasco Joel G. , Hubbard E. Jane Albert , Cadwell Ken 
Published: August 2021

SummaryA distinguishing feature of Trichuris nematodes is that these parasitic worms reproduce within the digestive tracts of humans and other mammalian hosts shedding thousands of eggs daily, facilitating their sustained presence in the environment and hampering eradication efforts. Although this aspect of the lifecycle places Trichuris in a microbiota-rich environment, metabolic byproducts of bacteria that facilitate the reproductive development of parasites are unknown. Here, we employ a pipeline using the well-characterized free-living nematode C. elegans to identify microbial factors with conserved roles in the reproduction of nematodes. A screen for E. coli mutants that impair C. elegans fertility identified genes in fatty acid biosynthesis and ethanolamine utilization pathways, including fabH and eutN. Trichuris muris eggs displayed defective hatching in the presence of E. coli deficient in fabH or eutN due to reduction in arginine or elevated levels of aldehydes, respectively. Remarkably, T. muris reared in gnotobiotic mice colonized with these E. coli mutants displayed profound abnormalities including morphological defects and a failure to lay viable eggs. These findings indicate that microbial byproducts mediate evolutionarily conserved transkingdom interactions that impact the reproductive fitness of distantly-related nematodes.
Effects of Cholesterol on the mechanism of fengycin, a biofungicide
Authors: Sur Sreyoshi , Grossfield Alan 
Published: August 2021

AbstractFengycins are a class of antifungal lipopeptides synthesized by the bacteria Bacillus subtilis, commercially available as the primary component of the agricultural fungicide Serenade®. They are toxic to fungi, but far less to mammalian cells. One key difference between mammalian and fungal cell membranes is the presence of cholesterol only in the former; recent experimental work showed that the presence of cholesterol reduces fengycin-induced membrane leakage. (1) Since our previous all-atom and coarse-grained simulations (2, 3) suggested that aggregation of membrane-bound fengycin is central to its ability to disrupt membranes, we hypothesized that cholesterol might reduce fengycin aggregation. Here, we test this hypothesis using coarse-grained molecular dynamics simulations, with sampling enhanced via the weighted ensemble method. The results indicate that cholesterol subtly alters the size distribution for fengycin aggregates, limits the lateral range of their membrane disordering, and reduces the ability of aggregates to bend the membrane. Taken together, these phenomena may account for cholesterol’s affects on fengycin activity.
NT-CRISPR: Combining natural transformation and CRISPR/Cas9 counterselection for markerless and scarless genome editing in Vibrio natriegens
Authors: Stukenberg Daniel , Hoff Josef , Faber Anna , Becker Anke 
Published: August 2021

AbstractThe fast-growing bacterium Vibrio natriegens has recently gained increasing attention as a novel chassis organism for a wide range of projects. To fully harness the potential of this fascinating bacterium, convenient and highly efficient genome editing methods are indispensable to create novel strains, tailored for specific applications. V. natriegens is able to take up free DNA and incorporate it into its genome by homologous recombination. This process, called natural transformation, was tamed for genome editing. It displays a high efficiency and is able to mediate uptake of multiple DNA fragments, thereby allowing multiple simultaneous edits. Here, we describe NT-CRISPR, a combination of natural transformation with CRISPR/Cas9 counterselection. In two temporally distinct steps, we first performed a genome edit by natural transformation and second, induced CRISPR/Cas9, targeting the wild type sequence, leading to death of non-edited cells. Through highly efficient cell killing with efficiencies of up to 99.999 %, integration of antibiotic resistance markers became dispensable and thus enabled scarless and markerless edits with single-base precision. We used NT-CRISPR for deletions, integrations and single-base modifications with editing efficiencies of up to 100 % and further demonstrated its applicability for the simultaneous deletion of multiple chromosomal regions. Lastly, we demonstrated that the near PAM-less Cas9 variant SpG Cas9 is compatible with NT-CRISPR and thereby massively broadens the target spectrum.
Automated, high-dimensional evaluation of physiological aging and resilience in outbred mice
Authors: Chen Zhenghao , Raj Anil , Prateek G.V. , Di Francesco Andrea , Liu Justin , Keyes Brice E. , Kolumam Ganesh , Jojic Vladimir , Freund Adam 
Published: August 2021

AbstractBehavior and physiology are essential readouts in many studies but have not benefited from the high-dimensional data revolution that has transformed molecular and cellular phenotyping. To address this, we developed an approach that combines commercially available automated phenotyping hardware with a systems biology analysis pipeline to generate a high-dimensional readout of mouse behavior/physiology, as well as intuitive and health-relevant summary statistics (resilience and biological age). We used this platform to longitudinally evaluate aging in hundreds of outbred mice across an age range from 6 months to 3.4 years. In contrast to the assumption that aging can only be measured at the limits of animal ability via challenge-based tasks, we observed widespread physiological and behavioral aging starting in early life. Using network connectivity analysis, we found that organism-level resilience exhibited an accelerating decline with age that was distinct from the trajectory of individual phenotypes. We developed a method, Combined Aging and Survival Prediction of Aging Rate (CASPAR), for jointly predicting chronological age and survival time and showed that the resulting model is able to predict both variables simultaneously, a behavior that is not captured by separate age and mortality prediction models. This study provides a uniquely high-resolution view of physiological aging in mice and demonstrates that systems-level analysis of physiology provides insights not captured by individual phenotypes. The approach described here allows aging, and other processes that affect behavior and physiology, to be studied with sophistication and rigor.
Single-sequence protein structure prediction using language models from deep learning
Authors: Chowdhury Ratul , Bouatta Nazim , Biswas Surojit , Rochereau Charlotte , Church George M. , Sorger Peter K. , AlQuraishi Mohammed 
Published: August 2021

ABSTRACTAlphaFold2 and related systems use deep learning to predict protein structure from co-evolutionary relationships encoded in multiple sequence alignments (MSAs). Despite dramatic, recent increases in accuracy, three challenges remain: (i) prediction of orphan and rapidly evolving proteins for which an MSA cannot be generated, (ii) rapid exploration of designed structures, and (iii) understanding the rules governing spontaneous polypeptide folding in solution. Here we report development of an end-to-end differentiable recurrent geometric network (RGN) able to predict protein structure from single protein sequences without use of MSAs. This deep learning system has two novel elements: a protein language model (AminoBERT) that uses a Transformer to learn latent structural information from millions of unaligned proteins and a geometric module that compactly represents Cα backbone geometry. RGN2 outperforms AlphaFold2 and RoseTTAFold (as well as trRosetta) on orphan proteins and is competitive with designed sequences, while achieving up to a 106-fold reduction in compute time. These findings demonstrate the practical and theoretical strengths of protein language models relative to MSAs in structure prediction.
Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity
Authors: Fu Rongjie , He Wei , Dou Jinzhuang , Villarreal Oscar D. , Bedford Ella , Wang Helen , Hou Connie , Zhang Liang , Wang Yalong , Chen Yiwen , Gao Xue Sherry , Depken Martin , Xu Han 
Published: August 2021

AbstractThe specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. Here we systematically investigated the sequence determinants governing CRISPR/Cas9 specificity by measuring the off-on ratios of 1,902 gRNAs on 13,314 target sequences using an improved synthetic system with dual-target design. Our study revealed a comprehensive set of rules including 3 factors in CRISPR/Cas9 off-targeting: 1) the nucleotide context and position of a single mismatch; 2) an “epistasis-like” combinatorial effect of multiple mismatches; and 3) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context. Notably, the combinatorial effect and GMT are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. Based on these rules, we developed a model-based off-target prediction tool (MOFF), which showed superior performance compared to the existing methods.
Microbiota-dependent and independent production of L-dopa in the gut of Daphnia magna
Authors: El-Shehawy Rehab , Luecke-Johansson Sandra , Ribbenstedt Anton , Gorokhova Elena 
Published: August 2021

AbstractThe host-microbiome interactions are essential for the physiological and ecological performance of the host, yet these interactions are challenging to identify. Neurotransmitters are commonly implicated in these interactions, but we know very little about the mechanisms of their involvement, especially in invertebrates. Here, we report a peripheral Catecholamine (CA) pathway involving the gut microbiome of the model species Daphnia magna. We demonstrate that: (1) tyrosine hydroxylase and dopa decarboxylase enzymes are present in the gut wall; (2) DOPA decarboxylase gene is expressed in the gut by the host, and its expression follows the molt cycle peaking after ecdysis; (3) biologically active L-Dopa, but not Dopamine, is present in the gut lumen; and (4) gut bacteria produce L-Dopa in a concentration-dependent manner when provided L-Tyrosine as a substrate. Impinging on gut bacteria involvement in host physiology and ecologically relevant traits, we suggest L-Dopa as a communication agent in the host-microbiome interactions in daphnids and, possibly, other crustaceans.