bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmembrane helices 5 and 12 control transport dynamics, substrate affinity and specificity in the elevator-type UapA transporter
Authors: Dimakis Dimitris , Pyrris Yiannis , Diallinas George 
Published: April 2022

AbstractAn increasing number of solute transporters have been shown to function with the so-called sliding-elevator mechanism. Despite structural and functional differences all elevator-type transporters use a common mechanism of substrate translocation via reversible movements of a mobile core domain (the elevator) hosting the substrate binding site along a rigid scaffold domain stably anchored in the plasma membrane via homodimerization. One of the best studied elevator transporters is the UapA uric acid-xanthine/H+ symporter of the filamentous fungus Aspergillus nidulans. Here, we present a novel genetic analysis for deciphering the role of transmembrane segments (TMS) 5 and 12 in UapA transport function. We show that specific residues in both TMS5 and TMS12 control, negatively or positively, the dynamics of transport, but also substrate binding affinity and specificity. More specifically, mutations in TMS5 can lead to increased rate of transport, but also to an inactive transporter due to high-affinity substrate-trapping, whereas mutations in TMS12 lead to apparently uncontrolled sliding, and thus broadened specificity and UapA-mediated purine toxicity. Our findings shed new light on how elevator transporters function or how their transport characteristics might be altered genetically or have been modified in the course of evolution.
Community adaptation to temperature explains abrupt soil bacterial community shift along a geothermal gradient on Iceland
Authors: Weedon James T. , Bååth Erland , Rijkers Ruud , Reischke Stephanie , Sigurdsson Bjarni D. , Oddsdottir Edda , van Hal Jurgen , Aerts Rien , Janssens Ivan A. , van Bodegom Peter M. 
Published: April 2022

AbstractUnderstanding how and why soil microbial communities respond to temperature changes is important for understanding the drivers of microbial distribution and abundance. A unique area in Iceland, where soil temperatures have increased due to geothermic activity four years prior to sampling, creating a stable gradient of ambient to +40°C, allowed us to investigate the shape of the response to warming of soil bacterial communities, and their associated community temperature adaptation. We used 16S rRNA amplicon sequencing to profile bacterial communities, and bacterial growth based assays (3H Leu-incorporation) to characterize community adaptation using a temperature sensitivity index (SI, log (growth at 40°C/4°C)). Samples were taken from ≥9 levels of warming (covering almost up to +40°C above ambient soil temperature), under both grassland (Agrostis capillaris) and forest (Picea sitchensis) vegetation. The soils had very different community composition, but temperature adaptation was the same. Both diversity and community composition as well SI showed similar threshold dynamics along the soil temperature gradient. There were no significant changes up to soil warming of approx. 6-9 °C, beyond which all indices shifted in parallel. The consistency of these responses gives strong support for a decisive role for direct temperature effects in driving bacterial community shifts along soil temperature gradients.
Prey resources are more important than climatic conditions for predicting the distribution of a broad-ranged apex predator
Authors: Sutton Luke J. , Anderson David L. , Franco Miguel , McClure Christopher J.W. , Miranda Everton B.P. , Vargas F. Hernán , de Vargas González José J. , Puschendorf Robert 
Published: April 2022

AbstractA current biogeographic paradigm states that climate regulates species distributions at continental scales and that biotic interactions are undetectable at coarse-grain extents. However, recent advances in spatial modelling show that incorporating food resource distributions are important for improving model predictions at large distribution scales. This is particularly relevant to understand the factors limiting distribution of widespread apex predators whose diets are likely to vary across their range. The harpy eagle (Harpia harpyja) is a large raptor, whose diet is largely comprised of arboreal mammals, such as sloths and primates, all with broad distributions across Neotropical lowland forest. Here, we used a hierarchical modelling approach to determine the relative importance of abiotic factors and prey resource distribution on harpy eagle range limits. Our hierarchical approach consisted of the following modelling sequence of explanatory variables: (a) abiotic covariates, (b) prey resource distributions predicted by an equivalent modelling for each prey, (c) the combination of (a) and (b), and (d) as in (c) but with prey resources considered as a single prediction equivalent to prey species richness. Incorporating prey distributions improved model predictions but using solely these biotic covariates still resulted in a high performing model. In the Abiotic model, Climatic Moisture Index (CMI) was the most important predictor, contributing 80 % to model prediction. Three-toed sloth (Bradypus spp.) was the most important prey resource, contributing 57 % in a combined Abiotic-Biotic model, followed by CMI contributing 29 %. Harpy eagle distribution had moderate to high environmental overlap across all prey distributions in geographic space when measured individually, but overlap was substantially lower in environmental space when prey distributions were combined. With strong reliance on prey distributions across its range, harpy eagle conservation programs must therefore consider its most important food resources as a key element in the protection of this threatened raptor.
Evidence for a widespread third system for bacterial polysaccharide export across the outer membrane comprising a composite OPX/β-barrel translocon
Authors: Schwabe Johannes , Pérez-Burgos María , Herfurth Marco , Glatter Timo , Søgaard-Andersen Lotte 
Published: April 2022

AbstractIn Gram-negative bacteria, secreted polysaccharides have multiple critical functions. In Wzx/Wzy- and ABC transporter-dependent pathways, an outer membrane (OM) polysaccharide export (OPX) type translocon exports the polysaccharide across the OM. The paradigm OPX protein WzaE. coli is an octamer, in which the eight C-terminal domains form an α-helical OM pore, and the eight copies of the three N-terminal domains (D1-D3) a periplasmic cavity. In synthase-dependent pathways, the OM translocon is a 16- to 18- stranded β-barrel protein. In Myxococcus xanthus, the secreted polysaccharide EPS is synthesized in a Wzx/Wzy-dependent pathway. Here, using experiments and computational structural biology, we characterize EpsX as an OM 18-stranded β-barrel protein important for EPS synthesis and identify AlgE, a β-barrel translocon of a synthase-dependent pathway, as its closest structural homolog. We also find that EpsY, the OPX protein of the EPS pathway, only consists of the periplasmic D1 and D2 domains and lacks the domain for spanning the OM (henceforth D1D2OPX protein). In vivo, EpsX and EpsY mutually stabilize each other, supporting their direct interaction. Based on these observations, we propose a model whereby EpsY and EpsX make up a novel type of translocon for polysaccharide export across the OM. Specifically, in this composite translocon, EpsX functions as the OM-spanning translocon together with the periplasmic D1D2OPX protein EpsY. Based on computational genomics, similar composite systems are present widespread in Gram-negative bacteria. This model provides a framework for these proteins’ future experimental characterization.
Biological responses to terahertz radiation with different power density in primary hippocampal neurons
Authors: Zhao Li , Yi Ruhan , Liu Sun , Chi Yunliang , Tan Shengzhi , Dong Ji , Wang Hui , Zhang Jing , Wang Haoyu , Xu Xinping , Yao Binwei , Wang Bo , Peng Ruiyun 
Published: April 2022

AbstractBackgroundTerahertz (THz) radiation is a valuable imaging and sensing tool which is widely used in industry and medicine. However, it biological effects including genotoxicity and cytotoxicity are not clear, particularly on the nervous system. In this study, we investigated how THz radiation with different frequency and intensity would affect the morphology, cell growth and function of rat hippocampal neurons in vitro.MethodsPrimary hippocampal neuronal cells were isolated from newborn Wistar rat pups and were exposed to THz radiation with the frequencies of 0.12 THz and 0.141 THz, at an power intensities of 10 mW/cm2 and 30 mW/cm2 respectively. The cellular activities were evaluated by Cell Counting Kit-8 after exposure for 10 min and 30 min. The cellular apoptosis was examined by Annexin V staining using flow cytometry and the ultrastructure was detected by electron microscopy. Moreover, the amount of amino acid in the cultured neurons was measured by high performance liquid chromatography (HPLC).ResultsNo obvious morphological changes, such as axon length and axon number, could be detected in primary neurons after exposure to 10mW/cm2 or 50 mW/cm2 THz for 30 min. However, the overall cellular activities were differentially affected by 10mW/cm2 and 50 mW/cm2 THz. Obvious cellular apoptosis was induced by both 10mW/cm2 and 50 mW/cm2 exposure. We also found that the amounts of most amino acids did not change significantly after exposure to these two types of THz radiation.ConclusionsThe effects of THz radiation on hippocampal neurons depend on frequency, power, exposure time as well as the measurement time after the exposure. These results will provide important information for further investigation of the effect of THz radiation on the nervous system.
Transcriptional profiling from whole embryos to single neuroblast lineages inDrosophila
Authors: Seroka Austin , Lai Sen-Lin , Doe Chris Q 
Published: April 2022

AbstractEmbryonic development results in the production of distinct tissue types, and different cell types within each tissue. A major goal of developmental biology is to uncover the “parts list” of cell types that comprise each organ. Here we perform single cell RNA sequencing (scRNA-seq) of theDrosophilaembryo to identify the genes that characterize different cell and tissue types during development. We assay three different timepoints, revealing a coordinated change in gene expression within each tissue. Interestingly, we find that theelavandmhcgenes, whose protein products are widely used as markers for neurons and muscles, respectively, show broad pan-embryonic expression, indicating the importance of post-transcriptional regulation. We next focus on the central nervous system (CNS), where we identify genes characterizing each stage of neuronal differentiation: from neural progenitors, called neuroblasts, to their immediate progeny ganglion mother cells (GMCs), followed by new-born neurons, young neurons, and the most mature neurons. Finally, we ask whether the clonal progeny of a single neuroblast (NB7-1) share a similar transcriptional identity. Surprisingly, we find that clonal identity does not lead to transcriptional clustering, showing that neurons within a lineage are diverse, and that neurons with a similar transcriptional profile (e.g. motor neurons, glia) are distributed among multiple neuroblast lineages. Although each lineage consists of diverse progeny, we were able to identify a previously uncharacterized gene,Fer3, as an excellent marker for the NB7-1 lineage. Within the NB7-1 lineage, transcriptional clusters are identifiable in neuroblasts and neurons, and each cluster is composed of current temporal transcription factor (e.g. Hunchback, Kruppel, Pdm, and Castor), novel temporal factors, and/or targets of the temporal transcription factors. In conclusion, we have characterized the embryonic transcriptome for all major tissue types and for three stages of development, as well as the first transcriptomic analysis of a single, identified neuroblast lineage, finding a lineage-enriched transcription factor.
MAECI: A Pipeline For Generating Consensus Sequence With Nanopore Sequencing Long-read Assembly and Error Correction
Authors: Lang Jidong 
Published: April 2022

ABSTRACTNanopore sequencing produces long reads and offers unique advantages over next-generation sequencing, especially for the assembly of draft bacterial genomes with improved completeness. However, assembly errors can occur due to data characteristics and assembly algorithms. To address these issues, we developed MAECI, a pipeline for generating consensus sequences from multiple assemblies of the same nanopore sequencing data and error correction. Systematic evaluation showed that MAECI is an efficient and effective pipeline to improve the accuracy and completeness of bacterial genome assemblies. The available codes and implementation are at https://github.com/langjidong/MAECI.
Engineering functional membrane-membrane interface by InterSpy
Authors: Moghimianavval Hossein , Patel Chintan , Mohapatra Sonisilpa , Hwang Sung-Won , Kayikcioglu Tunc , Bashirzadeh Yashar , Liu Allen P. , Ha Taekjip 
Published: April 2022

AbstractEngineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through SpyTag/SpyCatcher interaction. Inclusion of split fluorescent protein fragments in the designed InterSpy toolkit allows tracking the formation of membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. We first demonstrate InterSpy by testing split protein designs using a mammalian cell-free expression system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with a desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, since InterSpy is fully genetically encoded, the engineered system is adapted to cells and showcased. InterSpy demonstrates the power of cell-free expression systems in functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful for synthetic biology where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
Ischemic stroke and dietary vitamin B12 deficiency in old-aged females impaired motor function, increased ischemic damage size, and changed metabolite profiles in brain and cecum tissue
Authors: Poole Joshua , Jasbi Paniz , Pascual Agnes S. , North Sean , Kwatra Neha , Weissig Volkmar , Gu Haiwei , Bottiglieri Teodoro , Jadavji Nafisa M. 
Published: April 2022

AbstractThe global population is aging and the prevalence of age-related diseases, such as stroke, is predicted to increase. A vitamin B12 deficiency (vit. B12 def.) is common in the elderly, because of changes in metabolism. Clinical studies have reported that a vit. B12 def results in worse outcome after stroke, the mechanisms through which a vit. B12 def. changes the brain requires further investigation. This study investigated the role of vit. B12 def. on stroke outcome and mechanisms using aged female mice. Eighteen month old females were put on a control or vit. B12 def. diet for four weeks, after which an ischemic stroke was induced in the sensorimotor cortex. After damage, motor function was measured and animals were euthanized and tissues were collected for analysis. Vit. B12 def. animals had increased levels of total homocysteine in plasma and liver, choline levels were also increased in the liver. Vit. B12 def. animals had larger damage volume in brain tissue and more apoptosis. In the cecum, changes in creatinine and methylmalonic acid were observed in vit. B12 def. animals, pathway analysis showed dysfunction in B12 transport. Analysis of mitochondrial metabolomics in brain tissue showed reduced levels of metabolites involved in the TCA cycle in vit. B12 def animals. Meanwhile, pathway analysis showed significant, widespread dysfunction in phenylalanine, tyrosine, and tryptophan biosynthesis. Motor function after stroke was impaired in vit. B12 def. animals. A dietary vitamin B12 deficiency impairs motor function through increased apoptosis and changes in mitochondrial metabolism in brain tissue.
Mice expressing P301S mutant human tau have deficits in interval timing
Authors: Larson Travis , Khadelwal Vaibhav , Weber Matthew A. , Leidinger Mariah R. , Meyerholz David K. , Narayanan Nandakumar S. , Zhang Qiang 
Published: April 2022

ABSTRACTInterval timing is a key executive process that involves estimating the duration of an interval over several seconds or minutes. Patients with Alzheimer’s disease (AD) have deficits in interval timing. Since temporal control of action is highly conserved across mammalian species, studying interval timing tasks in animal AD models may be relevant to human disease. Amyloid plaques and tau neurofibrillary tangles are hallmark features of AD. While rodent models of amyloid pathology are known to have interval timing impairments, to our knowledge, interval timing has not been studied in models of tauopathy. Here, we evaluate interval timing performance of P301S transgenic mice, a widely studied model of tauopathy that overexpresses human tau with the P301S mutation. We employed the switch interval timing task, and found that P301S mice consistently underestimated temporal intervals compared to wild-type controls, responding early in anticipation of the target interval. Our study indicating timing deficits in a mouse tauopathy model could have relevance to human tauopathies such as AD.HIGHLIGHTSWe examined interval timing behavior in mice expressing P301S mutant tauP301S mice responded earler than littermate controlsThese data provide insight into animal models of tauopathy
Ralstonia solanacearum effector RipAF1 ADP-ribosylates host FBN1 to induce resistance against bacterial wilt
Authors: Wu Wei , Luo Xuming , Chen Xinyu , Wang Leyi , Wang Kang , Tian Siyao , Tong Ziqunfang , Zhao Tongxin , Fan Xiaojing , Zhuo Tao , Hu Xun , Zou Huasong 
Published: April 2022

AbstractRalstonia solanacearum (Rso) causes destructive bacterial wilt across a broad range of host plants by inducing jasmonic acid (JA) signaling while suppressing salicylic acid (SA) signaling pathways during disease development. In the present study, we show that Rso type III effector RipAF1 exerts a negative effect on bacterial virulence by subverting disease signaling in association with bacterial wilt. The ADP-ribosylation activity of RipAF1 was verified both in vivo and in vitro. Host fibrillin FBN1 was identified as a RipAF1-interacting protein that acted as a susceptible factor for bacterial wilt. In particular, RipAF1 directly ADP-ribosylates FBN1 at the E175/K207 residues, thus interfering with the mediation of disease signaling by FBN1. Together, these results suggest that RipAF1 exerts a role in defense induction by ADP-ribosylation of the susceptible factor FBN1 in the host plant.
Molecular basis of proteolytic cleavage regulation by the extracellular matrix receptor dystroglycan
Authors: Anderson MJM , Hayward AN , Smiley AT , Shi K , Pawlak MR , Aird EJ , Grant E , Greenberg L , Aihara H , Evans RL , Ulens C , Gordon WR 
Published: April 2022

ABSTRACTThe dystrophin glycoprotein complex (DGC), anchored by the transmembrane protein dystroglycan, functions to mechanically link the extracellular matrix to the actin cytoskeleton to drive critical aspects of development and adult homeostasis. Breaking this connection via mutation of the actin adaptor protein dystrophin or impaired glycosylation of dystroglycan are strongly associated with diseases such as Muscular Dystrophy, yet cleavage of the dystroglycan protein by matrix metalloproteinases (MMPs) remains an understudied mechanism to disrupt the DGC. We solved X-ray structures of the membrane-adjacent domain of dystroglycan to understand the molecular underpinnings of dystroglycan MMP cleavage regulation. Dystroglycan proteolysis occurs within the versatile SEAL domain, which supports proteolysis in diverse receptors to facilitate mechanotransduction, protection of cell membranes, and even viral entry. The structure reveals a c-terminal extension of the SEAL domain that buries the MMP cleavage site by packing into a hydrophobic pocket, a unique mechanism of MMP cleavage regulation. We further demonstrate that structure-guided and disease-associated mutations disrupt proteolytic regulation using a new cell-surface proteolysis assay. Finally, we find that disruption of proteolysis leads to altered cellular mechanics and migration using high-throughput DNA tension probe and wound healing assays. These findings highlight that disrupted proteolysis is a relevant mechanism for “breaking” the DGC link to contribute to disease pathogenesis and may offer new therapeutic avenues for dystroglycanopathies.
Surface detection of SARS-CoV-2 by lateral flow LAMP
Authors: Acker Isabelle Dahl , Ware Mark Joseph , Bracht John Russell 
Published: April 2022

AbstractSlowing the transmission of SARS-CoV-2 requires rapid and accurate diagnostic testing. Toward this end, loop-mediated isothermal amplification (LAMP), an isothermal genomic detection method, offers great promise but the readout tends to be difficult because it does not generate linear DNA products. Rapid antigen tests are coupled to lateral flow strips, with one (negative) or two (positive) bands providing simple rapid readout, but are less sensitive than genomic amplification methods. To address the need for a genomic amplification method that can be visualized on a lateral flow strip, we developed a novel strand-displacement probe. In this work we validate this pipeline for purified RNA, intact virus, and even virus deposited onto a surface. We demonstrate robust sensitivity (100 genomic copies) and and we demonstrate the utility of our assay as a surveillance system, with the capability to detect viral particles from surfaces, even after a week of complete dry-down. Our innovation couples the diagnostic advantages of a nucleic acid amplification test (NAAT) with the simplicity of lateral-flow readouts.
Shear displacement gradient in X-ray Bragg coherent diffractive imaging
Authors: Gorobtsov Oleg , Singer Andrej 
Published: April 2022

Bragg coherent X-ray diffractive imaging is a cutting-edge method for recovering three-dimensional crystal structure with nanoscale resolution. Phase retrieval provides an atomic displacement parallel to the Bragg peak reciprocal lattice vector. The derivative of the displacement along the same vector provides the normal strain field, which typically serves as a proxy for any structural changes. In this communication it is found that the other component of the displacement gradient, perpendicular to the reciprocal lattice vector, provides additional information from the experimental data collected from nanocrystals with mobile dislocations. Demonstration on published experimental data show how the perpendicular component of the displacement gradient adds to existing analysis, enabling an estimate for the external stresses, pinpointing the location of surface dislocations, and predicting the dislocation motion in in situ experiments.