bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice
Authors: Wanelik Klara M , Raulo Aura , Troitsky Tanya , Husby Arild , Knowles Sarah CL 
Published: August 2022

AbstractThe mammalian gut microbiota influences a wide array of phenotypes and is considered a key determinant of fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life. We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted to a similar extent by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we further identify a candidate maternally-transmitted bacterial family in wood mice, theLactobacillaceae. Overall, our findings suggest a shifting transmission landscape for wild mice, with a mother’s influence on microbiota composition waning as offspring age, while the impact of social contacts remains strong and consistent.
BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation
Authors: Witus Samuel R. , Tuttle Lisa M. , Li Wenjing , Zelter Alex , Wang Meiling , Kermoade Klaiten E. , Wilburn Damien B. , Davis Trisha N. , Brzovic Peter S. , Zhao Weixing , Klevit Rachel E. 
Published: August 2022

AbstractBRCA1/BARD1 is a tumor suppressor E3 ubiquitin (Ub) ligase with roles in DNA damage repair and in transcriptional regulation. BRCA1/BARD1 RING domains interact with nucleosomes to facilitate mono-ubiquitylation of distinct residues on the C-terminal tail of histone H2A. These enzymatic domains constitute a small fraction of the heterodimer, raising the possibility of functional chromatin interactions involving other regions such as the BARD1 C-terminal domains that bind nucleosomes containing the DNA damage signal H2A K15-Ub and H4 K20me0, or portions of the expansive intrinsically disordered regions found in both subunits. Herein, we reveal novel interactions that support robust H2A ubiquitylation activity mediated through a high-affinity, intrinsically disordered DNA-binding region of BARD1. These interactions support BRCA1/BARD1 recruitment to chromatin and sites of DNA damage in cells and contribute to their survival. We also reveal distinct BRCA1/BARD1 complexes that depend on the presence of H2A K15-Ub, including a complex where a single BARD1 subunit spans adjacent nucleosome units. Our findings identify an extensive network of multivalent BARD1- nucleosome interactions that serve as a platform for BRCA1/BARD1-associated functions on chromatin.
Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex
Authors: Rózsa Márton , Tóth Martin , Oláh Gáspár , Baka Judith , Lákovics Rajmund , Barzó Pál , Tamás Gábor 
Published: August 2022

AbstractNeural population activity determines the timing of synaptic inputs, which arrive to dendrites, cell bodies and axon initial segments (AISs) of cortical neurons. Action potential initiation in the AIS (AIS-APs) is driven by input integration, and the phase preference of AIS-APs during network oscillations is characteristic to cell classes. Distal regions of cortical axons do not receive synaptic inputs, yet experimental induction protocols can trigger retroaxonal action potentials (RA-APs) in axons distal from the soma. We report spontaneously occurring RAAPs in human and rodent cortical interneurons that appear uncorrelated to inputs and population activity. Network linked triggering of AIS-APs versus input independent timing of RA-APs of the same interneurons result in disparate temporal contribution of a single cell to in vivo network operation through perisomatic and distal axonal firing.One-Sentence SummaryNetwork linked triggering of AIS-APs versus input independent timing of RA-APs of the same interneurons result in disparate temporal contribution of a single cell to in vivo network operation.
Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought stress
Authors: Xu Duorong , Tang Qian , Leister Dario , Kleine Tatjana 
Published: August 2022

ABSTRACTPlants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used long non-coding RNA-sequencing to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0 and a mutant (protein phosphatase 7-like, pp7l), from which we demonstrated that it can survive long periods of drought stress. The changes detected in the pp7l mutant were marginal, while in the wild type chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Also, transcriptional activation of transposable elements played only a minor role. Conversely, alternative splicing (AS) affected nearly 2,000 genes (11% of expressed nuclear genes). Of these, 25% underwent isoform switching, and 15% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought. Moreover, altering the relative contributions of spliced isoforms might enhance drought resistance. For instance, our data imply that accumulation of a non-functional FLM (FLOWERING LOCUS M) isoform – and not the ratio of functional isoforms as suggested for temperature responses - accounts for the early-flowering phenotype under drought conditions.
Inhibition of PI3K p110δ activity reduces IgE production in IL-4 and anti-CD40 stimulated human B cell cultures
Authors: Cutrina-Pons Anna , De Sa Aloka , Fear David J , Gould Hannah J , Ramadani Faruk 
Published: August 2022

AbstractPhosphoinositide 3-kinase (PI3K) p110δ signalling negatively regulates the production of mouse IgE. However, there are disparities between the mouse and human IgE biology, and the role of PI3K p110δ in the production of human IgE is yet to be determined. To investigate the effect of PI3K p110δ inhibition in the production of human IgE we isolated human B cells from tonsil tissue and stimulated them with IL-4 and anti-CD40 antibody to induce class switching to IgE and IgG1 in the presence or absence of IC87114, a small molecule inhibitor of PI3K p110δ. Using FACS, RT-PCR and ELISA we examined the effect of PI3K p110δ inhibition on IgE production and also determined the mechanisms involved. Unlike in mice, we observed that PI3K p110δ inhibition significantly reduces the number of IgE+ switched cells and the amounts of secreted IgE in IL4 and anti-CD40 cultures. However, the number of IgG1+ cells and secreted IgG1 were largely unaffected by PI3K p110δ inhibition. The expression levels of AID, ε and γ1 germinal transcripts or other factors involved in the regulation of CSR to IgE and IgG1 were also unaffected by IC87114. However, we found that IC87114 significantly decreases the proliferation of tonsil B cells stimulated with IL-4 and anti-CD40, specifically reducing the frequency of cells that had undergone 4 divisions or more. Our data identifies proliferation as the key mechanism through which PI3K p110δ regulates CSR of human B cells to IgE and highlights PI3K p110δ as a pharmacological target for the treatment of allergic disease.
From empirical to data-driven host selection: a broad-host-range expression platform to facilitate chassis screening
Authors: Mol Viviënne , Falkenberg Kristoffer Bach , De Almeida Will Ácil , Pogrebnyakov Ivan , Beck Charlotte , Skøttrup Anna Lyhne , Nielsen Alex Toftgaard , Jensen Sheila Ingemann 
Published: August 2022

AbstractNature has provided a vast landscape of organisms through evolution, each with unique phenotypic traits adapted to varying environments. Nevertheless, host selection in biotechnological research is exceedingly dominated by empirical preference, where the endogenous physiology of the selected host is often not suited to the desired application. Considering that large parts of cellular regulation and metabolism remain obscure, empirical selection of a preferred model organism may lead to undue caveats in further engineering attempts, arising from intrinsic metabolism. One reason for the empirical host selection is the lack of engineering tools for screening novel organisms. In this study, we provide a modular, single vector-based expression platform, compatible with a wide range of prokaryotes. It centers around a tight and titratable promoter system, inducible by anhydrotetracyclin within an 84-fold dynamic range. It enables easy screening of recombinant proteins and pathways in both mesophilic and thermophilic Gram-negative and Gram-positive hosts. Overall, this platform enables simple screening of heterologous expression and production in a variety of hosts, including the exploration of previously unconsidered hosts thereby aiding the transition from empirical to data-driven host selection.
Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs
Authors: Leroy Elodie C. , Perry Thomas N. , Renault Thibaud T. , Innis C. Axel 
Published: August 2022

SUMMARYWith antibiotic-resistant bacteria threatening our ability to treat common infections, new lead compounds with distinct target binding sites and limited cross-resistance are urgently needed. Natural products that inhibit the bacterial ribosome – a target for more than half of the antibiotics in use today – are a promising source of such leads and have the potential to be developed into potent drugs through structure-guided design. However, because the mechanisms of action of many of these compounds are not well understood, they are often poor candidates for a structure-based approach. Here, we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X (TcmX) primarily inhibits the formation of a peptide bond between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3’ adenosine of peptidyl-tRNALysin the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of TcmX on the bacterial ribosome and suggests a path forward for the development of novel antibiotics based on a common aromatic polyketide scaffold.
Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles
Authors: Qin Boyang , Bassler Bonnie L. 
Published: August 2022

AbstractBacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a ΔrbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.
Uncovering structural ensembles from single particle cryo-EM data using cryoDRGN
Authors: Kinman Laurel F. , Powell Barrett M. , Zhong Ellen D. , Berger Bonnie , Davis Joseph H. 
Published: August 2022

ABSTRACTCryoDRGN is a machine learning system for heterogeneous cryo-EM reconstruction of proteins and protein complexes from single particle cryo-EM data. Central to this approach is a deep generative model for heterogeneous cryo-EM density maps, which we empirically find effectively models both discrete and continuous forms of structural variability. Once trained, cryoDRGN is capable of generating an arbitrary number of 3D density maps, and thus interpreting the resulting ensemble is a challenge. Here, we showcase interactive and automated processing approaches for analyzing cryoDRGN results. Specifically, we detail a step-by-step protocol for analysis of the assembling 50S ribosome dataset (Davis et al., EMPIAR-10076), including preparation of inputs, network training, and visualization of the resulting ensemble of density maps. Additionally, we describe and implement methods to comprehensively analyze and interpret the distribution of volumes with the assistance of an associated atomic model. This protocol is appropriate for structural biologists familiar with processing single particle cryo-EM datasets and with moderate experience programming in Python and navigating Jupyter notebooks. It requires 3-4 days to complete.
CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics
Authors: Rainey Markace A. , Watson Chandler A. , Asef Carter K. , Foster Makayla R. , Baker Erin S. , Fernández Facundo M. 
Published: August 2022

AbstractMetabolite annotation continues to be the widely accepted bottleneck in non-targeted metabolomics workflows. Annotation of metabolites typically relies on a combination of high resolution mass spectrometry (MS) with parent and tandem measurements, isotope cluster evaluations, and Kendrick mass defect (KMD) analysis. Chromatographic retention time matching with standards is often used at the later stages of the process, which can also be followed by metabolite isolation and structure confirmation utilizing nuclear magnetic resonance (NMR) spectroscopy. The measurement of gas phase collision cross section (CCS) values by ion mobility (IM) spectrometry also adds an important dimension to this workflow by generating an additional molecular parameter that can be used for filtering unlikely structures. The millisecond timescale of IM spectrometry allows the rapid measurement of CCS values and allows easy pairing with existing MS workflows. Here, we report on a highly accurate machine learning algorithm (CCSP 2.0) in an open-source Jupyter Notebook format to predict CCS values based on linear support vector regression models. This tool allows customization of the training set to the needs of the user, enabling the production of models for new adducts or previously unexplored molecular classes. CCSP produces predictions with accuracy equal to or greater than existing machine learning approaches such as CCSbase, DeepCCS and AllCCS, while being better aligned with FAIR (Findable, Accessible, Interoperable and Reusable) data principles. Another unique aspect of CCSP 2.0 its inclusion of a large library of 1613 molecular descriptors via the Mordred Python package, further encoding the fine aspects of isomeric molecular structures. CCS prediction accuracy was tested using CCS values in the McLean CCS Compendium with median relative errors of 1.25, 1.73 and 1.87% for the 170 [M-H]-, 155 [M+H]+ and 138 [M+Na]+ adducts tested. For class-matched data sets, CCS predictions via CCSP allowed filtering of 36.1% of incorrect structures while retaining a total of 100% of the correct annotations using a ΔCCS threshold of 2.8% and a mass error of 10 ppm.
Multi-site Performance Evaluation of the cobas 5800 System and Comparison to the cobas 6800/8800 Systems for Quantitative Measurement of HBV, HCV, and HIV-1 Viral Load
Authors: Tschäpe Jakob , Cobernuss-Rahn Anika , Boyle Sean , Parkin Neil , LaBrot Ben , Aslam Shagufta , Young Stephen , Gohl Peter 
Published: August 2022

AbstractBackgroundThe cobas® 5800 System (“cobas 5800”) is a new low to mid-throughput PCR-based nucleic acid testing system which performs both qualitative and quantitative testing, including viral load (VL) determination. cobas 5800 shares numerous design elements and technical characteristics with the existing cobas 6800/8800 Systems.Study DesignWe compared HBV, HCV, and HIV-1 VL results from cobas 5800 in three different laboratories to those from the same specimens tested on a cobas 6800 system. We also assessed cobas 5800 assay reproducibility by repetitive testing of specimens with VL close to values used as thresholds for patient management or classification.ResultsThe correlation between VL measurements generated using cobas 5800 vs 6800 was extremely high, with r2 correlation coefficients between 0.990 and 0.999 for the three targets at the different sites. The slope of the Deming regression line ranged from 0.994 (HBV, site 3) to 1.025 (HIV-1, site 1). The standard deviation values ranged from 0.04 to 0.19 log10 IU/mL for HBV, 0.05 to 0.31 log10 IU/mL for HCV, and 0.05 to 0.31 log10 copies/mL for HIV-1. In general, variability was higher at lower VL. Between 98.6% and 100% of results fell within the allowable total difference zone that defines expected variability on the existing 6800/8800 system.ConclusionsThis multi-site comparison study demonstrates equivalent performance of the new cobas 5800 system compared to cobas 6800. This establishes cobas 5800 as a new option for low to mid-throughout laboratories seeking to optimize efficiency of their viral molecular testing.
ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes
Authors: Bunch Heeyoun , Kim Deukyeong , Naganuma Masahiro , Nakagawa Reiko , Cong Anh , Jeong Jaehyeon , Ehara Haruhiko , Vu Hongha , Chang Jeong Ho , Schellenberg Matthew J. , Sekine Shun-ichi 
Published: August 2022

ABSTRACTThe transcription of stress-inducible genes requires synchronized and robust activation, which is critical for organismal survival and homeostasis. The function of the mitogen-activated protein kinase (MAPK) signaling pathway is required for the activation of immediate early genes (IEGs), includingEGR1andFOS, for cell growth and proliferation1–3. In addition, recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs4–6. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at theEGR1gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK1 can relax the DNA by itself and produces a semi-relaxed DNA, which is apparently resistant to TOP2B catalysis. Inhibition of ERK2 kinase activity or ERK2 knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we obtained the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with theEGR1transcriptional start site (50 nt; –30 to +20) that has the strongest affinity to TOP2B within –423 to +332. The structure elucidated in our studies showed TOP2B-mediated breakage and dramatic bending of the double-stranded DNA, comparable to previously reported structures of TOP2. Our cell-based analyses showed transcriptional activation by etoposide and transcriptional inhibition by ICRF193 atEGR1andFOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.
The evolution of the human DNA replication timing program
Authors: Bracci Alexa N. , Dallmann Anissa , Ding Qiliang , Hubisz Melissa J. , Caballero Madison , Koren Amnon 
Published: August 2022

AbstractDNA is replicated according to a defined spatiotemporal program that is linked to both gene regulation and genome stability. The evolutionary forces that have shaped replication timing programs in eukaryotic species are largely unknown. Here, we studied the molecular causes and consequences of replication timing evolution across 94 humans, 95 chimpanzees, and 23 rhesus macaques. Replication timing differences recapitulated the species’ phylogenetic tree, suggesting continuous evolution of the DNA replication timing program in primates. Hundreds of genomic regions had significant replication timing variation between humans and chimpanzees, of which 66 showed advances in replication origin firing in humans while 57 were delayed. Genes overlapping these regions displayed correlated changes in expression levels and chromatin structure. Many human-chimpanzee variants also exhibited inter-individual replication timing variation, pointing to ongoing evolution of replication timing at these loci. Association of replication timing variation with genetic variation revealed that DNA sequence evolution can explain replication timing variation between species. Taken together, DNA replication timing shows substantial and ongoing evolution in the human lineage that is driven by sequence alterations and impacts regulatory evolution.