bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning reveals signatures of promiscuous microbial amidases for micropollutant biotransformations
Authors: Marti Thierry D. , Schweizer Diana , Yu Yaochun , Schärer Milo R. , Probst Silke I. , Robinson Serina L. 
Published: August 2024

AbstractOrganic micropollutants - including pharmaceuticals, personal care products, pesticides and food additives - are prevalent in the environment and have unknown and potentially toxic effects. Humans are a direct source of micropollutants as the majority of pharmaceuticals are primarily excreted through urine. Urine contains its own microbiota with the potential to catalyze micropollutant biotransformations. Amidase signature (AS) enzymes are known for their promiscuous activity in micropollutant biotransformations, but the potential for AS enzymes from the urinary microbiota to transform micropollutants is not known. Moreover, characterization of AS enzymes to identify key chemical and enzymatic features predictive of biotransformation profiles is critical for developing benign-by-design chemicals and micropollutant removal strategies.In this study, we biochemically characterized a new AS enzyme with arylamidase activity from a urine isolate,Lacticaseibacillus rhamnosus,and demonstrated its capability to hydrolyze pharmaceuticals and other micropollutants. To uncover the signatures of AS enzyme-substrate specificity, we then designed a targeted enzyme library consisting of 40 arylamidase homologs from diverse urine isolates and tested it against 17 structurally diverse compounds. We found that 16 out of the 40 enzymes showed activity on at least one substrate and exhibited diverse substrate specificities, with the most promiscuous enzymes active on nine different substrates.Using an interpretable gradient boosting machine learning model, we identified chemical and amino acid features predictive of arylamidase biotransformations. Key chemical features from our substrates included the molecular weight of the amide carbonyl substituent and the number of charges in the molecule. Important amino acid features were found to be located on the protein surface and four predictive residues were located in close proximity of the substrate tunnel entrance.Overall, this work highlights the understudied role of urine-derived microbial arylamidases and contributes to enzyme sequence-structure-substrate-based predictions of micropollutant biotransformations.
Genesis and regulation of C-terminal cyclic imides from protein damage
Authors: Xu Wenqing , Zhao Zhenguang , Su Matthew , Jain Atul , Lloyd Hannah C. , Feng Ethan Yang , Cox Nick , Woo Christina M. 
Published: August 2024

AbstractC-Terminal cyclic imides are post-translational modifications (PTMs) that can arise from spontaneous intramolecular cleavage of asparagine or glutamine residues resulting in a form of irreversible protein damage. These protein damage events are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN), indicating that these aging-related modifications may require cellular quality control mechanisms to prevent deleterious effects. However, the factors that determine protein or peptide susceptibility to C-terminal cyclic imide formation or their effect on protein stability have not been explored in detail. Here, we characterize the primary and secondary structures of peptides and proteins that promote intrinsic formation of C-terminal cyclic imides in comparison to deamidation, a related form of protein damage. Extrinsic effects from solution properties and stressors on the cellular proteome additionally promote C-terminal cyclic imide formation on proteins like glutathione synthetase (GSS) that are susceptible to aggregation if the protein damage products are not removed by CRBN. This systematic investigation provides insight to the regions of the proteome that are prone to these unexpectedly frequent modifications, the effects of this form of protein damage on protein stability, and the biological role of CRBN.
Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities
Authors: Bueno de Mesquita Clifton P. , Walsh Corinne M. , Attia Ziv , Koehler Brady D. , Tarble Zachary J. , Van Tassel David L. , Kane Nolan C. , Hulke Brent S. 
Published: August 2024

AbstractAssociations with soil microorganisms are crucial for plants’ overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 common sunflower (Helianthus annuus) genotypes from 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogenSclerotiniawere present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.ImportanceDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial and fungal communities are driven primarily by site soil and climatic differences, but that genotype can interact with site to influence composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogenSclerotinia sclerotiorumwere widespread but significantly affected by site, while a subset were also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial and fungal community assembly, and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.
Reducing Offsite Modification using 2-mercaptoethanol for Proteome Analysis
Authors: Suto Arisa , Matsui Takashi , Kodera Yoshio 
Published: August 2024

AbstractAlkylation of the thiol group in cysteine (Cys) residues using halide reagents is a significant step in proteomics. However, non-specific modifications to the N-terminus and other amino acids are known. Thus promiscuous offsite alkylation in the peptide further complicated the MS spectra and thus made the difficulty of identification and quantification of all peptides. 2-mercaptoethanol (2-ME) is not only a regent for the reduction of the disulfide bond but also is bound to the Cys residue. Furthermore, it is known that dimethyl sulfoxide (DMSO) enhances the disulfide bond formation. Thus, based on these facts, we developed a method for specifical modification of Cys residues using 2-ME and DMSO. The specific modification of Cys residue by 2-ME were promoted by the concentration-dependent manner of DMSO with quite less offsite modification reaction compared with recent procedures. This Cys-specific modification technique may not only improve the quantification of peptides containing cysteine but also enhance the quantification accuracy of all peptides.
Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT
Authors: Seddon Chloe , David Sophia , Wong Joshua LC , Ishimoto Naito , He Shan , Bradshaw Jonathan , Low Wen Wen , Frankel Gad , Beis Konstantinos 
Published: August 2024

AbstractConjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same plasmid via entry (TraS) and surface (TraT) exclusion mechanisms. Here, we show that TraT from the pKpQIL and F plasmids (TraTpKpQILand TraTF) exhibits plasmid surface exclusion specificity. The cryo-EM structures of TraTpKpQILand TraTFrevealed that they oligomerise into decameric champagne bottle cork-like structures, which are anchored to the outer membrane via a diacylglycerol modified α-helical barrel domain. Unexpectedly, we identified chromosomal TraT homologues from multiple Gram-negative phyla which formed numerous deep-branching lineages in a phylogenetic tree of TraT sequences. Plasmid-associated TraT sequences largely cluster into two separate lineages that have more recently evolved, incorporating TraT from Enterobacterales IncF and Legionellaceae F-like plasmids. These findings suggest that different plasmid backbones have acquired and co-opted TraT on independent occasions.
Type I TARPs regulate Kv7.2 potassium channels and susceptibility to seizures
Authors: Rodrigues Marina V. , Inácio Ângela S. , Soldovieri Maria Virginia , Ribau Sara , Leal Telmo M. , Baurberg Theo , Mosca Ilaria , Ambrosino Paolo , Amado Luísa , Beltrão Nuno , Caldeira Gladys L. , Ribeiro Luís F. , Li Ka Wan , Groc Laurent , Ferreira Joana S. , Taglialatela Maurizio , Carvalho Ana Luisa 
Published: August 2024

SummaryThe M-current is a low-threshold potassium current that modulates neuronal excitability and suppresses repetitive firing. However, the mechanisms regulating M-channel function remain unclear. We identified type I Transmembrane AMPA receptor Regulatory Proteins (TARPs) as M-channel Kv7.2 subunit interactors in cortical neurons, with their interaction increasing upon neuronal depolarization. Co-expression of TARPs with Kv7.2 increased channel surface expression and Kv7.2-mediated currents, while disrupting TARP-γ2 expression in neurons perturbed dendritic Kv7.2 nano-clusters and decreased M-currents. Knock-in mice with an intellectual disability-associated TARP-γ2 variant showed reduced hippocampal M-currents and increased seizure susceptibility, indicating that disrupting TARP-γ2 regulation of Kv7.2-M-channels is epileptogenic. These findings show that TARP-γ2, a synaptic protein crucial for excitatory transmission, also controls intrinsic excitability via M-channels. This discovery provides a link between synaptic transmission and neuronal excitability, with implications for disease, as the interplay between synaptic and intrinsic plasticity is pivotal to how the brain adapts to varying input signals.HighlightsType I TARPs bind to Kv7.2-M-channels and enhance Kv7.2-mediated currents.TARP-γ2 governs the neuronal nano-organization and function of Kv7.2 channels.Intellectual disability-associated TARP-γ2 variant impairs M-currents and facilitates seizures.Type I TARPs can serve as molecular integrators of synaptic and intrinsic excitability.
EVE is an open modular data analysis software for event-based localization microscopy
Authors: Weber Laura M. , Martens Koen J.A. , Cabriel Clément , Gates Joel J. , Albecq Manon , Vermeulen Fredrik , Hein Katarina , Izeddin Ignacio , Endesfelder Ulrike 
Published: August 2024

AbstractEvent-based sensors (EBS), or neuromorphic vision sensors, offer a novel approach to imaging by recording light intensity changes asynchronously, unlike conventional cameras that capture light over fixed exposure times. This capability results in high temporal resolution, reduced data redundancy, and a wide dynamic range. This makes EBS ideal for Single-Molecule Localization Microscopy (SMLM) as SMLM relies on the sequential imaging of sparse, blinking fluorescent emitters to achieve super-resolution. Recent studies have shown that EBS can effectively capture these emitters, achieving spatial resolution comparable to traditional cameras. However, existing analyses of event-based SMLM (eveSMLM) data have relied on converting event lists into image frames for conventional analysis, limiting the full potential of the technology.To overcome this limitation, we developed EVE, a specialized software for analyzing eveSMLM data. EVE offers an integrated platform for detection, localization, and post-processing, with various algorithmic options tailored for the unique structure of eveSMLM data. EVE is user-friendly and features an open, modular infrastructure that supports ongoing development and optimization. EVE is the first dedicated tool for event-based SMLM, transforming the analysis process to fully utilize the spatiotemporal data generated by EBS. This allows researchers to explore the full potential of eveSMLM and encourages the development of new analytical methods and experimental improvements.
Genome-wide analysis of somatic non-coding mutation patterns and mitochondrial heteroplasmy in type B1 and B2 thymomas
Authors: Fujikura Kohei , Correa Isabel , Heck Susanne , King Juliet , McLean Emma , Bille Andrea , Nonaka Daisuke 
Published: August 2024

AbstractIntroductionType B1 and B2 thymomas are lymphocyte-rich malignant tumors with few somatic mutations in protein-coding regions of the nuclear genome; nonetheless, non-coding regions remain uncharacterized. Here, we developed a rigorous tumor isolation method from lymphocyte-rich thymoma tissues and identified somatic mutations in non-coding and mitochondrial DNA.MethodsCD205+CD45-pure tumor cells were isolated from fresh-frozen tissues using DEPArray system. Deep whole-genome sequencing was performed, and recurrent somatic alterations in coding, non-coding, and mitochondria regions were systemically identified by computational framework. The mutations were classified according to gene function, cis-regulatory element, and mutational signature.ResultsThe total number of somatic mutations was approximately 80 times higher in non-coding regions than in coding regions in type B1-2 thymomas (1,671.3 vs. 21.1 per case). Coding mutations were identified in epigenetic regulators, DNA repair genes, and some other genes. Nevertheless, 40% of cases exhibited fewer than four mutations in coding regions. A systematic non-coding analysis identified a total of 405.0 mutations per case on cis-regulatory elements, and detected six recurrent mutations: one interferon regulatory factor (IRF8), two E3 ubiquitin ligases (UBR2andRNF213), and three intergenic regions. Mitochondrial heteroplasmy was observed in 90% of cases, with a significant proportion of mutations located in D-loop region. The single-base substitution pattern was signature 12.ConclusionsNumerous non-coding mutations and mitochondrial heteroplasmy were detected in type B1 and B2 thymomas. Given the paucity of coding mutations observed in this disease entity, disruption of the non-coding landscape and mitochondrial heteroplasmic shift may be the primary cause of thymoma.
Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise
Authors: Khetan Neha , Zuckerman Binyamin , Calia Giuliana P. , Chen Xinyue , Arceo Ximena Garcia , Weinberger Leor S. 
Published: August 2024

SUMMARYStochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability. However, how best to quantify genome-wide noise, remains unclear. Here we utilize a small-molecule perturbation (IdU) to amplify noise and assess noise quantification from numerous scRNA-seq algorithms on human and mouse datasets, and then compare to noise quantification from single-molecule RNA FISH (smFISH) for a panel of representative genes. We find that various scRNA-seq analyses report amplified noise, without altered mean-expression levels, for ∼90% of genes and that smFISH analysis verifies noise amplification for the vast majority of genes tested. Collectively, the analyses suggest that most scRNA-seq algorithms are appropriate for quantifying noise including a simple normalization approach, although all of these systematically underestimate noise compared to smFISH. From a practical standpoint, this analysis argues that IdU is a globally penetrant noise-enhancer molecule—amplifying noise without altering mean-expression levels—which could enable investigations of the physiological impacts of transcriptional noise.MOTIVATIONCell-to-cell variability in isogenic populations is predominantly attributed to the stochastic fluctuations (i.e., noise) in transcription. However, the quantification of this noise, particularly on a genome-wide scale, remains an open question. To address this general question, here we utilize a small-molecule perturbation reported to amplify transcriptional noise. Previous single-cell RNA-sequencing (scRNA-seq) analysis indicated that the pyrimidine nucleobase 5′-iodo-2′-deoxyuridine (IdU) amplifies noise but technical drawbacks of scRNA-seq may have obscured the penetrance and degree of noise amplification. Consequently, here we assess numerous scRNA-seq algorithms, on two different scRNA-seq datasets for a human and mouse cell type, for their ability to quantify noise amplification and then compare the results to noise quantification from single-molecule RNA FISH (smFISH) imaging for a panel of representative genes. The specific questions addressed are whether IdU amplifies noise in a globally or partially penetrant manner, and what scRNA-seq algorithm is most appropriate for quantifying transcriptional noise.Graphical Abstract
Circadian and permanent pools of extracellular matrix co-exist in tendon tissue, but have distinct rates of turnover and differential responses to ageing
Authors: Hoyle Anna , Chang Joan , Cutiongco Marie FA , O’Cualain Ronan , Warwood Stacey , Knight David , Meng Qing-Jun , Kadler Karl E , Swift Joe 
Published: August 2024

ABSTRACTHeavy carbon isotopes in the tendons of people who grew up in the age of nuclear bomb testing have shown that the extracellular matrix (ECM), assembled during development, stays with us for life. However, recent work suggests that type-I collagen in ECM-rich mouse tendon exists in two pools: a permanent matrix, and a more soluble, circadian-regulated matrix. Despite this, the underlying regulation of such distinct pools is not understood. Here, we demonstrate using stable isotope labelling coupled with mass spectrometry proteomics that circadian and permanent matrix pools have significantly different half-lives. Furthermore, the properties of the matrix pools are altered during development and ageing. Tail tendon tissue was harvested from mice fed on a heavy-lysine diet; protein was then extracted for analysis using a sequential two-step protocol. The first, soluble fraction (‘F1’) was found to contain intracellular proteins, and a range of core and associated extracellular matrix proteins, including a pool of type-I collagen shown to be circadian-regulated. The remaining fraction (‘F2’) contained primarily collagens, including type-I collagen which did not show rhythmicity. In adult mice, matrix proteins extracted in the F1 pool had significantly shorter half-lives than F2, including type-I collagen which had half-lives of 4 ± 2 days in F1, compared to 700 ± 100 days in F2. Circadian-regulated matrix proteins were found to have significantly faster turnover than non-circadian in adult mice, but this distinction was lost in older animals. This work identifies protein turnover as the underlying mechanism for the circadian/permanent model of tendon matrix, and suggests a loss of circadian regulation as a characteristic of ECM ageing.
Phosphate transporter(Pht) gene families in rye (Secale cerealeL.) – genome-wide identification and sequence diversity assessment
Authors: Chan-Rodriguez David , Koboyi Brian Wakimwayi , Werghi Sirine , Till Bradley J. , Maksymiuk Julia , Shoormij Fatemeh , Hilderlith Abuya , Hawliczek Anna , Królik Maksymilian , Bolibok-Brągoszewska Hanna 
Published: August 2024

AbstractBackgroundPhosphorus is a macronutrient indispensable for plant growth and development. Plants utilize specialized transporters (PHT) to take up inorganic phosphorus and distribute it throughout the plant. The PHT transporters are divided into five families: PHT1 to PHT5. Each PHT family has a particular physiological and cellular function. Rye (Secale cereale L.) is a member ofTriticeae, and an important source of variation for wheat breeding. It is considered to have the highest tolerance of nutrient deficiency, amongTriticeae. To date, there is no report about genes involved in response to phosphorus deficiency in rye. The aim of this study was to: (i) identify and characterize putative members of different phosphate transporter families in rye, (i) assess their sequence diversity in a collection of diverse rye accessions via low-coverage resequencing (DArTreseq), and (iii) evaluate the expression of putative ryePhtgenes under phosphate-deficient conditions.ResultsWe identified 29 and 35 putativePhttransporter genes in the rye Lo7 and Weining reference genomes, respectively, representing all knownPhtfamilies. Phylogenetic analysis revealed a close relationship of rye PHT with previously characterized PHT proteins from other species. Quantitative RT PCR carried out on leaf and root samples of Lo7 plants grown in Pi-deficient and control condition demonstrated thatScPht1;6, ScPht2andScPht3;1are Pi-deficiency responsive. Based on DArTreseq genotyping of 94 diverse rye accessions we identified 820 polymorphic sites within ryeScPht, including 12 variants with a putatively deleterious effect. SNP density varied markedly betweenScPhtgenes.ConclusionsThis report is the first step toward elucidating the mechanisms of rye’s response to Pi deficiency. Our findings point to multiple layers of adaptation to local environments, ranging from gene copy number variation to differences in level of polymorphism acrossPhtfamily members. DArTreseq genotyping permits for a quick and cost-effective assessment of polymorphism levels across genes/gene families and supports identification and prioritization of candidates for further studies. Collectively our findings provide the foundation for selecting most promising candidates for further functional characterization.