bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local and dynamic regulation of neuronal glycolysisin vivo
Authors: Wolfe Aaron D. , Koberstein John N , Smith Chadwick B , Stewart Melissa L , Hammarlund Marc , Hyman Anthony , Stork Philip JS , Goodman Richard , Colón-Ramos Daniel A. 
Published: August 2023

AbstractEnergy metabolism supports neuronal function. While it is well established that changes in energy metabolism underpin brain plasticity and function, less is known about how individual neurons modulate their metabolic states to meet varying energy demands. This is because most approaches used to examine metabolism in living organisms lack the resolution to visualize energy metabolism within individual circuits, cells, or subcellular regions. Here we adapted a biosensor for glycolysis, HYlight, for use inC. elegansto image dynamic changes in glycolysis within individual neurons andin vivo. We determined that neurons perform glycolysis cell-autonomously, and modulate glycolytic states upon energy stress. By examining glycolysis in specific neurons, we documented a neuronal energy landscape comprising three general observations: 1) glycolytic states in neurons are diverse across individual cell types; 2) for a given condition, glycolytic states within individual neurons are reproducible across animals; and 3) for varying conditions of energy stress, glycolytic states are plastic and adapt to energy demands. Through genetic analyses, we uncovered roles for regulatory enzymes and mitochondrial localization in the cellular and subcellular dynamic regulation of glycolysis. Our study demonstrates the use of a single-cell glycolytic biosensor to examine how energy metabolism is distributed across cells and coupled to dynamic states of neuronal function, and uncovers new relationships between neuronal identities and metabolic landscapesin vivo.Significance statementWhile it is generally accepted that energy metabolism underpins neuronal function, how it is distributed and dynamically regulated in different tissues of the brain to meet varying energy demands is not well understood. Here we utilized a fluorescent biosensor, HYlight, to observe glycolytic metabolism at cellular and subcellular scalesin vivo. By leveraging both the stereotyped identities of individual neurons inC. elegans,and genetic tools for manipulating glycolytic metabolism, we determined that neurons perform and dynamically regulate glycolysis to match changing cellular demands for energy. Our findings support a model whereby glycolytic states should be considered distinct and related to individual neuron identitiesin vivo, and introduce new questions about the interconnected nature of metabolism and neuronal function.
Single-molecule visualization of twin-supercoiled domains generated during transcription
Authors: Janissen Richard , Barth Roman , Polinder Minco , van der Torre Jaco , Dekker Cees 
Published: August 2023

ABSTRACTTranscription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model within vitroreal-time visualization at the single-molecule scale. Upon binding to the promoter site on a supercoiled DNA molecule, RNAP merges all DNA supercoils into one large pinned plectoneme with RNAP residing at its apex. Transcription by RNAP in real time demonstrates that up- and downstream supercoils are generated simultaneously and in equal portions, in agreement with the twin-supercoiled-domain model. Experiments carried out in the presence of RNases A and H, revealed that an additional viscous drag of the RNA transcript is not necessary for the RNAP to induce supercoils. The latter results contrast the current consensus and simulations on the origin of the twin-supercoiled domains, pointing at an additional mechanistic cause underlying supercoil generation by RNAP in transcription.
Disease Resistance correlates with Core Microbiome Diversity in Cotton
Authors: Aqueel Rhea , Badar Ayesha , Roy Nazish , Ijaz Umer Zeeshan , Malik Kauser Abdulla 
Published: August 2023

AbstractUnderstanding the resident microbial communities and their above and below ground interactions with plants will provide necessary information for crop disease protection and stress management. In this study, we show how diversity of core microbiome varies with disease susceptibility of a crop. To test this hypothesis, we have focused on identifying the core microbial species of Cotton Leaf Curl Disease (CLCuD) susceptibleGossypium hirsutumand CLCuD resistantGossypium arboreumunder viral infestation. Derivation of core membership is challenging as it depends on an occupancy threshold of microbial species in a sampling pool, whilst accounting for different plant compartments. We have used an abundance-occupancy distribution approach where we dynamically assess the threshold for core membership, whilst marginalizing for occupancy in four compartments of the cotton plant, namely, leaf epiphyte, leaf endophyte, rhizosphere, and root endophyte. Additionally, we also fit a neutral model to the returned core species to split them into three groups, those that are neutral, those that are selected by the plant environment, and finally those that are dispersal limited. We have found strong inverse relationship between diversity of core microbiome and disease susceptibility. A deeper understanding of this association will aid in the development of biocontrol agents for improving plant immunity against biotrophic pathogens.
Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping
Authors: Fink Emily E. , Nanavaty Vishal , Lee Byron H. , Ting Angela H. 
Published: August 2023

ABSTRACTAlternative cleavage and polyadenylation (APA) is a gene regulatory mechanism used by cells under stress to upregulate proteostasis-promoting transcripts, but how cells achieve this remains poorly understood. Previously, we elucidated a DNA methylation-regulated APA mechanism, in which gene body DNA methylation enhances distal poly(A) isoform expression by blocking CTCF binding and chromatin loop formation at APA control regions. We hypothesized that DNA methylation-regulated APA is one mechanism cells employ to induce proteostasis-promoting poly(A) isoforms. At theDNAJB6co-chaperone gene locus, acute heat shock resulted in binding of stress response transcription factors HSF1, ATF6, and YY1 at the APA control region and an increase in the expression of the proximal poly(A) isoform known to prevent protein aggregation. Furthermore, TET1 was recruited to rapidly demethylate DNA, facilitating CTCF binding and chromatin loop formation, thereby reinforcing preferential proximal poly(A) isoform expression. As cells recovered, the transcription factors vacated the APA control region, and DNMT1 was recruited to remethylate the region. This process resolved chromatin looping and reset the poly(A) isoform expression pattern. Our findings unveil an epigenetic mechanism enabling cells to dynamically modulate poly(A) isoforms in response to stress while shedding light on the interplay between DNA methylation, transcription factors, and chromatin looping.
CryoEM architecture of a native stretch-sensitive membrane microdomain
Authors: Kefauver Jennifer M. , Hakala Markku , Zou Luoming , Alba Josephine , Espadas Javier , Tettamanti Maria G. , Estrozi Leandro F. , Vanni Stefano , Roux Aurélien , Desfosses Ambroise , Loewith Robbie 
Published: August 2023

AbstractBiological membranes are partitioned into functional zones containing specific lipids and proteins, termed membrane microdomains. Their composition and organization remain controversial owing to a paucity of techniques that can visualize lipidsin situwithout disrupting their native behavior1,2. The yeast eisosome, a membrane compartment scaffolded by the BAR-domain proteins Pil1 and Lsp1, senses and responds to mechanical stress by flattening and releasing sequestered factors3–7. Here, we isolated native eisosomes as helical filaments of Pil1/Lsp1 lattice bound to plasma membrane lipids and solved their structures by helical reconstruction. We observe remarkable organization within the lipid bilayer density from which we could assign headgroups of PI(4,5)P2and phosphatidylserine bound to Pil1/Lsp1 and a pattern of membrane voids, signatures of sterols, beneath an amphipathic helix. We verified these assignments usingin vitroreconstitutions and molecular dynamics simulations. 3D variability analysis of the native eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects functionally important lipid sequestration, supporting a mechanism in which membrane stretching liberates lipids otherwise anchored by the Pil1/Lsp1 coat. Our results provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain and, more globally, resolve long-standing controversies about the architecture and nature of lipid microdomains.
An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin
Authors: Hill Jake A , Nyathi Yvonne , Horrell Sam , von Stetten David , Axford Danny , Owen Robin L , Beddard Godfrey , Pearson Arwen R , Ginn Helen Mary , Yorke Briony A 
Published: August 2023

1AbstractHuman gamma-D crystallin (HGD) is the major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin shows no post-translational modifications. After aging for nine months in the absence of light, a covalently bound reducing agent modifying surface cysteines is observed for the first time by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system.
Cdc42 couples septin recruitment to the axial landmark assembly via Axl2 in budding yeast
Authors: Kang Pil Jung , Mullner Rachel , Lian Kendra , Park Hay-Oak 
Published: August 2023

ABSTRACTCell polarization generally occurs along a single axis that is directed by a spatial cue. Cells of the budding yeastSaccharomyces cerevisiaeundergo polarized growth and oriented cell division in a spatial pattern by selecting a specific bud site. Haploidaor α cells bud in the axial pattern in response to a transient landmark that includes Bud3, Bud4, Axl1, and Axl2. Septins, a family of filament-forming GTP-binding proteins, are also involved in axial budding and recruited to an incipient bud site, but the mechanism of recruitment remains unclear. Here, we show that Axl2 interacts with Bud3 and the Cdc42 GTPase in its GTP-bound state. Axl2 also interacts with Cdc10, a septin subunit, promoting efficient recruitment of septins near the cell division site. Furthermore, acdc42mutant defective in the axial budding pattern at a semi-permissive temperature had a reduced interaction with Axl2 and compromised septin recruitment in the G1 phase. We thus propose that active Cdc42 brings Axl2 to the Bud3-Bud4 complex and that Axl2 then interacts with Cdc10, linking septin recruitment to the axial landmark.
Automappa: An interactive interface for metagenome-derived genome bins
Authors: Rees Evan R. , Waterworth Samantha C. , Chanana Shaurya C. , Kwan Jason C. 
Published: August 2023

AbstractBackgroundStudies attempting to observe microbes commonly considered uncultivable under standard laboratory conditions are turning to so-called “deep” environmental sequencing approaches whereby they may access these unculturable organisms’ genomes viain silicoapproaches. A typical workflow involves metagenome assembly, annotation, and binning for reconstruction of each respective organism’s genome (or metagenome-assembled genome, MAG). Many automated genome binning approaches have been developed and have displayed a wide range of variation in performance. Therefore, refinement methods have been developed in order to aid manual curation following the automated genome binning process. Current manual curation tools were developed with a focus towards teaching metagenomics concepts and may fail when handling complex datasets containing many microbes. Automappa was developed with a focus on overlaying a variety of annotations such as taxonomy, coverage and marker-gene prevalence while maintaining an implementation that may scale to the complexity of environmental samples.ResultsWe present Automappa, a companion tool and interactive interface for exploration and refinement of Autometa taxon and genome binning results from metagenomes. Selections provide real-time updates of MAG metrics to aid manual curation. Furthermore, researchers may detect unbinned MAGs as well as manually improve their draft-quality MAGs with contigs that closely match the MAG’s genome characteristics. Automappa’s utility has previously been demonstrated on host-associated, marine and terrestrial systems with a total of 242 curated MAGs across fourteen published metagenomes. Of these refined MAGs, the number of high-quality and medium-quality bins increased, consequently lowering the number of low-quality bins and decreasing the amount of data discarded from downstream analyses. The recovery of higher quality MAGs improved the confidence in results and strengthened the resultant conclusions of these respective studies. Automappa consists of three tabs, one for uploading a user’s metagenome data, another for exploration and refinement and the last for providing an overall summary of the refined MAG results.ConclusionsAutomappa is an open source software package that allows researchers to easily assess and refine undetected or draft-quality MAGs from their respective metagenomes. It is freely available under the GPLv3 license athttps://github.com/WiscEvan/Automappaand through Figshare (doi: 10.6084/m9.figshare.22593235).
Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate
Authors: Hoang Don Q. , Wilson Lindsay R. , Scheftgen Andrew J. , Suen Garret , Currie Cameron R. 
Published: August 2023

AbstractDisturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the generaCellvibrio,Lacunisphaera, andAsticaccacaulisare the most abundant microbes. However,Lacunisphaerais only abundant in the lower disturbance frequency treatments, whileAsticaccaulisis more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are twoPseudomonassequence variants, and aCohnellasequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37-3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.Abstract ImportanceA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community’s response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose, and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.
Genome analyses reveal the secondary metabolites potentially influence the geographical distribution ofFusarium pseudograminearumpopulations
Authors: Li Wei , Cao Shulin , Sun Haiyan , Yang Xiaoyue , Xu Lei , Zhang Xin , Deng Yuanyu , Pavlov Igor N. , Litovka Yulia A. , Chen Huaigu 
Published: August 2023

AbstractFusarium crown rot (FCR), caused byFusarium pseudograminearum, significantly impacts wheat yield and quality in China’s Huanghuai region. The rapidF. pseudograminearumepidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes ofF. pseudograminearumstrains producing 3-acetyl-deoxynivalenol (3AcDON) and 15-acetyl-deoxynivalenol (15AcDON) toxins were assembled. Additionally, 38 related strains were resequenced. Genomic differences such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) amongF. pseudograminearumstrains were analyzed. The whole-genome SNP locus based population classification mirrored the toxin chenotype (3AcDON and 15AcDON)-based classification, indicating the presence of genes associated with the trichothecene toxin gene cluster. Further analysis of differential SNP, indel, and SV loci between the 3AcDON and 15AcDON populations revealed a predominant connection to secondary metabolite synthesis genes. Notably, the majority of the secondary metabolite biosynthesis gene cluster (SMGC) loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution toF. pseudograminearumpopulation structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution ofF. pseudograminearum, and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.
Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
Authors: Filandr Frantisek , Sarpe Vladimir , Raval Shaunak , Alex Crowder D. , Khan Morgan F. , Douglas Pauline , Coales Stephen , Viner Rosa , Syed Aleem , Tainer John A. , Lees-Miller Susan P. , Schriemer David C. 
Published: August 2023

AbstractWe developed a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS2) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS1-based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS2straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-validation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.
The G protein alpha Chaperone and Guanine-Nucleotide Exchange Factor RIC-8 Regulates Cilia Morphogenesis inCaenorhabditis elegansSensory Neurons
Authors: Campagna Christina M. , McMahon Hayley , Nechipurenko Inna 
Published: August 2023

AbstractHeterotrimeric G (αβγ) proteins are canonical transducers of G-protein-coupled receptor (GPCR) signaling and play critical roles in communication between cells and their environment. Many GPCRs and heterotrimeric G proteins localize to primary cilia and modulate cilia morphology via mechanisms that are not well understood. Here, we show that RIC-8, a cytosolic guanine nucleotide exchange factor (GEF) and chaperone for Gα protein subunits, shapes cilia membrane morphology in a subset ofCaenorhabditis eleganssensory neurons. Consistent with its role in ciliogenesis,C. elegansRIC-8 localizes to cilia in different sensory neuron types. Using domain mutagenesis, we demonstrate that while the GEF function alone is not sufficient, both the GEF and Gα-interacting chaperone motifs of RIC-8 are required for its role in cilia morphogenesis. We identify ODR-3 as the RIC-8 Gα client and demonstrate that RIC-8 functions in the same genetic pathway with another component of the non-canonical G protein signaling AGS-3 to shape cilia morphology. Notably, despite severe defects in AWC cilia morphology,ags-3null mutants exhibit normal chemotaxis toward benzaldehyde unlikeodr-3mutant animals. Collectively, our findings describe a novel function for the evolutionarily conserved protein RIC-8 and non-canonical RIC-8-AGS-3-ODR-3 signaling in cilia morphogenesis and uncouple Gα ODR-3 functions in ciliogenesis and olfaction.Author SummaryPrimary cilia are specialized cellular compartments that mediate communication between cells and their environment. In humans, deficits in cilia assembly and function lead to genetic diseases called ciliopathies. While the molecular machinery that sends out and receives major signaling cues is present inside cilia of different cell types, the mechanisms by which these signaling factors modulate cilia structure or cilia-dependent cellular functions are not well understood. In this study, we identify a new role for the RIC-8-AGS-3-ODR-3 signaling module in formation of specialized ciliary structures inC. elegansneurons. Our findings provide new insight into mechanisms of cilia assembly and highlight how the same signaling component (i.e. ODR-3) can be differentially regulated to mediate distinct cellular functions (cilia formation versus olfactory behavior).