bluuebunny/crossref_metadata_2025_split huggingface dataset:
Niche cytoskeletal architecture is required for proper stem cell signaling and oriented division in theDrosophilatestis
Authors: Vida Gabriela S. , Botto Elizabeth , DiNardo Stephen 
Published: June 2024

AbstractStem cells are critical to repair and regenerate tissues, and often reside in a niche that controls their behavior. TheDrosophilatestis niche has been a paradigm for niche-stem cell interactions and is used here to address the cell biological features that maintain niche structure and function during its steady-state operation. We report enrichment of the Myosin II (MyoII) and a key regulator of acto-myosin contractility (AMC), Rho Kinase (ROK), within the niche cell cortex at the interface with germline stem cells (GSCs). Compromising MyoII and ROK disrupts niche architecture, suggesting that AMC in niche cells is important to maintain the reproducible structure of this niche. Furthermore, defects in niche architecture cause changes in stem cell function. Our data suggest that the niche signals less robustly to adjacent germ cells, yet the disrupted structure permits increased numbers of cells to respond to the signal. Finally, compromising Myo II in niche cells leads to an increase in mis-oriented centrosomes in GSCs as well as defects in the centrosome orientation checkpoint. Ultimately, this work identifies a critical role for AMC-dependent maintenance of niche structure to ensure a proper complement of stem cells with correct execution of stem cell divisions.Summary statementActomyosin contractility regulated niche architecture is critical for proper signaling and oriented division of germline stem cells.
Biases in routine influenza surveillance indicators used to monitor infection incidence and recommendations for improvement
Authors: Eales Oliver , McCaw James M. , Shearer Freya M. 
Published: June 2024

AbstractBackgroundMonitoring how the incidence of influenza infections changes over time is important for quantifying the transmission dynamics and clinical severity of influenza. Infection incidence is difficult to measure directly, and hence other quantities which are more amenable to surveillance are used to monitor trends in infection levels, with the implicit assumption that they correlate with infection incidence.MethodHere we demonstrate, through mathematical reasoning, the relationship between the incidence of influenza infections and three commonly reported surveillance indicators: 1) the rate per unit time of influenza-like illness reported through sentinel healthcare sites, 2) the rate per unit time of laboratory-confirmed influenza infections, and 3) the proportion of laboratory tests positive for influenza (‘test-positive proportion’).ResultsOur analysis suggests that none of these ubiquitously reported surveillance indicators are a reliable tool for monitoring influenza incidence. In particular, we highlight how these surveillance indicators can be heavily biased by: the dynamics of circulating pathogens (other than influenza) with similar symptom profiles; changes in testing rates; and differences in infection rates, symptom rates, and healthcare-seeking behaviour between age-groups and through time. We make six practical recommendations to improve the monitoring of influenza infection incidence. The implementation of our recommendations would enable the construction of more interpretable surveillance indicator(s) for influenza from which underlying patterns of infection incidence could be readily monitored.ConclusionThe implementation of all (or a subset) of our recommendations would greatly improve understanding of the transmission dynamics, infection burden, and clinical severity of influenza, improving our ability to respond effectively to seasonal epidemics and future pandemics.
Structure ofGeobacillus stearothermophilusCas9: insights into the catalytic process and thermostability of CRISPR-Cas9
Authors: Shen Panpan , Zhang Lilan , Liu Beibei , Li Xian , Min Jian , Huang Jian-Wen , Chen Chun-Chi , Guo Rey-Ting 
Published: June 2024

AbstractCRISPR-Cas9 has been developed as a powerful gene editing tool, but the mechanism governing the intricate catalytic process remains incompletely resolved. Here, the cryo-electron microscopy structures of thermostable Cas9 fromGeobacillus stearothermophilus(GeoCas9) in complex with sgRNA and target DNA are reported. The structure of GeoCas9 in complex with sgRNA reveals a slit termed L1-crevice comprising HNH, RuvC, and L1 helix as a transient storage site of 5’ spacer of sgRNA. When 5’ spacer is extracted to pair with the target DNA, L1-crevice collapses to trigger the subsequent HNH domain translocation. In addition, structural and biochemical analyses suggest that the resilience of GeoCas9 at elevated temperature is related to the unique PI domain conformation. These results advance our understanding into the catalytic process of Cas9 and unveil the molecular mechanism that accounts for the superior thermal profile of GeoCas9.
Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state
Authors: Pahl Vanessa , Lubrano Paul , Petras Daniel , Link Hannes 
Published: June 2024

AbstractSimultaneous measurements of library barcodes and metabolites can facilitate the screening of metabolically engineered bacterial libraries. Here, we introduce a scalable method for the parallel measurement of protein-based library barcodes and metabolites using flow-injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin, a small 76-amino-acid protein, which we labeled with N-terminal tags of six amino acids to identify bacterial strains. We demonstrate that FI-MS effectively detects intact ubiquitin proteins and identifies the N-terminal barcodes. In the same analysis, we semi-quantify relative concentrations of primary metabolites. As a proof of concept, we engineered six ubiquitin-barcoded CRISPRi strains targeting metabolic enzymes, and analyzed their metabolic profiles and ubiquitin barcodes using FI-MS. Our results show distinct metabolome changes within metabolic pathways targeted by CRISPRi. This method enables fast and simultaneously detection of library barcodes and intracellular metabolites, opening up new possibilities to measure metabolomes of engineered bacteria at scale.
A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization
Authors: Cao Xiaofu , Huang Shiying , Wagner Mateusz M. , Cho Yuan-Ting , Chiu Din-Chi , Wartchow Krista M. , Lazarian Artur , McIntire Laura Beth , Smolka Marcus B. , Baskin Jeremy M. 
Published: June 2024

ABSTRACTTools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled Anchor-away/Recruiter System (MARS) comprises an engineered, 15-kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP–GFP nanobody interaction. Applications of MARS include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
Contractile fibroblasts are recruited to the growing mammary epithelium to support branching morphogenesis
Authors: Sumbal Jakub , Journot Robin P. , Faraldo Marisa M. , Koledova Zuzana Sumbalova , Fre Silvia 
Published: June 2024

AbstractFibroblasts are stromal cells found in connective tissue that are critical for organ development, homeostasis, and disease. Single-cell transcriptomic analyses have revealed a high level of inter- and intra-organ heterogeneity of fibroblasts. However, the functional implications and lineage relations of different fibroblast subtypes remain unexplored, especially in the mammary gland. Here we provide a comprehensive characterization of pubertal mammary fibroblasts, achieved using single-cell RNA sequencing, spatial mapping, and in vivo lineage tracing. Notably, we discovered a transient niche-forming population of specialized contractile fibroblasts that exclusively localize around the tips of the growing mammary epithelium and are recruited from the surrounding fat pad. Using functional organoid-fibroblast co-cultures we reveal that different fibroblast populations can acquire contractile features when in direct contact with the epithelium, promoting morphogenesis. In summary, our exhaustive characterization of these specialized cells provides new insights into mammary fibroblast heterogeneity and implicates their functional relevance for branching morphogenesis and lineage hierarchy during mouse mammary gland development.
Spectrin condensates provide a nidus for assembling the periodic axonal structure
Authors: Boyer Nicholas P. , Sharma Rohan , Wiesner Theresa , Delamare Antoine , Pelletier Florence , Leterrier Christophe , Roy Subhojit 
Published: June 2024

ABSTRACTCoordinated assembly of individual components into higher-order structures is a defining theme in biology, but underlying principles are not well-understood. In neurons, α/β spectrins, adducin, and actinfilaments assemble into a lattice wrapping underneath the axonal plasma membrane, but mechanistic events leading to this periodic axonal structure (PAS) are unclear. Visualizing PAS components in axons as they develop, we found focal patches in distal axons containing spectrins and adducin (but sparse actin filaments) with biophysical properties reminiscent of biomolecular condensation. Overexpressing spectrin-repeats – constituents of α/β-spectrins – in heterologous cells triggered condensate formation, and preventing association of βII-spectrin with actin-filaments/membranes also facilitated condensation. Finally, overexpressing condensate-triggering spectrin repeats in neurons before PAS establishment disrupted the lattice, presumably by competing with innate assembly, supporting a functional role for biomolecular condensation. We propose a condensation-assembly model where PAS components form focal phase-separated condensates that eventually unfurl into a stable lattice-structure by associating with subplasmalemmal actin. By providing local ‘depots’ of assembly parts, biomolecular condensation may play a wider role in the construction of intricate cytoskeletal structures.
EARLY NEUTROPHIL ACTIVATION AND NETs RELEASE IN THE PRISTANE-INDUCED LUPUS MICE MODEL
Authors: Carrasco Solange , Liphaus Bernadete L. , Peixoto Tatiana Vasconcelos , Lima Thais Martins , Ariga Sueli Kunimi Kubo , Jesus Queiroz Zelita Aparecida , de Matos Lobo Thays , Catanozi Sergio , Rodrigues Letícia Gomes , Filho Antônio Santos , Teodoro Walcy Rosolia , Velosa Ana Paula Pereira , Levy Débora , Soriano Francisco Garcia , Goldenstein-Schainberg Cláudia 
Published: June 2024

AbstractBackgroundNETosis is recognized as an important source of autoantigens. Therefore, we hypothesized whether the pristane-induced lupus mice model shows early activation of neutrophils, the presence of low-density granulocytes (LDGs), and neutrophil extracellular traps (NETs) release, which could contribute to the development of a lupus phenotype.MethodsTwelve female wild-type Balb/c mice were intraperitoneally injected with pristane (n=6; pristane group) or saline (n=6; control group). Five days after the injection, blood, peritoneal lavage, bone marrow, and spleen samples were collected for flow cytometry analyses of activated neutrophils (Ly6G+CD11b+), LDGs (CD15+CD14low), and NETs release (Sytox Green+).ResultsThe pristane-induced mice group had a significantly increased number of blood activated neutrophils and LDGs as well as NETs released by these cells compared to the saline-injected control group and the basal values determined 12 days before the injection. The pristane group also had a significantly increased number of activated neutrophils, LDGs, and NETs released compared to the control group for the peritoneal lavage, bone marrow, and spleen.ConclusionsWe demonstrated early changes in the innate immune response such as an increased number of activated neutrophils and LDGs and mainly increased NETosis in the pristane-induced mice model which may be considered as the primary event triggering lupus development.
Dispensable genome and segmental duplications drive the genome plasticity inFusarium solani
Authors: Navasca Abbeah , Singh Jatinder , Rivera-Varas Viviana , Gill Upinder , Secor Gary , Baldwin Thomas 
Published: June 2024

AbstractFusarium solaniis a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunisticF. solaniassociated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of theF. solanisugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. SB1 has a large genome (59.38 Mb) organized into 15 chromosomes. The genome expansion is due to the high repeats and massive segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly,F. vanettenii77-13-4. The extensive segmental duplications between the two SB1 chromosomes suggest that this isolate may have doubled its accessory genes. Further comparison of theF. solanistrain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome ofF. vanettenii77-13-4. The pan-genome of 12 publicly availableF. solaniisolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity,F. solaniis not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits inFusarium solaniare driven by the dispensable genome with significant contributions from segmental duplications.
UNC-6/Netrin promotes both adhesion and directed growth within a single axon
Authors: Nichols Ev L. , Lee Joo , Shen Kang 
Published: June 2024

SummaryDuring development axons undergo long-distance migrations as instructed by guidance molecules and their receptors, such as UNC-6/Netrin and UNC-40/DCC. Guidance cues act through long-range diffusive gradients (chemotaxis) or local adhesion (haptotaxis). However, how these discrete modes of action guide axonsin vivois poorly understood. Using time-lapse imaging of axon guidance inC. elegans, we demonstrate that UNC-6 and UNC-40 are required for local adhesion to an intermediate target and subsequent directional growth. Exogenous membrane-tethered UNC-6 is sufficient to mediate adhesion but not directional growth, demonstrating the separability of haptotaxis and chemotaxis. This conclusion is further supported by the endogenous UNC-6 distribution along the axon’s route. The intermediate and final targets are enriched in UNC-6 and separated by a ventrodorsal UNC-6 gradient. Continuous growth through the gradient requires UNC-40, which recruits UNC-6 to the growth cone tip. Overall, these data suggest that UNC-6 stimulates stepwise haptotaxis and chemotaxisin vivo.
Implementing a clinical pathway for diagnosing and treating acute HIV infection among key populations attending sexual health clinics in Indonesia: cohort profile of the INTERACT study
Authors: Irwanto  , Kawi Nurhayati H. , Luis Hendry , Sihotang Erik P. , Januraga Pande Putu , Oktaviani Margareta , Suwarti  , Rahmawati Dwi P. , Sukmaningrum Evi , Yanihastuti Evy , Dijkstra Maartje , Sanders Eduard J. , Wignall F. Stephen , Gedela Keerti , Hamers Raph L. ,   INTERACT Study Group
Published: June 2024

ABSTRACTBackgroundTo reduce the high HIV incidence among key populations in Indonesia, we implemented a clinical pathway for screening, diagnosis and treatment of acute HIV infection (AHI) in sexual health clinics in Jakarta and Bali. This paper presents a cohort profile and analysis of baseline data on the study uptake, diagnostic yield, and estimated AHI prevalence and screening cascade outcomes.MethodsWe performed a baseline analysis of 1879 individuals who underwent AHI screening at three sexual health clinics in Jakarta and Bali between May and December 2023, comprising a risk-score assessment, fourth-generation antibody/p24 antigen-based rapid diagnostic test (RDT; Abbott Determine HIV Early Detect) and HIV-PCR (Xpert) testing.ResultsMedian age was 27 years (IQR24-31), and 75.4% were male. Men who have sex with men (MSM) accounted for 50.4%, clients of sex workers 20.1%, and sex workers 5.2%. Of 1866 participants tested at study enrolment, 113 (6.1% [113/1866]) had chronic HIV (antibody-positive) and 6 (0.34% [6/1748]) had AEHI. HIV-PCR testing led to a 5.3% (95%CI1.9-11.2) increase in confirmed HIV diagnoses. The number needed to test to detect one AEHI case was 291 (1748/6) overall and 169 (842/5) among MSM. Overall HIV and AHI prevalence was 6.4% (95%CI 5.3-7.6; 119/1866) and 0.34% (95%CI0.12-0.74; 6/1748) overall; and 10.8% (95%CI8.9-13.0; 102/940) and 0.53% (95%CI 0.17-1.2; 5/940) among MSM. The Abbott Determine HIV Early Detect RDT only detected 2 (18.2%) of 11 AEHI cases. 113 (95.0%) newly diagnosed individuals were linked to care and started ART, of whom 75 (66.4%) on the same day and 104 (92.0%) within a week (median 0 days, range 0-93).ConclusionAHI screening, diagnosis and prompt treatment is feasible among high-risk urban MSM in Indonesia. Further evaluations are needed to estimate clinical impact and cost-effectiveness of AHI screening in this setting. The study continues accrual and follow-up, and provides a platform for future immuno-virological, social science, and intervention studies in Indonesia.
Combinatorial Design Testing in Genomes with POLAR-seq
Authors: Ciurkot Klaudia , Lu Xinyu , Malyshava Anastasiya , Soro Livia , Lees Aidan , Gorochowski Thomas E. , Ellis Tom 
Published: June 2024

AbstractSynthetic biology projects increasingly use modular DNA assembly or synthetic in vivo recombination to generate diverse combinatorial libraries of genetic constructs for testing. But as these designs expand to multigene systems it becomes challenging to sequence these in a cost-effective way that reveals the genotype to phenotype relationships in the libraries. Here, we introduce a new quick, low-cost method designed for assessing combinational designs of genome-integrated multigene constructs that we callPoolofLongAmplifiedReads (POLAR) sequencing. POLAR-seq takes genomic DNA isolated from library pools and uses long range PCR to amplify target genomic regions up to 35 kb long containing combinatorial designs. The pool of long amplicons is then directly read by nanopore sequencing with full length reads then used to identify the gene content and structural variation of individual genotypes in the library and read count indicating how abundant a genotype is within the pool. Using yeast cells with loxP-containing synthetic gene clusters that rearrange in vivo in the presence of Cre recombinase, we demonstrate how POLAR-seq can be used to identify global patterns from combinatorial experiments, find the most abundant genotypes in a pool and also be adapted to sequence-verify gene clusters from isolated strains.
Spatial distribution of local elastic moduli in nanocrystalline metals
Authors: Krief Menahem , Ashkenazy Yinon 
Published: June 2024

Elastoplastic properties of nanocrystalline metals are nonuniform on the scale of the grain size, and this nonuniformity affects macroscopic quantities as, in these systems, a significant part of the material is at or adjacent to a grain boundary. We use molecular dynamics simulations to study the spatial distributions of local elastic moduli in nanograined pure metals and analyze their dependence on grain size. Calculations are performed for copper and tantalum with grain sizes ranging from 5 to 20 nm. Shear-modulus distributions for grain and grain-boundary atoms were calculated. It is shown that the noncrystalline grain boundary has a wide shear-modulus distribution, which is grain-size independent, while grains have a peaked distribution, which becomes sharper with increasing grain size. Average elastic moduli of the bulk, grains, and grain boundary are calculated as a function of grain size. The atomistic simulations show that the reduction of total elastic moduli with decreasing grain size is mainly due to a resulting larger grain-boundary atoms fraction, and that the total elastic moduli can be approximated by a simple weighted average of larger grain elastic moduli and a lower grain-boundary elastic moduli.

Published by the American Physical Society
2024
Clinical characteristics of adolescents and emerging adults presenting for integrated posttraumatic stress and substance use treatment
Authors: Peach Natalie , Kihas Ivana , Isik Ashling , Cassar Joanne , Barrett Emma Louise , Cobham Vanessa , Back Sudie E. , Perrin Sean , Bendall Sarah , Brady Kathleen , Ross Joanne , Teesson Maree , Bezzina Louise , Dobinson Katherine A. , Schollar-Root Olivia , Milne Bronwyn , Mills Katherine L. 
Published: June 2024

Purpose
Adolescence and emerging adulthood are key developmental stages with high risk for trauma exposure and the development of mental and substance-use disorders (SUDs). This study aims to compare the clinical profiles of adolescents (aged 12–17 years) and emerging adults (aged 18–25 years) presenting for treatment of posttraumatic stress disorder (PTSD) and SUD.

Design/methodology/approach
Data was collected from the baseline assessment of individuals (n = 55) taking part in a randomized controlled trial examining the efficacy of an integrated psychological therapy for co-occurring PTSD and SUDs (PTSD+SUD) in young people.

Findings
Both age groups demonstrated complex and severe clinical profiles, including high-frequency trauma exposure, and very poor mental health reflected on measures of PTSD, SUD, suicidality and domains of social, emotional, behavioral and family functioning. There were few differences in clinical characteristics between the two groups.

Research limitations/implications
Similarity between the two groups suggests that the complex problems seen in emerging adults with PTSD + SUD are likely to have had their onset in adolescence or earlier and to have been present for several years by the time individuals present for treatment.

Originality/value
To the best of the authors’ knowledge, this is the first study to compare the demographic and clinical profiles of adolescents and emerging adults with PTSD + SUD. These findings yield important implications for practice and policy for this vulnerable group. Evidence-based prevention and early intervention approaches and access to care are critical. Alongside trauma-focused treatment, there is a critical need for integrated, trauma-informed approaches specifically tailored to young people with PTSD + SUD.