bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes
Authors: Aroney Samuel T. N. , Newell Rhys J. P. , Tyson Gene W. , Woodcroft Ben J. 
Published: November 2024

AbstractRecovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm which substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritised, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample-groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes, and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.
Bridging the Python Training Gap for Bioscientists in Brazil: Improvements and Challenges
Authors: Crestana Gustavo Schiavone , da Silva Batista Ubiratan , Gonçalves Funnicelli Michelli Inácio , Braga Larissa Graciano , Zuvanov Luíza , Bizarria Rodolfo , de Sousa Raissa Melo , Narciso Ferreira Pedro Henrique , Winck Flavia Vischi , Alves Margarido Gabriel Rodrigues , de Mello Varani Alessandro , Riaño-Pachón Diego Mauricio , Corrêa dos Santos Renato Augusto 
Published: November 2024

AbstractThe rapid evolution of high-throughput technologies in biosciences has generated diverse and voluminous datasets, requiring bioscientists to develop data manipulation and analysis skills. Python, known for its versatility and powerful libraries, has become a crucial tool for managing these datasets. However, there is a significant lack of programming training for bioscientists in many countries. To address this knowledge gap among scientists in Brazil, the Brazilian Python Workshop for Biological Data was introduced several years ago, focusing on basic programming concepts and data handling techniques using popular Python libraries. Despite the progress and positive feedback from earlier editions, challenges persisted, necessitating continuous adaptation and improvement to meet the evolving needs of bioscientists.This work describes the advancements made in the 2021 and 2022 editions of the workshop and discusses new suggestions for its ongoing enhancement. Key innovations were introduced in the workshop structure and coordination, including the creation of new committees and the establishment of a code of conduct. Feedback forms were updated to enable real-time adjustments during the event, improving its overall effectiveness. The workshop also expanded its reach by increasing geographical diversity among participants. New didactic strategies, such as pair-teaching, code clubs, and the integration of information and communication technologies (ICTs), were implemented to enhance learning outcomes. Programming best practices and scientific reproducibility were emphasized through talks and hands-on activities, guided by PEP8 conventions. Furthermore, efforts to enhance scientific dissemination were intensified, with an increased presence on social media and participation in international scientific events and communication networks. Finally, we present updated recommendations for students, researchers, and educators interested in organizing and promoting similar events, building on those previously described.
Saccharibacteria deploy two distinct Type IV pili, driving episymbiosis, host competition, and twitching motility
Authors: Grossman Alex S. , Lei Lei , Botting Jack M. , Liu Jett , Nahar Nusrat , Souza João Gabriel S. , Liu Jun , McLean Jeffrey S. , He Xuesong , Bor Batbileg 
Published: November 2024

AbstractAll cultivated Patescibacteria, or CPR, exist as obligate episymbionts on other microbes. Despite being ubiquitous in mammals and environmentally, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts are largely unknown. Type 4 pili (T4P) are well conserved in this group and predicted to facilitate symbiotic interactions. To test this, we targeted T4P pilin genes in SaccharibacteriaNanosynbacter lyticusstrain TM7x to assess their essentiality and roles in symbiosis. Our results revealed thatN. lyticusassembles two distinct T4P, a non-essential thin pili that has the smallest diameter of any T4P and contributes to host-binding, episymbiont growth, and competitive fitness relative to other Saccharibacteria, and an essential thick pili whose functions include twitching motility. Identification of lectin-like minor pilins and modification of host cell walls suggest glycan binding mechanisms. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that are vital mediators of their underexplored episymbiotic lifestyle.
Sirt5 preserves cardiac function in ischemia-reperfusion injury by inhibiting ANT2 lactylation
Authors: Li Simeng , Shen Siman , Hong Yongfang , Ding Kun , Chen Suyun , Chen Jianning , Wang Changsen , Wen Yaofeng , Mo Guixi , Yu Lili , Shi De-Li , Zhang Liangqing 
Published: November 2024

AbstractMyocardial ischemia-reperfusion (IR) injury is the most common type of heart disease. IR-disrupted mitochondrial homeostasis affects heart energy metabolism and function, but the mechanism remains poorly understood. Here we report a cardioprotective role of the mitochondrial protein Sirt5 in a mouse model of cardiac IR injury. The down-regulation of Sirt5 in IR-injured heart is associated with an increased protein lactylation and impaired mitochondrial function. Overexpression ofSirt5alleviates, whereas conditional knockout ofSirt5aggravates, mitochondrial damage and cardiac injury. Mechanistically, Sirt5 interacts with the inner mitochondrial membrane protein adenine nucleotide translocase 2 (ANT2), inhibiting its lysine lactylation to promote its association with the outer mitochondrial membrane protein voltage-dependent anion-selective channel 1 (VDAC1). Lactylation-resistant ANT2 efficiently complexes with VDAC1 and improves cardiac function after injury. Therefore, we uncover a Sirt5-regulated interaction of ANT2 and VDAC1 in maintaining mitochondrial homeostasis, highlighting the potential of targeting ANT2 lactylation as a therapeutic strategy in the treatment of cardiac injury.TeaserSirt5 promotes the interaction of mitochondrial proteins to protect mitochondrial homeostasis and improve heart function in ischemia-reperfusion injury.
Revealing the Ultrastructure of LiveCandida albicansusing Stimulated Emission Depletion Microscopy
Authors: Baxter Katherine J. , Rooney Liam M. , Foylan Shannan , Gould Gwyn W. , McConnell G. 
Published: November 2024

SUMMARYCandida albicans, a commensal fungal pathogen, is a major cause of opportunistic infections in immunocompromised individuals. Understanding its cellular structures and pathogenic mechanisms is critical for developing targeted antifungal therapies. Stimulated emission depletion (STED) microscopy enables nanoscale visualization of cellular components, surpassing the diffraction limit of conventional light microscopy. In this study, we employed STED microscopy to investigate the ultrastructural organization ofC. albicansin live specimens. We showed that dyes commonly used in STED microscopy of mammalian cells are ineffective for the study ofC. albicans, and we showed the utility of Nile Red staining for visualising the organisation of dynamic cellular components, including tracking of lipid droplets, using time-lapse recording in experiments exceeding 12 hours. STED microscopy offered more than a two-fold improvement in resolution compared to confocal laser scanning microscopy applied to the same specimens with negligible photobleaching. This study demonstrates the utility of STED microscopy in advancing our understanding ofC. albicansbiology at the nanoscale, providing a platform for future investigations into fungal pathogenicity and antifungal development.GRAPHICAL ABSTRACTWe present an optimised fluorescence staining method for super-resolution live-cell imaging ofCandida albicans, using Stimulated Emission Depletion (STED) microscopy to resolve and track sub-cellular structures. We compare the performance of conventional confocal laser scanning microscopy (CLSM) to STED imaging, providing a three-fold resolution improvement beyond the diffraction limit. Finally, we perform live cell tracking to visualise and quantify the trajectories of multiple sub-diffraction limit-sized objects over a period of 12 hours, demonstrating the potential for live-cell STED imaging ofCandidato visualise key processes involved in pathogenesis, drug resistance and infection.
HsbA represses stationary phase biofilm formation inPseudomonas putida
Authors: Pulido-Sánchez Marta , Montero-Beltrán Elisa , López-Sánchez Aroa , Govantes Fernando 
Published: November 2024

ABSTRACTPseudomonas putidabiofilm growth is associated to nutrient-sufficient conditions and biofilm dispersal is induced by nutrient starvation, signaled by the stringent response-associated nucleotide alarmone (p)ppGpp. We have used transcriptomic analysis to show that (p)ppGpp regulates thehsbAR-hptBgene cluster, encoding components of a phosphorelay pathway and an anti-α factor antagonist, andcfcR, encoding a response regulator with diguanylate cyclase (DGC) activity. Transcription ofhsbAR-hptBandcfcRis RpoS-dependent and induced by stationary phase and the stringent response. A ΔhsbAmutant resumed biofilm formation after dispersal in late stationary phase, stimulated liquid-air biofilm formation and increased Congo Red adsorption. All these phenotypes were traced down to increased c-di-GMP levels in stationary phase dependent on the activity of CfcR and its cognate sensor kinase, CfcA. HsbA was reversibly phosphorylated by the combined action of HptB and HsbR HsbA phosphorylation conditioned its interaction with CfcR and CfcA and the intracellular distribution of the three proteins, but did not greatly influence biofilm regulation. Our results support a model in which HsbA forms a complex with CfcR to inhibit its DGC activity regardless of its phosphorylation state. Upon HsbA dephosphorylation, this complex is recruited to the cell membrane by CfcA to strengthen the inhibitory effect. This system contributes to biofilm dispersal by denying biofilm formation, but allows quick onset ofde novobiofilm formation in response to physiological cues that release HsbA inhibition to restore CfcR DGC activity.
Evaluating bacteriophage impact on gut microbiome composition in broad-nosed pipefish (Syngnathus typhle)
Authors: Parker Jamie , Marten Silke-Mareike , Rajkov Jelena , Theising Franziska I. , Dubin Arseny , Roth Olivia 
Published: November 2024

ABSTRACTBacteriophages play a crucial role in shaping microbial community dynamics in marine systems and have the potential to stimulate surges in pathogenic bacteria facilitating disease outbreaks. Notwithstanding, bacteriophages also serve as valuable biocontrol agents, underscoring their huge potential for aquaculture therapy treatments. Insights into the intricate tripartite interplay upon an infection with a virulent bacterium, its specific phages and the eukaryotic microbiome could improve our understanding of how bacteria-phage interactions behave in a natural microbial system. This investigation assessed the influence of a virulentVibrio alginolyticus(K01M1) infection, in tandem with lytic (фSt2) and filamentous (фK04M1)Vibrio-specific phages, on the broad-nosed pipefish (Syngnathus typhle) gut microbiome using 16S rRNA amplicon sequencing and non-intrusive gastric swabbing. Microbial communities and diversity metrics were not permanently impacted byVibrioand phage introductions, while the different infection regimes shapedVibrio-specific dynamics. In the filamentous phage andVibrio-only treatments,V. alginolyticusabundances spiked 12 hours post-ingestion. In contrast,V. alginolyticusnumbers in the lytic phage and control treatment were significantly reduced, suggesting phage activity and specific elimination of the introduced bacteria. Assisted by relative true-gut tissue samples, a newly implemented non-intrusive swabbing method was successful at discerning the activity of two contrasting phages and supports previous work that encourages the use of фSt2 in bacteriophage treatments. IdentifyingVibrio-specific phages with similar positive characteristics could be beneficial for the aquaculture trade, which is currently heavily impacted by the antibiotic crisis.
InvasiveVespa velutina nigrithoraxhornets are more susceptible to entomopathogenic fungus than two other hymenopteran species, the waspVespa vulgarisand the bumblebeeBombus terrestris
Authors: Lacombrade Mathilde , Rocher Naïs , Mahot-Castaing Blandine , Vogelweith Fanny , Lihoreau Mathieu , Thiéry Denis 
Published: November 2024

AbstractEntomopathogenic fungi are commonly used as biological control agents. Recently, a strain ofMetarhizium robertsii(Sorokin, 1883) (Hypocreales: Clavicipitaceae) collected in France was identified as a good candidate for controlling invasive populations of yellow-legged hornet,Vespa velutina nigrithorax(Buysson, 1905) (Hymenoptera: Vespidae) in Europe. SinceM. robertsiiis generalist, its use as bioagent could be damaging for non-targeted species. Here, we compared the lethal effects of three concentrations of thisM. robertsiistrain on the invasive hornet and two non-targeted species commonly found in Europe, the common waspVespa vulgaris(Linnaeus, 1758) (Hymenoptera: Vespidae) and the buff-tailed bumblebeeBombus terrestris(Linnaeus, 1758) (Hymenoptera: Apidae). Exposure toM. robertsiispores altered the survival of all three species but at different degrees. Hornets had consistently lower survival, even under low concentrations of spores, when compared to wasps and bumblebees. Such lower susceptibility of beneficial Hymenoptera is encouraging in the perspectives of usingM. robertsiias biocontrol agent against invasive hornets.
The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain
Authors: Warner James L. , Lux Vanda , Veverka Václav , Winston Fred 
Published: November 2024

SummaryThe disassembly and reassembly of nucleosomes by histone chaperones is an essential activity during eukaryotic transcription elongation. This highly conserved process maintains chromatin integrity by transiently removing nucleosomes as barriers and then restoring them in the wake of transcription. While transcription elongation requires multiple histone chaperones, there is little understanding of how most of them function and why so many are required. Here, we show that the histone chaperone Spt6 acts through its acidic, intrinsically disordered N-terminal domain (NTD) to bind histones and control chromatin structure. The Spt6 NTD is essential for viability and its histone binding activity is conserved between yeast and humans. The essential nature of the Spt6 NTD can be bypassed by changes in another histone chaperone, FACT, revealing a close functional connection between the two. Our results have led to a mechanistic model for dynamic cooperation between multiple histone chaperones during transcription elongation.
The glycosyltransferase POGLUT1 regulates muscle stem cell development and maintenance in mice
Authors: Cho Soomin , Servián-Morilla Emilia , Garrido Victoria Navarro , Rodriguez-Gonzalez Beatriz , Yuan Youxi , Cano Raquel , Rambhiya Arjun A. , Darabi Radbod , Haltiwanger Robert S. , Paradas Carmen , Jafar-Nejad Hamed 
Published: November 2024

AbstractMutations in proteinO-glucosyltransferase 1 (POGLUT1) cause a recessive form of limb-girdle muscular dystrophy (LGMD-R21) associated with reduced satellite cell number and NOTCH1 signaling in adult patient muscles and impaired myogenic capacity of patient-derived muscle progenitors. However, thein vivoroles of POGLUT1 in the development, function, and maintenance of satellite cells are not well understood. Here, we show that conditional deletion of mousePoglut1in myogenic progenitors leads to early lethality, postnatal muscle growth defects, reducedPax7expression, abnormality in muscle extracellular matrix, and impaired muscle repair.Poglut1-deficient muscle progenitors exhibit reduced proliferation, enhanced differentiation, and accelerated fusion into myofibers. Inducible loss ofPoglut1in adult satellite cells leads to their precocious differentiation and impairs muscle repair upon serial injury. Cell-based signaling assays and mass spectrometric analysis indicate that POGLUT1 is required for the activation of NOTCH1, NOTCH2, and NOTCH3 in myoblasts and that NOTCH3 is a target of POGLUT1 like NOTCH1 and NOTCH2. These observations provide insight into the roles of POGLUT1 in muscle development and repair and the pathophysiology of LGMD-R21.
Constraining
λBs
by
Bs→γ*
and
Bs→ϕ
form factors
Authors: Ivanov Mikhail A. , Melikhov Dmitri , Simula Silvano 
Published: November 2024

We calculate the form factors FV(q2,q′2) and FTV(q2,q′2) describing the Bs→γ* transition induced by the vector and tensor weak currents in a broad range of values of q2 and q′2 far below the quark thresholds in both q2 and q′2 channels. These form factors are calculated via the distribution amplitudes of the Bs-meson. We then interpolate the obtained results by a formula that contains pole at q′2=Mϕ2 and extract the residue which gives the Bs→ϕ transition form factors V(q2) and T1(q2). In this way we obtain theoretical predictions for these form factors without invoking quark-hadron duality and QCD sum rules. Furthermore, we calculate the relationship between V(0) and T1(0) and the parameter λBs(μ), the inverse moment of the Bs-meson distribution amplitude. Using the available predictions for V(0) and T1(0) coming from approaches not referring to the Bs-meson distribution amplitudes, we obtain the estimate λBs(μ≃mb)=(0.62±0.10)  GeV.

Published by the American Physical Society
2024
Giant superhydrophobic slip of shear-thinning liquids
Authors: Schnitzer Ory , Ray Prasun K. 
Published: November 2024

We theoretically illustrate how complex fluids flowing over superhydrophobic surfaces may exhibit giant flow enhancements in the double limit of small solid fractions (ε≪1) and strong shear thinning (β≪1, β being the ratio of the viscosity at infinite shear rate to that at zero shear rate). Considering a Carreau liquid within the canonical scenario of longitudinal shear-driven flow over a grooved superhydrophobic surface, we show that, as β is decreased, the scaling of the effective slip length at small solid fractions is enhanced from the logarithmic scaling ln(1/ε) for Newtonian fluids to the algebraic scaling 1/ε1−nn, attained for β=O(ε1−nn), n∈(0,1) being the exponent in the Carreau model. We illuminate this scaling enhancement and the geometric-rheological mechanism underlying it through asymptotic arguments and numerical simulations.

Published by the American Physical Society
2024
Estimating farmers’ willingness to pay for crop insurance with application of choice experiment: case study in South Gondar Zone, Ethiopia
Authors: Wassie Asmamaw Getnet , Nesibu Shegaw Getu , Mengistu Yismaw Ayelign 
Published: November 2024

PurposeThis study aims to estimate farmers’ willingness to pay for crop insurance, utilizing a choice experiment case study in the South Gondar Zone, Ethiopia.Design/methodology/approachPrimary cross-sectional data were collected in 2023 from 240 farm households. The choice experiment method was employed to elicit farmers’ willingness to pay for crop insurance. Five attributes, including monetary cost, were identified for the choice experiment, with two improved scenarios and a status quo presented to respondents. The mixed logit model and extended mixed logit model were used for analysis.FindingsThe econometric model indicated that, with the exception of one attribute, all were positive and statistically significant. Farmers showed a preference for improved scenarios over the status quo, demonstrating a willingness to pay for crop insurance. The extended mixed logit model revealed that factors such as livestock ownership, household head’s sex, family size, income, farming experience, crop risk exposure, and additional occupations significantly influenced farmers’ preferences for crop insurance.Research limitations/implicationsThe study’s sample size was limited to 240 farm households, which is relatively small. More reliable results could be obtained with a larger sample size. Another significant limitation is the study’s failure to account for institutional setups when assessing farmers’ willingness to pay for crop insurance.Practical implicationsAgricultural risk, particularly crop risk, is severe in the study area. The results suggest that farmers have a genuine need for risk mitigation mechanisms, such as crop insurance. The findings reflect farmers’ interest in crop insurance, indicating that responsible entities, whether governmental or private insurance companies, can readily implement crop insurance schemes.Social implicationsThe study has significant social implications, as the society in the study area is highly vulnerable to crop risk, which adversely affects their livelihood. Introducing a crop insurance scheme could enhance the welfare and livelihood of the local population.Originality/valueTo the best of our knowledge, this study is novel in both concept and methodology. Unlike previous studies, which focused on specific crop risks, this study considers multiple crop risks. The findings offer valuable insights for policymakers and other stakeholders involved in crop insurance. Understanding farmers’ preferences for crop insurance is crucial for designing effective crop insurance policies.
Driving mechanism of attentional bias toward safety of construction workers: case study in China
Authors: Wu Xiang , Li Xiaochuan , Chen Jianwu , Gao Jingqi , Luo Xiaowei 
Published: November 2024

PurposeAttentional bias toward safety (ABS) is a positive safety cognitive ability that could encourage individuals to engage in proactive safety behaviors; however, there is a lack of systematic sorting out of the driving mechanism of ABS. This study aims to identify the influencing factors and underlying mechanisms of ABS among construction workers (CWs) in China, thereby enhancing the practice of construction safety management.Design/methodology/approachAn exploratory study using the open-ended approach of grounded theory was conducted, including 25-depth interviews with CWs. Based on the interviews’ records, a scale for measuring CWs’ ABS was developed and an empirical study on 554 workers was performed. The ABS scale was validated in conjunction with an ABS modification training experiment published by the authors’ team, and the theoretical model of the driving mechanism of CWs’ ABS was obtained.FindingsThe results showed that the six driving factors of construction workers’ ABS include organizational factors, risk perception, safety awareness, safety investment, job stress and workers’ educational level. This paper also identified the critical approach to improving workers’ ABS as an effective intervention on risk perception. In addition, the ABS scale was found to be effective in measuring the ABS level.Originality/valueThis paper is of importance in reducing the unsafe behaviors of construction workers and preventing and promoting the sustainable development of construction enterprises.