bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanistic basis of gene-specific transcription regulation by the Integrator complex
Authors: Sabath Kevin , Nabih Amena , Arnold Christian , Moussa Rim , Domjan David , Zaugg Judith B. , Jonas Stefanie 
Published: January 2024

ABSTRACTThe Integrator complex (INT) regulates gene expression via premature transcription termination of RNA polymerase II (RNAP2) at promoter-proximal pausing sites. This attenuation of transcription is required for cellular response to external stimuli, cell differentiation and neurodevelopment. How gene-specific regulation is achieved by INT in an inducible manner remains unclear. Here, we identify two sites on INT subunits 13/14 that serve as direct binding hubs for diverse sets of sequence-specific transcription factors (TFs) and other transcription effector complexes. The TFs co-localize with INT genome-wide, increase INT abundance on target genes and co-regulate inducible transcriptional programs. Consistently, disruption of INT-TF contacts impairs sensory cilia formation in response to glucose starvation. Structural analysis places INT’s TF binding hubs upstream of the transcription bubble when attached to paused RNAP2, consistent with simultaneous TF-promoter association. Our data establish TF-mediated recruitment of INT to promoters as a widespread mechanism for targeted and inducible transcription attenuation.
Rat anterior cingulate neurons responsive to rule or strategy changes are modulated by the hippocampal theta rhythm and sharp-wave ripples
Authors: Khamassi M , Peyrache A , Benchenane K , Hopkins DA , Lebas N , Douchamps V , Droulez J , Battaglia FP , Wiener SI 
Published: January 2024

AbstractTo better understand neural processing during adaptive learning of stimulus-response-reward contingencies, we recorded synchrony of neuronal activity in anterior cingulate cortex (ACC) with hippocampal rhythms in male rats acquiring and switching between spatial and visual discrimination tasks in a Y-maze. ACC population and single unit activity responded shortly after task rule changes, or just before the rats adopted different task strategies. Hippocampal theta oscillations (associated with memory encoding) modulated an elevated proportion of rule-change responsive neurons (70%), but other neurons that were correlated with strategy-change, strategy value, and reward-rate were not. However, hippocampal sharp wave-ripples modulated significantly higher proportions of rule-change, strategy-change and reward-rate responsive cells during post-session sleep but not pre-session sleep. This suggests an underestimated mechanism for hippocampal mismatch and contextual signals to facilitate ACC detection of contingency changes for cognitive flexibility, a function that is attenuated after it is damaged.
Pinpointing the microbiota of tardigrades: what is really there?
Authors: Surmacz Bartłomiej , Stec Daniel , Prus-Frankowska Monika , Buczek Mateusz , Michalczyk Łukasz , Łukasik Piotr 
Published: January 2024

AbstractMicrobiota have been proposed as an important aspect of tardigrade biology, but little is known about their diversity and distribution. Here, we attempted to characterize the microbiota of 44 cultured species of tardigrades using 16S rRNA amplicon sequencing, using different specimen pooling strategies, various DNA extraction kits, and multiple types of controls. We also estimated the number of microbes in samples using synthetic DNA spike-ins. Additionally, we reanalyzed data from previous studies.Our results suggest that the microbial community profiles of cultured tardigrades are dominated by bacterial OTUs and genotypes originating from food, medium, or laboratory reagents. We found microbial strains consistently enriched in certain tardigrades (relative to the culture media and controls), which indicates likely symbiotic associations, but the reads representing putative true tardigrade-associated microbes rarely exceeded 20% of the datasets. Some of the identified tardigrade-associated microbes matched symbionts identified by other studies. However, we also identified serious contamination issues with previous studies of tardigrade microbiome, making some of their conclusions questionable. We conclude that tardigrades are not universally dependent on specialized microbes and highlight the necessary safeguards in future studies of the microbiota of microscopic organisms.
Thiosulfinate tolerance gene clusters are common features ofBurkholderiaonion pathogens
Authors: Paudel Sujan , Zhao Mei , Stice Shaun P. , Dutta Bhabesh , Kvitko Brian H. 
Published: January 2024

AbstractBurkholderia gladiolipv.alliicola, B.cepacia, andB. orbicolaare common bacterial pathogens of onion. Onions produce organosulfur thiosulfinate defensive compounds after cellular decompartmentalization. Using whole genome sequencing andin silicoanalysis, we identified putative thiosulfinate tolerance gene (TTG) clusters in multiple onion-associatedBurkholderiaspecies similar to those characterized in otherAllium-associated bacterial endophytes and pathogens. Sequence analysis revealed the presence of threeBurkholderiaTTG cluster types with both Type A and Type B being broadly distributed inB. gladioli,B. cepacia, andB. orbicolain both the chromosome and plasmids. Based on isolate natural variation and generation of isogenic strains, we determined thein vitroandin vivocontribution of TTG clusters inB. gladioli,B. cepacia, andB. orbicola. TheBurkholderiaTTG clusters contributed to enhanced allicin tolerance and improved growth in filtered onion extract by all three species. TTG clusters also made clear contributions toB gladiolifoliar necrosis symptoms and bacterial populations. Surprisingly, the TTG cluster did not contribute to bacterial populations in onion bulb scales by these three species. Based on our findings, we hypothesize onion-associatedBurkholderiamay evade or inhibit the production of thiosulfinates in onion bulb tissues.
Extracellular ATP is an environmental cue in bacteria
Authors: Tronnet Sophie , Pandey Vikash , Lloret-Berrocal Miriam , Pérez-del-Pozo Mario , Söderholm Niklas , Hernández-Ortego Carlos , Billker Oliver , Nordström Anders , Puhar Andrea 
Published: January 2024

AbstractIn animals and plants extracellular ATP (eATP) functions as signal and regulates the immune response. During inflammation intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here we show that non-pathogenicEscherichia coliresponds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is time-, concentration-, and medium-dependent and ATP-specific. The second messenger cAMP and genes related to metabolism, quorum sensing, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties on the host or bacteria. Combined genome-scale modelling revealed global metabolic and biomass building blocks modifications. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes which broadly regulates physiology, antimicrobial resistance, and virulence.
Development of a qPCR assay and a LAMP assay forVerticillium longisporumdetection and a triplex qPCR assay for simultaneous detection ofV. longisporum,Leptosphaeria biglobosaandL. maculansfrom canola samples
Authors: Fu Heting , Yang Yalong , Jiang Junye , Daniels Greg C. , Hill Blake , Xue Shiming , Zahr Kher , Stellar L. , Harding Michael W. , Feindel David , Bvindi Carol , Fernando Dilantha , Wang Lipu , Feng Jie 
Published: January 2024

AbstractVerticillium wilt, Verticillium stem striping, and Verticillium stripe, are common disease names that all denote infection caused byVerticillium longisporum, on canola, or other Brassica crops. In this study, a quantitative PCR (qPCR) assay and a loop-mediated isothermal amplification (LAMP) assay were developed for the detection ofV. longisporumfrom canola stem samples. Both assays are specific toV. longisporumat the species level and ubiquitous at the strain level. The low limit for positive detection of the two assays is 1 pg fungal DNA in a 20-µ L reaction or 1,400 fungal cells in 100-mg plant tissue. The qPCR assay was combined with the duplex qPCR assay for the two blackleg pathogens,Leptosphaeria biglobosaandL. maculansto constitute a triplex qPCR system for simultaneous detection of all three pathogens. The usefulness of this triplex qPCR system was verified on canola samples collected from various locations in Alberta, Canada. Using this triplex qPCR system,V. longisporumwas detected from one sample, while the two blackleg pathogens were detected at higher frequencies. Since it is sometimes difficult to differentiate Verticillium stripe and blackleg on Alberta canola samples based on visual symptoms, the triplex qPCR system is an important tool for the detection ofV. longisporum, especially when its presence is masked or obscured by symptoms of blackleg.
Measuring excitation-inhibition balance through spectral components of local field potentials
Authors: Diehl Geoffrey W , Redish A David 
Published: January 2024

AbstractThe balance between excitation and inhibition is critical to brain functioning, and dysregulation of this balance is a hallmark of numerous psychiatric conditions. Measuring this excitation-inhibition (E:I) balancein vivohas remained difficult, but theoretical models have proposed that characteristics of local field potentials (LFP) may provide an accurate proxy. To establish a conclusive link between LFP and E:I balance, we recorded single units and LFP from the prefrontal cortex (mPFC) of rats during decision making. Dynamic measures of synaptic coupling strength facilitated direct quantification of E:I balance and revealed a strong inverse relationship to broadband spectral power of LFP. These results provide a critical link between LFP and underlying network properties, opening the door for non-invasive recordings to measure E:I balance in clinical settings.
Harnessing the diversity ofBurkholderiaspp. prophages for therapeutic potential
Authors: Nordstrom Hayley R. , Griffith Marissa P. , Srinivasa Vatsala Rangachar , Wallace Nathan R. , Li Anna , Cooper Vaughn S. , Shields Ryan K. , Van Tyne Daria 
Published: January 2024

AbstractBurkholderiaspp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment forBurkholderiaspp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified withinBurkholderiaspp. and may represent a source of useful phages for therapy. Here we investigate whether prophages withinBurkholderiaspp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-twoBurkholderiaspp. isolates were induced for prophage release, and harvested prophages were tested for lytic activity against the same 32 isolates. Lytic phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35Burkholderiaspp. clinical isolate genomes, and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed thatB. cenocepaciaisolates were more phage-susceptible thanBurkholderia multivoransisolates. Overall, our findings suggest that prophages present withinBurkholderiaspp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population
Authors: Gamage Bawantha Dilshan , Ranasinghe Diyanath , Sahankumari AGP , Malavige Gathsaurie Neelika 
Published: January 2024

AbstractObjectiveThe gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.DesignThe gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n=112) and colonic tissue (n=36) in 112 individuals. Of these had CRC (n=24), premalignant lesions (n=10), healthy individuals (n=50) and in those with diabetes (n=28).ResultsOverall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium, were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p< 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.ConclusionDespite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, withPrevotellaspecies, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.
Promoting
p
-based Hall effects by
p−d−f
hybridization in Gd-based dichalcogenides
Authors: Zeer Mahmoud , Go Dongwook , Schmitz Peter , Saunderson Tom G. , Wang Hao , Ghabboun Jamal , Blügel Stefan , Wulfhekel Wulf , Mokrousov Yuriy 
Published: January 2024

We conduct a first-principles study of Hall effects in rare-earth dichalcogenides, focusing on monolayers of the H-phase EuX2 and GdX2, where X=S, Se, and Te. Our predictions reveal that all EuX2 and GdX2 systems exhibit high magnetic moments and wide band gaps. We observe that while in the case of EuX2 the p and f states hybridize directly below the Fermi energy, the absence of f and d states of Gd at the Fermi energy results in the p-like spin-polarized electronic structure of GdX2, which mediates p-based magnetotransport. Notably, these systems display significant anomalous, spin, and orbital Hall conductivities. We find that in GdX2, the strength of correlations controls the relative position of the p, d, and f states and their hybridization, which has a crucial impact on p-state polarization and the anomalous Hall effect, but not the spin and orbital Hall effects. Moreover, we find that the application of strain can significantly modify the electronic structure of the monolayers, resulting in quantized charge, spin, and orbital transport in GdTe2 via a strain-mediated orbital inversion mechanism taking place at the Fermi energy. Our findings suggest that rare-earth dichalcogenides hold promise as a platform for topological spintronics and orbitronics.

Published by the American Physical Society
2024
Two levels of topology in skyrmion lattice dynamics
Authors: Schick Daniel , Weißenhofer Markus , Rózsa Levente , Rothörl Jan , Virnau Peter , Nowak Ulrich 
Published: January 2024

Skyrmions are localized, topological spin structures that can be described as quasiparticles. Skyrmions in thin films are an ideal model system to study Brownian motion and lattice formation in two dimensions. They follow an equation of motion, the Thiele equation, which includes a topology-dependent chiral term, linear in velocity, causing a skyrmion Hall effect and a drastic reduction of the diffusion coefficient for individual skyrmions, as compared to normal Brownian particles. Using Brownian dynamics simulations, we show that this topological suppression of the diffusion can be partially lifted in two-dimensional lattices of skyrmions. Counterintuitively, this causes enhanced diffusive properties with increasing particle density, similar to odd-diffusive Brownian particles. We show how the topological charge of the skyrmions influences the dynamics of topological lattice defects, which also affects the dynamics of the phase formation.

Published by the American Physical Society
2024
Impact of Isotopic Exchange on Hydrated Protein Dynamics Revealed by Polarized Neutron Scattering
Authors: Nidriche Agathe , Moulin Martine , Oger Philippe , Stewart J. Ross , Mangin-Thro Lucile , Schmidt Wolfgang , Kneller Gerald , Peters Judith 
Published: January 2024

Within the last decades, it was often assumed that in hydrogen-rich disordered samples, such as proteins in solution or hydrated powder form, incoherent neutron scattering from hydrogen nuclei dominated the scattering signal to an extent that allowed all other contributions to be neglected. As incoherent scattering arises solely from self-correlations, it further justified such a choice. Consequently, heavy water was often used as a contrast tool to highlight molecular motions in live samples. Coherent scattering, which implies the scattering from many nuclei and therefore collective processes, is another non-negligible contribution to neutron scattering where cross sections of other nuclei than hydrogen are significant. The recent advent of instrumentation based on polarization of neutron beams and the analysis of their polarization state after scattering for dynamical studies allows us to separate and shed light on the two contributions. In the present study we reveal that, unexpectedly, the isotopic exchange of water in the hydration shell of proteins arises on a much faster timescale than assumed so far. Moreover, the collective and local D-bond network relaxation of hydration water contributes to a high extent to the coherent scattering signal, at odds with usual “static” approaches used to estimate the relative impacts of dynamics in the sample. Hence, hydration water necessarily contaminates nonpolarized standard experiments. The findings are of paramount importance for all neutron scattering experiments where partial or full deuteration is used.

Published by the American Physical Society
2024
The impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay: the mediating role of job engagement
Authors: Uraon Ram Shankar , Kumarasamy Ravikumar 
Published: January 2024

PurposeThis study examines the direct impact of justice perceptions of performance appraisal practices (procedural, distributive, interpersonal and informational justice) on job satisfaction, intention to stay and job engagement. Further, it investigates the effect of job engagement on job satisfaction and intention to stay. Moreover, the study tests the mediating role of job engagement on the impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay.Design/methodology/approachA total of 650 self-report structured questionnaires were distributed among the employees of 50 information technology companies, and 503 samples were received. Partial least square-structural equation modeling was used to test the hypothesized model.FindingsThis study revealed that justice perception of performance appraisal practices positively affects job satisfaction, intention to stay and job engagement. In addition, job engagement positively affects job satisfaction and intention to stay. Further, job engagement significantly transfers the impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay, thus confirming the mediating role of job engagement. However, the significant direct impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay in the presence of a mediator, i.e. job engagement, revealed partial mediation.Research limitations/implicationsThe findings of this study augment the social exchange theory by explicating that an individual who perceives justice in performance appraisal practices is likely to have greater job engagement, which ultimately leads to higher job satisfaction and intention to stay. This study filled the research gap by examining the role of four justice components of performance appraisal practices on job satisfaction and intention to stay and the mediating role of job engagement in transferring the impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay.Practical implicationsThis study showed the importance of four justice components of performance appraisal practices in enhancing employee job engagement. Hence, this study would motivate information technology companies to maintain fairness in performance appraisal practices to enhance employee job engagement and ultimately increase job satisfaction and intention to stay.Originality/valueThis study is one of its kind that tested the direct impact of comprehensive justice components (procedural, distributive, interpersonal and informational justice) of performance appraisal practices on job satisfaction and intention to stay. In addition, this is a unique study that examined the mediating effect of job engagement on the impact of justice perceptions of performance appraisal practices on job satisfaction and intention to stay.
Effect of process parameters on the growth and wear resistance of CrAlN coating on silicon nitride surface
Authors: Lu He , Wu Yuhou , Liu Zijin , Wang He , Yan Guangyu , Bai Xu , Guo Jiancheng , Zheng Tongxiang 
Published: January 2024

Purpose
Preparing CrAlN coatings on the surface of silicon nitride bearings can improve their service life in oil-free lubrication. This paper aims to match the optimal process parameters for preparing CrAlN coatings on silicon nitride surfaces, and reveal the microscopic mechanism of process parameter influence on coating wear resistance.

Design/methodology/approach
This study used molecular dynamics to analyze how process parameters affected the nucleation density, micromorphology, densification and internal stress of CrAlN coatings. An orthogonal test method was used to examine how deposition time, substrate temperature, nitrogen-argon flow rate and sputtering power impacted the wear resistance of CrAlN coatings under dry friction conditions.

Findings
Nucleation density, micromorphology, densification and internal stress have a significant influence on the surface morphology and wear resistance of CrAlN coatings. The process parameters for better wear resistance of the CrAlN coatings were at a deposition time of 120 min, a substrate temperature of 573 K, a nitrogen-argon flow rate of 1:1 and a sputtering power of 160 W.

Originality/value
Simulation analysis and experimental results of this paper can provide data to assist in setting process parameters for applying CrAlN coatings to silicon nitride bearings.