bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs
Authors: Liu Qianli , Helmin Kathryn A. , Dortzbach Zachary D. , Reyes Flores Carla P. , Torres Acosta Manuel A. , Gurkan Jonathan K. , Joudi Anthony M. , Mambetsariev Nurbek , Morales-Nebreda Luisa , Kang Mengjia , Rasmussen Luke , Pérez-Leonor Xóchitl G. , Abdala-Valencia Hiam , Singer Benjamin D. 
Published: May 2024

AbstractDNA methylation at cytosine-phospho-guanine (CpG) residues is a vital biological process that regulates cell identity and function. Although widely used, bisulfite-based cytosine conversion procedures for DNA methylation sequencing require high temperature and extreme pH, which lead to DNA degradation, especially among unmethylated cytosines. Enzymatic methylation sequencing (EM-seq), an enzyme-based cytosine conversion method, has been proposed as a less biased alternative for methylation profiling. Compared to bisulfite-based methods, EM-seq boasts greater genome coverage with less GC bias and has the potential to cover more CpGs with the same number of reads (i.e., higher signal-to-noise ratio). Reduced representation approaches enrich samples for CpG-rich genomic regions, thereby enhancing throughput and cost effectiveness. We hypothesized that enzyme-based technology could be adapted for reduced representation methylation sequencing to enable high-resolution DNA methylation profiling on low-input samples, including those obtained from clinical specimens. We leveraged the well-established differences in methylation profile between mouse CD4+ T cell populations to compare the performance of a novel reduced representation EM-seq (RREM-seq) procedure against an established reduced representation bisulfite sequencing (RRBS) protocol. While the RRBS method failed to generate reliable DNA libraries when using <2 ng of DNA (equivalent to DNA from around 350 cells), the RREM-seq method successfully generated reliable DNA libraries from 1–25 ng of mouse and human DNA. Ultra-low-input (<2-ng) RREM-seq libraries’ final concentration, regulatory genomic element coverage, and methylation status within lineage-defining Treg cell-specific super-enhancers were comparable to RRBS libraries with more than 10-fold higher DNA input. RREM-seq also successfully detected lineage-defining methylation differences between alveolar Tconv and Treg cells obtained from mechanically ventilated patients with severe SARS-CoV-2 pneumonia. Our RREM-seq method enables single-nucleotide resolution methylation profiling using low-input samples, including from clinical sources.
Effective real-time transmission estimations incorporating population viral load distributions amid SARS-CoV-2 variants and pre-existing immunity
Authors: Meng Yu , Lin Yun , Xiong Weijia , Lau Eric H. Y. , Ho Faith , Wong Jessica Y. , Wu Peng , Tsang Tim K. , Cowling Benjamin J. , Yang Bingyi 
Published: May 2024

AbstractBackgroundPopulation-level viral load distribution, measured by cycle threshold (Ct), has been demonstrated to enable real-time estimation of Rtfor SARS-CoV-2 ancestral strain. Generalisability of the framework under different circulating variants and pre-existing immunity remains unclear.AimThis study aimed to examine the impact of evolving variants and population immunity on the generalizability of Ct-based transmission estimation framework.MethodsWe obtained the first Ct record of local COVID-19 cases from July 2020 to January 2023 in Hong Kong. We modeled the association between daily viral load distribution and the conventional estimates of Rtbased on case count. We trained the model using data from wave 3 (i.e., ancestral strain with minimal population immunity) and predicted Rtfor wave 5, 6 and 7 (i.e., omicron subvariants with > 70% vaccine coverage). Cross-validation was performed by training on the other 4 waves. Stratification analysis by disease severity was conducted to evaluate the impact of the changing severity profiles.ResultsTrained with the ancestral dominated wave 3, our model provided accurate estimation of Rt, with the area under the ROC curve of 0.98 (95% confidence interval: 0.96, 1.00), 0.62 (95% CI: 0.53, 0.70) and 0.80 (95% CI: 0.73, 0.88) for three omicron dominated waves 5 to 7, respectively. Models trained on the other four waves also had high accuracy. Stratification analysis suggested potential impact of case severity on model estimation, which coincided with the fluctuation of sampling delay.DiscussionOur findings suggested that incorporating population viral shedding can provide accurate real-time estimation of transmission with evolving variants and population immunity. Application of the model needs to account for sampling delay.
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Authors: Abramsson Mia L. , Corey Robin A. , Škerle Jan , Persson Louise J. , Andén Olivia , Oluwole Abraham O. , Howard Rebecca J. , Lindahl Erik , Robinson Carol V. , Strisovsky Kvido , Marklund Erik G. , Drew David , Stansfeld Phillip J. , Landreh Michael 
Published: May 2024

AbstractIntegral membrane proteins carry out essential functions in the cell, and their activities are often modulated by specific protein-lipid interactions in the membrane. Here, we elucidate the intricate role of cardiolipin (CDL), a regulatory lipid, as a stabilizer of membrane proteins and their complexes. Using thein silico-designed model protein TMHC4_R (ROCKET) as a scaffold, we employ a combination of molecular dynamics simulations and native mass spectrometry to explore the protein features that facilitate preferential lipid interactions and mediate stabilization. We find that the spatial arrangement of positively charged residues as well as local conformational flexibility are factors that distinguish stabilizing from non-stabilizing CDL interactions. However, we also find that even in this controlled, artificial system, a clear-cut distinction between binding and stabilization is difficult to attain, revealing that overlapping lipid contacts can partially compensate for the effects of binding site mutations. Extending our insights to naturally occurring proteins, we identify a stabilizing CDL site within theE. colirhomboid intramembrane protease GlpG and uncover its regulatory influence on enzyme substrate preference. In this work, we establish a framework for engineering functional lipid interactions, paving the way for the design of proteins with membrane-specific properties or functions.
RNA adapts its flexibility to efficiently fold and resist unfolding
Authors: Jang Sukjin S. , Ray Korak Kumar , Lynall David G. , Shepard Kenneth L. , Nuckolls Colin , Gonzalez Ruben L. 
Published: May 2024

AbstractRecent studies have demonstrated that the mechanisms through which biopolymers like RNA interconvert between multiple folded structures are critical for their cellular functions. A major obstacle to elucidating these mechanisms is the lack of experimental approaches that can resolve these interconversions between functionally relevant biomolecular structures. Here, we dissect the complete set of structural rearrangements executed by an ultra-stable RNA, the UUCG stem-loop, at the single-molecule level using a nano-electronic device with microsecond time resolution. We show that the stem-loop samples at least four conformations along two folding pathways leading to two distinct folded structures, only one of which has been previously observed. By modulating its flexibility, the stem-loop can adaptively select between these pathways, enabling it to both fold rapidly and resist unfolding. This paradigm of stabilization through compensatory changes in flexibility broadens our understanding of stable RNA structures and is expected to serve as a general strategy employed by all biopolymers.
Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome
Authors: Goel Abhishek , Shete Omprakash , Goswami Sourav , Samal Amit , CB Lavanya , Kedia Saurabh , Ahuja Vineet , O’Toole Paul W , Shanahan Fergus , Ghosh Tarini Shankar 
Published: May 2024

AbstractVariations in the normal gut microbiome and the existence of context-dependent disease associations have confounded the identification of microbiome markers of health. A reliable indexing of taxa based on their association with host health and microbiome resilience could accelerate development of microbiome-based therapeutics including selection of live biotherapeutics and facilitate microbiome comparisons in diverse study populations.Here we first investigated 196 taxa for their association with three hallmark properties of health and microbiome-resilience, namely prevalence/community-influence in non-diseased subjects, longitudinal stability and host health, using a discovery cohort of 39,926 publicly available adult (> 18 years) gut microbiomes from 127 studies spanning 42 countries and 28 disease conditions (including 9,434 longitudinal samples). We identified 18 species-level-taxa, referred to as ‘Health-Associated Core Keystones’ (HACKs), with association-strengths in the top 30 percentile for all three properties. We integrated these association-strengths into a single value, the HACK-index, that ranks taxa based on their estimated contribution to both microbiome stability and host health. We then demonstrate the reproducibility of these indices for the taxon associations with the three properties, using a validation cohort of 4,500 gut microbiomes (from 11 studies with various demographics and diseases). Specific consortia of high HACK-index taxa are also associated with positive response to Mediterranean Diet interventions and Immuno-Checkpoint-Inhibitor therapies. We finally identify the distinguishing microbial genomic functions associated with high HACK-indices/HACK-taxa that can be investigated using targeted mechanistic studies to identify microbiome effectors of improved health.The availability of HACK-indices provides a rational basis for microbiome comparisons and will facilitate the selection and design of microbiome-based therapeutics.
Strong conservation of spacer lengths in NrdR repressor DNA binding sites
Authors: Shahid Saher , Balka Mateusz , Lundin Daniel , Daley Daniel O. , Sjöberg Britt-Marie , Grinberg Inna Rozman 
Published: May 2024

AbstractThe ribonucleotide reductase-specific repressor NrdR, from the human pathogensListeria monocytogenesandStreptococcus pneumoniae, form tetramers that bind to DNA when loaded with dATP and ATP. If loaded with only ATP they form different oligomeric complexes that cannot bind to DNA. The DNA binding site inL. monocytogenesis a pair of NrdR boxes separated by 15-16 bp, whereas inStreptococcus pneumoniaethe NrdR boxes are separated by 25-26 bp. However,Streptococcus pneumoniaeNrdR binds stronger to the relatedStreptococcus thermophilusbinding sites with NrdR boxes separated by 15-16 bp. This observation triggered a comprehensive binding study of four NrdRs fromL. monocytogenes, Streptococcus pneumoniae, Escherichia coliandStreptomyces coelicolorto a series of synthetic dsDNA fragments where the NrdR boxes were separated by 12-27 bp. All four NrdRs bound well to NrdR boxes separated by 14-17 bp, and also to NrdR boxes separated by 24-27 bp. The worst binding occurred when NrdR boxes were separated by 20 bp. Thein vitroresults were confirmedin vivoinE. colifor spacer distances 12-27 bp. We conclude that NrdR repressors bind most efficiently when there is an integer number of DNA turns between the center of the two NrdR boxes.
The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution
Authors: Lemke Oliver , Heineike Benjamin Murray , Viknander Sandra , Cohen Nir , Steenwyk Jacob Lucas , Spranger Leonard , Li Feiran , Agostini Federica , Lee Cory Thomas , Aulakh Simran Kaur , Nielsen Jens , Rokas Antonis , Berman Judith , Zelezniak Aleksej , Gossmann Toni Ingolf , Ralser Markus 
Published: May 2024

AbstractThe functions of cells and proteins depend on their biochemical microenvironment. To understand how biochemical constraints shaped protein structural evolution, we coupled the extensive genetic and metabolic data from theSaccharomycotinasubphylum with the capability of AlphaFold2 to systematically predict protein structures from sequence. Determining how 11,269 enzyme structures catalysing 361 different metabolic reactions evolved over 400 million years alongside their molecular functions, we report that metabolism has shaped the structural evolution of enzymes at different levels: the organism’s overall metabolism; the topological organisation of the metabolic network; and each enzyme’s molecular properties. For example, structural evolution depends on each enzyme’s reaction mechanism, on the variability rather than the amount of metabolic flux, and on biosynthetic cost. Evolutionary cost-optimization is stronger on highly abundant enzymes and acts differently on different structural domains, with the exception of small-molecule binding sites, which are prioritised over other structural domains and lack cost-optimisation. Finally, while enzyme surfaces are less constrained, surface residues can also be exposed to positive selection for the co-evolution of protein-protein interaction sites. Accessing AlphaFold’s power to predict protein structures systematically and across species barriers, facilitating the integration of protein structures with functional genomics, we were thus able to map biological constraints which shape protein structural evolution at scale and over long timelines.
Conjugation mediates large-scale chromosomal transfer inStreptomycesdriving diversification of antibiotic biosynthetic gene clusters
Authors: Choufa Caroline , Gascht Pauline , Leblond Hugo , Gauthier Anthony , Vos Michiel , Bontemps Cyril , Leblond Pierre 
Published: May 2024

AbstractStreptomycesare ubiquitous soil dwelling bacteria of special importance as a source of metabolites used in human and veterinary medicine, agronomy and industry. Conjugation is the main mechanism ofStreptomycesHorizontal Gene Transfer, and this process has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains ofStreptomycesresult in the large-scale, genome-wide distributed replacement of up to one third of the recipient chromosome, a phenomenon for which we propose the name ‘StreptomycesChromosomal Transfer’ (SCT). Such chromosome blending results in the acquisition, loss and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated SMBGC diversification holds great promise in the discovery of new bioactive compounds including antibiotics.
Unifying the analysis of bottom-up proteomics data with CHIMERYS
Authors: Frejno Martin , Berger Michelle T. , Tüshaus Johanna , Hogrebe Alexander , Seefried Florian , Graber Michael , Samaras Patroklos , Fredj Samia Ben , Sukumar Vishal , Eljagh Layla , Brohnshtein Igor , Mamisashvili Lizi , Schneider Markus , Gessulat Siegfried , Schmidt Tobias , Kuster Bernhard , Zolg Daniel P. , Wilhelm Mathias 
Published: May 2024

AbstractProteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent (DDA), data-independent (DIA) or parallel reaction monitoring (PRM), separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a novel, spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in DDA, DIA and PRM experiments.
Screening clinicalCandida albicansisolates for invasiveness by mimicking the human environment
Authors: Vulin Clément , Sutter Julian , Schweizer Tiziano A. , Andreoni Federica , Baer Julian , Bernasconi Alexandra , Bulut Karl , Posteraro Brunella , Saunguinetti Maurizio , Zinkernagel Annelies S. 
Published: May 2024

AbstractObjectivesCandida albicanscolonizes a wide range of human body niches, but also causes severe invasive infections, such as candidemia. No screening method exists to predict which colonizer may lead to invasive infections. Invasiveness and virulence are associated with yeast filamentation, triggered by environmental factors encountered in the host. Here, we monitored the filamentation profile and colony appearance time of aC.albicansstrain isolated from a patient’s abscess. Using eight additionalC.albicansclinical isolates, we established anin vitroscreening-framework of filamentation to assess the invasiveness potential of individual isolates.MethodsWe monitored the filamentation pattern of nineC.albicansclinical isolates over 14 days in 48 environmental conditions, including combinations of glucose/nitrogen concentrations, pH and temperature, to mimic host environment variations. Additionally, we tested invasiveness by growing isolates on modified filtration membranes, mimicking physical human body barriers usually colonized byCandida. An automated image analysis pipeline was developed to quantify filamentation.ResultsTwo types of colony filamentation morphology were differentiated, star and hazy. The total filamentation area depended on environmental factors. Based on their filamentation response to environmental changes, the isolates clustered in three distinct groups reflecting their site of isolation in the host. We moreover found that filamentation morphologies on modified filtration membranes could be predictors of invasiveness.ConclusionThis work lays the ground for screening assays, which could help assessing the potential of a colonizingCandidaisolate to cause invasive disease, paving the way for tailored preventive therapy regimens in the future.
Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils
Authors: Barnett Samuel E. , Shade Ashley 
Published: May 2024

AbstractViruses are important components of the soil microbiome, influencing microbial population dynamics and the functions of their hosts. However, the relationships and feedbacks between virus dynamics, microbial host dynamics, and environmental disturbance is not understood. Centralia, PA, USA, is the site of an underground coal seam fire that has been burning for over 60 years. As the fire moves along the coal seam, previously heated soils cool to ambient temperature, creating a gradient of heat disturbance intensity and recovery. We examined annual soil viral population dynamics over seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed over time and were distinct between fire-affected and reference sites. Dissimilarity in viral communities was greater across sites (space) than within a site across years (time), and cumulative viral diversity more rapidly stabilized within a site across years than within a year across sites. There also were changes in CRISPR investment as soils cooled, corresponding to shifts in viral diversity. Finally, there were also differences in viral-encoded auxiliary metabolic genes between fire-affected and reference sites. These results indicate that despite high site-to-site soil viral diversity, there was surprising viral community consistency within a site over the years and shifting host-viral interactions in soils recovering from disturbance. Together, these results provide insights into how viral and host communities collectively respond to unpredicted environmental disturbance.HighlightsIn a seven-year annual study of temperate soils affected by an underground fire, viral communities displayed greater variability across sites (spatial) than over time (temporal).Viral communities were distinct between heated and unheated soils throughout sampling.Soil bacterial community composition correlated to viral community composition, though this relationship weakened when accounting for edaphic properties of soil temperature and pH.Soil viral communities may be less resilient to press disturbance than their host bacterial communities.Viral-host interactions may shift during soil recovery from long-term heating.
Chordin-mediated BMP shuttling patterns the secondary body axis in a cnidarian
Authors: Mörsdorf David , Prünster Maria Mandela , Genikhovich Grigory 
Published: May 2024

AbstractBMP signaling patterns secondary body axes throughout Bilateria and, strikingly, in the bilaterally symmetric corals and sea anemones – members of the bilaterian sister clade Cnidaria. It has been suggested that the secondary, “directive” axis in the sea anemoneNematostella vectensisrequires Chordin-mediated “shuttling” of BMP ligands, like inDrosophilaor frog, however, an alternative “local inhibition” model is also possible. To choose between these two options, we generated localized Chordin sources in the Chordin morphant background and showed that in the presence of BMP ligands inNematostella, mobile Chordin is necessary and sufficient to establish a peak of BMP signaling at the side of the embryo opposing the Chordin source. In contrast, membrane-tethered Chordin-CD2 promotes weak BMP signaling within the Chordin-CD2 source. These results provide the first mechanistic evidence for BMP shuttling in a cnidarian and suggest that BMP shuttling may have been functional in the cnidarian-bilaterian ancestor.
Managing workplace interpersonal conflicts: Harnessing employees’ emotional intelligence and organizational learning
Authors: Vapiwala Fatima , Pandita Deepika 
Published: May 2024

Purpose
The present study explores the need to strengthen the organizational learning culture to aid constructive conflict management through high levels of employees’ emotional intelligence.

Design/methodology/approach
In the current study, with relevant support from the literature, the authors review the need to develop a high degree of emotional intelligence through knowledge acquisition, sharing and utilization for constructive conflict management in the workplace.

Findings
Emotional intelligence significantly aids employees in integrating newly obtained information with the organization’s established processes. Individuals with a high degree of emotional intelligence possess the aptitude to deal with dysfunctional task, process, and relationship conflicts with a centralized focus on organizational learning.

Originality/value
The authors have proposed a learning model which indicates that individuals with a high degree of emotional intelligence possess the aptitude to deal with dysfunctional task, process and relationship conflicts. With a focus on organizational learning, the model can aid managers in developing training initiatives for knowledge acquisition, knowledge sharing and knowledge utilization among employees.