bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting, mapping, and suppressing the spread of a decade-longPseudomonas aeruginosanosocomial outbreak with genomics
Authors: Stribling William , Hall Lindsey R. , Powell Aubrey , Harless Casey , Martin Melissa J. , Corey Brendan W. , Snesrud Erik , Ong Ana , Maybank Rosslyn , Stam Jason , Bartlett Katie , Jones Brendan T. , Preston Lan N. , Lane Katherine F. , Thompson Bernadette , Young Lynn M. , Kwak Yoon I. , Barsoumian Alice E. , Markelz Ana-Elizabeth , Kiley John L. , Cybulski Robert J. , Bennett Jason W. , Mc Gann Patrick T. , Lebreton Francois 
Published: July 2023

ABSTRACTWhole-genome sequencing is revolutionizing bacterial outbreak investigation but its application to the clinic remains limited. In 2020, prospective and retrospective surveillance detected aPseudomonas aeruginosaoutbreak with 254 isolates collected from 82 patients in 27 wards of a hospital. Its origin was dated to the late 90s, just after the facility opened, and patient-to-patient and environment-to-patient cases of transmission were inferred. Over time, two epidemic subclones evolved in separate hosts and hospital areas, including newly opened wards, and hospital-wide sampling confirmed reservoirs persisted in the plumbing. Pathoadaptive mutations in genes associated with virulence, cell wall biogenesis, and antibiotic resistance were identified. While the latter correlated with the acquisition of phenotypic resistances to 1st (cephalosporin), 2nd (carbapenems) and 3rd (colistin) lines of treatment, maximum parsimony suggested that a truncation in a lipopolysaccharide component coincided with the emergence of a subclone prevalent in chronic infections. Since initial identification, extensive infection control efforts guided by routine, near real-time surveillance have proved successful at slowing transmission.SIGNIFICANCE STATEMENTEvery year, millions of hospital-associated infections are threatening patient lives. This, in a world in which rates of resistances to existing antibiotics are increasing. And this, at a time dubbed the post-antibiotic era when new drugs are scarce. But now is also the golden age of genomics. Here, applying this transformative technology to the clinic revealed an outbreak ofPseudomonas aeruginosa, resistant to last line antibiotics, that had escaped detection for decades. The mapping of transmission chains, through hospital floors, pointed to environmental reservoirs in intensive care units but also provided critical insights into the evolution and adaptation of this pathogen. Genomic data, shared in near real-time with the hospital, resulted in targeted interventions and the prevention of new cases.
Structural Coverage of the Human Interactome
Authors: Kosoglu Kayra , Aydin Zeynep , Tuncbag Nurcan , Gursoy Attila , Keskin Ozlem 
Published: July 2023

AbstractComplex biological processes in cells are embedded in the interactome, representing the complete set of protein-protein interactions. Mapping and analyzing the protein structures are essential to fully comprehending these processes’ molecular details. Therefore, knowing the structural coverage of the interactome is essential to show the current limitations. Structural modeling of protein-protein interactions requires accurate protein structures. In this study, we mapped all experimental structures to the reference human proteome. Later, we found the enrichment in structural coverage when complementary methods such as homology modeling and deep learning (AlphaFold) are included. We then collected the interactions from the literature and databases to form the reference human interactome resulting in 117,897 non-redundant interactions. When we analyzed the structural coverage of the interactome, we found that the number of experimentally determined protein complex structures is scarce, corresponding to 3.95% of all binary interactions. We also analyzed known and modeled structures to potentially construct the structural interactome with a docking method. Our analysis showed that 12.97% of the interactions from HuRI, 73.62%, and 32.94% from the filtered versions of STRING and HIPPIE could potentially be modeled with a high structural coverage or accuracy, respectively. Overall, this paper provides an overview of the current state of structural coverage of the human proteome and interactome.Significance StatementWe gathered binary protein-protein interactions from three prominent interactome databases to create a comprehensive human reference interactome. We quantified the structural coverage of the human interactome using already available structural data from four different sources. We further evaluate the percentage of interactions that can be accurately predicted using docking methods.
ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole genome sequencing data
Authors: Calendo Gennaro , Kusic Dara , Madzo Jozef , Gharani Neda , Scheinfeldt Laura 
Published: July 2023

AbstractLong-read sequencing technologies offer new opportunities to generate high confidence phased whole genome sequencing data for robust pharmacogenetic annotation. Here we describe a new user-friendly R package, ursaPGx, designed to accept multi-sample phased whole genome sequencing data VCF input files and output star allele annotations for pharmacogenes annotated in PharmVar.
Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses
Authors: Gupta Sandeep , Heinrichs Eric , Novitch Bennett G. , Butler Samantha J. 
Published: July 2023

AbstractDorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itch, and proprioception. While previous studies using genetic strategies in animal models have revealed important insights into dI development, the molecular details by which dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse ESC-derived dIs with pseudotime analyses. To validate thisin silicoresource as a useful tool, we used it to first identify novel genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them usingin situhybridization analyses in the developing mouse spinal cordin vivo. We have also identified a novel endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogenous during terminal differentiation. Together, this study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility clarifying dI lineage relationships.Summary statementPseudotime analyses of embryonic stem cell-derived dorsal spinal interneurons reveals both novel regulators and lineage relationships between different interneuron populations.
Exome capture of Antarctic krill (Euphausia superba) for cost effective population genetics of historical collections
Authors: White Oliver , Tarling Geraint , Hughes Lauren , Walkington Sarah , Clark Matt 
Published: July 2023

AbstractAntarctic Krill (Euphausia superba) is a pivotal keystone species in the Southern Ocean ecosystem, with immense ecological and commercial significance. However, its vulnerability to climate change necessitates urgent investigation of its population genetics and adaptive responses. Historical spirit collections of Antarctic krill from the early 20th century represent an ideal opportunity for genomic research, to investigate how krill have changed over time and been impacted by predation, fishing and climate change. In this study, we assessed the utility of shotgun sequencing and exome capture for genomic analyses with historical spirit collections of Antarctic krill. Because the krill genome is very large (48Gb) two full-length transcriptomes were generated and used to identify putative targets for targeted resequencing. Skim genome sequencing allowed sample and library quality control. By comparing genome to exome resequencing of the same libraries we calculate enrichment and variant calling metrics. Full-length mitochondrial and nuclear ribosomal sequences were successfully assembled from genomic data demonstrating that endogenous DNA sequences could be assembled from historical collections. We find that exome capture provided enrichment of on-target sequence data, with increased depth and higher variant quality for targeted loci. Our findings demonstrate the feasibility of extracting genomic information from historical krill samples, despite the challenges of fragmented DNA and huge genome size unlocking such collections to provide valuable insights into past and present krill diversity, resilience, and adaptability to climate change. This approach unlocks the potential for broader genomic studies in similar samples, and for enhancing conservation efforts and fisheries management in the Southern Ocean ecosystem.
Direct and culture-independent detection of low-abundantClostridioides difficilein environmental DNA via PCR
Authors: Schüler Miriam A. , Schneider Dominik , Poehlein Anja , Daniel Rolf 
Published: July 2023

AbstractClostridioides difficilerepresents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examinedC. difficilestrains originated from clinical specimen and were isolated under selective conditions emplyoing antibiotics. This suggests a significant bias among analysedC. difficilestrains, which impedes a holistic view on this pathogen. In order to support extensive isolation ofC. difficilestrains from environmental samples, we designed a detection PCR that targets thehpdBCAoperon and thereby identifies low abundances ofC. difficilein environmental samples. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific forC. difficileand successfully detectedC. difficiledespite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of thehpdBCAdetection PCR sequence for initial phylogenetic classification, which allows assessingC. difficilediversity in environmental samples via amplicon sequencing. Our findings furthermore showed thatC. difficilestrains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to detection PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias inC. difficileisolation and research.ImportanceClostridioides difficileis mainly responsible for hospital-acquired infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence focused on bacterial isolation from clinical specimen under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies however require an unbiased strain collection, which is accomplished by isolation ofC. difficilefrom diverse environmental samples and avoiding antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from ourC. difficile-specific detection PCR, which rapidly verifiesC. difficilepresence in environmental samples and further allows estimation of theC. difficilediversity by using NGS.
Does soil history decline in influencing the structure of bacterial communities ofBrassica napushost plants across different growth stages?
Authors: Blakney Andrew J.C. , St-Arnaud Marc , Hijri Mohamed 
Published: July 2023

AbstractSoil history has been shown to condition future plant-soil microbial communities up to a year after being established. However, previous experiments have also illustrated that mature, adult plants can “re-write”, or mask, different soil histories through host plant-soil microbial community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Therefore, in this experiment we tested the hypothesis that previously established soil histories will decrease in influencing the structure ofBrassica napusbacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B.napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere and roots ofB.napusat different growth stages— the initial seeding conditions, seedling, rosette, bolting, and flower— from all three soil history plots. We compared the taxonomic composition and diversity of bacterial communities, as estimated using 16S rRNA metabarcoding, to identify any changes associated with soil history and growth stages on the differentB. napussoil bacterial communities. We found that soil history remained significant across each growth stage in structuring the bulk soil and rhizosphere communities, but not the roots. This suggests that the host plant’s capacity to “re-write” different soil histories may be quite limited as key components that constitute the soil history’s identity remain present and continue to impact bacterial communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
Smart Leginon enables cryoEM screening automation across multiple grids
Authors: Sawh-Gopal Anjelique , Ishemgulova Aygul , Chua Eugene Y.D. , Aragon Mahira F. , Mendez Joshua H. , Eng Edward T. , Noble Alex J. 
Published: July 2023

AbstractSummaryCryoEM multi-grid screening is often a tedious process that demands hours of attention. Here, this protocol shows how to set up standardLeginoncollection andSmart Leginon Autoscreento automate this process. This protocol can be applied to the majority of cryoEM holey foil grids.Advancements in cryo-electron microscopy (cryoEM) techniques over the past decade have allowed structural biologists to routinely resolve macromolecular protein complexes to near-atomic resolution. The general workflow of the entire cryoEM pipeline involves iterating between sample preparation, cryoEM grid preparation, and sample/grid screening before moving on to high-resolution data collection. Iterating between sample/grid preparation and screening is typically a major bottleneck for researchers, as every iterative experiment must optimize for sample concentration, buffer conditions, grid material, grid hole size, ice thickness, and protein particle behavior in the ice, amongst other variables. Furthermore, once these variables are satisfactorily determined, grids prepared under identical conditions vary widely in whether they are ready for data collection, so additional screening sessions prior to selecting optimal grids for high-resolution data collection are recommended. This sample/grid preparation and screening process often consumes several dozen grids and days of operator time at the microscope. Furthermore, the screening process is limited to operator/microscope availability and microscope accessibility. Here, we demonstrate how to useLeginonandSmart Leginon Autoscreento automate the majority of cryoEM grid screening.Autoscreencombines machine learning, computer vision algorithms, and microscope-handling algorithms to remove the need for constant manual operator input.Autoscreencan autonomously load and image grids with multi-scale imaging using an automated specimen-exchange cassette system, resulting in unattended grid screening for an entire cassette. As a result, operator time for screening 12 grids may be reduced to ∼10 minutes withAutoscreencompared to ∼6 hours using previous methods which are hampered by their inability to account for high variability between grids. This protocol and video tutorial first introduces basicLeginonsetup and functionality, then demonstratesAutoscreenfunctionality step-by-step from the creation of a template session to the end of a 12 grid automated screening session.
Improving healthcare team harmony through collaborative team reflection and mindfulness
Authors: Kang Matthew JY , Aung Ar Kar , Gibbs Jo , Gibbs Harry 
Published: July 2023

AbstractHospital wards, staffed by the multidisciplinary team, are complex environments where teamwork, communication and psychological safety is essential for coordinated care delivery, yet are faced with challenges such as staffing changes and complex care needs. However, there is little literature on interventions to assist staff connect as a team. We evaluated a brief daily group based on team reflection and mindfulness aimed at a multidisciplinary general medicine team, using measures of team functioning (effectiveness, communication, and psychological safety).We found that participants reported significant improvement in the meeting’s effectiveness (U=184, p=0.013), team morale (U=123, p<0.001), and focus (U=183, p<0.001) after the program’s commencement. Furthermore, participants who attended the program for at least a week reported they felt more psychologically safe (U=116, p=0.032). We also found significant positive correlation between measures of team functioning and the number of sessions they attended the program (effectiveness of the interdisciplinary meeting r=0.509, p<0.001; team’s communication and functioning (r=0.509, p<0.001). The post-intervention focus group highlighted the program helped build relationships within the team, improve psychological safety, and subsequently shifted the team’s behaviour to be more supportive of the overall team. Our program improved the functioning of a multidisciplinary healthcare team, with the overall aim to deliver better patient care.
Community structure of known and previously unknown endobacteria associated with spores of arbuscular mycorrhizal fungi
Authors: Lastovetsky Olga A. , Caruso Tancredi , Brennan Fiona P. , Wall David , Pylni Susanna , Doyle Evelyn 
Published: July 2023

AbstractArbuscular mycorrhizal fungi (AMF) are ubiquitous plant root symbionts which can house two endobacteria:Ca.Moeniiplasma glomeromycotorum (CaMg) andCa. Glomeribacter gigasporarum (CaGg). However, little is known about their distribution and population structure in natural AMF populations and whether AMF can harbour other endobacteria. We isolated AMF from two environments and surveyed the surface-sterilized spores for endobacteria. We found thatCaMg andCaGg differed significantly in distribution wherebyCaMg were extremely abundant (80%) andCaGg were extremely rare (2%) in both environments. Unexpectedly, we discovered an additional and previously unknown level of bacterial diversity within AMF spores which extended beyond the known endosymbionts, with as many as 277 other bacterial taxa detected in individual spores. Detailed analysis of endobacterial communities inside AMF spores revealed that: (i)CaGg were not limited in distribution to theGigasporaceafamily of AMF, as previously thought, (ii)CaMg community structure was driven by AMF host genotype, (iii) a significant inverse correlation existed between the diversity ofCaMg and diversity of all other endobacteria. The latter suggests the existence of competition dynamics between different bacterial populations inside AMF spores and provides a basis for generation of testable hypotheses regarding the function ofCaMg in AMF biology.
CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data
Authors: Phung Toan K. , Berndsen Kerryn , Phan Tran Le Cong Huyen Bao , Muqit Miratul M. K. , Alessi Dario R. , Nirujogi Raja S. 
Published: July 2023

AbstractTo facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data we created tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info). These enable the non-MS expert to interactively peruse volcano plots; deconvolute primary experimental data to individual replicates that can be visualized in bar charts or violin plots allowing statistical analysis; and export of plots in SVG format. They also permit assessment of experimental quality by correlation matrix and profile plot. Within CURTAIN, the user can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression, disease and pharmaceutical links, and mutagenesis information on all selected hits. Moreover, CURTAIN-PTM permits the comparison of all identified PTM sites on protein(s) of interest with PTM information contained within selected databases. For phosphorylation site analysis CURTAIN-PTM links with the kinase library to predict upstream kinases that phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson’s LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing new data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open-source and will enable researchers to share and maximize the analysis and impact of their proteomics data. We advocate that differential expression proteomic data should be published containing a shareable CURTAIN web-link, allowing readers to better explore their data.Significance StatementTo enable non-experts to better share and explore mass spectrometry data, we have generated using open-source software, interactive tools termed CURTAIN and CURTAIN-PTM. These tools enable users’ to save their analysis sessions with a sharable unique web-link, enabling other researchers to visualize and further analyze these datasets. These links can also be reported in publications allowing readers to further survey the reported data. We discuss benefits for the research community of publishing proteomic data containing a shareable web-link.
Lariat debranching by RNA DEBRANCHING ENZYME 1 depends on SICKLE inArabidopsis thaliana
Authors: Kovak Emma E. , Marshall Carine M. , Molinari Mayla D. C. , Nepomuceno Alexandre L. , Harmon Frank G. 
Published: July 2023

ABSTRACTSpliceosome mediated intron removal from precursor mRNAs (pre-mRNAs) generates circular RNAs called intron lariats. RNA DEBRANCHING ENZYME 1 (DBR1) ribonucleases linearize, or debranch, intron lariats to allow their degradation.DBR1genes occur across eukaryotes and are essential in animals and plants. High levels of intron lariats in the weakArabidopsis thaliana dbr1-2allele inhibits primary microRNA (pri-miRNA) processing, disrupting miRNA production and miRNA-regulated growth and development. Arabidopsissickle(sic) mutants alter pri-miRNA processing and pre-mRNA splicing. This study demonstratessicmutants accumulate intron lariats matching those in weakdbralleles. The strongsic-1and weakdbr1-3alleles together cause synthetic lethality, while weaksic-3withdbr1-3has intron lariat accumulation likesic-3. Further,sic-3,dbr1-3, andsic-3 dbr1-3similarly alter circadian rhythms and growth of roots and rosettes. The conserved MPLKIP amino acid motif in SIC mediates physical interaction with DBR1in vitroand is required for intron lariat debranchingin vivo. Thus, MPLKIP containing proteins, like SIC and human TTDN1, act with cognate DBR1 proteins to maintain RNA homeostasis critical for growth and development.