bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic exploration of trimethylamine N-oxide metabolism in human gut bacteria
Authors: Dawson Samuel , Hoyles Lesley 
Published: May 2022

Trimethylamine N-oxide (TMAO) is a microbial metabolite that has been shown to have protective effects on the blood–brain barrier, while elevated serum levels of TMAO and its precursors have been linked to cardiometabolic diseases in Western populations. Previous work examined the prevalence of TorA to determine which groups of bacteria were responsible for the metabolism of TMAO in the human gut. This study examined 6 TMAO metabolism pathways to provide a more in-depth analysis of bacterial TMAO metabolism. These results were then filtered for hits with >90% coverage and >70% identity.
Results showed that Tor proteins were largely limited to members of the Enterobacteriaceae, mostly appearing in Escherichia coli and Citrobacter spp. >1% of 9898 Klebsiella spp. genomes examined encode any Tor proteins, despite previous work highlighting Klebsiella spp. as one of the prevalent genera encoding TorA. Dms proteins were much more prevalent than TorA in other genera of bacteria, along with MsrP and BisC. 118 of the HGRGs were found to encode for at least 1 TMAO metabolism protein.
Overall, this work highlights the need for more comprehensive methods to be used to examine large genomic and metagenomic datasets and the need for in vitro work to be done alongside in silico analyses to improve functional annotations and our understanding of the roles of gut bacteria.
Transcriptional profiles of Streptococcus pneumoniae associated with adaptation to the nasopharynx environment
Authors: Barton Thomas E , Green Angharad E , Neill Daniel R 
Published: May 2022

Streptococcus pneumoniae is a major cause of global morbidity and mortality. It behaves as a commensal in the host nasopharynx, but can become pathogenic, invading the lungs, blood, and meninges. As such, identification of pneumococcal virulence and colonisation factors remains a major research objective. We previously described an experimental evolution approach for the identification of pneumococcal genes that make niche-specific contributions to fitness and virulence. Sequential passage of pneumococci through mouse models of nasopharyngeal-carriage and pneumonia was performed, generating bacterial lineages adapted to the nasopharynx and lungs, respectively.
Using RNA-Seq differential gene expression analysis, this study compared the transcriptomic profile of a nasopharynx-evolved pneumococcal lineage that showed evidence of enhanced nasopharyngeal colonisation potential, with a lab-adapted ancestor strain. Here, we describe how the genomic adaptations acquired by this lineage, and which we have demonstrated facilitate survival in the nasopharynx, can influence bacterial gene expression.
One key finding was the identification of five adjacent upregulated genes, representing a putative pneumococcal operon. These poorly characterised genes are predicted to encode a carbohydrate-scavenging pathway. Expression of the operon within the nasopharynx may facilitate sugar acquisition from host glycoproteins. Of note, the nasopharynx evolved pneumococcal lineage carries a single nucleotide insertion mutation immediately adjacent to the -10 element of the operon predicted promotor sequence. This may contribute to increased operon gene expression in the nasopharynx-adapted pneumococcus, thereby enhancing colonisation potential. Confirmatory mechanistic investigations are underway, which will aid the identification of pneumococcal virulence factors involved in the commensal to pathogen switch.
Immunoproteomic analysis of surface proteins in bovine-adapted lineages of Staphylococcus aureus
Authors: Drumm Shauna D , Cormican Paul , Owens Rebecca , Mitchell Jennifer , Keane Orla M. 
Published: May 2022

In Ireland, Staphylococcus aureus is the most frequent cause of bovine intramammary infection (IMI) with the bovine-adapted lineages CC151 and CC97 most commonly found. While bovine mastitis vaccines are available that target S. aureus, this pathogen is still a significant source of infection in dairy cows. Therefore, there’s a clear need for a more effective vaccine against S. aureus. However, S. aureus is considered a clonal organism, therefore identifying new potential protein targets common to all major lineages is an important step for vaccine design.
Two S. aureus strains, one belonging to ST151 and another to ST3170 (CC97), were used to infect two groups of dairy cows. Antibodies raised by individual cows were used to identify immunodominantsurface proteins for each strain. One-dimensional serum blotting determined that the antibody response to S. aureus infection was largely strain specific, and to a lesser extent, animal specific.
Two-dimensional serum blotting followed by mass spectrometry of immunoreactive spots was used to identify potential vaccine candidates that were immunodominant for both strains. These blots showed that proteins to which an antibody response was generated in the ST151 infected cows were generally different to those generated in the ST3170 infected cows. However, mass spectrometry also identified immunoreactive proteins common to both strains including Clumping factor B and Iron-regulated surface determinant protein A. Common immunoreactive secreted proteins are also currently being identified.
This study will identify immunodominant proteins expressed by the bovine-adapted strains ST3170 and ST151 that could potentially be used as candidates in vaccine research.
Non-typeable Haemophilus influenzae biofilm formation on primary human airway epithelia cultured at air-liquid interface
Authors: Horton Katie L , Coles Janice L , Hueppe Jana F , Cleary David W , Jackson Claire L , Lucas Jane S , Allan Raymond N 
Published: May 2022

Introduction
Primary ciliary dyskinesia (PCD) is an inherited heterogeneous disorder associated with defective motile cilia on airway epithelia, resulting in impaired mucociliary function and ultimately, bronchiectasis. Non-typeable Haemophilus influenzae (NTHi) is frequently isolated from PCD airways where it resides in biofilms. It is unclear if biological pathways in response to NTHi infection differ in PCD, contributing to increased susceptibility to biofilm-associated infection.

Aim
The development of a biologically representative co-culture model to investigate the interactions between PCD airway epithelia and NTHi biofilms.

Methods
Air-liquid interface (ALI)-cultured non-PCD primary nasal cells were grown in transwells. Barrier properties were assessed by trans-epithelial electrical resistance (TEER), FITC-dextran passage and tight junction staining. Ciliary function was assessed by high-speed video microscopy at 37°C. ALI cultures were infected with a PCD NTHi isolate at multiplicity of infections (MOIs) 10, 50 or 100 and co-cultured to form biofilms over 3 days. TEER was measured pre- and post-infection, NTHi recoverability assessed by conventional culture, and biofilm formation confirmed by scanning electron microscopy (SEM).

Results
Epithelial culture at ALI was successful, with tight barriers being formed and normal ciliary beat pattern and frequency recorded (mean 14Hz). Following co-culture, TEER increased relative to pre-infection at all MOIs but maximum NTHi recoverability was at MOI 50 (median colony forming units, 6.8x106per cm2). SEM confirmed NTHi biofilm formation at MOI 50.

Conclusions
A successful NTHi biofilm co-culture model on human primary epithelia was established. This will be used with PCD epithelia to investigate host-pathogen interactions during NTHi biofilm colonisation.
Amoeba & Biofilms in UK Chlorinated Drinking Water Distributions Systems: Impact on Water Safety
Authors: Olmo Gonzalo Del , Puzon Geoffrey J. , Preciado Carolina Calero , Douterelo Isabel 
Published: May 2022

Amoeba-related diseases have been related with the presence of certain amoebas in domestic water, including drinking water. Biofilms in drinking water distribution systems are able to support amoeba growth by providing a food source and protecting them against disinfectants. Additionally, amoeba growth can be favoured by warm temperatures and climate change appears to contribute to its geographic spread.
The presence of amoeba and its association with potential pathogenic bacteria was studied in a real-scale chlorinated DWDS. The test facility comprised three independent pipe loops fed with water from the local water supply and for this study a varied flow hydraulic profile was applied based on daily patterns observed in real UK distribution networks. The daily regime was repeated for a biofilm growth phase of 30 days. Amoeba viability was tested by a culture-based method, non-nutrient agar (NNA)-E. coli plates, and then confirm by qPCR using specific primers to detect species of amoeba including Naegleria and Acanthamoeba. Amplicon sequencing of the 16s rRNA gene was used to characterise the biofilm and planktonic bacterial communities.
Several amoeba species belonging to the genera Acanthamoeba, Vermamoeba and Naegleria were identified in 30-day old biofilm samples. While the bacterial communities in biofilms were dominated by Variovorax, Pseudomonas and Aquabacterium. This study yielded new insights on the dynamics of amoeba and bacterial communities in DWDS. However, more research is required to accurately establish the impact of these inter-kingdom associations on human health.
How to sequence 10,000 bacterial genomes and retain your sanity: an accessible, efficient and global approach
Authors: Perez-Sepulveda Blanca , Heavens Darren , Pulford Caisey , Predeus Alexander , Low Ross , Webster Hermione , Dykes Gregory , Schudoma Christian , Rowe Will , Lipscombe James , Watkins Chris , Kumwenda Benjamin , Shearer Neil , Costigan Karl , Baker Kate , Feasey Nicholas , Hinton Jay , Hall Neil ,   The 10KSG Consortium
Published: May 2022

Non-typhoidal Salmonella(NTS)are typically associated with enterocolitis and linked to the industrialisation of food production. In recent years, NTS has been associated with invasive disease (iNTS disease) causing an estimated 77,000 deaths each year worldwide; 80% of mortality occurs in sub-Saharan Africa. New clades of S. Typhimurium and S. Enteritidis have been identified, which are characterised by genomic degradation, altered prophage repertoires and novel multidrug resistant plasmids. To understand how these clades are contributing to the burden and severity of iNTS disease, it is crucial to expand genome-based surveillance to cover more countries, and incorporate historical isolates to generate an evolutionary timeline of the development of iNTS.
We developedand validateda robust and inexpensive method for large-scale collection and sequencing of bacterial genomes. The “10,000 Salmonella genomes” project established a worldwide research collaboration to generate information relevant to the epidemiology, drug resistance and virulence factors of Salmonellae using a whole-genome sequencing approach. By streamlining collection of isolates and developing an efficient logistics pipeline, we gathered 10,419 clinical and environmental isolates from collections in low and middle-income countries within six months. Genome sequences are now available for isolates from 51 countries/territories dating from 1949 to 2017, with ~80 % representing African and Latin-American datasets. Our method can be applied to other large sample collections that require maximisation of resources within a limited timeframe. Detailed genome analyses are in progress and it is hoped that the resulting data will contribute to public health control strategies in low and middle-income countries.
Piperacillin/tazobactam resistance in a clinical isolate of Escherichia colidue to IS26-mediated amplification of blaTEM-1B
Authors: Hubbard Alasdair , Mason Jenifer , Roberts Paul , Parry Christopher , Corless Caroline , Aartsen John van , Howard Alex , Bulgasim Issra , Fraser Alice , Adams Emily , Roberts Adam , Edwards Thomas 
Published: May 2022

We identified a clinical isolate of Escherichia coli displaying an unusual, emerging phenotype; piperacillin/tazobactam (TZP)-resistant, 3rd generation cephalosporin-susceptible. Prior to treatment with TZP, a TZP-susceptible E. coli isolate was isolated from the same patient. Hyperproduction of a class A β-lactamase has previously been linked to this phenotype, but the mechanism of hyperproduction in isolates lacking promoter region mutations is not well understood.
Clonality of the two isolates was initially assessed with RFLP, and β-lactamase activity was determined using a nitrocefin assay. Both isolates were sequenced on Illumina and Oxford Nanopore Technology platforms and fitness assessed competitively. A plasmid construct containing the insertion sequence IS26was used to capture a translocatable unit (TU) in vitro.
The two E. coli clinical isolates were confirmed to be clonal, with the TZP-resistant isolate hyperproducing blaTEM-1. However, no promoter region mutations were identified in the TZP-resistant isolate. Hybrid assembly revealed that an ~11kb segment of DNA was excised from a IS26 flanked pseudo-compound transposon in the TZP-resistant isolate, forming a circular TU containing blaTEM-1. Multiple re-insertion events of the TU, mediated by IS26, led to tandem repeats of the TU within the chromosome, increasing the copy number of blaTEM-1. Excision and insertion events were confirmed via capture of the TU. Amplification of the TU in the TZP-resistant isolate incurred no significant change in fitness in different environmental conditions.
This study improves the understanding of the TZP-resistant, 3rd generation cephalosporin-susceptible phenotype in E. coli and antimicrobial resistance prediction of this phenotype from genotypic data.
Use of Equine Herpesvirus 1 glycoprotein pseudotyped lentiviral particles for the development of serological tests and assessment of lyophilisation for transport and storage
Authors: Genova Cecilia Di , Sutton Gabrielle , Paillot Romain , Temperton Nigel , Pronost Stéphane , Scott Simon D 
Published: May 2022

Equine herpesviruses (EHVs) are enveloped DNA viruses predominantly infecting members of the Equidae family. EHVs primarily cause respiratory disease, however EHV-1 can produce cases of a neurological disease, abortion and neonatal death. Thus, these viruses represent a welfare issue for the equine industry and scientific focus for researchers. EHV-1 exhibits a complex array of 12 glycoproteins on its surface envelope, but it is unclear precisely which are important for virus cell entry and the role of each in host immune response. In order to investigate the contribution of these glycoproteins, pseudotype viruses (PVs) could provide a useful study tool. We have successfully generated functional EHV-1 pseudotyped lentiviruses bearing four glycoproteins, gB, gD, gH and gL (sequences derived from an aborted foetus during a large EHV1 outbreak strain in Normandy, France). PVs were employed in a pseudotype virus neutralisation test (PVNT) to measure levels of specific neutralising antibodies serum samples (n=52) taken longitudinally from experimentally infected ponies, compared with uninfected controls.
PVs routinely require -80oC for long term storage and a dry ice cold-chain during transport which can impede dissemination and utilisation in other laboratories. Consequently, we further investigated whether freeze-drying (lyophilisation) of EHV-1 PV could address this issue. PVs were lyophilised and pellets either reconstituted immediately or stored under various temperature conditions, sampling at different timepoints. The recovery and functionality of these lyophilised PVs was compared with standard frozen aliquots in titration and neutralisation tests.
Embedding 21st century employability into assessment and feedback practice through a student-staff partnership
Authors: Veitch Nicola , Mcgregor Anna , Stubbs Fiona , Broom Miranda , Zainudden Dzachary 
Published: May 2022

Although commonly thought to be only a measure of academic performance, assessments can also provide students with an opportunity to apply skills and knowledge acquired at university into written literacies that prepare them for the transition into prospective careers. Within a Level 2 Microbiology and Immunology course, students struggled to engage with standalone timetabled careers-related sessions, yet they showed enthusiasm when employability was embedded into assessments. A staff-student partnership project explored these issues, with the overall aim of understanding how to effectively embed employability skills into assessment and feedback, which supports the theme of supporting students to position themselves for the future.
Through student-run focus groups, this project investigated the reasons for low student engagement with the timetabled employability session and used student views to develop digital initiatives that could be applied to assessment and feedback practice with an emphasis on developing 21st-century competencies. These initiatives were then implemented as pre-session self-directed activities, which helped students link course feedback with employment skills and future career planning, followed by a newly developed in-class reflective feedback session that allowed students time to consider what skills they have developed and make links with future careers. Project evaluation was conducted using a quantitative survey of students involved.
This project aims to make feedback more meaningful and better valued by students. The approaches were designed in partnership with former students from the course, this project possesses the unique ability to deliver a genuine student voice both on employability concerns and the role of assessment.
The effect of GLP-1RA exenatide on Idiopathic Intracranial Hypertension: Randomised Clinical Trial
Authors: Mitchell James L. , Lyons Hannah S. , Walker Jessica K. , Yiangou Andreas , Grech Olivia , Alimajstorovic Zerin , Greig Nigel H. , Li Yazhou , Tsermoulas Georgios , Brock Kristian , Mollan Susan P. , Sinclair Alexandra J. 
Published: May 2022

AbstractTherapeutics to reduce intracranial pressure are an unmet need. Pre-clinical data has demonstrated a novel strategy to lower intracranial pressure using glucagon-like peptide-1 receptor signaling.Here, we translate these findings into patients by conducting a randomized, placebo controlled, double-blind trial to assess the effect of exenatide, a glucagon-like peptide-1 receptor agonist, on intracranial pressure in idiopathic intracranial hypertension. Telemetric intracranial pressure catheters enabled long-term intracranial pressure monitoring. The trial enrolled adult women with active idiopathic intracranial hypertension (intracranial pressure >25 cmCSF and papilloedema) who receive subcutaneous exenatide or placebo. The three primary outcome measures were intracranial pressure at 2.5 hours, 24 hours and 12 weeks and alpha set a priori at less than 0.1.Among the 16 women recruited, 15 completed the study (mean age 28 ± 9, body mass index 38.1 ± 6.2 kg/m2, intracranial pressure 30.6 ± 5.1 cmCSF). Exenatide significantly and meaningfully lowered intracranial pressure at 2.5 hours -5.7 ± 2.9 cmCSF (p=0.048); 24 hours of -6.4 ± 2.9 cmCSF (p=0.030); and 12 weeks -5.6 ± 3.0 cmCSF (p=0.058). No serious safety signals were noted.This data provides confidence to proceed to a phase 3 trial in idiopathic intracranial hypertension and highlights the potential to utilise glucagon-like peptide-1 receptor agonist in other conditions characterised by raised intracranial pressure.
Men’s preconception health and the social determinants of health: What are we missing?
Authors: Anakwe Adaobi , Xian Hong , BeLue Rhonda , Xaverius Pamela 
Published: May 2022

ABSTRACTBackgroundLife course perspectives suggest that optimizing men’s health before conception is requisite to equitably improve population health, an area of increasing public health focus. Although scholarship on the social determinants of health (SDOH) suggests that men’s health and health behaviors do not occur in a vacuum, preconception health studies have not explicitly examined how these factors influence men’s preconception health.ObjectiveTo identify latent classes of men’s preconception health and the role of the SDOHs in predicting class membership.MethodsPooled data from the 2011-2019 male file of the National Survey of Family Growth were analyzed (n= 10,223). Latent class analysis was used to identify distinct classes of men’s preconception health. Eight manifest variables were used to fit latent class models. A classify-analyze approach was subsequently used to create a preconception health phenotype (PhP) outcome variable. SDOHs (exposure variable) were assessed in four domains (residential context, health access, socioeconomic status, and sociocultural context) to predict class membership. Survey weighted multinomial regression models were fitted to examine the association between the exposure and the outcome.ResultsThree unique PhPs were identified (lowest risk (69%), substance users (22.9%), and sexual risk-takers (8.1%) (SRT)) from the LCA model. Health access, socioeconomic status, and sociocultural contexts were significant predictors of class membership but not residential context. Sexual risk takers were more likely to be uninsured (aOR: 1.25, 95% CI 1.02, 1.52), college-educated (aOR: 1.94 95% CI: 1.34, 2.79), and non-Hispanic Black (aOR: 1.99 95% CI: 1.55, 2.54) while substance users were more likely to have unstable employment (aOR: 1.23 95% CI:1.04, 1.45) and have a high school degree or higher (aOR 1.48 95% CI: 1.15, 1.90) than men in the lowest risk category.ConclusionFindings suggest that social determinants may impact men’s preconception health in ways that are not conventionally understood and raises important questions about how preconception health interventions should be created, tailored, and/or retooled. Specifically, studies that examine the sociocultural and political contexts underpinning the relationship between social class, masculinity, and men’s preconception health are needed to provide nuanced insights on factors that shape these outcomes.
SMAD4 suppresses colitis-associated carcinoma through inhibition of CCL20/CCR6-mediated inflammation
Authors: Hanna David N. , Smith Paula Marincola , Novitskiy Sergey V. , Washington M. Kay , Zi Jinghuan , Weaver Connie J. , Hamaamen Jalal A. , Lewis Keeli B. , Zhu Jing , Yang Jing , Liu Qi , Beauchamp R. Daniel , Means Anna L. 
Published: May 2022

AbstractBackground & AimsChronic inflammation in the colon is a predisposing factor for colon cancer. We previously reported that colon epithelial cell silencing of Smad4, the central downstream mediator of TGFβ family signaling, increased epithelial expression of inflammatory genes, including the chemokine CCL20, and increased susceptibility to colitis-associated cancer. Here, we examine the role of the chemokine/receptor pair CCL20/CCR6 in mediating colitis-associated colon carcinogenesis induced by SMAD4 loss.MethodsMice with conditional, epithelial-specific Smad4 loss with and without germline deletion of the Ccr6 gene were subjected to three rounds of dextran sodium sulfate and followed for up to 3 months. Tumors were quantified histologically, and immune cell populations were analyzed by flow cytometry and immunostaining.ResultsIn humans, SMAD4 expression inversely correlated with CCL20 expression. Smad4 loss in mouse colon epithelium led to enlarged gut-associated lymphoid tissues and recruitment of specific immune cell subsets to the mouse colon epithelium and underlying stroma, particularly Treg, Th17, and dendritic cells. Loss of CCR6 abrogated these immune responses and significantly reduced the incidence of colitis-associated tumors observed with loss of SMAD4 alone.ConclusionsRegulation of mucosal inflammation is a critical role of SMAD4 signaling within the colon epithelium and central to its tumor suppressor function in the colon. A key downstream node in this regulation is suppression of CCL20 signaling by the epithelium to CCR6 in immune cells. Loss of SMAD4 in the colon epithelium increases CCL20 expression and chemoattraction of CCR6+ immune cells, contributing to greater susceptibility to colon cancer.