bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histopathological analysis of placental lesions caused by Chlamydia abortus 1B vaccine strain in vaccinated ewes
Authors: Caspe Sergio Gastón , Livingstone Morag , Wattegedera Sean , Aitchison Kevin , Underwood Clare , Milne Elspeth , Sargison Neil , Chianini Francesca , Palarea-Albaladejo Javier , Longbottom David 
Published: May 2022

Background
Chlamydia abortus is one of the most diagnosed causes of infectious abortion in small ruminants. Infections can be controlled using the live, attenuated C. abortus strain 1B vaccine, which has been associated with infection and abortion in animals. This study aimed to compare the severity and the distribution of lesions caused by this vaccine strain (vt) with those resulting from a wild-type (wt) infection.

Methods
Two grossly affected and 1B-positive (by qPCR and RFLP analysis) placentas from a vaccinated sheep flock were analysed. Histopathological lesions and immunohistochemical labelling (IHC) were graded (increasing score from 0 to 5) according to their severity and distribution. Pathology in the vt infected placentas was compared with that in two wt infected placentas. Datasets generated for observed histological and pathological features were analysed using principal component analysis (PCA).

Results
Histopathologically, the lesions in both vt and wt-placentas presented as typical multifocal necrosuppurative placentitis, associated with vasculitis, mural necrosis, and thrombosis. IHC for C. abortus revealed intense staining with a multifocal distribution in most cotyledons in both vt and wt placentas. Comparison of the pathological lesions between vt and wt by PCA revealed a similar distribution and severity, revealing a strong association with features such as necrosis and inflammatory infiltration between vt and wt placentas. A weaker association with IHC was observed.

Conclusion
This study shows that the C. abortus attenuated 1B vaccine strain presents no significant differences in severity and distribution of pathological lesions from those typically observed following a wt infection.
Defining the pknH Transcriptional Network in the Animal Tuberculosis bacillus, Mycobacterium bovis
Authors: Kerins Anne , Farrell Damien , Gordon Stephen V. 
Published: May 2022

The Mycobacterium tuberculosiscomplex (MTBC) is a group of bacteria that show more than 99% genetic identity, yet they diverge in their host preference and the severity of associated disease. Mycobacterium bovis causes the disease in cattle and poses an economic challenge, with the cost of Irelands TB Eradication Scheme predicted to exceed €90 million in 2020.
The aim was to focus on the RD900 and pknH gene network in MTBC members. ThepknH gene encodes a transmembrane serine threonine protein kinase, that plays a role in the regulation of signalling pathways in the mycobacterial cell and has been linked to virulence. The RD900 or “region of difference 900” contains the tbD2 and pknH2 genes. The part of the genome that contains this region varies substantially across MTBC members.
The results of RNA-seq analysis showed that there are statistically significant levels of differential gene expression in wildtype and knock-in M. bovis strains.
The RD900 analysis across the MTBC showed that there is variation in this important genomic region. Analysis carried out by Mata et al. 2020, showed that this RD900 region had been independently lost in different MTBC lineages and strains. M. bovis has retained the RD900 region and this is believed to be linked to its increased virulence.
The majority of the M . africanum strains were found to possess the standard pknH, tbD2, pknH2, embR gene arrangement as is found in M. africanum GM041182, the strain that is typically used as a reference.
Based on work of Mata et al., 2020.
Assessing the interspecies relationship betweenPseudomonas aeruginosa and Staphylococcus aureus in mixed biofilms grown in alginate beads and collagen scaffolds
Authors: Khalid Ammara , Beeton Michael , Maddocks Sarah 
Published: May 2022

Polymicrobial biofilms in chronic infected wounds harbour different bacterial species that interact with each other, competing or co-operating to survive. The two most common pathogens co-isolated from chronic wound biofilms are Pseudomonas aeruginosa and Staphylococcus aureus. Evidence from in vitrobiofilms models have shown these two bacteria interactand data suggests that P. aeruginosa inhibits the growth of S. aureusin mixed biofilms. This study aimed to assess the growth of these two species in a complex polymicrobial biofilm in a 3D matrix comprised of either alginate (1.5% w/v) or a collagen scaffold.
Using a five-species biofilm (S. aureus, P. aeruginosa, Citrobacter freundii, Enterococcus faecalisand Escherichia coli), with all bacteria inoculated at time zero, it was consistently observed that P. aeruginosa was not recoverable over a 72h period, with sampling every 24h. However, P. aeruginosagrew well if it was added to a pre-formed four-species biofilm. Further, P. aeruginosa was seen to inhibit the growth of S. aureus after 24h subsequent co-culture in the pre-formed biofilm, which resulted in the emergence of small colony variants of S. aureus. Interestingly when P. aeruginosawas co-inoculated in a four species biofilm that did not contain S. aureus,its growth was not inhibited, suggesting a competitive interaction between these two bacteria during establishment of the early biofilm. These data were consistent in alginate beads and collagen scaffolds. In a chronic wound P. aeruginosais regarded as a late coloniser and the phenomena observed in this study might be reflective of this.
Functional responses of neutrophils to Fusobacterium nucleatum subspecies
Authors: Muchova Maria , Kuehne Sarah A. , Grant Melissa , Chapple Iain , Hirschfeld Josefine 
Published: May 2022

Introduction
Fusobacterium nucleatum is an opportunistic oral pathogen with five subspecies: animalis, fusiforme, nucleatum, polymorphumandvincentii. These play an important role in biofilms associated with chronic gum disease (periodontitis). Neutrophils form the first line of defence against these and other oral pathogens, employing a multitude of anti-microbial strategies, which, alongside bacterial killing, also cause collateral host-tissue damage. The immunogenic properties of F. nucleatum subspecies are poorly understood. The purpose of this study was to investigate specific neutrophil responses to all F. nucleatum subspecies.

Methods
AllF. nucleatumsubspecieswere grown planktonically overnight and inactivated using 10% neutral buffered formalin. Peripheral blood neutrophils (PBN) and neutrophil-like cells (differentiated from HL-60 cells) were challenged with inactivated bacteria (MOI 100) and production of reactive oxygen species (ROS) was quantified by Luminol/Iso-luminol enhanced chemiluminescence assays. Release of neutrophil extracellular traps (NETs) was quantified fluorescently using Sytox-green. Additionally, phagocytosis of fluorescently labelled F. nucleatum subspecies was analysed in both cell groups by flow cytometry.

Results
In addition to differences in ROS generation by PBN and neutrophil-like cells in response to individual F. nucleatum subspecies, variations in the amount of extracellular DNA extruded during NETosis was evident. Moreover, distinct levels of phagocytic activity of both cell types will be shown.

Conclusion
F. nucleatum pathogenicity has been reported in oral as well as systemic diseases (colorectal cancer, cardiovascular disease). Understanding subspecies-specific effects of F. nucleatum on neutrophils will enhance our knowledge of the interactions between this bacterium and the host immune response and may help to identify new therapeutic targets.
Understanding the bug that make our drugs: Cellular responses to therapeutic protein secretion in E. coli
Authors: Seleiro Alice , Evans Caroline , Green Jeff , Lennon Chris , Stafford Graham 
Published: May 2022

Production of therapeutic proteins is a $200 billion industry with E. coli being one of the main expression systems used and proteins often being secreted to the periplasm to produce disulphide bonds. However, little is known about how E. coliresponds to secretion of these therapeutic proteins into the periplasm under industrial conditions.
Proteomics and transcriptomics were conducted on cultures grown at high cell density in industrial production conditions to look at the effect of secreting a model therapeutic protein (scFv) to the periplasm compared to expressing the same protein in the cytoplasm.
82 proteins and 1653 transcripts were differentially expressed when overexpressing the scFv in different cellular compartments. ScFv secretion had a significant effect on expression of genes involved in the envelope stress response. However, while certain envelope stress pathways where upregulated upon secretion others were downregulated (including expression of some periplasmic chaperones). Scfv secretion also led to an increase in expression of genes involved in degradation of membrane proteins and the SEC secretion system, as well as iron transport, Outer membrane porins and flagella operons.
In future and current experiments, we are testing whether knocking out and overexpressing a selection of these genes improves secretion and folding of scFvs and other recombinant proteins.
Characterisation of the Rh50 protein from the ammonia-oxidising bacterium Nitrosomonas europaea
Authors: Bizior Adriana , Williamson Gordon , Mirandela Gaëtan Dias , Boeckstaens Mélanie , Hoskisson Paul , Marini Anna Maria , Zachariae Ulrich , Javelle Arnaud 
Published: May 2022

The transport of ammonium through the cell membranes, an essential process in all kingdoms of life, is accomplished by the ubiquitous Amt/Mep/Rh superfamily of proteins. The functional context of Amt/Mep and Rh transporters is diverse: bacteria, fungi, and plants use Amt/Mep proteins to scavenge ammonium for biosynthetic assimilation, whereas mammals use the Rh proteins for ammonium detoxification in erythrocytes, kidney, and liver tissues. While RH50 genes are widespread in eukaryotes they are present in some prokaryotes: an example is a chemolithoautotroph Nitrosomonas europaeawhich gains all its energy from the oxidation of ammonia to nitrate.
While Amt/Mep/Rh proteins have divergent physiological functions, they are structurally very similar, which raises the important question about the universality of the transport mechanism. We have recently proposed an elegant new model for the mechanism of electrogenic ammonium transport in bacteria Amt protein: after deprotonation of NH4+ at the periplasmic side of the transporter, a previously undiscovered polar conduction route enables H+ transfer into the cytoplasm. A parallel pathway, lined by hydrophobic groups within the protein core, facilitates the simultaneous transfer of uncharged NH3. In this context, we propose to elucidate at the molecular level the mechanism of ammonium translocation through rhesus protein from Nitrosomonas europaeaand establish whether there is a universal mechanism for biological ammonium transport. Beyond the elucidation of a central biological process, this work has important medical implications, as some Rh mutations have been associated with human pathologies. We propose to demonstrate how specific Rh mutations affect the activity of the protein to establish the relationship between Rh malfunction and the associated diseases.
Uncovering the residues responsible for Dis3L2 specificity
Authors: Costa Susana M. , Matos Rute G. , Viegas Sandra C. , Arraiano Cecília M. 
Published: May 2022

Exoribonucleases from the RNB-family of enzymes are widely distributed in nature. DIS3 is the eukaryotic homolog of the bacterial exoribonuclease II and is the only catalytic subunit of the core exosome complex. In humans, there are three members of DIS3 family that can be distinguished according to the sequence conservation of the active site:
DIS3, DIS3L (DIS3L1) and DIS3L2. Unlike its family counterparts, DIS3L2 does not interact with the exosome since it lacks the PIN domain, which is essential for the interaction with this multiprotein complex. Dis3L2 is involved in several cellular mechanisms, such as apoptosis, cellular differentiation and proliferation and its mutations have been associated with Wilms tumor formation and Perlman syndrome in children. Distinct studies on Dis3L2 enzyme unraveled a novel eukaryotic RNA decay pathway that challenged the models already established. Dis3L2 activity is stimulated by the addition of untemplated uridine residues to mRNAs, tRNAs, microRNAs, snRNAs among other classes of RNA.
The first insight on the uridylation involvement in controlling the stability of poly(A)-containing mRNAs was reported in S. pombe. However, the precise mechanism of action of this enzyme is not yet fully understood. In this work, the activity of fission yeast Dis3L2 mutant proteins was analyzed over different RNA substrates. The aim was to characterize the amino acid residues that distinguish Dis3L2 substrate specificities regarding its family homologues, namely the preference for uracil residues. The results show that some of the mutant Dis3L2 ribonucleases lose or acquire activity regarding the degradation of different RNAs. Furthermore, this will enable us to understand the mechanism of action of Dis3L2 and its function in different eukaryotic cells.
How do bacteria change their coats? Structural analysis of acyltransferases involved in O-antigen modification
Authors: Tindall Sarah , Woude Marjan van der , Thomas Gavin 
Published: May 2022

Acyltransferase-3 (AT3) domain-containing proteins are involved in acylation of a diverse range of carbohydrates across all domains of life. In bacteria they are essential in processes including symbiosis, antimicrobial resistance, and antibiotic biosynthesis. Despite this, the mechanism of action is largely unknown. AT3 proteins fromSalmonellaspp. are responsible for acetylation of lipopolysaccharides which can generate a specific immune response upon infection. Here we analysed two AT3 proteins fromSalmonellaspp., some differences exist but both contain an integral membrane AT3 domain fused to a periplasmic SGNH domain. Identification of essential residues from each domain suggests both domains are required for acylation.
The crystal structure of the SGNH domain and periplasmic linking region was determined. Novel structural features are seen in comparison to other SGNH domains. In particular, the periplasmic linking region is structured and forms an extension of the SGNH domain (SGNH-extension). Removal of the SGNH-extension suggests that this region is important for stability of the SGNH domain. The structure of the SGNH-extension suggests the SGNH domain is in close proximity to the acyltransferase domain and the domains may interact. In silicoco-evolution analysis, used to make predictions about the structure of both domains, suggests likely inter-domain interactions. This analysis also predicted which transmembrane helices in the acyltransferase domain interact giving an insight into the overall structure.
Combining these data we propose a refined model of AT3-SGNH proteins which enhances our understanding of the mechanism and function of AT3 proteins required for modification of cell-surface carbohydrates.
Investigation of the Localisation of FtsZ in Pathogenic E. coli Upon Bacteriophage Addition in a Human Cell Model as a Biomarker for Antibacterial Agents
Authors: Dhanoa Gurneet , Roper David , Sagona Antonia 
Published: May 2022

Antimicrobial resistance is a growing problem worldwide and has created a need for novel antibacterial agents and strategies. Escherichia coli is one of the most common Gram-negative pathogens and is responsible for infection leading to neonatal meningitis and sepsis. The FtsZ protein is a bacterial tubulin homolog required for cell division in most species, including E. coli. Agents that block cell division have been shown to mis-localise FtsZ, including the bacteriophage λ encoded Kil peptide, resulting in defective cell division and a filamentous phenotype, and therefore FtsZ may be an attractive target for new antimicrobials.
In this project, we are interested in studying the localisation of FtsZ in pathogenic E. coli in the presence and absence of human cell cultures, in order to establish how and if this localisation changes upon infection. We are also interested in whether bacteriophages specifically attacking pathogenic E. coli have an effect on the localisation of FtsZ in a human cell environment and want to study the mechanism of this process. We have observed E. coliFtsZ localising to the cell midbody as a ring in both a K12 strain and in the K1 strain EV36 using confocal microscopy. These strains were used to infect human cerebral microvascular endothelial cells (hCMEC/D3) to create a meningitis model. We will present our results showing the effect of the Kil peptide and bacteriophages on this localisation within the model system, in an effort to validate FtsZ as a potential biomarker for antibacterial agents.
A Legionella’s outbreak in a COVID-19 pandemic setting
Authors: Oliveira Catarina , Leite Carla , Rodrigues Helena , Fonseca Fernando 
Published: May 2022

In this report, the author intends to reinforce the need to test for another potencial causes of pneumonia which present with similar symptoms of SARS-CoV-2 infection and can also be responsible for outbreaks and sometimes fatal, particularly Legionnaires’ disease.
Legionellabacteria are aerobic, gram-negative, ubiquitous freshwater and soil inhabitants. Pneumonia is the most commonly described manifestation of Legionella infection (Legionnaires’ disease), acquired through inhalation of aerosolized water droplets containing the bacteria.
Legionella pneumophilais the most consistently reported species, being an important cause of severe community-acquired pneumonia that often requires hospitalization and is fatal in approximately 10% of cases. Most cases present sporadically, however, outbreaks can occur when there are appropriate conditions for bacteria to grow and spread, like stagnating water in piping systems in large facilities. Furthermore, the pathogenesis of Legionella pneumonia is complex and it is clinically and radiographically similar to other forms of pneumonia.
In the context of pandemic COVID-19, the use of Legionella urinary antigen testing continues to be crucial and strongly recommended. Thus, in the outbreak faced in the author’s hospital, this screening method proved to be effective and all cases of Legionellapneumonia were promptly recognized and notified, allowing public health measures to be taken to prevent the development of other potencial clusters.
Bacteriological and Physicochemical Assessment of Sachet and Bottled Drinking Water Sold in Makurdi Metropolis, Benue State, Nigeria
Authors: Agbendeh Lubem , Ogbonna Innocent 
Published: May 2022

Background
Packaged drinking water popularly known as “sachet and bottled water” serves a large percentage in increasing access to clean drinking water in Nigeria. But little attention is given to investigate the bacteriological assessment of these water which may be harmful for human consumption.

Objective
This study was to assess the bacteriological and physicochemical characteristics of sachet and bottled water sold in Makurdi metropolis.

Methodology
A cross sectional study was carried out with a total of one hundred and sixty-five samples collected. These comprised of triplicates of fifty sachet water and five bottled water brands purchased using simple random sampling from street vendors within Makurdi metropolis and analyzed using standard methods and results were compared with the recommended guidelines for water quality.

Results
The presence of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus sp., Klebsiella sp., Salmonella sp. and Shigella sp. were detected in the water samples with a total bacteria count (MPN/100ml) ranging from 0 – 1100 MPN/100ml. Escherichia coli had the highest incidence of 80% followed by Staphylococcus aureus 66%, Salmonella species 48%, Pseudomonas aeruginosa 46%, Streptococcus sp 36%, Shigella species 36%, Klebsiella species 22%. The pH, conductivity, total dissolved solids, dissolved oxygen and sodium chloride levels ranged from 6.0 to 7.6, 8.4 to 188.4μS/cm, 4.2 to 94.2mg/l, 0.08 to 0.16mg/l and 0 to 0.4 respectively.

Conclusion
There is urgent need to intensify the monitoring of activities of this rapidly expanding industry and enforcing strict hygienic measures with a view to raising standards to improve packaged water quality.
Teaching Microbial Genomics in the COVID-19 age: principles, theory, and practice
Authors: Stach Jem , Marles-Wright Jon , Montero-Calasanz Maria del Carmen 
Published: May 2022

The importance of genomics in the COVID-19 age cannot be overstated and genomics has a key place in the advanced undergraduate microbiology curriculum. The COVID-19 pandemic, and its attendant lockdowns, have necessitated a change in the delivery of our microbial genomics module. The key challenges for delivering a remote computer-based genomics module, are ensuring student engagement and learning; and supporting the technical aspects of remote computer work.
In the absence of in-person classes, we have adapted our material covering the principles and theory of microbial genomics, to asynchronous videos and synchronous online workshops. Practical training for all undergraduate microbiologists in the UK has been severely reduced, which has forced us to focus skills training towards computational aspects of genome assembly, analysis, and interpretation. The set up and implementation of a robust and scalable Linux-based genome analysis pipeline for students presents many challenges: from organising remote access to computer clusters; software support; and managing hardware.
Assessment for the module is based on the demonstrating learning and skills development through the analysis of SARS-CoV2 genomes to identify spike protein variation and mapping this to published structures. Terminal assessment is through the analysis of newly sequenced bacterial genomes and the preparation of a genome report suitable for publication.
We will outline the implementation and management of our Microbial Genomics module as a model for computer-based skills training for undergraduate microbiologists. Furthermore, we will discuss the impact of the COVID-19 pandemic on the module and the opportunities it has presented.