bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial coping mechanisms for aging: using an individual-based model to study aging in biofilms
Authors: Wright Robyn , Clegg Robert , Kreft Jan-Ulrich
Published: April 2019

Aging can be defined as an accumulation of damage, or a loss of function, with increasing age. For bacteria, it has generally been assumed that the mechanism used to cope with aging is the asymmetric segregation of damage at division, so that all of the damage is inherited by one cell and the other is therefore rejuvenated. Another, often neglected, mechanism is to repair the damage; our previous computational modelling work has found that an optimized, fixed rate of repair is fitter than damage segregation in well-mixed environments such as chemostats. The predominant mode of growth for bacteria is in biofilms, however, and here we investigate aging in biofilms using the individual-based model iDynoMiCS. In addition to the previously used damage segregation and fixed repair strategies, we introduced adaptive repair: sensing the current damage levels within the cell and responding to this by investing in damage repair machinery. We found that the optimal method for dealing with cellular damage varies with the environment being investigated. The investment of additional resources into adaptive repair is only beneficial when competition is sufficiently strong, in the chemostat and in biofilms, and the speed at which the fittest strategy becomes apparent depends upon the initial density of cells. When the bacterial cells are dense initially, and thus the competition between strategies is stronger, the adaptive repair strategy emerges as the winner much more rapidly.
Properties and directionality of intragenic promoters in E. coli
Authors: Warman Emily , Singh Shivani , Grainger David
Published: April 2019

The histone-like nucleoid structuring (H-NS) protein targets and binds AT-rich DNA. Oligomerisation of H-NS along AT-rich genes represses transcription from spurious intragenic promoters within the coding sequences of AT-rich genes. In this work, we sought to better understand why promoters occur so frequently within AT-rich DNA. To do this, we compared the properties of (i) canonical promoters (ii) promoters within H-NS bound genes and (iii) promoters generated by random combinations of nucleotides. We have identified and analysed many active intragenic promoters distributed within AT-rich genes in the E. coli genome. We show that these promoters, and promoters from randomly generated AT-rich DNA, differ from canonical promoters in several ways. In particular, spurious promoters are often dependent on AT-tracts upstream of the promoter −10 element. These AT-tracts play a key role by altering DNA curvature and facilitating interactions between the promoter and RNA polymerase sigma factor. Promoter regions inside genes are also often bidirectional.
An uncharacterised protein mediates motility, biofilm formation, and host colonisation in adherent invasive Escherichia coli
Authors: Cogger-Ward Robert , Collins Adam , Dehinsilu Jacob , Huett Alan
Published: April 2019

Adherent Invasive Escherichia coli (AIEC) is a non-diarrhoeagenic intestinal E. coli patho type with a putativea etiological role in Crohn’s Disease (CD). AIEC pathogenes is ischaracterised by adhesion to, invasion of, and replication within intestinal epithelial cells and macrophages, and biofilm formation. Using a heterologous expression screen, we identified a gene in the AIEC LF82 genome encoding a protein which self-assembles into filaments in HeLa cells, which we hypothesised was a novel pilin or biofilm matrix component, designated bcmA (biofilm coupled to motility in AIEC). Using a crystal violet-based assay, we found LF82ΔbcmA have defective biofilm formation, which can be fully complemented by episomal bcmA expression. Microscopic analysis of LF82 biofilms demonstrated LF82ΔbcmA form patchy, sparse biofilms, and revealed an intracellular localisation for GFP-tagged bcmA, suggesting the protein is not a surface-exposed adhesin or biofilm matrix component. We therefore assessed the role of bcmA in flagellar-mediated motility and found that – despite displaying wild-type flagellar morphologies – LF82ΔbcmA have profound swimming and swarming defects. Work in a Caenorhabdit is elegans infection model suggests bcmA is not required for full virulence; however, preliminary evidence suggests LF82ΔbcmA have defective C. elegans gut colonisation. Taken together, our data demonstrates roles for bcmA in AIEC host colonisation via an undefined role in motility. bcmA is highly conserved among pathogenic gammaproteobacteria, including Salmonella Typhi, Shigella boydii and Klebsiella pneumoniae. This suggests bcmA may not only be significant for AIEC pathogenesis, but may also represent an important virulence determinant in several major gammaproteobacterial pathogens.
Genotypic and phenotypic diversity in Candida tropicalis
Authors: O’Brien Caoimhe , Oliveira-Pacheco João , Butler Geraldine
Published: April 2019

Candida tropicalis is a human pathogen with significant mortality rates, which is particularly prevalent in tropical regions. The first genome sequence of C. tropicalis was published in 2009. In this study, we sequenced 75 C. tropicalis isolates with the aim of studying the intra-species diversity of this pathogen at a phenotypic and genetic level. These isolates were collected from both clinical and environmental sources, and sequenced using Illumina technology. Phylogenetic analysis of the sequenced isolates using SNP trees and PCA analysis reveals several multi-isolate clusters, which are unrelated to geographical origin. Overall, the genomes of the isolates were stable, with only 4 out of 75 isolates demonstrating any aneuploidy. However, the genomes are highly heterozygous, with one variant, on average, every 136 bases. Variant analysis revealed three highly divergent isolates, with one variant, on average, every 7 bases. Further examination of these isolates revealed that they are the products of hybridisation between two parents; one which is almost identical to the reference strain (>99.9 %), and a second, unidentified parent, which is approximately 4.5 % different in its sequence to the reference strain. Differences in sequence indicate that these hybrids arose from separate hybridisation events. Phenotypic differences are also observed between isolates under certain conditions, particularly in the presence of cell wall stressors, metal stressors and antifungal drugs. Cosine similarity was used to identify correlations between genetic variants and phenotypic variation in all isolates, identifying variants that may be responsible for particular phenotypes. Work is ongoing to confirm these observed correlations.
Development of low bio-containment assays to characterise the antibody responses in pigs to Nipah virus vaccine candidates
Authors: Thakur Nazia , Nath Barman Nagendra , Chang Li-Yen , Chappell Keith , Gilbert Sarah , Lambe Teresa , Marsh Glenn , McLean Rebecca , Mourino Mercedes , Pedrera Miriam , Raue Rudiger , Tchilian Elma , Watterson Daniel , Young Paul , Graham Simon , Bailey Dalan
Published: April 2019

Nipah virus (NiV) is a zoonotic paramyxovirus that causes severe and often fatal respiratory and neurological disease in humans. Since 1998, NiV outbreaks have occurred in Malaysia, Bangladesh and India. NiV poses a significant pandemic threat due to its broad host range and the widespread distribution of its natural host, the Pteropus fruit bat. Despite this, there are currently no licenced therapeutics or vaccines for use in either humans or livestock. Aiming to develop a safe and inexpensive vaccine to protect livestock in future outbreaks and to prevent onward transmission to humans, we are evaluating the immunogenicity and efficacy of three candidate vaccines in pigs. These vaccines are based on the NiV G or F surface glycoproteins, proteins which are essential for mediating virus-cell or cell-cell entry. The candidate vaccines include: (i) a recombinant soluble NiV G protein subunit, (ii) a recombinant molecular clamp stabilised NiV F protein subunit and (iii) a replication deficient, adenoviral vectored NiV G protein. We have developed low biocontainment assays to characterise the antibody responses to NiV and to aid identification of immune correlates of protection through quantification of both antigen-specific and neutralising antibody responses to our vaccine candidates. This includes anti-NiV F/G indirect ELISAs, a microneutralisation test using pseudotyped particles, and a microfusion inhibition test using a quantifiable cell-cell fusion assay. Using these assays we have demonstrated that all three of our novel vaccines are immunogenic in pigs and capable of generating a robust antibody response, with evidence for neutralising antibodies.
Motilimonas cestriensis sp. nov., isolated from a Cheshire brine spring
Authors: Kelbrick Matthew , Abed Raeid , Antunes André
Published: April 2019

The Cheshire Salt District (UK) is home to a wide range of largely unexplored inland brine springs, whose increased salinity originates from subterranean Triassic salt rock deposits. Our study focused on the Anderton Brine Spring System, a set of pools of varying salinity which are subjected to regular salinity fluctuations depending on drainage and evaporation (recorded salinities have ranged from 1.2% to 13% NaCl). Preliminary investigation of samples obtained from one of these pools (with 4.2 % NaCl) revealed a wealth of novel isolates which were analysed by 16S rRNA gene sequencing. Within these isolated strains, we have detected that strain MKS20 had a 97 % similarity to its closest relative, Motilimonas eburnea, which is currently the only characterised species in a newly discovered genus of the order Alteromonadales. All reported strains within this genus have been isolated from marine environments, namely marine-sediments and the gut of a sea cucumber. MKS20 is the first strain in the genus to be reported from an inland brine spring and thus significantly extends the ecological range of the genus Motilimonas. The distinctiveness of our strain is further supported by preliminary results from polyphasic taxonomic characterisation (e.g. metabolic and enzymatic profiling). Based on these, strain MKS20 represents a putative new species within the genus for which we propose the name Motilimonas cestriensis, referring to Cheshire, the place of isolation.
The macrophage intracellular niche and its role in cryptococcosis
Authors: Pline Katherine , Johnston Simon , Bradford James
Published: April 2019

Cryptococcus neoformans is an opportunistic fungal infection that causes cryptococcal meningitis in immunocompromised individuals. Macrophages play a critical role in determining the outcome of infection, and can either phagocytose and kill the cryptococcal cells, or disseminate infection. While it is known that macrophages impact the progression of cryptococcal disease, it is not known how the macrophage intracellular niche contributes to complex infection outcomes. Clinical and experimental studies have identified potential genetic differences, in both host and pathogen, but statistical robustness has been difficult to achieve due the large variability in the outcome of infections. Therefore, in attempt to quantitatively explain this variability, we have used a zebrafish model of cryptococcal infection where we can directly relate the initial level of fungal infection with final infection outcome. We find that at low levels of initial fungal burden the outcome of infection is stochastic, while over high ranges of initial infection the outcome is linearly related to the initial burden, but with a further stochastic component that contributes to increased variability. Using these experimental data and data from clinical trials we have generated a computational simulation of in vivo cryptococcal infections which allows us to consider different infection variables and how they alter the progression of cryptococcosis. By combining such computational simulations with our experimental models we demonstrate that the macrophage intracellular niche determines the unknown stochastic component, independent of fungal burden. Using this knowledge, we can better identify the molecular, population genetic, and clinical parameters associated with the outcome of cryptococcosis.
Characterization of Enterococcus faecium SP15, a novel isolate with probiotic and therapeutic potential
Authors: Aziz Fauzia , Khan Muhammad , Ahmed Safia , Jones Ian , Andrews Simon
Published: April 2019

Aims

To characterise the genome and enterocin content of Enterococcus faecium SP15, a new isolate from natural spring water.

Methods and Results

Enterococcus faecium strain SP15 was isolated from natural spring water and its identity confirmed using 16S rDNA sequence. The bacterial strain produced antimicrobial compounds (enterocins) against pathogenic bacteria including Listeria monocytogenesis as determined by the agar spot method. In addition, an anti-cancer activity was observed on human cancer cell line HT-29 by cytotoxicity assay (MTT) and apoptosis study. A draft genome sequence revealed the presence of several enterocin genes capable of activity against a panel of pathogenic bacteria including L. monocytogenesis. The active production of enterocins was also supported by the presence of peptides in part purified fermentates following trypsin digest and mass spectrometry. The genome showed no classical virulence factors or hemolysins and was free of antibiotic resistance genes. To confirm enterocin related killing, select enterocin genes were cloned and expressed as His-tagged proteins in E. coli. Purified enterocin retained activity in L. monocytogenes overlay assay.

Conclusion

E. faecium SP15 is a promising strain for probiotic use and/or food preservation. Purified enterocins retain their activity suggesting them a template for structure-function studies and future improvements as antimicrobial and cancer cell therapeutics. Significance and Impact of the Study: New antibacterial and anticancer agents are required to combat antibiotic resistance and a limited drug repertoire. Enterocins from Enterococcus faecium SP15 could fulfil these goals in addition to use of the strain as a whole organism probiotic.
Glucose metabolism via the Entner-Doudoroff Pathway in a select subgroup of Campylobacter jejuni
Authors: Almimoni Nourah , Macintyre Sheila
Published: April 2019

Campylobacter jejuniis is the most common cause of bacterial gastroenteritis worldwide. It is often considered a ‘commensal’ in chickens where it rapidly colonises the caecum of young chicks and is present in around 80 % of farmed poultry. C. jejuni has a small genome and most strains are unable to transport or metabolize glucose. Instead they use amino acids, TCA cycle intermediates and short chain fatty acids as energy and carbon sources. Recently, a WGS project identified an unusual group of C. jejuni (RG-2 group) within a bank of C. jejuni strains isolated from farm associated Norway rats. These strains had acquired an entire locus (glc) of seven genes which enable uptake and metabolism of glucose via the Entner Doudoroff (ED) pathway. This project is addressing the impact of these genes on metabolism and niche survival of these strains. Campylobacter are microaerophilic bacteria. Good growth of C. jejuni NCTC 11168 and of aglcnegative Norway rat C. jejuni isolate was recorded in the presence of 5 % O2up to 13 %in a Whitley M35 workstation. In contrast, two glcpositive strains of C. jejuni, Dg275 and Dg95, exhibited the unusual ability to grow well in an atmosphere of 16 % oxygen, as monitored by c.f.u. and OD600. Current studies are also focusing on the contribution of glucose utilization via the ED pathway to influence survival and growth in oxygen.
Film-forming agents as potential barriers to fungal skin infections
Authors: Ho Kaho , Delgado-Charro Begona , Bolhuis Albert
Published: April 2019

Background

Superficial fungal infections are one of the most common causes of human disease caused by dermatophytes or yeasts. Dermatophyte infections are caused by fungi that can digest keratin, infecting the keratinised tissues e.g. skin, hair and nails. It has a higher prevalence than the other superficial mycoses, and its incidence has increased continuously over the last few decades, probably because of the change in lifestyle and frequent usage of antibiotics. Therefore, the aim of the project is to develop a physical barrier that can prevent the early stages of infection to the skin, to avoid development of antifungal resistance and cross-contamination.

Materials/methods

We developed an ex vivo model using porcine skin to study the potential of film-forming agents in prevention and treatment of dermatophytosis caused by Trichophyton rubrum. We used cell viability assays, confocal and electron microscopy to study the effects of film-forming agents on T. rubrum, followed by using QTOF-LCMS and NMR to analyse the carbohydrates binding and chelation to study its mechanism of action.

Results

A cationic polymer used in pharmaceutical and cosmetic products inhibited growth of T. rubrum on porcine skin. Viability assays indicated that the polymer has a fungistatic activity and microscopy imaging indicated it formed a coating on top of T. rubrum. The QTOF-LCMS and NMR indicated the polymer inhibits fungal growth by removing the carbohydrate content and chelation.

Conclusions

The present study suggests this cationic polymer has considerable antifungal activity against Trichophyton rubrum by preventing the supply of nutrients to the fungi.
Meeting the rare earth expanding circle
Authors: Barnett Megan , Gregory Simon , Deady Eimear , Palumbo-Roe Barbara
Published: April 2019

The increasing demand for rare earth elements (REE) is fuelled by their importance in a green energy future, with the demand for dysprosium predicted to increase by 5 % annually by 2026. Bioleaching approaches are being investigated for the recovery of REE and other precious metals from waste materials, however even 100 % recovery will not be able to meet increasing demand. Therefore, extraction from primary sources will be required. REE do not form high concentration ores, so their extraction can require processing large volumes of material, however REE are frequently associated with other raw materials and REE are sold as by-products of iron mining from Chinese deposits. Bioleaching offers the potential to produce valuable by-products from existing mining operations or to remediate historical mine waste. The diverse nature of REE-bearing minerals means that a variety of established and emerging bioleaching approaches could be applied: organic acid leaching, oxidative leaching of sulphidic ores, and reductive leaching of oxidised ores. We have applied these processes to three bauxites, demonstrating varied responses to bioleaching with each bauxite. The combination of low concentration ores and varied sources provide a challenge to recovery: however, it is one that microbes could take on.
Molecular characterization of the activity and requirements of a novel and promiscuous bacteriophage integrase
Authors: Mohaisen Mohammed , Allison Heather , McCarthy Alan
Published: April 2019

Stx bacteriophages are responsible for the dissemination and production of Shiga toxin genes (stx) across the Shigatoxigenic E. coli (STEC). These toxigenic bacteriophage hosts can cause severe, life-threatening illness, and Shiga toxin (Stx) is responsible for the severe nature of EHEC infection, a subset of pathogenic STEC. At the point of Stx phage infection, the injected phage DNA can direct its integration into the bacterial chromosome becoming a prophage; the host cell is then known as a lysogen. Unusually, our model Stx phage, Φ24B, can integrate into at least four distinct sites within the E. coli genome that shared no easily identifiable recognition sequence pattern. The identification of what are actually required for phage and bacterial DNAs recombination has been tested using both in vitro and in situ recombination assays. These assays enabled the simple manipulation of bacterial attachment site (attB) and phage attachment site (attP) sequences. The aim of the study is to fully characterize the requirements of this promiscuous integrase, carried by the Stx phage Φ24B (IntΦ24B), to drive integration. These assays enabled us to identify the minimal necessary flanking sequences for attB site identified (21 bp and 49 bp from the right and left the cross over region, respectively) and the attP site (200 bp each side). Furthermore, we identified that the Φ24B integrase does not need Integration Host Factor (IHF) to drive integration. Fi
Molecular studies on iron metabolism, redox stress and pathogenicity in Bartonella
Authors: Alali Sheama , Andrews Simon
Published: April 2019

For bacteria, mechanisms of resistance to redox stress are utilised to increase survival. Although B. henselae has the ability to resist redox stress, its genome sequence is characterised by a paucity of genes responsible for redox-stress resistance, particularly hydrogen peroxide degradation systems. However, our results show a surprisingly high resistance to peroxides, given the lack of peroxide disposal systems. To determine how B. henselae achieves resistance to H2O2 stress, the potential role of MbfA (membrane-bound bacterioferritin), which in other α-Proteobacteria is believed to function as an iron exporter, was investigated. The results show that B. henselae has the ability to export iron and that this export activity is promoted by H2O2as export was inhibited by exogenous catalase and anaerobiosis. The form of iron exported was largely ferric. The impact of the iron export process on the resistance to, and degradation of, H2O2, by B. henselae was determined and the results showed that B. henselae mediates a rapid consumption of exogenously supplied H2O2. This degradation was entirely inhibited when iron chelators were included along with the H2O2. The resistance of B. henselae to NO was also tested since NO is generated by phagocytic host cells along with H2O2, and is suggested to potentiate the toxicity of H2O2 towards engulfed bacteria through inhibition of haem-dependent catalases and alkylhydroperoxidases. Our results suggest that NO does not cause a marked increase in H2O2 toxicity for B. henselae, in contrast to E. coli (a haem-catalayse/peroxidase dependent bacterium).
Novel antimicrobial agents for clinical applications
Authors: Allen Nyasha , Mulvihill Daniel P , Hiscock Jennifer R
Published: April 2019

Since their discovery, antimicrobial compounds have been vital for the treatment and prevention of disease; making many previously fatal diseases treatable or at worst, manageable conditions. The inappropriate use of these compounds has led to the rapid development of resistance mechanisms within bacteria to the majority of compounds currently marketed. A recent UK governmental review predicted that by 2050 global deaths caused by antimicrobial resistant bacteria will outnumber those attributed to cancer [1]. As new resistance mechanisms emerge and resistance within microbial populations increases, so does the need to further understand the molecular basis of resistance, develop new antimicrobial molecules and use better strategies to manage their use [2]. In response to this, we discovered a novel class of antimicrobials and have created 50 structurally related members of this class [3-6]. We sought to understand the structure-activity relationships which will result in the determination of the mode of action of these molecules. Consequently, each variant was screened against Staphylococcus aureus and Escherichia coli and the minimum inhibitory concentration was calculated for effective compounds. This will enable us to identify predictive tools that will aid the synthesis of the next generation of these novel therapeutic molecules. We will present our latest findings in the ongoing analysis of the antimicrobial activity for each variant of this new class of antimicrobial compound. In addition, we will discuss the insights provided by the detailed structure-function analysis. This project is in collaboration with Public Health England and NHS East Kent Trust.
Global mapping of protein subcellular location in apicomplexans: the parasite as we’ve never seen it before
Authors: Barylyuk Konstantin , Koreny Ludek , Ke Huiling , Butterworth Simon , Lassadi Imen , Mourier Tobias , Breckels Lisa , Gatto Laurent , Pain Arnab , Lilley Kathryn , Waller Ross
Published: April 2019

Apicomplexans are human and animal protozoan pathogens responsible for diseases including malaria, cryptosporidiosis and toxoplasmosis. As obligate intracellular parasites they are highly organised cells with numerous novel and specialised sub-compartments that form the basis of their invasion biology, host defence evasion, and novel metabolic traits. However, our understanding of these cells is highly constrained by our limited knowledge of the locations and functions of most of the cell’s proteome. Even in the best-studied apicomplexans (Plasmodium spp. and Toxoplasma gondii) only a small fraction of proteins’ locations have been experimentally determined, with most assignments based on predictions from orthologues in distant relatives. Moreover, many parasite proteins are annotated as ‘hypotheticals’, for example 4113 of 8121 Toxoplasma proteins, and many are unique to parasites stymying even predictions of location or function by comparative biology. To address this deficit in our basic understanding of the compositional organisation of the apicomplexan cell, we have used a spatial proteomics method called hyper LOPIT to simultaneously capture the steady-state subcellular association of thousands of proteins in the apicomplexan Toxoplasma. These protein atlases reveal: extensive protein association networks throughout the cell providing testable hypotheses of their function; conservation and novelty of compartment proteomes between apicomplexans; differential selective pressures across the different cell compartments; and clear instances of protein relocation from one organelle to a different one during apicomplexan speciation. This new, global view of the organisation of the apicomplexan cell proteome provides a much more complete framework for understanding the mechanisms of function and biology of these cells.
Prevalence of extended spectrum beta-lactamase producing Enterobacteriaceae in urine samples from Thumbay hospitals, U.A.E
Authors: Rahamathullah Nazeerullah , Ahamed Khan Sajith Khan , Arshad Khan Zahra , Farrukh Amina , Bashir Hamdallah M , Ahmad Asmau
Published: April 2019

Beta Lactamases is proven to be one of the leading cause of resistance to β-lactam antibiotics among gram-negative bacteria. Many up to date researches have shown increase in the incidence and prevalence of ESBL worldwide. This study aimed to determine the prevalence of ESBL strains of Klebsiella spp. and Escherichia coli species in urinary isolates from the patients admitted in Thumbay hospitals around United Arab Emirates. Furthermore, drug resistant genes (SHV and CTX-M) in the ESBL positive samples were detected. 237 urine samples were collected from November 2017 to January 2018. Based on the lactose utilization, colony morphology, and biochemical utilization of the gram negative bacilli were identified as E. coli (53), Klebsiella pneumoniae (10) and Citrobacter species (2). Antibiotic sensitivity test, double disc diffusion test and combination disc tests all confirmed that the 65 (27.4 %) out of 237 isolates were ESBL producing bacteria. There was high prevalence of bacteria in females than male and the number of E. coli strains is higher than Klebsiella spp. DNA isolation was performed on the 65 samples, out of which 50 samples were selected for PCR based on their concentration. The selected DNA samples were used to detect the presence of bla CTX-M and bla SHV genes. Only 24 DNA samples (48 %) contains blaCTX-M genes, bla SHV or both the genes. 14 samples had bla CTX-M gene, 2 bla SHV genes, and 8 with both bla SHV and bla CTX-M. At the rate at which ESBL is spreading, further research, close observation and cautious use of antibiotics is important.
Human Cytomegalovirus pUL83 targets core histones to inhibit interferon synthesis and promote viral spread
Authors: Deb Anasua , Paulus Christina , Nevels Michael
Published: April 2019

Tegument protein pUL83 is the most abundant component of human cytomegalovirus (hCMV) particles. The viral protein is predicted to be composed of three domains: a pyrin association domain (PAD), a carboxy-terminal domain (CTD), and an intrinsically disordered linker domain (amino acids 388–479) located between the PAD and CTD. Although pUL83 has been shown to antagonize interferon (IFN) responses, it has not been fully elucidated how the viral protein may contribute to hCMV replication. In this study we demonstrate that pUL83 associates broadly with viral and host chromatin including condensed chromosomes during mitosis. We further show that the linker domain in pUL83 is both required and sufficient for host chromatin targeting, and that this interaction depends on two evolutionary conserved arginine residues (R453 and R455) in the viral protein. Our data indicate that the pUL83 linker domain specifically associates with human core histones (but not linker histones). Furthermore, pUL83 inhibits IFN-beta and IFN-lambda gene induction, but not expression of other cytokine genes, via a mechanism that largely depends on the linker domain including R453/455. Although earlier studies suggested that pUL83 is dispensable for productive hCMV infection in fibroblasts, we find that the viral protein is necessary for efficient plaque formation in these cells, specifically in the presence of IFN. Finally, the pUL83 linker domain including R453/455 contributes significantly to the plaque size in hCMV-infected fibroblasts. Overall, we propose that pUL83 promotes spread of hCMV by selectively inhibiting induction of IFN gene expression via a novel chromatin-based molecular mechanism involving core histones.
Harnessing novel bacterial peptides for antimicrobial activity in the gut microbiome
Authors: Sterling Amy , Dooley James , Ternan Nigel , Naughton Patrick
Published: April 2019

The Enterococci are a resilient collection of species, found in the human intestine, river sediment and even certain cheeses. Human infection by this genus is dominated by E. faecalis and E. faecium. Vancomycin resistant enterococci (VRE) are associated with higher mortality rates over non-VRE strains. Enterococci can utilise the highly efficient pheromone responsive plasmid (PRP) system to transfer plasmid DNA between cells. Plasmid containing donor cells respond to small peptide pheromones (7–8 amino acids) and transfer plasmid DNA to pheromone-producing plasmid-free recipient cells. PRP can encode antibiotic resistance (including vancomycin) and virulence enhancing factors. Investigation into the PRP system between donor and recipient E. faecalis environmental isolates has indicated a 40 % decrease in PRP transfer in colder environments. Additionally, PRP efficiencies under other conditions, including in presence of synthetic pheromone peptides, have been calculated. Future assays will utilise pheromone imitative fluorescently labelled synthetic peptides to visualise the pheromone binding receptor (PrgZ) on the E. faecalis donor cell membrane. Later experiments will focus on varying the synthetic pheromone amino acid composition so to interfere with the PRP system machinery, with the aim of reducing PRP transfer efficiency or preventing PRP transfer completely.
Mapping the pH sensors critical for host cell entry by a complex Nonenveloped Virus
Authors: Wu Weining , Roy Polly
Published: April 2019

Bluetongue virus (BTV), in family Reoviridae, is an insect-borne, double capsid virus causing haemorrhagic disease in livestock around the world. Here, we elucidate how outer capsid proteins VP2 and VP5 coordinate cell entry of BTV. The recently solved high-resolution structures reveal unique features of BTV VP2 and VP5. To identify key functional residues, we used atomic-level structural data to guide mutagenesis of VP2 and VP5 and a series of biological and biochemical approaches, including site-directed mutagenesis, reverse genetics-based virus recovery, expression and characterization of individual recombinant mutant proteins, and various in vitro and in vivo assays. We demonstrate the dynamic nature of the conformational change process, revealing that a unique zinc finger (CCCH) in VP2 acts as the major low pH sensor, coordinating VP2 detachment, subsequently allowing VP5 to sense low pH via specific histidine residues at key positions. We show that single substitution of only certain histidine residues has a lethal effect, indicating that the location of histidine in VP5 is critical to inducing changes in VP5 conformation that facilitates membrane penetration. Further, we show that the VP5 anchoring domain alone recapitulates sensing of low pH. Our data reveal a novel, multiconformational process that overcomes entry barriers faced by this multicapsid nonenveloped virus.
Epidemiological characteristics of the Manchurian plague pandemic of 1910-1911
Authors: Dou Xiangfeng , Chen Meng , Li Shuang , Chen Yanwei , Pang Xinghuo , Wang Quanyi
Published: April 2019

Objective

To investigate the epidemiological characteristics of the Manchurian plague pandemic of 1910–1911 with descriptive epidemiological methods.

Methods

The epidemiological data were distracted from Report of Manchurian Plague, which is a summary of local official reports about plague in 1910–1911. The time distribution by day, and the space distribution by country was recorded, and also the source of infection.

Results

The pandemic of plague continued from October 25th, 1910 to April 18th, 1911. There were 46 747 dead cases on record in the three provinces of Manchuria. There were 24 867 dead cases and 7068 dead cases were reported, and the average mortality rates were 41.21 and 10.25 per ten thousands in Jilin and Liaoning province, respectively. In Heilongjiang province, 14 812 dead cases of plague were reported. The huge difference was found in different epidemic regions, the highest mortality rate was 4121 per ten thousands in Binjiang country of Jilin province. Patient zero of pneumonic plague had been infected in Russia and got sick and died in Manzhouli, a northern country in Heilongjiang province. Then the pneumonic plague was mainly spread through railway to other cities.

Conclusion

The epidemiological characteristics of the Manchurian plague pandemic of 1910–1911 were first described with modern epidemiological methods.
Investigation of the Candida–host interaction using dual RNA-seq
Authors: Iracane Elise , Hovhannisyan Hrant , Miguel Oliveira Pacheco João , Pekmezovic Marina , Hube Bernhard , Gabaldón Toni , Butler Geraldine
Published: April 2019

Candida species are commensal yeasts but are also responsible of life-threatening infection in at-risk populations, like new-born or immunocompromised patients. Candida albicans is the most common causative species, and the most studied. Moreover, non-albicans
Candida species as Candida glabrata, Candida parapsilosis and Candida tropicalis cause a large proportion of infections. In our study we investigated the interaction between four Candida species and human vaginal epithelial cells A431 by using a dual RNA-seq method. Our aim is to identify the different transcriptomic response of each yeast, and of the host, during the infection of human cells. Gene Ontology analysis of up-regulated genes in the yeasts during infection implicated the ergosterol (ERG) pathway in C. parapsilosis only. We therefore investigated the role of the ERG pathway in the three Candida species in which it is currently possible to generate gene knockouts. The transcriptional factor Upc2 is the main regulator of ERG gene expression in C. albicans and C. parapsilosis. C. glabrata has two UPC2 orthologs, called CgUPC2A and CgUPC2B. We found that deleting CgUPC2A or CgUPC2B or both together does not reduce the damage inflicted by C. glabrata on host cells. However, deleting UPC2in C. albicans greatly reduces damage. Deleting UPC2 in C. parapsilosis appears to reduce damage of host cells; however further investigation is required. Our results show the that the role of ergosterol pathway in the host pathogen interaction differs between Candida species.
Modulation of arbovirus infection by mosquito saliva
Authors: Lefteri Daniella , Pondeville Emilie , Bryden Steven , Pingen Marieke , McKimmie Clive
Published: April 2019

Arboviruses constitute a major public health problem, in particular mosquito-borne arboviruses that continue to emerge and re-emerge. Arbovirus infection of mammals is enhanced by the presence of a mosquito bite at the inoculation site, in comparison to virus experimentally administered by needle inoculation in the absence of a bite. Inflammatory responses to bites appear to be a key factor in this enhancement. However, the experimental inoculation of mosquito saliva with virus inoculum by needle, in the absence of bite trauma, also has the ability to enhance viral infections. In this study, we have studied the mechanistic basis for these observations. We have studied whether saliva from different mosquito species can enhance virus infection. Interestingly, while saliva from Aedes genus enhanced virus infection, An. gambiae saliva did not. Instead, An. gambiae saliva actively inhibited infection compared to inoculation with virus alone. This could partly explain why An. gambiae mosquitos are unsuitable vectors for transmitting most arboviruses. By comparing the effects that saliva of these different mosquitoes have at the bite site we have further specified which inflammatory responses at the inoculation site modulate arbovirus infection in the skin. Using an in vivo mouse model we have shown that An. gambiae causes significantly less oedema but a higher up-regulation of key inflammatory genes in the skin than A. aegypti. As such, we are providing important insights into how mosquito saliva modulates infection. A better understanding of this will aid the development of anti-viral treatments by targeting factors within the mosquito bite that are common to many distinct infections.
Fungal biodeterioration of copper metal
Authors: Zhao Jiayue , Gadd Geoffory
Published: April 2019

In this work, geoactive fungi including Aspergillus niger, Beauveria caledonica and Paecilomyces javanicus, were used to investigate their biocorrosion and deteriorative effects on copper metal to gain an understanding of the roles that fungi may play in biodeterioration of such a material in the built environment. It was clearly demonstrated that the test fungi possessed a high tolerance to copper metal. New biominerals resulted from fungal interactions with copper metal mainly arising from organic acid excretion. Copper oxalate was formed by oxalate excretion from the fungi and different patterns of bioweathering and biomineralization were generated on the copper surfaces. In addition, copper could be dissolved by certain fungi, result in significant biodeterortive effects such as etching and pitting. These results provide compelling evidence for deteriortion of copper metal by fungi and that organic acids, particularly oxalate, play an important role in this process. Such properties of metal biocorrosion and deterioration indicate the potential significance of fungi in biodeterioration of metal substrates and the importance of considering methods of protection and preservation in the built environment.
Investigating the influence of host genetics on the metagenome: the intestinal microbiome of two arid mammalian species
Authors: Osborne Peter , Pasternak Ella , Kronfield-Schor Noga , Hall Lindsay , Caim Shabhonam , Thybert David
Published: April 2019

Numerous factors have been shown to influence microbiome composition, including host genetics, diet and environmental variables. Recent studies have explored how host genetics influence human gut microbial communities, and those of pre-clinical models e.g. mice. However to date no studies have determined the influence of host genetics and extreme environments on wild animal microbiomes. Furthermore, when ‘wild’ species have been utilised this has typically involved working on captive individuals, restricted to a single species or limited to single sampling without replicates. Here we present work which takes advantage of a unique opportunity to directly investigate host organism genetic influences and environment on the resident microbiome. Our dataset comprised samples from individuals of two closely related sympatric, independently adapted arid mouse species, subject to the same stresses and diet; Acomys cahirinus and Acomys russatus. These desert dwellers are very highly adapted to the extreme environment they live in, and therefore represent an exciting opportunity to probe key microbiome-environment-host genetic questions. Samples are replicates from wild individuals, separated by a period of four months. Wild individuals were captured on two occasions and faecal samples collected. DNA extracted and subjected to shotgun metagenomic sequencing, generating NGS data. Preliminary analysis allowed us to probe community composition and relative abundance within individuals, and between members of the same species. Utilising Kraken, Centrifuge and Metaphlan we have found that abundant taxa include Lactobacillus and Roseburia. Ongoing analysis will enable us to establish the relative influence of host genetics on the metagenome composition of the two species.
Incorporation of V. vulnificus into marine snow for oyster uptake and in vivo bacterial competition assays
Authors: Hubert Cam , Michell Steve
Published: April 2019

Vibrio vulnificus is a significant human pathogen found in high numbers in oysters. Despite the environmental prevalence of V. vulnificus, clinical cases are uncommon. We hypothesised that in vivo competition between V. vulnificus and other strains/species resulted in the killing of hypervirulent strains, reducing clinical incidence. To assess this, we have developed an oyster model into which we can ensure ingestion of high quantities of V. vulnificus using a defined ‘marine snow’. Marine snow describes the aggregation of naturally occurring phytoplankton, bacteria, debris and other organic materials. Our marine snow substrate is comprised solely of the diatom, Thalassiosira pseudonana. Bottles containing artificial seawater, 109 T. pseudonana, V. vulnificus culture and hyaluronic acid were rotated at 16 r.p.m. for 24 h to generate aggregates. V. vulnificus-containing marine snow was added to beakers holding individual oysters. Following 24 h uptake, oyster stomachs were excised and homogenised in PBS. The resulting suspension was serially diluted for plate-counts and DNA extracted for downstream qPCR analysis. Diatom-based aggregates present a controllable and reproducible model for incorporating V. vulnificus into marine snow. Using this methodology, we demonstrate greater uptake of V. vulnificus by oysters than any current study. This has potential applications for future in vivo work studying a range of microorganisms in oysters, such as other human pathogens or those of interest to aquaculture. Future work will undertake in vivobacterial competition assays to determine the role that intra-/inter-species competition has on the ecology of V. vulnificus and whether this impacts the clinical incidence.
Metagenomic analysis of open-air and indoor spent fuel storage ponds at Sellafield, UK
Authors: Ruiz Lopez Sharon , Foster Lynn , Song Hokyung , Cole Nick , Adams Jonathan , Lloyd Jonathan
Published: April 2019

Nuclear power is an important energy source that can compensate for carbon emissions from fossil fuel power plants. However, processing of radioactive waste from nuclear plants is a significant challenge. The current treatment prior to final geological disposal involves wet storage of spent fuel in designated ponds, and microbial colonisation of these ponds can complicate plant operation. To help identify the key microbes that colonise hydraulically interlinked spent fuel storage ponds at Sellafield, UK, a series of samples were collected and analysed using next generation (Illumina) sequencing. Samples were taken from the facility’s indoor Fuel Handling Plant (FHP) pond (feeding head tank, main and subponds), and also from the open-air First Generation Magnox Storage Pond (FGMSP). 16S rRNA gene sequencing revealed that the FHP is colonized mainly by Bacteria (99%), affiliated with species of Curvibacter, Rhodoferax, Sphingomonas and Roseococcus, in addition to the hydrogen-oxidising bacterium Hydrogenophaga. In contrast the open-air FGSMP pond contained species of Hydrogenophaga, Nevskia, and Roseococcus, and also photosynthetic cyanobacteria (Pseudanabaena). Biological function was also assessed by metagenomic sequencing and analyses. The most abundant genes were associated with carbohydrate and protein metabolism, cell wall and capsule synthesis, stress responses and respiration. Genes involved in respiration were also more abundant in the indoor pond microbiome, including genes underpinning hydrogen metabolism, whilst photosynthesis genes were more abundant in the open-air ponds. These datasets give valuable insight into the microbial communities inhabiting nuclear storage facilities, the metabolic processes that underpin their colonisation and can help inform appropriate control strategies.
Single-particle measurements reveal damage to filamentous influenza virions during laboratory handling
Authors: Hirst Jack , Burke Amy , Hutchinson Edward
Published: April 2019

Most laboratory strains of influenza virus produce near-spherical virions, but clinical isolates also produce extended filaments whose biophysical properties are understudied. Most functional studies of filamentous influenza viruses do not include data on the concentration or lengths of the virions, making it hard to interpret their sometimes contradictory results. Furthermore, anecdotal reports suggest that filaments are damaged during routine laboratory handling. Therefore, to understand filament function we require a tool to assess the number and dimensions of filaments in a sample and an assessment of how filaments respond to standard handling procedures. We initially sought to analyse filament populations using negative stain particle counting, but found that this was low-throughput and could not detect particles longer than 10 µm. Instead, we used confocal microscopy with semi-automated image analysis. This allowed a high-throughput, quantitative analysis of length distributions in filament populations. Using this, we assessed the effects of pipetting, vortexing, sonicating, clarification and freezing on filaments. Most procedures did not appreciably alter filament dimensions. Pipetting and vortexing both slightly reduced filament numbers, but their effects were only appreciable after extended treatment. In contrast, freezing substantially reduced the number and median length of filaments, as well as creating ‘kinks’ in filaments which suggest damage to the capsid. We conclude that confocal microscopy can provide the basic measurements needed to interpret functional studies of filamentous strains. Using this approach, we found that freezing filaments causes previously unappreciated damage, which should be considered when planning further research.