bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in gastrointestinal microbial communities influence HIV-specific CD8+ T-cell responsiveness to immune checkpoint blockade
Authors: SahBandar Ivo N. , Chew Glen M. , Corley Michael J. , Pang Alina P.S. , Tsai Naoky , Hanks Nancy , Khadka Vedbar S. , Klatt Nichole R. , Hensley-McBain Tiffany , Somsouk Ma , Vujkovic-Cvijin Ivan , Chow Dominic C. , Shikuma Cecilia M. , Ndhlovu Lishomwa C.
Published: July 2020

Objectives:

The aim of this study was to examine the relationship between gut microbial communities in HIV-infected individuals on suppressive antiretroviral therapy (cART), and the peripheral HIV-Gag-specific CD8+ T-cell responses before and after ex-vivo immune checkpoint blockade (ICB).

Design:

Thirty-four HIV-seropositive, 10 HIV-seronegative and 12 HIV-seropositive receiving faecal microbiota transplant (FMT) participants were included. Gut microbial communities, peripheral and gut associated negative checkpoint receptors (NCRs) and peripheral effector functions were assessed.

Methods:

Bacterial 16s rRNA sequencing for gut microbiome study and flow-based assays for peripheral and gut NCR and their cognate ligand expression, including peripheral HIV-Gag-specific CD8+ T-cell responses before and after ex-vivo anti-PD-L1 and anti-TIGIT ICB were performed.

Results:

Fusobacteria abundance was significantly higher in HIV-infected donors compared to uninfected controls. In HIV-infected participants receiving Fusobacteria-free FMT, Fusobacteria persisted up to 24 weeks in stool post FMT. PD-1 TIGIT and their ligands were expanded in mucosal vs. peripheral T cells and dendritic cells, respectively. PD-L1 and TIGIT blockade significantly increased the magnitude of peripheral anti-HIV-Gag-specific CD8+ T-cell responses. Higher gut Fusobacteria abundance was associated with lower magnitude of peripheral IFN-γ+ HIV-Gag-specific CD8+ T-cell responses following ICB.

Conclusion:

The gut colonization of Fusobacteria in HIV infection is persistent and may influence anti-HIV T-cell immunity to PD-1 or TIGIT blockade. Strategies modulating Fusobacteria colonization may elicit a favourable mucosal immune landscape to enhance the efficacy of ICB for HIV cure.
High abundance of genus Prevotella is associated with dysregulation of IFN-I and T cell response in HIV-1-infected patients
Authors: Pinacchio Claudia , Scagnolari Carolina , Iebba Valerio , Santinelli Letizia , Innocenti Giuseppe P. , Frasca Federica , Bitossi Camilla , Scordio Mirko , Oliveto Giuseppe , Ceccarelli Giancarlo , Antonelli Guido , Mastroianni Claudio Maria , d’Ettorre Gabriella
Published: July 2020

Objective:

HIV-1-associated dysbiosis is most commonly characterized by overall decreased diversity, with abundance of the genus Prevotella, recently related to inflammatory responses.

Design:

A pilot study including 10 antiretroviral therapy-treated HIV-1-infected men and 50 uninfected controls was performed to identify the main gut dysbiosis determinants (e.g. Prevotella enrichment), that may affect mucosal antiviral defenses and T cell immunity in HIV-1-infected individuals.

Methods:

16rRNA gene sequencing was applied to the HIV-1-infected individuals’ fecal microbiota and compared with controls. Measurements of CD4+ and CD8+ T cell activation [CD38, human leukocyte antigen (HLA)-DR, CD38 HLA-DR] and frequencies of Th17, obtained from lamina propria lymphocytes isolated from five different intestinal sites, were performed by flow cytometry. IFNβ, IFNAR1 and MxA gene expression level was evaluated by real-time PCR in lamina propria lymphocytes. Nonparametric t tests were used for statistical analysis.

Results:

HIV-1-infected men had a significant fecal microbial communities’ imbalance, including different levels of genera Faecalibacterium, Prevotella, Alistipes and Bacteroides, compared with controls. Notably, Prevotella abundance positively correlated with frequencies of CD4+ T cells expressing CD38 or HLA-DR and coexpressing CD38 and HLA-DR (P < 0.05 for all these measures). The same trend was observed for the activated CD8+ T cells. Moreover, Prevotella levels were inversely correlated with IFN-I genes (P < 0.05 for IFNβ, IFNAR1 and MxA genes) and the frequencies of Th17 cells (P < 0.05). By contrast, no statistically significant correlations were observed for the remaining bacterial genera.

Conclusion:

Our findings suggest that Prevotella enrichment might affect gut mucosal IFN-I pathways and T cell response in HIV-1-infected patients, thus contributing to immune dysfunction.
The Anatomical Distribution of the Pudendal Nerve Block Injection: A Cadaveric Study
Authors: Takashima Yoko , Handler Stephanie J. , Zeno Aldene , Alvarez Pedro , Miyazaki Brian , Del Canto Isabel , Khamis Charles , Yazdany Tajnoos , Le Tam Hoang
Published: July 2020

Objective

The objective of this study was to assess the accuracy of commonly used injection locations of the pudendal nerve block by examining the proximity of the injected dye to the pudendal nerve in a cadaveric model.

Methods

Pudendal block injections at 4 sites were placed transvaginally on 5 cadaveric pelvises. These sites were 1 cm proximal to the ischial spine (black dye), at the ischial spine (red dye), 1 cm distal to the ischial spine (blue dye), and 2 cm lateral and 2 cm distal to the ischial spine (green dye). The cadavers were dissected via a posterior approach.

Results

We measured the shortest distance from the center of the dye-stained tissue to the pudendal nerve. As expected, the injections at the ischial spine (red) resulted in a distribution of dye closest to the pudendal nerve, averaging 3.0 ± 0.95 mm. Dyes at other sites were close to the nerve: 3.1 ± 1.00 mm (black), 3.6 ± 1.14 mm (blue), and 4.05 ± 1.28 mm (green).

Conclusions

Regardless of the injection site, all dyes were close the pudendal nerve, indicating accuracy. We observed wide variation in the dye distribution even though all injections were performed by the same provider, implicating lack of precision. Based on our findings, we propose that the most effective injection location is at the ischial spine because it is the closest to the pudendal nerve; however, all injections were within 4 mm of the pudendal nerve, suggesting that only 1 to 2 injections may be sufficient.
Telomere attrition with age in a wild amphibian population
Authors: Sánchez-Montes Gregorio , Martínez-Solano Íñigo , Díaz-Paniagua Carmen , Vilches Antonio , Ariño Arturo H. , Gomez-Mestre Ivan
Published: July 2020

Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (
Epidalea calamita
). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout their ontogeny, and that most attrition occurs during the first 1–2 years. We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.
The dawn of social bonds: what is the role of shared experiences in non-human animals?
Authors: Busia Laura , Griggio Matteo
Published: July 2020

Group-living animals can develop social bonds. Social bonds can be considered a type of social relationship characterized by frequent and consistent affiliative (non-reproductive) interactions. Social bonds with conspecifics bring many advantages, also in terms of direct fitness. A characteristic of social bonds is that they need time to develop. Several studies on humans have emphasized the fact that sharing experiences can affect the strength of social bonds. A similar trend can be spotted in non-human species. For example, a recent experiment showed that if chimpanzees watched a video together with a conspecific, they spent more time in proximity compared to conspecifics with whom they did not actively watch a video. Another experiment on fish showed that individuals who experienced a situation of high predation risk together, showed preference for each other compared to those who did not. As the link between shared experiences and social bonds is not explicitly recognized in non-human animals, the main goal of this work is to propose the exploration of this novel research path. This exploration would contribute to shed light on the evolutionary mechanisms of social bond (or friendship) development and maintenance between individuals in different vertebrate species, from fish to non-human primates.
Science-based approach to using growth rate to assess coral performance and restoration outcomes
Authors: Edmunds Peter J. , Putnam Hollie M.
Published: July 2020

One response to the coral reef crisis has been human intervention to enhance selection on the fittest corals through cultivation. This requires genotypes to be identified for intervention, with a primary basis for this choice being growth: corals that quickly grow on contemporary reefs might be future winners. To test for temporal stability of growth as a predictor of future performance, genotypes of the coral
Porites
spp. were grown in common gardens in Mo'orea, French Polynesia. Growth was measured every two to four months throughout 2018, and each period was used as a predictor of growth over the subsequent period. Area-normalized growth explained less than 29% of the variance in subsequent growth, but for biomass-normalized growth this increased to 45–60%, and was highest when summer growth was used to predict autumn growth. The capacity of initial growth to predict future performance is dependent on the units of measurement and the time of year in which it is measured. The final choice of traits to quantify performance must be informed through consideration of the species and the normalization that best capture the information inherent in the biological processes mediating variation in traits values.
Effects of 9,10-phenanthrenequione on antioxidant indices and metabolite profiles in
Takifugu obscurus
plasma
Authors: Jiang Shulun , Yang Jian , Fang Dian
Published: July 2020

Derived from polycyclic aromatic hydrocarbons (PAHs), oxygenated-PAHs (oxy-PAHs) may pose hazards to aquatic organisms, which remain largely unknown.
Takifugu obscurus
is an important anadromous fish species of high economic and ecological values. In the present study,
T. obscurus
was acutely exposed to 44.29 µg l
−1
9,10-phenanthrenequione (9,10-PQ) for 96 h. Changes of antioxidant indices and metabolite profiles in plasma were compared between 9,10-PQ treatment and the control. The results showed that 9,10-PQ treatment significantly increased malondialdehyde (MDA) content during 6 to 96 h, increased superoxide dismutase (SOD) and catalase (CAT) activities at 6 h, but decreased them at 96 h. These results indicated that 9,10-PQ induced oxidative stress to fish. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis revealed that four metabolic pathways were influenced in response to treatment with 9,10-PQ, including glycerophospholipid metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, purine metabolism and sulfur metabolism. These pathways are associated with antioxidant mechanisms, biosynthesis of neurotransmitters and innate immune functions. Thus, the as-obtained results confirmed that 9,10-PQ induced oxidative stress and raised concerns of neurotoxicity and immunotoxicity to fish. Overall, the present study posed a high environmental risk of oxy-PAHs to aquatic ecosystems.
Gait coordination in overground walking with a virtual reality avatar
Authors: Soczawa-Stronczyk Artur A. , Bocian Mateusz
Published: July 2020

Little information is currently available on interpersonal gait synchronization in overground walking. This is caused by difficulties in continuous gait monitoring over many steps while ensuring repeatability of experimental conditions. These challenges could be overcome by using immersive virtual reality (VR), assuming it offers ecological validity. To this end, this study provides some of the first evidence of gait coordination patterns for overground walking dyads in VR. Six subjects covered the total distance of 27 km while walking with a pacer. The pacer was either a real human subject or their anatomically and biomechanically representative VR avatar driven by an artificial intelligence algorithm. Side-by-side and front-to-back arrangements were tested without and with the instruction to synchronize steps. Little evidence of spontaneous gait coordination was found in both visual conditions, but persistent gait coordination patterns were found in the case of intentional synchronization. Front-to-back rather than side-by-side arrangement consistently yielded in the latter case higher mean synchronization strength index. Although the mean magnitude of synchronization strength index was overall comparable in both visual conditions when walking under the instruction to synchronize steps, quantitative and qualitative differences were found which might be associated with common limitations of VR solutions.
Exogenous testosterone increases the audience effect in healthy males: evidence for the social status hypothesis
Authors: Wu Yin , Zhang Yinhua , Ou Jianxin , Hu Yang , Zilioli Samuele
Published: July 2020

Several studies have implicated testosterone in the modulation of altruistic behaviours instrumental to advancing social status. Independent studies have also shown that people tend to behave more altruistically when being watched (i.e. audience effect). To date, little is known about whether testosterone could modulate the ﻿audience effect. In the current study, we tested the effect of testosterone on altruistic behaviour using a donation task, wherein participants were asked to either accept or reject a monetary transfer to a charity organization accompanying a personal cost either in the presence or absence of an observer. We administered testosterone gel or placebo to healthy young men (
n
= 140) in a double-blind, placebo-controlled, mixed design. Our results showed that participants were more likely to accept the monetary transfer to the charity when being observed compared to when they completed the task alone. More importantly, this audience effect was amplified among people receiving testosterone versus placebo. Our findings suggest that testosterone administration increases the ﻿audience effect and further buttress the social status hypothesis, according to which testosterone promotes status-seeking behaviour in a context-dependent manner.
Self-organization of river vegetation leads to emergent buffering of river flows and water levels
Authors: Cornacchia Loreta , Wharton Geraldene , Davies Grieg , Grabowski Robert C. , Temmerman Stijn , van der Wal Daphne , Bouma Tjeerd J. , van de Koppel Johan
Published: July 2020

Global climate change is expected to impact hydrodynamic conditions in stream ecosystems. There is limited understanding of how stream ecosystems interact and possibly adapt to novel hydrodynamic conditions. Combining mathematical modelling with field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution triggers spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a spatial separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. This self-organization process decouples both local flow velocities and water levels from the forcing effect of changing stream discharge. Field data from two lowland, baseflow-dominated streams support model predictions and highlight two important stream-level emergent properties: vegetation controls flow conveyance in fast-flowing channels throughout the annual growth cycle, and this buffering of discharge variations maintains water depths and wetted habitat for the stream community. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity.
Effects of ultraviolet-C on the spores of Bacillus subtilis and Bacillus velezensis suspension in phosphate buffered saline with their structural and molecular analysis using Raman-AFM imaging
Authors: Elegbeleye James , Gervilla Ramon , Roig-Sagues Artur , Buys Elna
Published: July 2020

Bacterial spores are of concern in food processing due to their ubiquity and resistance. This study seeks to determine the effect of ultraviolet C (UV-C) in the inactivation of spores of Bacillus subtilis and Bacillus velezensis that can result in enzymatic spoilage in foods using PBS as the suspension medium. Purified spore samples were treated under 1 pass in a UV-C reactor using 10 mL of spore inoculum with one dose of the radiation (410 mJ/cm2) for 10secs at room temperature. Aliquots of the treated samples were plated on tryptone soy agar supplemented with 0.6% glucose and the colonies counted. Flow cytometry analysis was done using 500 μL of both treated and control samples with a cell concentration of a ≥106 CFU/ml with propidium iodide (15 μM) and SYTO 9 (500 nM) used as live/dead stains. Samples were processed for microscopy (SEM and Raman-AFM Imaging). The maximum lethality is 2.5 for B. velezensis and the minimum is 0.1 for B. subtilis. Microscopic imaging of treated spores shows significant morphological disruption of the spore structure. The Raman spectroscopy analysis reveals the B. subtilis isolates to have the highest concentrations of dipicolnic acid (Ca+2DPA) as well as other compounds belonging to other functional groups. Flow cytometric analysis of treated spores reveals sub-populations unaccounted for by plate count. UV-C shows a promising application in the inactivation of resistant spores during processing of liquid foods such as milk.
Effects of Vibrio cholerae infection and colonization on the zebrafish intestinal microbiome
Authors: Breen Paul , Winters Andrew , Theis Kevin , Withey Jeffrey
Published: July 2020

Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae needs to colonize the intestine of an exposed host for any type of pathogenicity to occur. It is suspected that members of the resident intestinal microbial community need to be eliminated by V. cholerae in order for colonization, and subsequently disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal community. In this study, 16S rRNA gene sequencing was utilized to investigate how various strains of V. cholerae alter the aforementioned microbial profiles following an infection. We found that V. cholerae infection and subsequent colonization induced significant changes in the zebrafish intestinal microbiome, with specific members of the microbial community targeted. Additional salient differences to the microbial profile were observed based on the particular strain of V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae causes significant modulation to the zebrafish intestinal microbiome in order for infection and subsequent disease to occur.
Skin microbiome profiling and cultivation of healthy adult Indonesian skin
Authors: Malik Amarila , Sitti Khayyira Amalia , Elfa Rosdina Aulia , Ika Irianti Marina
Published: July 2020

Studies on the impact of skin microbiota on human health have been gaining more attention. The skin microbiome is considered to provide several probiotics for skin therapeutic. Beneficial bacteria mixtures (bacterial cocktail) isolated from targeted organs have shown promising modulatory activities for use in skin therapeutics. The objectives of this study were to determine and identify the microbial communities on the skin that can be potentially used as probiotics-postbiotics. Determination and identification of skin microbiota were carried out simultaneously by employing next-generation sequencing (NGS) of direct sampling, as well as by bacterial cultivation; twenty bacterial isolates with different characteristics were selected and identified by both culture-based methods and 16sRNA sequencing. We found that Actinobacteria and Firmicutes are the most abundant phylum present on the skin as presented by NGS data, which constitute to 67% and 28.59% of the whole bacterial population, consecutively. Three strains, i.e., Staphylococcus hominis (AN MK968325.1), Staphylococcus warneri (AN MK968315.1), and Micrococcus luteus (MK968318.1), were obtained from cultivable samples. They were potential to be developed further as probiotics in skin microbiome therapeutic as well as for postbiotic formulation. However, the promising formula of bacterial cocktail for skin microbiome therapeutic must be elucidated thoroughly to avoid unwanted effects by performing visual observation on agar plate and by molecular approach, q-PCR.
The Type VI secretion system in commensal Neisseria spp.
Authors: Calder Alan , Snyder Lori
Published: July 2020

A type 6 secretion system (T6SS) was recently identified in the genome sequence data of an isolate sourced from a throat swab of a volunteer that is believed to be N. subflava. The T6SS is one of the most recently discovered bacterial secretion systems and this is the first time it has been reported in Neisseriaceae. Since this discovery, genome sequence analyses for a number of other commensal Neisseria spp. has identified that in fact, two distinct T6SS types exist across Neisseriaceae. These two types are clearly defined and are different to one another in both their core gene sequences and organisation. The two systems also differ in the number of VgrG proteins required for toxic effector protein delivery, as well as type of effector associated with them. The predicted VgrG/effector combinations identified in our isolate are not common to all members of the same species and further analysis has identified a wide range of diversity in these components between different strains of the same species. The data provides possible evidence that T6SS positive commensal Neisseria spp. can acquire new VgrG/effector combinations through competitor killing. A number of putative effectors have so far been identified within the genome of our original isolate, including hydrolases, phospholipases, and nucleases. Whilst these are predicted to be antibacterial effectors, the conditions under which the T6SS system is activated, as well as demonstration of the function of the effectors still needs to be investigated experimentally.
Failing to control Maedi-Visna
Authors: Jones Scott , Houghton Lily , Eden Laura , McKay Heather , Curwen Alice , Davies Peers , Dunham Stephen , Lovatt Fiona , Tarlinton Rachael
Published: July 2020

Maedi-Visna is a lentivirus of sheep that causes lung disease and chronic wasting. It has been designated an “Iceberg disease” by the UK sheep industry levy board with a very large burden of subclinical disease that is often not apparent until losses in an individual flock become catastrophic. Disease prevalence in the UK is thought to have doubled in the last 10 years, however farmer and veterinary awareness of the disease is poor. There is no vaccine and treatment is not cost effective, meaning that the only realistic control option is culling of affected animals.

Current testing protocols use MV gag protein ELISAs. A long lag time between infection and antibody production means that many animals are missed on flock screening and repeated rounds of testing over a period of years are necessary remove all infected animals. Preliminary testing of flocks that have attempted eradication indicates that those that do not keep testing until all animals are negative fail to eliminate the disease and that prevalence rates can even increase substantially in these flocks. The viruses extreme variability confounded attempts to develop a qPCR capable of detecting all variants, indeed deep sequencing was required to establish which strains of virus are currently present in UK sheep as there has been substantial genetic drift since the last sequencing studies (performed more than 20 years ago). More promisingly virus was detectable in nasal swabs of experimental animals at least offering a possibility for sampling methods that can be done by farmers themselves.
Testing for novel inhibitors of periodontitis-associated sialidases
Authors: R.P Galleh , Chen Xi , D.W Lambert , G.P Stafford
Published: July 2020

The microorganisms associated with severe periodontitis are the periodontal pathogens of the red complex: Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola. These organisms cleave sialic acids found at the terminal end of host glycoconjugates by hydrolysing the glycosidic linkages with their expressed sialidases, thereby affecting the integrity of the host periodontium and promoting disease progression. Both P. gingivalis (SiaPG) and T. forsythia (NanH) sialidase enzymes were purified using HisTag affinity chromatography and a range of putative synthetic and plant-based inhibitors were tested for their ability to inhibit both enzymes using a MUNANA cleavage assay. Investigation of sialidase inhibitory activity of these compounds revealed that the plant derived alkaloids: Epicatechin gallate (IC50 = 21.75μM and 120.9μM) and Berberine chloride (IC50 = 106.2μM and 125.5μM) were more effective inhibitors of both SiaPg and NanH enzymes than the anti-influenza drug Zanamivir, an FDA approved viral neuraminidase inhibitor. Finally, a range of newly synthesized sialic acid analogues were effective in the micromolar to nanomolar range against both SiaPg and NanH enzymes with compound 2e3aDFNeu5Ac9N3 having an IC50 of (3.846μM and 49.40nM) respectively. The data suggests several novel inhibitors of these enzymes that might have future use as novel drugs against diseases such as periodontitis, and which we are currently testing further in host-pathogen interaction studies.
Functional antimicrobial substance and their bioactive compounds extracted from secondary metabolites of Aspergillus terreus
Authors: Olanbiwoninu Afolake , Oleru Kelechi , Olayiwola Olusola , Popoola Bukola
Published: July 2020

Methods: Fungal isolates were isolated fromsoil samples using Potato Dextrose Agar (PDA). The plates were incubated at 25°C for 72 – 96 h and identification was based on molecular techniques by targeting 18S rRNA. Isolation of bioactive compounds from the extracts was carried out by GC-MS analysis. The extracted secondary metabolites was concentrated by evaporation of the solvents at room temperature. Concentrated extract was constituted by dissolving it in DMSO and stored at 4°C for antimicrobial assay.

Results: Two hundred and fifty six (256) fungal isolates were isolated and sixteen (16) of them showed promising antimicrobial potential. Phylogenetic tree showed evolutionary trend of the fungus with 99% similar to Aspergillus terreus. The broad spectrum activity of the antimicrobial substance were observed to be24.7±4.619 and 26.0±0.000 against Gram positive and negative respectively.The bioactive compounds isolated were phenols, amines, terpenes and fatty acid esters.

Conclusion: The functional and new antibiotics can be obtained from fungal family especially in this era of multi-drug resistant (MDR) bacteria. It is observed that there are functional antimicrobial substances associated with Aspergillus terreus. The extracted substances was found to be active against MDR bacteria in vitro. The bioactive compounds obtained from the GC MS analysis revealed the nature of compounds and some of these compounds have been documented in different areas of antimicrobial and related properties.
Characterisation of anti-pseudomonad activity of hyper-arid Micromonospora species
Authors: Mark David , DeWald Jan , Dorador Cristina , Tucker Nicholas , Herron Paul
Published: July 2020

The opportunistic pathogen Pseudomonas aeruginosa is a major cause of nosocomial infections, and has been categorised by the World Health Organisation as a “Priority 1: Critical” target for research and development of novel antibiotics owing to its intrinsic multi-resistance and ability to acquire novel resistance mechanisms.

One strategy for discovering novel antibiotics is the identification and characterisation of metabolites with antimicrobial activity. Members of the bacterial phylum Actinobacteria are historic source of these metabolites, in particular the genus Streptomyces. However, other genera have not received this same level of interest despite sharing the capacity to biosynthesise a diverse array of metabolites. One such genus is Micromonospora, responsible for production of the broad-spectrum aminoglycoside antibiotic gentamicin (M. purpurea).

Here we present three Micromonospora species isolated from the Atacama Desert, Chile; that possess anti-pseudomonad bioactivity inducible by culture on International Streptomyces Project (ISP) Media. In addition, preliminary data indicates that this activity can be affected by the addition of P. aeruginosa conditioned media. In parallel, short-read Illumina sequencing was used to assemble draft genomes for these strains, enabling antiSMASH analysis of putative biosynthetic gene clusters. In addition to this, estimated Average Nucleotide Identity (ANI) as calculated by the autoMLST server indicates that these strains may all be novel Micromonospora species.

The results of this work serve to highlight the biosynthetic capacity of an understudied genus of bacteria, as well as the value of examining underexplored environments and habitats in the search for novel bioactive molecules.
Selection and niche trade-offs in biofilm-forming bacterial communities in experimental microcosms
Authors: Jerdan Robyn , Cameron Scott , Donaldson Emily , Spiers Andrew
Published: July 2020

Static microcosms are a well-established system used to study the adaptive radiation of Pseudomonas fluorescens SBW25 and the adaptive biofilm-forming mutants known as the Wrinkly Spreaders (WS). We have developed this system to investigate selection within multi-species communities using a soil-wash inoculum dominated by biofilm-competent pseudomonads. Here we present community and isolate-level analyses of one serial-transfer experiment in which replicate populations were selected for over ten transfers and 60 days. Although no significant trends in improving community biofilm characteristics or total microcosm productivity were observed, a significant shift in biofilm-formation and microcosm growth by individual isolates recovered from the initial soil-wash inoculum and final transfers indicated that these communities were subject to selection for growth in these microcosms. Surprisingly, the fitness of the archetypal WS was poor when competing against community samples, and having compared the cell densities in the low-O2 region of liquid column below the biofilm, we suggest that part of the community’s fitness advantage comes from the ability to colonise this under-utilised niche as well as to compete at the A-L interface. Samples from the community biofilms and the low-O2 region were able to re-colonize both niches and many final transfer isolates grew throughout the liquid column as well as forming A-L interface biofilms. This suggests that there is a trade-off between fast growth under highly competitive conditions at the A-L interface and slower growth with less competition in the low-O2 region, with some isolates taking a bet-hedging approach a colonizing both niches in our microcosm system.
Enhancing the natural toxicity of Salmonella Typhimurium towards tumours
Authors: Alfaqeer Najla , Wall Donal
Published: July 2020

Background and objective:
Salmonella is the underlying cause of foodborne diseases and poses a major public health problem worldwide. Research has developed a method to efficiently treat cancer using some of the same bacteria behind food poisoning, one of these bacteria is Salmonella which targets and penetrats tumours specifically by being attracted to the compounds produced by tumour cells and accumulating at the tumour site and inducing inflammation. In this project we aim to investigate the mechanism of Salmonella Typhimurium which has a tremendous ability to invade, replicate and compete to survive inside the cells by virtue of effector proteins such as: sipA, sipB, and AvrA which it possesses.

Method: The S.Typhimurium strains used are wild-type SL1344 ( ΔsipA, ΔsipB, ΔavrA and VV341) and attenuated strain of SL7207. Bacteria were cultured in LB broth in a 37 °C shaker overnight to reach a stationary phase before using it to infect B16F10 (mouse melanoma).

Results: The initial results show that the infection of B16F10 with wild-type SL1344 had a high level of invasion compared to the low number of bacteria with the deletion of sipB which impaired its entry into the cell. Similarly, the mutant strains ΔsipA and ΔavrA show an increasing number of intracellular bacteria, like the wild-type strain. We will be investigating further on the innate mechanisms of Salmonella in disrupting tumour growth and progression, that might help maximize the potential of using these bacteria in monotherapy or in tandem with other useful therapies.
The selection and co-selection of antimicrobial resistance by non-antibiotic drugs and plant protection products
Authors: Murray Laura , Boxall Alistair , Snape Jason , Gaze William , Murray Aimee
Published: July 2020

Non-antibiotic compounds including metals and biocides co-select for clinically relevant antimicrobial resistance (AMR) genes. Presently, there is little research looking at the effects of plant protection products (PPPS) such as herbicides and insecticides on the development and spread of resistance. Agricultural activities require the direct application of PPPs in large quantities and at high concentrations to soil. These chemicals are applied alongside antibiotics and manures which may contain antibiotic residues, other selective agents and resistant bacteria. The selection pressure exerted by this mixture of chemicals may result in enrichment of resistant bacteria and/or the exchange of resistance genes between environmental and clinically relevant bacteria. The impact of these chemicals on AMR and microbial diversity in terrestrial environments is poorly understood.

PPPs from different substance groups were tested for antimicrobial activity using the SELECT method developed by Murray et al. (2019; under review). In this method, bacterial communities were exposed to PPPs and selective concentrations were identified by a significant reduction in community growth. Results from these experiments determined the concentration at which long term evolution experiments were carried out in soil microcosms. Selection for AMR was investigated using metagenomic analysis and targeted real-time PCR.
A potential new paradigm of denitrification in pathogenic Neisseria
Authors: Bolton Jack , Djoko Karrera , Waldron Kevin
Published: July 2020

Metals are bacterial nutrients. Upon infection by microorganisms, the animal host innate immune system typically reduces the availability of metals. In response, bacterial pathogens can activate pathways for metal uptaketo avoid metal starvation. This competition for metals at the host-pathogen interface is termed “nutritional immunity”.

We are interested in how the obligate human pathogen Neisseria gonorrhoeae acquires nutrient copper (Cu). This Gram-negative bacterium expresses several respiratory cuproenzymes that are required for growth and metabolism in both aerobic and anaerobic conditions. These cuproenzymes include the putative nitrous oxide reductase (NosZ). NosZ contains 12 Cu atoms per functional dimer and it catalyses the reduction of nitrous oxide (N2O) to dinitrogen (N2). This reduction is an intermediate step in the denitrification pathway, in which nitrite (NO2) is used as the terminal electron acceptor for respiration instead of O2. In this project, we will determine whether NosZ is expressed as a functional enzyme in N. gonorrhoeae. We will then examine how this enzyme acquires nutrient Cu and subsequently assembles its active site.

Given the rise in antibiotic resistance and the worldwide recognition of multidrug-resistant N. gonorrhoeae as a major threat to public health, we hope that a fundamental understanding of the physiology and metabolism of this organism will yield new strategies for anti-infectives, for instance by manipulating Cu availability at the site of infection.
Fatty acids as novel treatment options for Pseudomonad and Staphylococcal infection
Authors: Ukachukwu Faith , Snyder Lori , Alany Raid
Published: July 2020

Pseudomonas aeruginosa and Staphylococcus aureus are bacteria pathogens that cause a myriad of infections affecting various sites in the body including the eyes, ears, lungs, skin, heart, bones, and blood amongst others. These bacteria can be disseminated via the blood to other parts of the body away from the primary site of infection and consequences vary from mild to severe with death occurring in certain instances. Both bacterial infections can occur individually, as well as in co-infection resulting in even worse outcomes. P. aeruginosa and S. aureus exhibit multidrug resistance against current antibiotic treatment regimens, which accentuates the challenge in managing the infections caused by these bacteria. To prevent the looming era of untreatable bacterial infections, alternative treatment regimens that are cost effective and accessible are needed. To explore novel treatment options, twenty-five organic compounds comprising fatty acids and their derivatives were screened for antibacterial activity in broth microdilution assay to determine the minimum inhibitory concentration and minimum bactericidal concentration against both P. aeruginosa and S. aureus. Five candidates (N–nonanoic acid, butyric acid, heptanoic acid, palmitoleic acid, and isopropyl myristate) were effective against P. aeruginosa. Seven candidates (N–nonanoic acid, palmitoleic acid, tridecanoic acid, sebaic acid, undecanoic acid, monolaurin, and monocaprin) were effective against S. aureus. Candidates such as N–nonanoic acid and palmitoleic acid were effective against both P. aeruginosa and S. aureus, demonstrating that the same fatty acids show potential to be used against both Gram negative and Gram positive bacterial infections.
Foot-and-mouth disease virus non-structural protein 3A modulates cellular innate immune responses to influence host tropism
Authors: Chakravarti Soumendu , Wright Caroline , Howes Emma , Kock Richard , Jackson Terry , Tuthill Toby
Published: July 2020

The picornavirus foot-and-mouth disease virus (FMDV) is responsible for one of the most significant diseases of livestock, leading to large economic losses due to reduced productivity and trade embargoes for areas not certified as disease-free. The picornavirus non-structural protein 3A is involved in replication of the viral RNA genome and is implicated in host tropism of several picornaviruses. Deletions in the C-terminus of 3A have been observed in FMDV outbreaks specific for swine and such viruses are non-pathogenic in cattle. The mechanism for species specific attenuation of FMDV is unknown.

We have shown that FMDV containing a C-terminal deletion in 3A is attenuated in bovine cell culture and that the attenuated phenotype can be reversed by the JAK1/2 inhibitor Ruxolitinib (Rux), identifying a role for the induction of interferon stimulated genes (ISGs) in the restricted bovine tropism of the 3A-deleted virus.
Generation of Equine Herpesvirus type 1 glycoprotein pseudotyped lentiviral particles for use as a tool for tropism and diagnostic studies
Authors: Di Genova Cecilia , Paillot Romain , Pronost Stéphane , Sutton Gabrielle , Temperton Nigel , Scott Simon
Published: July 2020

Equine herpesviruses (EHVs) are enveloped DNA viruses infecting mainly members of the Equidae family and also members of other taxa. EHVs primarily causing respiratory disease, however EHV type 1 (EHV-1) can produce cases of a neurological disease, abortion and neonatal death, sometimes as regional outbreaks. Thus these viruses represent a welfare issue for the equine industry and scientific focus for researchers. EHV-1 presents a complex array of 12 glycoproteins on its surface envelope, but it is unclear which ones 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 perfect study tool. In 2016, Rogalin & Heldwein successfully generated the first functional herpesvirus pseudotype, bearing the four glycoproteins gB, gD, gH and gL from human Herpes simplex 1. Our study is the first to attempt pseudotyping of EHV-1. We have employed homologous glycoproteins of EHV-1 in lentivirus PV generation, using different mammalian cells (e.g. epithelial, dermal, CNS) as transduction targets. The glycoprotein sequences obtained from an EHV-1 strain isolated from organs of aborted foetus during a significant outbreak in Normandy (France) in 2010. Future work will focus on the development of a PV assay for detection of neutralising antibodies in naturally infected horses for diagnostics and for vaccine evaluation.
Microwaves can reverse the tumour phenotype of human papillomavirus type 16 (HPV16)-positive keratinocytes in 3D cell culture models: a novel therapy for HPV-associated disease?
Authors: Epifano Ilaria , J. Conley Michaela , Stevenson Andrew , Doorbar John , V. Graham Sheila
Published: July 2020

High-risk human papillomavirus (HPV) is the causative agent of benign, precancerous and cancerous lesions, in both anogenital and oropharyngeal sites. Increased expression of the viral oncoproteins E6 and E7 are responsible for tumour progression. The treatment of these precancerous and cancerous lesions is invasive, painful and with long-term side effects. Localised microwaves have been used successfully in the clinic for the treatment of verrucas, which are caused by low-risk HPV genotypes (>75% success rate versus >33% for cryotherapy). Moreover, local hyperthermia is known to have anti-tumour effects.

Ten-second microwave treatment of 3D in vitro-grown cervical tumour tissues (HPV16-positive SiHa cell) resulted in cell death in the treated zone while the tissue integrity was disrupted in the adjacent area. Microwaves induced apoptosis (induction of cleaved caspase 3) and autophagy (induction of LC3) and inhibited cell proliferation (loss of Ki67 and MCM2) in the entire tissue. Furthermore, HPV16 E6 and E7 expression was reduced in cells in the treated and transition zones, with subsequent induction of expression of the apoptosis-regulator, p53 over a 24 hour period following microwave treatment. Thermal stress, identified with the Heat Shock Protein 70 (HSP70) and translational stress identified by G3BP expression, was observed in the transition zone.

In conclusion, we demonstrate that the microwave treatment induces cell stress pathways and inhibits HPV oncoprotein expression that causes tumour progression. Induction of apoptosis and reduced cell proliferation suggest a reversal of the cervical tumour phenotype in the 3D tissues.
Characterisation of surfactant-expressing bacteria and their potential bioremediation properties from hydrocarbon-contaminated and uncontaminated soils
Authors: Bamanga Raji , Y. Deeni Yusuf , Spiers Andrew , Cameron Scott
Published: July 2020

We are investigating characteristics associated with oil degradation amongst bacteria isolated from clean and hydrocarbon contaminated soils from Nigeria and the UK.Our focus has been to identify bacteria expressing surfactants following isolation on Pseudomonas selective (PSA-CFC) and non-selective nutrient media and investigate the nature of surfactants, heavy metal resistance and hydrocarbon-degrading enzymes expressed by the bacteria. Of five sites sampled, a total of 1460 colonies were tested using the drop collapse assay, and 110 were found to express surfactants reducing liquid surface tensions as assessed by quantitative tensiometry to between 24.7 and 26.7 mN.m-1 (Tukey-Kramer HSD, α=0.05). We undertook a range of growth and behaviour-based assays on 60 selected strain which, when investigated by Hierarchical cluster analysis (HCA) demonstrated that this collection showed considerable phenotypic diversity. Eight out of the 60 strains could grow at a high temperature (50 °C), 35 of the 60 strains utilized diesel as a sole carbon source, and most of the strains could tolerate high concentrations (up to 20 mM) of heavy metals. Identification by 16S rDNA sequencing revealed that some of the strains belong to Pseudomonas, Bacillus, and Stenotrophomonas genera. We found using bioinformatics analysis of eight-selected draft genome sequences (AntiSMASH and RAST) NRPS-like (probable surfactants), cytochrome P450, catechol-1,2/2,3-dioxygenase, lipase, and heavy metal resistance gene sequences. We intend to use the information provided in this research to select strains for potential applications in in-situor ex-situ bioremediation of hydrocarbon-contaminated soils.
Design of stable Enterovirus 71 virus like particles (VLPs) as a potential approach to vaccine development
Authors: Martyna Agnieszka , Fox Helen , Macadam Andrew
Published: July 2020

We have previously described the design of stable and immunogenic polio virus-like particles (VLPs) (Fox, et al. 2017) as an alternative approach to vaccine production. Unlike current polio vaccines, recombinantly-expressed VLP vaccines are non-infectious so would pose no risk of accidental escape from production plants, threatening eradication. To do this we devised a pipeline for the identification of stabilising mutations which could then be combined in a single construct to produce suitable particles; this strategy may have applications for other enterovirus vaccines.

Enterovirus 71 (EV71) is one of causative agents of hand, foot and mouth disease which is usually mild but in some cases neurological and systemic complications may occur. Recently there have been several outbreaks with significant mortality in South East Asia as well as increasing numbers of reports of outbreaks in Europe. VLP vaccines might be a useful alternative to inactivated vaccines currently in use or development.

EV71, like poliovirus, produces empty particles that are antigenically different from the virion. If, like poliovirus, these empty particles are less immunogenic than the virion, it would be necessary to stabilise them in the native conformation. We are attempting to do this (1) by incorporating modifications that proved successful in the context of poliovirus and (2) by identifying new candidate mutations using an analogous pipeline. Here we will report the characterisation of a range of different modifications that have stabilising and de-stabilising effects on EV71 particles as well as unexpected effects on morphogenesis.