bluuebunny/crossref_metadata_2025 huggingface dataset:
Iontophoretic Transepithelial Collagen Cross-Linking Versus Epithelium-Off Collagen Cross-Linking in Pediatric Patients: 3-Year Follow-Up
Authors: Buzzonetti Luca , Petrocelli Gianni , Valente Paola , Iarossi Giancarlo , Ardia Roberta , Petroni Sergio , Parrilla Rosa
Published: April 2019

Purpose:

To compare 3-year iontophoretic transepithelial corneal cross-linking (I-ON CXL) outcomes with epithelium-off collagen cross-linking (epi-off CXL) in pediatric patients.

Methods:

Forty eyes of 28 consecutive pediatric patients [mean age 14.3 ± 2.5 (SD) years; range, 9–18 years] with keratoconus were evaluated. Twenty eyes of 15 patients underwent I-ON and 20 eyes of 13 patients epi-off CXL. Mean corrected distance visual acuity, spherical equivalent, maximum keratometry (Kmax), posterior elevation of the thinnest point, and thickness of the thinnest point were evaluated. The Student t test was used to compare baseline and postoperative data. Keratoconus progression as a function of preoperative Kmax and cone location was evaluated.

Results:

At 36 months, corrected distance visual acuity statistically improved (from 0.18 ± 0.1 to 0.10 ± 0.1 logarithm of the minimum angle of resolution) in epi­off CXL, whereas spherical equivalent and posterior elevation of the thinnest point did not significantly change. Mean Kmax increased from the baseline +0.8 diopters (D) in epi-off and +2.9D in I-ON. In both groups, the thinnest point decreased. Keratoconus progression, defined by an increase of Kmax reading of the anterior corneal surface of at least 1.00D, occurred in 25% of epi-off and 50% of I-ON CXL over the 3-year period. Kmax value in I-ON, and cone location in both groups, seemed to be factors influencing the disease progression.

Conclusions:

In pediatric patients, 3 years after treatment, epi-off CXL halted keratoconus progression in 75% of eyes, whereas I-ON CXL seemed to slow down keratoconus progression in 50% of eyes, mainly in those with highest Kmax and paracentral cone.
Continued Disparities in Postpartum Follow-Up and Screening Among Women With Gestational Diabetes and Hypertensive Disorders of Pregnancy
Authors: Jones Emily J. , Hernandez Teri L. , Edmonds Joyce K. , Ferranti Erin P.
Published: April 2019

The postpartum period represents a critical window to initiate targeted interventions to improve cardiometabolic health following pregnancies complicated by gestational diabetes mellitus and/or a hypertensive disorder of pregnancy. The purpose of this systematic review was to examine studies published since 2011 that report rates of postpartum follow-up and risk screening for women who had gestational diabetes and/or a hypertensive disorder of pregnancy and to identify disparities in care. Nine observational studies in which postpartum follow-up visits and/or screening rates were measured among US women following pregnancies complicated by gestational diabetes and/or a hypertensive disorder of pregnancy were reviewed. Rates of postpartum follow-up ranged from 5.7% to 95.4% with disparities linked to black race and Hispanic ethnicity, low level of education, and coexisting morbidities such as mental health disorders. Follow-up rates were increased if the provider was an obstetrician/endocrinologist versus primary care. Payer source was not associated with follow-up rates. The screening rate for diabetes in women who had gestational diabetes did not exceed 58% by 4 months across the studies analyzed, suggesting little improvement in the last 10 years. While women who had a hypertensive disorder appear to have had a postpartum blood pressure measured, it is unclear whether follow-up intervention occurred. Overall, postpartum screening rates for at-risk women remain suboptimal and vary substantially. Further research is warranted including reliable population-level data to inform equitable progress to meeting the evidence-informed guidelines.
Inconsistency Between Contrast-Enhanced CT and Bone Scintigraphy in Revealing Radiation Nephritis
Authors: Zhu Wenjia , Zhen Hongnan , Ding Ning , Jing Hongli , Huo Li
Published: April 2019

A 34-year-old woman with pancreatic acinar cell carcinoma underwent a 99mTc-MDP bone scan to rule out potential bone metastasis because of back pain 18 months after radiation therapy. The bone scintigraphy revealed increased uptake over the upper pole of both kidneys corresponding to the portions of the kidneys included within the radiation field, consisting with radiation nephritis.
Synchronous Paraganglioma Masquerading as 68Ga-PSMA PET/CT–Avid Metastasis in Carcinoma Prostate—How Specific Is 68Ga-PSMA PET/CT?
Authors: Tyagi Shantanu , Singh Shrawan Kumar , Narain Tushar Aditya , Singh Harmandeep , Kumar Rajender , Vadi Shelvin Kumar
Published: April 2019

We present a case of biopsy-proven prostatic adenocarcinoma with a tracer-avid left paravertebral location at D4 to D5 vertebrae, suggestive of metastasis. However, in view of uncommon location of single-site metastasis at paravertebral region with no tracer-avid regional lymphadenopathy, image-guided biopsy was done, which was suggestive of paraganglioma. 68Ga-PSMA is known to have variable tracer avidity in multiple nonprostatic benign as well as malignant lesions, and our case adds to the list of nonspecific uptake by this once considered “specific” to prostate PET radiotracer.
Alloreactive T Cells Display a Distinct Chemokine Profile in Response to Conditioning in Xenogeneic GVHD Models
Authors: Kawasaki Yasufumi , Sato Kazuya , Nakano Hirofumi , Hayakawa Hiroko , Izawa Junko , Takayama Norihito , Mashima Kiyomi , Oh Iekuni , Minakata Daisuke , Yamasaki Ryoko , Morita Kaoru , Ashizawa Masahiro , Yamamoto Chihiro , Hatano Kaoru , Fujiwara Shin-ichiro , Ohmine Ken , Muroi Kazuo , Ito Ryoji , Hayakawa Morisada , Ohmori Tsukasa , Kanda Yoshinobu
Published: April 2019

Background.

Chemokines and chemokine receptors are potential targets for the prevention and treatment of graft-versus-host disease (GVHD). The objective of the current study is to determine the clinical relevance of xenogeneic transplantation models in terms of host and donor chemokine profiles and, if this is the case, to assess the clinical efficacy of C–C chemokine receptor (CCR) 5 antagonist maraviroc for the prevention of GVHD using this model.

Methods.

Xenogeneic GVHD was induced by intravenous injection of 5 × 106 human pan T cells into NOD/Shi-scid-IL2rγ
null
(NOG) mice or MHC class I/II-deficient NOG mice in the presence or absence of total body irradiation before transplantation.

Results.

Extensive tissue destruction with human T-cell infiltration was observed throughout the body, particularly in lungs and liver, but relatively mild in gut. Consistent with this finding, quantitative polymerase chain reaction confirmed the upregulation of mouse CXC chemokine ligand (CXCL) 9 and CXCL10 in lungs and CCL4 in lungs and liver but not in gut. The addition of total body irradiation (1) led to the early release of mouse CCL4 and CXCL10, (2) upregulated a number of chemokine-related genes in human T cells, (3) induced higher expression of CCR5 on human CD4+ and CD8+ T cells and CXCR3 on human CD4+ T cells, and (4) promoted their migration and proliferation in organs, resulting in more severe tissue damage. In this context, pharmacological CCR5 blockade neither ameliorated GVHD nor prolonged survival in NOG mice.

Conclusions.

Our experimental data do not demonstrate clinical benefit of CCR5 antagonist for the prevention of GVHD in a myeloablative setting.
Impact of Induction Immunosuppression Strategies in Simultaneous Liver/Kidney Transplantation
Authors: Kamal Layla , Yu Jonathan W. , Reichman Trevor W. , Kang Le , Bandyopadhyay Dipankar , Kumar Dhiren , King Anne , Gautam Ujwal , Bhati Chandra , Yakubu Idris , Lacy Kevin , Levy Marlon , Gupta Gaurav
Published: April 2019

Background.

There is scant data on the use of induction immunosuppression for simultaneous liver/kidney transplantation (SLKT).

Methods.

We analyzed the Organ Procurement and Transplant Network registry from 1996 to 2016 to compare outcomes of SLKT, based on induction immunosuppression.

Results.

Of 5172 patients, 941 (18%) received T-cell depletion induction, 1635 (32%) received interleukin 2 receptor antagonist (IL2-RA), and 2596 (50%) received no induction (NI). At 5 years, patient survivals were 68% in the T-cell group, 74% in the IL2-RA group, and 71% in the NI group (P = 0.0006). Five-year liver and kidney allograft survivals were 67% and 64% in the T-cell group, 73% and 70% in the IL2-RA group, and 70% and 68% in the NI group (P = 0.001 and 0.003), respectively. On multivariate analysis, the type of induction had no impact on patient or allograft survival. Maintenance steroids and calcineurin inhibitors (CNIs) at discharge were associated with improved patient and graft survival (steroids: patient survival hazard ratio [HR] 0.37 [0.27–0.52], liver survival HR 0.43 [0.31–0.59], kidney survival HR 0.46 [0.34–0.63]; P < 0.0001, CNI: patient survival HR 0.3 [0.21–0.43], liver survival HR 0.3 [0.2–0.44], kidney survival HR 0.4 [0.26–0.59]; P < 0.0001). CNI maintenance in patients who received T-cell induction was associated with decreased patient, liver, and kidney allograft survivals (respective HR: 1.4 [1.1, 1.8]; 1.5 [1.1, 1.9]; 1.3 [1.08, 1.7]; P < 0.05)

Conclusion.

Induction immunosuppression had no impact on patient and allograft survival in SLKT, while maintenance steroids and CNI were associated with improved patient and graft survivals. Given the inherent limitations of a registry analysis, these findings should be interpreted with caution.
Micro/nano-hierarchical structured TiO
2
coating on titanium by micro-arc oxidation enhances osteoblast adhesion and differentiation
Authors: Pan Xumeng , Li Yada , Abdullah Adil O. , Wang Weiqiang , Qi Min , Liu Yi
Published: April 2019

Nano-structured and micro/nano-hierarchical structured TiO
2
coatings were produced on polished titanium by the micro-arc oxidation (MAO) technique. This study was conducted to screen a suitable structured TiO
2
coating for osteoblast adhesion and differentiation in dental implants. The formulation was characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD) and wettability testing. Adhesion, proliferation and osteogenic differentiation of MG63 cells were analysed by SEM, Cell Counting Kit-8 (CCK-8) and quantitative real-time PCR. The micro/nano-hierarchical structured TiO
2
coating with both slots and pores showed the best morphology and wettability. XRD analysis revealed that rutile predominated along with a minor amount of anatase in both TiO
2
coatings. Adhesion and extension of MG63 cells on the micro/nano-hierarchical structured TiO
2
coating were the most favourable. MG63 cells showed higher growth rates on the micro/nano-hierarchical structured TiO
2
coating at 1 and 3 days. Osteogenic-related gene expression was markedly increased in the micro/nano-hierarchical structured TiO
2
coating group compared with the polished titanium group at 7, 14 and 21 days. These results revealed the micro/nano-hierarchical structured TiO
2
coating as a promising surface modification and suitable biomaterial for use with dental implants.
Opsin genes of select treeshrews resolve ancestral character states within Scandentia
Authors: Duytschaever Gwen , Janiak Mareike C. , Ong Perry S. , Wells Konstans , Dominy Nathaniel J. , Melin Amanda D.
Published: April 2019

Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (
OPN1LW
) of the Bornean smooth-tailed treeshrew (
Dendrogale melanura
). The opsin, by inference, is red-shifted by
ca
6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (
Dendrogale murina
) and the Mindanao treeshrew (
Tupaia everetti
, the senior synonym of
Urogale everetti
). We found that the opsin genes are under purifying selection and that
D. murina
shares the same substitution as its congener, a result that distinguishes
Dendrogale
from other treeshrews, including
T. everetti.
We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.
Behavioural patterns of vocal greeting production in four primate species
Authors: Fedurek Pawel , Neumann Christof , Bouquet Yaëlle , Mercier Stéphanie , Magris Martina , Quintero Fredy , Zuberbühler Klaus
Published: April 2019

Social animals have evolved a range of signals to avoid aggressive and facilitate affiliative interactions. Vocal behaviour is especially important in this respect with many species, including various primates, producing acoustically distinct ‘greeting calls’ when two individuals approach each other. While the ultimate function of greeting calls has been explored in several species, little effort has been made to understand the mechanisms of this behaviour across species. The aim of this study was to explore how differences in individual features (individual dominance rank), dyadic relationships (dominance distance and social bond strength) and audience composition (presence of high-ranking or strongly bonded individuals in proximity), related to vocal greeting production during approaches between two individuals in the philopatric sex of four primate species: female olive baboons (Papio anubis), male chimpanzees (Pan troglodytes), female sooty mangabeys (Cercocebus atys) and female vervet monkeys (Chlorocebus pygerythrus). We found that female vervet monkeys did not produce greeting calls, while in the other three species, low-ranking individuals were more likely to call than high-ranking ones. The effects of dyadic dominance relationships differed in species-specific ways, with calling being positively associated with the rank distance between two individuals in baboons and chimpanzees, but negatively in mangabeys. In none of the tested species did we find strong evidence for an effect of dyadic affiliative relationships or audience on call production. These results likely reflect deeper evolutionary layers of species-specific peculiarities in social style. We conclude that a comparative approach to investigate vocal behaviour has the potential to not only better understand the mechanisms mediating social signal production but also to shed light on their evolutionary trajectories.
Asynchrony induces polarization in attraction-based models of collective motion
Authors: Strömbom Daniel , Hassan Tasnia , Hunter Greis W. , Antia Alice
Published: April 2019

Animal groups frequently move in a highly organized manner, as represented by flocks of birds and schools of fish. Despite being an everyday occurrence, we do not fully understand how this works. In particular, what social interactions between animals give rise to the flock structures we observe? This question is often investigated using self-propelled particle models where particles represent the individual animals. These models differ in the social interactions used, individual particle properties, and various technical assumptions. One particular technical assumption relates to whether all particles update their headings and positions at exactly the same time (synchronous update) or not (asynchronous update). Here, we investigate the causal effects of this assumption in an attraction-only model and find that it has a dramatic impact. Polarized groups do not form when synchronous update is used, but are produced with asynchronous update, and this phenomenon is robust with respect to variation in particle displacements and inclusion of noise. Given that many important models have been implemented with synchronous update only, we speculate that our understanding of the social interactions on which they are based may be incomplete. Perhaps previously unobserved phenomena will emerge if other potentially more realistic update schemes are used.
Evolution and phylogeography analysis of diploid and polyploid
Misgurnus anguillicaudatus
populations across China
Authors: Zhong Jia , Yi Shaokui , Ma Laiyan , Wang Weimin
Published: April 2019

The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used
Misgurnus anguillicaudatus
, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers (
cytochrome b
and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of
M. anguillicaudatus
was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.
A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Authors: Wolfe Joanna M. , Breinholt Jesse W. , Crandall Keith A. , Lemmon Alan R. , Lemmon Emily Moriarty , Timm Laura E. , Siddall Mark E. , Bracken-Grissom Heather D.
Published: April 2019

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, ‘lobster’ and ‘crab’ groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species
Authors: Grieneisen Laura E. , Charpentier Marie J. E. , Alberts Susan C. , Blekhman Ran , Bradburd Gideon , Tung Jenny , Archie Elizabeth A.
Published: April 2019

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host–population
F
ST,
perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
Release from intralocus sexual conflict? Evolved loss of a male sexual trait demasculinizes female gene expression
Authors: Rayner Jack G. , Pascoal Sonia , Bailey Nathan W.
Published: April 2019

The loss of sexual ornaments is observed across taxa, and pleiotropic effects of such losses provide an opportunity to gain insight into underlying dynamics of sex-biased gene expression and intralocus sexual conflict (IASC). We investigated this in a Hawaiian field cricket,
Teleogryllus oceanicus
, in which an X-linked genotype (
flatwing
) feminizes males' wings and eliminates their ability to produce sexually selected songs. We profiled adult gene expression across somatic and reproductive tissues of both sexes. Despite the feminizing effect of
flatwing
on male wings, we found no evidence of feminized gene expression in males. Instead, female transcriptomes were more strongly affected by
flatwing
than males’, and exhibited demasculinized gene expression. These findings are consistent with a relaxation of IASC constraining female gene expression through loss of a male sexual ornament. In a follow-up experiment, we found reduced testes mass in flatwing males, whereas female carriers showed no reduction in egg production. By contrast, female carriers exhibited greater measures of body condition. Our results suggest sex-limited phenotypic expression offers only partial resolution to IASC, owing to pleiotropic effects of the loci involved. Benefits conferred by release from intralocus conflict could help explain widespread loss of sexual ornaments across taxa.
In vitro screening of antibacterial and antioxidant properties of stem of Sphaeranthus indicus Linn
Authors: Tandon Dhananjay , Gupta Ashwini Kumar
Published: April 2019

This study aimed to identify the bioactive compound (s) possessing both the antimicrobial and antioxidant activity. The antibacterial activity of hexane, ethyl acetate, methanol polar fraction and aqueous extract of stem of Sphaeranthus indicus was evaluated against MTCC bacterial strains Bacillus cereus-430, B. subtilis-441, Staphylococcus aureus-96, S. epidermidis-435, Escherichia coli-1687, Klebsiella pneumoniae-3384, Pseudomonas aeruginosa-741 and Proteus vulgaris-744 with their corresponding clinical isolates. The results revealed inhibitory activity of hexane extract against most of the bacterial pathogens except MTCC K. pneumonia and clinical B. cereus. The ethyl acetate extract inhibited growth of MTCC B. cereus, B. subtilis, S. epidermidis, P. aeruginosa and clinical isolates of B. cereus, S. aureus, S. epidermidis, E. coli, K. pneumonia. The methanol polar fraction exhibited activity against clinically isolated S. aureus, S. epidermidis, P. aureginosa, P. vulgaris while aqueous extracts had no activity against any of the organisms. Among all the extracts showing antioxidant activity, aqueous extract was found to possess highest activity when tested by reducing power, DMPD and DPPH assay. Phytochemical analysis revealed that methanol polar fraction had highest quantity of terpenoids while aqueous extract was rich in phenols and flavonoids. The active compound from hexane extract was isolated by TLC and the active band was detected via bioautography. DPPH was used for detecting antioxidant (s) in TLC plate. A total of 13 bands were obtained after separation in which two bands showed both the antibacterial as well as antioxidant activities. Hence it is speculated that bioactive compound showing antibacterial activity may also possesses antioxidant activity.
What factors contribute to the long-term persistence of Shigella species as pathogens?
Authors: Bennett Rebecca
Published: April 2019

The genus Shigella is a globally important pathogen responsible for the infectious disease shigellosis which causes an estimated 125 million cases worldwide and up to 100 000 deaths. Shigella species are now recognised as a priority organism by the World Health Organisation due to the increasing antimicrobial resistance (AMR) observed. For adults, treatment of Shigella infections commonly consists of ciprofloxacin, however, recently there have been confirmed cases of ciprofloxacin-resistant strains. Most Shigella is already resistant to ampicillin and trimethoprim so added resistance to ciprofloxacin is a worrying development. Also of note is the role played by toxin-antitoxin systems where they are critical for maintaining large plasmids that typically contain genes of interest such as AMR genes and virulence factors. The Murray collection comprises of several hundred bacterial strains from the pre-antibiotic era (1917–1954) from a range of geographic locations. Within this collection there are many Shigella isolates which are now publicly available for analysis. There are also available datasets for modern collections which have been sequenced for past studies. We will use these data sets to perform bioinformatic analysis and characterise the dynamic changes in the genetic composition across time. The Murray Collection isolates provide a prospective from the pre-antibiotic era and so from the comparisons with modern isolates we will observe the effect of routine antibiotic use has on the evolution of antimicrobial resistance. Through this investigation the hope is to provide unprecedented insight into how AMR and toxin-anti-toxin systems contribute to the long-term persistence and success of Shigella.
Community assembly in the microbiome: ecological insights into infant microbiome development
Authors: Coyte Katharine , Rao Chitong , Rakoff-Nahoum Seth , Foster Kevin
Published: April 2019

In healthy adults, the gastrointestinal tract harbours a diverse community of microbes that play critical roles in health and wellbeing. However, we are not born with this microbiome. Over the first months and years of life the gut microbiome gradually develops, undergoing a process akin to classic primary succession. We here develop ecological theory in order to study the factors that drive these assembly processes. We find that interactions between species can enforce order on microbiome development, with interspecies dependencies driving the predictability of succession. We combine this theory with novel sample processing techniques to interrogate both bacterial and fungal microbiome development in premature infants. We utilize machine learning to infer how members of the microbiome are affected by both one another and clinical interventions. Preliminary results identify specific inter-microbial interactions that may in part drive community dynamics, and identify the impact of antibiotic interventions in perturbing healthy microbiome development. Taken together, these results highlight the importance of disentangling microbial interactions if we are to understand and ultimately manipulate our microbiome communities.
Antimicrobial resistance in non-O157 Shiga-toxin producing Escherichia coli
Authors: Gentle Amy , Jenkins Claire , Day Martin , Greig David , Painset Anais , Do Nascimento Vivienne
Published: April 2019

Objectives

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause severe gastrointestinal disease in humans. Monitoring antimicrobial resistance (AMR) in STEC from symptomatic human cases may provide evidence for the extent of transmission of resistant strains and resistance genes from ruminants to humans. The aim of this study was to assess AMR in non-O157 STEC in England and Wales between 2014 and 2016, and to compare phenotypic and Whole Genome Sequencing (WGS) derived AMR profiles.

Methods

Six hundred and fifty-three non-O157 STEC isolates were analysed. WGS and bioinformatic analysis were performed on 457 isolates in the top 10 Clonal Complexes (CC) (193 were excluded on the basis of CC) and phenotypic susceptibility typing via breakpoint and minimum inhibitory concentration testing was undertaken on 100 isolates exhibiting resistance to at least one antimicrobial.

Results

Of 457 isolates, 332 lacked identifiable resistance genes and were predicted to be fully susceptible to 11 diverse classes of antimicrobials, 125 were found to carry one or more resistance genes and 83 were multi-drug resistant. Four isolates were identified as extended-spectrum b-lactamase-producers. In total, 46 different genes were detected – which conferred resistance to 8 different antibiotic classes. An overall concordance of 97.5  % was demonstrated between the two methods.

Conclusions

Phenotypic and genome-derived AMR comparisons showed good correlation for non-O157 STEC. This has added to the evidence base to support the use of genotypic approaches for antimicrobial susceptibility typing, to replace phenotypic typing for surveillance purposes, and guide clinical decision making in the more distant future.
Fitness costs of methicillin resistance in Staphylococcus aureus
Authors: Gill Jacqueline
Published: April 2019

Staphylococcus aureus is a Gram-positive bacteria, and a common human pathogen. It is a leading cause of healthcare-associated infections worldwide, causing potentially fatal bacteraemia. Infections can be treated using antibiotics, but many strains have quickly developed resistance to the most common antibiotics. Methicillin resistance in Staphylococcus is acquired through the uptake of the Staphylococcal Cassette Chromosome mec (SCCmec). SCCmec is a large mobile genetic element, which can integrate into the Staphylococcus genome. It carries the mecA gene, which confers resistance to broad-spectrum β-lactam antibiotics, including methicillin. Several different SCCmec elements have been described, some of which can carry additional antibiotic resistance genes, alongside mecA. These can include resistance to common antibiotics or resistance to heavy metals. Smaller SCCmec types do not encode any additional antibiotic resistance genes. These have been shown to confer no fitness cost to the bacteria. Because of this, smaller SCCmec types are becoming increasingly more common, particularly in community-associated MRSA infections.
A novel enterovirus protein modulates infection in gut epithelial cells
Authors: Lulla Valeria , Dinan Adam , Hosmillo Myra , Chaudhry Yasmin , Sherry Lee , Irigoyen Nerea , Nayak Komal , Stonehouse Nicola , Zilbauer Matthias , Goodfellow Ian , Firth Andrew
Published: April 2019

Enteroviruses comprise a large group of mammalian pathogens that includes poliovirus. Pathology in humans ranges from sub-clinical to acute flaccid paralysis, myocarditis and meningitis. Until now, all the enteroviral proteins were thought to derive from proteolytic processing of a polyprotein encoded in a single open reading frame (ORF). We report that many enterovirus genomes also harbor an upstream ORF (uORF) that is subject to strong purifying selection. Using echovirus 7 and poliovirus 1, we confirmed expression of uORF protein (UP) in infected cells. Using ribosome profiling (a technique for global footprinting of translating ribosomes), we also demonstrated translation of the uORF in representative members of the predominant human enterovirus species, namely Enterovirus A, B and C. In differentiated human intestinal organoids, UP-knockout echoviruses are attenuated compared to wild-type virus at late stages of infection where membrane-associated UP facilitates virus release. Thus we have identified a previously unknown enterovirus protein that facilitates virus growth in gut epithelial cells – the site of initial viral invasion into susceptible hosts. These findings overturn the 50-year-old dogma that enteroviruses use a single-polyprotein gene expression strategy, and have important implications for understanding enterovirus pathogenesis.
Infectious bronchitis virus modulates cellular stress granule signalling
Authors: Brownsword Matthew , Doyle Nicole , Brocard Michele , Locker Nicolas , Maier Helena
Published: April 2019

Infectious bronchitis virus (IBV), a gammacoronavirus, causes the economically important poultry disease, infectious bronchitis, resulting in reduced weight gain and egg quality. As observed for many viruses, during replication, IBV shuts off translation of host proteins, preventing synthesis of important products of the innate immunity, which are pivotal in fighting viral infection. This work investigates the role of stress granules in IBV translational control. Stress granules are membranes-less aggregations of stalled translation initiation complexes comprising translation initiation factors, 40S ribosome and RNA binding proteins. These structures serve as sites of storage and sequestration of translational machinery and cellular mRNA while simultaneously enabling intracellular signalling and antiviral responses. It is shown here by immunofluorescence that IBV induces stress granules in only a proportion of infected cells. These stress granules occur late in the virus life cycle and appear canonical, containing multiple stress granule markers and showing mRNA exchange with ribosomes. In addition, stress granule markers are not diverted to sites of virus replication, as seen during replication of some other viruses. Interestingly, IBV infection results in resistance to chemicals that induce stress granules via eukaryotic initiation factor 2α (eIF2α). Consistent with this, eIF2α is not phosphorylated at any time during IBV infection. This also indicates a non-canonical signalling pathway for IBV-induced stress granules. Significantly, stress granule formation is uncoupled from translational arrest as visualised using ribopuromycylation. Therefore, IBV replication both induces and inhibits cellular stress granule signalling in a process that is uncoupled from shut off of host translation.
Evolvability of orthologous genes
Authors: Abdalaal Hind , Näsvall Joakim
Published: April 2019

The project aims to generate a library of laboratory orthologous genes for studying evolvability. In this study, we have taken one of histidine biosynthetic genes hisA from Salmonella enterica through alternating rounds of weak selection (simulated by random mutagenesis through error-prone PCR and screens for partial loss of hisA function) followed by strong purifying selection (simulated by additional rounds of random mutagenesis and screens for restored hisA function). We have started from the wild-type hisA gene expressed from relatively weak arabinose inducible promoter ParaBAD. Twenty different single nucleotide polymorphisms (SNPs) that cause slow growth in the absence of histidine were isolated. In twelve of these deleterious mutants the activity was restored to wild-type levels by additional SNP after another round of random mutagenesis. In this study, in some of the compensated his A variants it was difficult to isolate further deleterious mutations, suggesting that these compensating mutations can mask the effects of additional deleterious mutations. By combining the compensating mutations with known deleterious mutations, complete or partial compensation was seen. Orthologs from one of the diverging lineages were also compared for their evolvability toward TrpF activity (ability to synthesize tryptophan) using fluctuation test. Two orthologs in this lineage showed higher evolvability compared to the wild type hisA.
Exploring the role of VpsT in Vibrio cholerae lifestyle switching
Authors: Guest Tom , Haycocks James , Warren Gemma , Grainger David
Published: April 2019

Biofilm formation is an important stage of the Vibrio cholerae lifecycle. The transcription factor VpsT is a master regulator of biofilm formation that activates the expression of biofilm matrix components in response to elevated intracellular c-di-GMP. VpsT has also been shown to repress the expression of rpoSand genes involved in motility. This suggests VpsT may have a wider role in the transition from a motile to sessile lifestyle. To better understand the role of VpsT in V. cholerae lifestyle switching ChIP-seq (chromatin immunoprecipitation and DNA sequencing) was used to map VpsT binding across the genome. Our data reveals many additional targets, defines the DNA binding motif for VpsT, and expands the VpsT regulon to include genes involved in c-di-GMP metabolism, motility and virulence. The VpsT interaction at target promoters is c-di-GMP dependent and can repress or activate gene expression.
Functional RNA structures as targets in emerging arboviruses
Authors: Prosser Oliver , Merits Andres , Stonehouse Nicola , Tuplin Andrew
Published: April 2019

Emerging arthropod-borne viruses, such as Zika virus (ZIKV) and Chikungunya virus (CHIKV), represent a significant and increasing threat to global health. Despite the expanding prevalence of their vectors, the Aedes sp.mosquitoes, and the potential for major epidemics, there are currently no specific antiviral compounds or vaccines available for either viral pathogen. The positive-strand genomes of ZIKV and CHIKV, members of the flavivirus and alphavirus genera respectively, contain functional, structured cis-acting RNA elements. We are investigating a range of approaches for targeting these RNA elements and analysing the effect on virus replication at different stages of their life cycle. Gaining high resolution structural data is essential prior to targeting RNA elements, and consequently, we mapped RNA structural elements within the ZIKV 5’ genome region using a combination of biochemical SHAPE probing, thermodynamic predictions and phylogenetic analysis. We are currently validating our structural data by analysis of mutant phenotypes in a reverse genetic system. Using antisense locked nucleic acid oligonucleotides (antisense-LNA), we demonstrated that functional RNA elements in CHIKV can be specifically targeted – inhibiting replication in both sub-genomic replicon and infectious virus systems. Surface plasmon resonance confirmed that the antisense-LNA binds to a specific stem-loop target with aKd of 310 nM and has an IC50 of 35 nM in the sub-genomic replicon system. In future work, we aim to investigate selection of RNA-aptamers against CHIKV and target ZIKV genomic stem-loops using antisense-LNAs.
Effect of temperature increase in bacterial and fungal communities of chlorinated drinking water distribution systems
Authors: Preciado Carolina Calero , Boxall Joby , Soria-Carrasco Víctor , Douterelo Isabel
Published: April 2019

Drinking Water Distribution Systems (DWDS) are diverse ecosystems where the majority of microorganisms live forming biofilms, which can alter the water quality if they are mobilised to the bulk water. Biofilm communities can be affected by the increase of temperature due to climate change, thus compromise the distribution of safe water. To understand the effect of temperature on biofilms in DWDS, biofilm was developed for 30 days at 16 °C and 24 °C using a full-scale experimental DWDS facility. Samples were collected at the end of the experiment from removable coupons inserted into the pipes. DNA was extracted and the 16S rRNA and ITS rRNA genes were sequenced and analysed, for the bacterial and fungal diversity respectively. Differences in bacterial and fungal diversity at both temperatures were observed at family level. At 16 °C bacterial community was dominated by Comamonadaceae (21.48 %), Pseudomonadaceae (16.41 %) and Sphingobacteriaceae (12.99 %). However, at 24 °C the most abundant family was Pseudomonadaceae (50.60 %) followed by Sphingomonadaceae (9.59 %) and Sinobacteraceae (7.82 %). Fungal diversity showed that at 16 °C the most abundant family was Nectriaceae (68.9 %), followed by Helotiales (24.5 %) and Filobasidiales (1.5 %). However, at 24 °C the community was dominated by Nectriaceae (98.15 %) and the following families showed a low relative abundance, Rhizopodaceae (0.95 %) and Cryptomycota (0.24 %). Temperature is a key factor for microbial growth in DWDS and affect the composition of the microbial communities. Temperature increase leads changes and a loss in complexity in bacterial and fungal communities of biofilms, which can affect the water quality.
Flavivirus membrane (M) proteins as potential ion channel antiviral targets
Authors: Brown Emma , Beaumont Hannah , Lefteri Daniella , Bentham Matthew , Foster Richard , McKimmie Clive , Kalli Antreas , Griffin Stephen
Published: April 2019

The Flavivirus small integral membrane (M) protein resides within mature infectious particles yet, unlike the envelope (E) protein which mediates membrane fusion upon encountering low pH within the acidifying endosome, the function of M within this context is unknown. We are investigating whether Zika virus (ZIKV) M protein exhibits channel activity, acting as a viroporin playing a role mediating virus entry and uncoating. Importantly, ZIKV entry was blocked in a dose-dependent fashion by the prototypic channel blocker rimantadine and the drug also prevented virus spread in mouse models of ZIKV infection. Molecular dynamics simulations supported that M protein is able to oligomerise into a hexameric viroporin channel, opening of which is promoted in an acidified environment via protonation of a conserved histidine residue. Rimantadine is predicted to bind onto this structure in silico at a lumenal binding site, against which we are currently designing improved small molecule inhibitors that could form the basis of novel M protein targeted drug discovery. Importantly, drugs targeting M might either prevent or reduce the severity of ZIKV infections, including those crossing the placenta, and could also be translated for use against other Flaviviruses.
Unravelling a co-nsP-iracy: the role of chikungunya virus non-structural protein 3 in replication and pathogenesis
Authors: Lee Siu Yi , Stonehouse Nicola , Harris Mark
Published: April 2019

Chikungunya virus (CHIKV) is a member of the Alphavirus genus, transmitted to humans by mosquitoes of the Aedesgenera. Infection with CHIKV causes chikungunya fever, which in many cases can lead to chronic joint disease, leaving patients with reduced ambulation. Despite its rising potential as a threat to global health, no effective vaccine or antiviral agent for protection or treatment are available. The CHIKV non-structural protein 3 (nsP3) is essential to the virus lifecycle and is believed to be a component of the genome replication complex. However, to date, the exact role of this protein has yet been determined. Although a conserved polyproline motif in the C-terminal hypervariable domain of nsP3 has been reported to interact with cellular SH3 domains, the function of this motif remains enigmatic. To address this question we generated a panel of mutations in this motif and tested the phenotype in the context of both a subgenomic replicon and full-length infectious virus, in both mammalian and mosquito-derived cell lines. Most of the mutations were well tolerated in the sub-genomic replicon, however, a subset either attenuated or completely abolished production of infectious CHIKV. These results suggest that as well as its role in genome replication, nsP3 also functions during assembly and release of infectious virus particles and that the C-terminal polyproline motif is a critical determinant of this function.
Nature and consequences of Salmonella infections in cattle
Authors: Vohra Prerna , Vrettou Christina , Hope Jayne , Hopkins John , Stevens Mark
Published: April 2019

Salmonella enterica is a human and veterinary pathogen of global importance. Cattle are a key reservoir of S. enterica serotypes that cause non-typhoidal salmonellosis in humans and infections are often acquired via consumption of contaminated food. Salmonella can survive within the bovine lymphatic system and contaminated peripheral lymph nodes often enter the food chain via ground beef production because they are small and deeply embedded in fat, making it impossible to remove them during food production. S. enterica serotypes can also cause acute enteritis and systemic typhoid-like disease in cattle, thereby exerting a significant burden on bovine welfare and productivity. Existing vaccines confer limited serotype-specific protection and a need exists to better understand the host and bacterial factors involved in pathogenesis and protection to inform the design of new vaccines and other intervention strategies. Most of our knowledge about salmonellosis comes from the mouse typhoid model. Here, we sought to understand the effects of infection by Salmonella Dublin, which causes typhoid-like disease in cattle, in its natural host. By infecting cattle with S. Dublin expressing green fluorescent protein and using flow cytometry we have been able to isolate and characterise the bovine cells infected by S. Dublin, study changes in their cell surface marker expression post-infection and compare tropism in the intestine and draining lymph nodes. We have also studied the survival of S. Dublin in the main infected host cell type in vitro using primary cells to determine the consequences of infection on the pathogen itself.
High throughput screening to identify host-factors involved in RSV fusion
Authors: Kelly James , Logan Leanne , Hiscox Julian , Armstrong Stuart , Wilson Sam , Bailey Dalan
Published: April 2019

Respiratory syncytial virus (RSV) is the major cause of childhood respiratory disease; however, currently there is no licenced vaccine available and the only therapeutic, a monoclonal antibody against the viral Fusion (F) protein, is expensive and applied sparingly. RSV particles enter cells by membrane fusion, orchestrated by F – a type I integral membrane protein. This process was recently shown to involve macropinocytosis of the particle. Separately, RSV can spread through induction of direct cell-cell fusion – again orchestrated by F. Little is currently known about the host-factors involved in regulating or inhibiting RSV F-mediated fusion. Here, using two different high-throughput screening approaches, we have identified host-factors involved in regulating RSV fusion. Using quantitative mass-spectrometry analysis of isolated cell membrane fractions from mock and RSV-infected cells we have identified membrane proteins which are differentially regulated during RSV infection. Furthermore, using lentiviral libraries expressing individual interferon stimulated genes (ISGs) from different mammalian species we have investigated ISG-mediated inhibition of RSV fusion. Our data provides important insights into host-factors involved in RSV spread, furthering our understanding of the fusion process and identifying potential targets for antiviral therapy.