Publications by authors named "David J Kelly"

125 Publications

Preface.

Adv Microb Physiol 2021 ;79:xiii

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http://dx.doi.org/10.1016/S0065-2911(21)00025-4DOI Listing
January 2021

Differential Circulating MicroRNA Expression in Age-Related Macular Degeneration.

Int J Mol Sci 2021 Nov 15;22(22). Epub 2021 Nov 15.

Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland.

This study explored the expression of several miRNAs reported to be deregulated in age-related macular degeneration (AMD). Total RNA was isolated from sera from patients with dry AMD ( = 12), wet AMD ( = 14), and controls ( = 10). Forty-two previously investigated miRNAs were selected based on published data and their role in AMD pathogenesis, such as angiogenic and inflammatory effects, and were co-analysed using a miRCURY LNA miRNA SYBR Green PCR kit via quantitative real-time polymerase chain reaction (qRT-PCR) to validate their presence. Unsupervised hierarchical clustering indicated that AMD serum specimens have a different miRNA profile to healthy controls. We successfully validated the differentially regulated miRNAs in serum from AMD patients versus controls. Eight miRNAs (hsa-let-7a-5p, hsa-let-7d-5p, hsa-miR-23a-3p, hsa-miR-301a-3p, hsa-miR-361-5p, hsa-miR-27b-3p, hsa-miR-874-3p, hsa-miR-19b-1-5p) showed higher expression in the serum of dry AMD patients than wet AMD patients and compared with healthy controls. Increased quantities of certain miRNAs in the serum of AMD patients indicate that these miRNAs could potentially serve as diagnostic AMD biomarkers and might be used as future AMD treatment targets. The discovery of significant serum miRNA biomarkers in AMD patients would provide an easy screening tool for at-risk populations.
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http://dx.doi.org/10.3390/ijms222212321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8625913PMC
November 2021

Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated serotype HS:19.

Microb Genom 2021 Nov;7(11)

Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA.

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http://dx.doi.org/10.1099/mgen.0.000660DOI Listing
November 2021

Infants show pupil dilatory responses to happy and angry facial expressions.

Dev Sci 2021 Oct 11:e13182. Epub 2021 Oct 11.

School of Psychology, University of Kent, Canterbury, UK.

Facial expressions are one way in which infants and adults communicate emotion. Infants scan expressions similarly to adults, yet it remains unclear whether they are receptive to the affective information they convey. The current study investigates 6-, 9- and 12-month infants' (N = 146) pupillary responses to the six "basic" emotional expressions (happy, sad, surprise, fear, anger, and disgust). To do this we use dynamic stimuli and gaze-contingent eye-tracking to simulate brief interactive exchanges, alongside a static control condition. Infants' arousal responses were stronger for dynamic compared to static stimuli. And for dynamic stimuli we found that, compared to neutral, infants showed dilatory responses for happy and angry expressions only. Although previous work has shown infants can discriminate perceptually between facial expressions, our data suggest that sensitivity to the affective content of all six basic emotional expressions may not fully emerge until later in ontogeny.
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http://dx.doi.org/10.1111/desc.13182DOI Listing
October 2021

MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen .

J Bacteriol 2021 Oct 4:JB0042121. Epub 2021 Oct 4.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.

The paralogues RrpA and RrpB which are members of MarR family of DNA binding proteins are important for the survival of the global bacterial foodborne pathogen under redox stress. We report that RrpA is a positive regulator of , encoding a flavin-dependent quinone reductase that contributes to the protection from redox stress mediated by structurally diverse quinones, whilst RrpB negatively regulates the expression of (renamed for NADPH-flavin reductase A), encoding a flavin reductase. NfrA reduces riboflavin at a greater rate than its derivatives, suggesting exogenous free flavins are the natural substrate. MdaB and NfrA both prefer NADPH as an electron donor. Cysteine substitution and post-translational modification analyses indicated that RrpA and RrpB employ a cysteine-based redox switch. Complete genome sequence analyses revealed is frequently found in and related ., whilst is predominant in strains. Quinones and flavins are redox cycling agents secreted by a wide range of cell-types that can form damaging superoxide by one-electron reactions. We propose a model for stress adaptation where MdaB and NfrA facilitate a two-electron reduction mechanism to the less toxic hydroquinones, thus aiding survival and persistence of this major pathogen. Changes in cellular redox potential results in alteration in the oxidation state of intracellular metabolites and enzymes, consequently, cells make adjustments that favor growth and survival. The work we present here answers some of the many questions that have remained elusive over the years of investigation into the enigmatic microaerophile bacterium, . We employed molecular approaches to understand the regulation mechanisms and functional analyses to reveal the roles of two novel quinone and flavin reductases, both serve as major pools of cellular redox-active molecules. This work extends our knowledge on bacterial redox sensing mechanisms and the significance of hemostasis.
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http://dx.doi.org/10.1128/JB.00421-21DOI Listing
October 2021

Badger territoriality maintained despite disturbance of major road construction.

PLoS One 2021 3;16(9):e0242586. Epub 2021 Sep 3.

Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.

Road ecology has traditionally focused on the impact of in-situ and functional roads on wildlife. However, road construction also poses a major, yet understudied, threat and the implications for key aspects of animal behaviour are unknown. Badgers (Meles meles) have been implicated in the transmission of tuberculosis to cattle. There are concerns that environmental disturbances, including major road construction, can disrupt badger territoriality, promoting the spread of the disease to cattle. To address these knowledge gaps the ranging behaviour of a medium-density Irish badger population was monitored using GPS-tracking collars before, during, and after a major road realignment project that bisected the study area. We estimated badgers' home range sizes, nightly distances travelled, and the distance and frequency of extra-territorial excursions during each phase of the study and quantified any changes to these parameters. We show that road construction had a very limited effect on ranging behaviour. A small increase in nightly distance during road construction did not translate into an increase in home range size, nor an increase in the distance or frequency of extra-territorial excursions during road construction. In addition, suitable mitigation measures to prevent badger deaths appeared to ensure that normal patterns of ranging behaviour continued once the new road was in place. We recommend that continuous badger-proof fencing be placed along the entire length of new major roads, in combination with appropriately sited underpasses. Our analysis supports the view that road construction did not cause badgers to change their ranging behaviour in ways likely to increase the spread of tuberculosis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0242586PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415604PMC
November 2021

The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters.

FEBS J 2021 Aug 10. Epub 2021 Aug 10.

Department of Molecular Biology and Biotechnology, The University of Sheffield, UK.

The organic polymer lignin is a component of plant cell walls, which like (hemi)-cellulose is highly abundant in nature and relatively resistant to degradation. However, extracellular enzymes released by natural microbial consortia can cleave the β-aryl ether linkages in lignin, releasing monoaromatic phenylpropanoids that can be further catabolised by diverse species of bacteria. Biodegradation of lignin is therefore important in global carbon cycling, and its natural abundance also makes it an attractive biotechnological feedstock for the industrial production of commodity chemicals. Whilst the pathways for degradation of lignin-derived aromatics have been extensively characterised, much less is understood about how they are recognised and taken up from the environment. The purple phototrophic bacterium Rhodopseudomonas palustris can grow on a range of phenylpropanoid monomers and is a model organism for studying their uptake and breakdown. R. palustris encodes a tripartite ATP-independent periplasmic (TRAP) transporter (TarPQM) linked to genes encoding phenylpropanoid-degrading enzymes. The periplasmic solute-binding protein component of this transporter, TarP, has previously been shown to bind aromatic substrates. Here, we determine the high-resolution crystal structure of TarP from R. palustris as well as the structures of homologous proteins from the salt marsh bacterium Sagittula stellata and the halophile Chromohalobacter salexigens, which also grow on lignin-derived aromatics. In combination with tryptophan fluorescence ligand-binding assays, our ligand-bound co-crystal structures reveal the molecular basis for high-affinity recognition of phenylpropanoids by these TRAP transporters, which have potential for improving uptake of these compounds for biotechnological transformations of lignin.
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http://dx.doi.org/10.1111/febs.16156DOI Listing
August 2021

Infants scan static and dynamic facial expressions differently.

Infancy 2021 11 20;26(6):831-856. Epub 2021 Jul 20.

School of Psychology, University of Kent, Canterbury, UK.

Despite being inherently dynamic phenomena, much of our understanding of how infants attend and scan facial expressions is based on static face stimuli. Here we investigate how six-, nine-, and twelve-month infants allocate their visual attention toward dynamic-interactive videos of the six basic emotional expressions, and compare their responses with static images of the same stimuli. We find infants show clear differences in how they attend and scan dynamic and static expressions, looking longer toward the dynamic-face and lower-face regions. Infants across all age groups show differential interest in expressions, and show precise scanning of regions "diagnostic" for emotion recognition. These data also indicate that infants' attention toward dynamic expressions develops over the first year of life, including relative increases in interest and scanning precision toward some negative facial expressions (e.g., anger, fear, and disgust).
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http://dx.doi.org/10.1111/infa.12426DOI Listing
November 2021

Genes Linking Copper Trafficking and Homeostasis to the Biogenesis and Activity of the -Type Cytochrome Oxidase in the Enteric Pathogen .

Front Microbiol 2021 25;12:683260. Epub 2021 Jun 25.

Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom.

Bacterial C-type haem-copper oxidases in the family are widespread in microaerophiles, which exploit their high oxygen-binding affinity for growth in microoxic niches. In microaerophilic pathogens, C-type oxidases can be essential for infection, yet little is known about their biogenesis compared to model bacteria. Here, we have identified genes involved in -oxidase (Cco) assembly and activity in the Gram-negative pathogen , the commonest cause of human food-borne bacterial gastroenteritis. Several genes of unknown function downstream of the oxidase structural genes were shown to be essential ( and ) or important ( and ) for Cco activity; Cj1483 is a CcoH homologue, but Cj1484 (designated CcoZ) has structural similarity to MSMEG_4692, involved in Qcr-oxidase supercomplex formation in . Blue-native polyacrylamide gel electrophoresis of detergent solubilised membranes revealed three major bands, one of which contained CcoZ along with Qcr and oxidase subunits. Deletion of putative copper trafficking genes () and () abolished Cco activity, which was partially restored by addition of copper during growth, while inactivation of encoding a CcoG homologue led to a partial reduction in Cco activity. Deletion of an operon encoding PCu C (Cj0909) and Sco (Cj0911) periplasmic copper chaperone homologues reduced Cco activity, which was partially restored in the mutant by exogenous copper. Phenotypic analyses of gene deletions in the cluster, encoding several genes involved in intracellular metal homeostasis, showed that inactivation of (), or () led to both elevated intracellular Cu and reduced Cco activity, effects exacerbated at high external Cu. Our work has therefore identified (i) additional Cco subunits, (ii) a previously uncharacterized set of genes linking copper trafficking and Cco activity, and (iii) connections with Cu homeostasis in this important pathogen.
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http://dx.doi.org/10.3389/fmicb.2021.683260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267372PMC
June 2021

The Role of Deregulated MicroRNAs in Age-Related Macular Degeneration Pathology.

Transl Vis Sci Technol 2021 02;10(2):12

Mater Retina Research Group, Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland.

Purpose: We previously identified three microRNAs (miRNAs) with significantly increased expression in the serum of patients with age-related macular degeneration (AMD) compared with healthy controls. Our objective was to identify potential functional roles of these upregulated miRNAs (miR-19a, miR-126, and miR-410) in AMD, using computational tools for miRNAs prediction and identification, and to demonstrate the miRNAs target genes and signaling pathways. We also aim to demonstrate the pathologic role of isolated sera-derived exosomes from patients with AMD and controls using in vitro models.

Methods: miR-19a, miR-126, and miR-410 were investigated using bioinformatic approaches, including DIANA-mirPath and miR TarBase. Data on the resulting target genes and signaling pathways were incorporated with the differentially expressed miRNAs in AMD. Apoptosis markers, human apoptosis miRNAs polymerase chain reaction arrays and angiogenesis/vasculogenesis assays were performed by adding serum-isolated AMD patient or control patient derived exosomes into an in vitro human angiogenesis model and ARPE-19 cell lines.

Results: A number of pathways known to be involved in AMD development and progression were predicted, including the vascular endothelial growth factor signaling, apoptosis, and neurodegenerative pathways. The study also provides supporting evidence for the involvement of serum-isolated AMD-derived exosomes in the pathology of AMD, via apoptosis and/or angiogenesis.

Conclusions: miR-19a, miR-126, miR-410 and their target genes had a significant correlation with AMD pathogenesis. As such, they could be potential new targets as predictive biomarkers or therapies for patients with AMD.

Translational Relevance: The functional analysis and the pathologic role of altered miRNA expression in AMD may be applicable in developing new therapies for AMD through the disruption of individual or multiple pathophysiologic pathways.
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http://dx.doi.org/10.1167/tvst.10.2.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7881277PMC
February 2021

Bovine Tuberculosis: The Emergence of a New Wildlife Maintenance Host in Ireland.

Front Vet Sci 2021 25;8:632525. Epub 2021 Mar 25.

Discipline of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland.

Despite advances in herd management, tuberculosis (TB) continues to affect ~0. 5% of Ireland's national cattle herd annually. It is clear that any "final" eradication of TB in cattle will need to address all TB maintenance hosts in the same environment. In Ireland and the UK, European Badgers (Meles meles) are a known TB maintenance host, while deer are recognised as spillover hosts. However, deer have been identified as maintenance hosts in other countries and Sika deer, specifically, have been identified with TB in Ireland. We examined the power of cattle, badger and Sika deer densities (at the county level) to predict cattle TB-breakdowns in Ireland, at both the herd and the individual level, using data collected between 2000 and 2018. Our hypothesis was that any positive correlations between deer density and cattle TB-breakdowns would implicate deer as TB maintenance hosts. Using linear multiple regressions, we found positive correlations between deer density and cattle TB-breakdowns at both the herd and individual levels. Since Sika deer in County Wicklow are known to have TB, we ran further regressions against subsets of data which excluded individual Irish counties. Analyses excluding Wicklow data showed much weaker correlations between Sika deer density and cattle TB-breakdowns at both the herd and individual levels, suggesting that these correlations are strongest in County Wicklow. A similar effect for badger density was seen in County Leitrim. While locally high densities of Sika deer persist in Irish counties, we believe they should be considered an integral part of any TB-control programme for those areas.
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http://dx.doi.org/10.3389/fvets.2021.632525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027074PMC
March 2021

The flavodoxin FldA activates the class Ia ribonucleotide reductase of Campylobacter jejuni.

Mol Microbiol 2021 07 3;116(1):343-358. Epub 2021 Apr 3.

Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.

Campylobacter jejuni is a microaerophilic zoonotic pathogen with an atypical respiratory Complex I that oxidizes a flavodoxin (FldA) instead of NADH. FldA is essential for viability and is reduced via pyruvate and 2-oxoglutarate oxidoreductases (POR/OOR). Here, we show that FldA can also be reduced by FqrB (Cj0559), an NADPH:FldA reductase. An fqrB deletion mutant was viable but displayed a significant growth defect. FqrB is related to flavoprotein reductases from Gram-positive bacteria that can reduce NrdI, a specialized flavodoxin that is needed for tyrosyl radical formation in NrdF, the beta subunit of class 1b-type (Mn) ribonucleotide reductase (RNR). However, C. jejuni possesses a single class Ia-type (Fe) RNR (NrdAB) that would be expected to be ferredoxin dependent. We show that CjFldA is an unusually high potential flavodoxin unrelated to NrdI, yet growth of the fqrB mutant, but not the wild-type or a complemented strain, was stimulated by low deoxyribonucleoside (dRNS) concentrations, suggesting FldA links FqrB and RNR activity. Using purified proteins, we confirmed the NrdB tyrosyl radical could be regenerated in an NADPH, FqrB, and FldA dependent manner, as evidenced by both optical and electron paramagnetic resonance (EPR) spectroscopy. Thus, FldA activates RNR in C. jejuni, partly explaining its essentiality.
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http://dx.doi.org/10.1111/mmi.14715DOI Listing
July 2021

Eye Movements and Behavioural Responses to Gaze-Contingent Expressive Faces in Typically Developing Infants and Infant Siblings.

Autism Res 2021 05 10;14(5):973-983. Epub 2020 Nov 10.

University of Kent, School of Psychology, Keynes College, Canterbury, Kent, UK.

Studies with infant siblings of children with Autism Spectrum Disorder have attempted to identify early markers for the disorder and suggest that autistic symptoms emerge between 12 and 24 months of age. Yet, a reliable first-year marker remains elusive. We propose that in order to establish first-year manifestations of this inherently social disorder, we need to develop research methods that are sufficiently socially demanding and realistically interactive. Building on Keemink et al. [2019, Developmental Psychology, 55, 1362-1371], we employed a gaze-contingent eye-tracking paradigm in which infants could interact with face stimuli. Infants could elicit emotional expressions (happiness, sadness, surprise, fear, disgust, anger) from on-screen faces by engaging in eye contact. We collected eye-tracking data and video-recorded behavioural response data from 122 (64 male, 58 female) typically developing infants and 31 infant siblings (17 male, 14 female) aged 6-, 9- and 12-months old. All infants demonstrated a significant Expression by AOI interaction (F(10, 1470) = 10.003, P < 0.001, ŋ  = 0.064). Infants' eye movements were "expression-specific" with infants distributing their fixations to AOIs differently per expression. Whereas eye movements provide no evidence of deviancies, behavioural response data show significant aberrancies in reciprocity for infant siblings. Infant siblings show reduced social responsiveness at the group level (F(1, 147) = 4.10, P = 0.042, ŋ  = 0.028) and individual level (Fischer's Exact, P = 0.032). We conclude that the gaze-contingency paradigm provides a realistically interactive experience capable of detecting deviancies in social responsiveness early, and we discuss our results in relation to subsequent infant sibling development. LAY SUMMARY: We investigated how infant siblings of children with autism spectrum disorder respond to interactive faces presented on a computer screen. Our study demonstrates that infant siblings are less responsive when interacting with faces on a computer screen (e.g., they smile and imitate less) in comparison to infants without an older sibling with autism. Reduced responsiveness within social interaction could potentially have implications for how parents and carers interact with these infants. Autism Res 2021, 14: 973-983. © 2020 International Society for Autism Research and Wiley Periodicals LLC.
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http://dx.doi.org/10.1002/aur.2432DOI Listing
May 2021

Dataset of the phospholipidome and transcriptome of under different growth conditions.

Data Brief 2020 Dec 28;33:106349. Epub 2020 Sep 28.

Department of Biomolecular Health Sciences, Utrecht University, 3584 CL Utrecht, the Netherlands.

The membrane phospholipid composition is not a stable bacterial characteristic but can change in response to altered environmental conditions. Here we provide the dataset of the phospholipidome and transcriptome of the microaerophilic human pathogen under different environmental conditions. These data have been used in (2020), The unique phospholipidome of the enteric pathogen : Lysolipids are required for motility at low oxygen availability. Here the abundance of each phospholipid is shown during the growth of for 0-108 h under low and high oxygen conditions (0.3 vs 10% O). The phospholipid data were obtained by applying high performance liquid chromatography tandem-mass spectrometry (LC-MS/MS). The transcriptomic data obtained by RNA-seq show the differential expressed genes between logarithmic and stationary grown bacteria. In addition, our data might serve as a reference information for further in-depth investigation to understand the relation between specific phospholipids and the activity of membrane associated proteins.
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http://dx.doi.org/10.1016/j.dib.2020.106349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7548934PMC
December 2020

Adapt taxonomy to conservation goals.

Science 2020 09;369(6508):1172

Operation Wallacea Ltd, Wallace House, Old Bolingbroke, Spilsby, Lincolnshire, PE23 4EX, UK.

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http://dx.doi.org/10.1126/science.abd7717DOI Listing
September 2020

Identification of Novel Serum MicroRNAs in Age-Related Macular Degeneration.

Transl Vis Sci Technol 2020 03 30;9(4):28. Epub 2020 Mar 30.

Mater Misericordiae University Hospital, Dublin, Ireland.

Purpose: To identify circulating microRNAs (miRNA) associated with age-related macular degeneration (AMD). Thus differentially expressed serum miRNA could be used as AMD biomarkers.

Methods: This study involved total RNA isolation from sera from patients with atrophic AMD (n = 10), neovascular AMD (n = 10), and age- and sex-matched controls (n = 10). A total of 377 miRNAs were coanalyzed using array technologies, and differentially regulated miRNAs were determined. Extensive validation studies (n = 90) of serum from AMD patients and controls confirmed initial results. Total RNA isolation was carried out from sera from patients with atrophic AMD (n = 30), neovascular AMD (n = 30), and controls (n = 30). Fourteen miRNAs from the discovery dataset were coanalyzed using quantitative real-time polymerase chain reaction (qRT-PCR) to validate their presence.

Results: Unsupervised hierarchical clustering indicated that AMD serum specimens have a different miRNA profile to healthy controls. We successfully identified and validated the differentially regulated miRNAs in serum from AMD patients versus controls. The biomarker potential of three miRNAs (miR-126, miR-19a, and miR-410) was confirmed by qRT-PCR, with significantly increased quantities in serum of AMD patients compared with healthy controls.

Conclusions: Increased quantities of miR-126, miR-410, and miR-19a in serum from AMD patients indicate that these miRNAs could potentially serve as diagnostic AMD biomarkers. All three miRNAs significantly correlated with AMD pathogenesis.

Translational Relevance: The discovery of new AMD miRNA may act as biomarkers in evaluating AMD diagnosis and prognosis.
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http://dx.doi.org/10.1167/tvst.9.4.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396178PMC
March 2020

The Unique Phospholipidome of the Enteric Pathogen Campylobacter jejuni: Lysophosholipids Are Required for Motility at Low Oxygen Availability.

J Mol Biol 2020 09 22;432(19):5244-5258. Epub 2020 Jul 22.

Department Biomolecular Health Sciences, Utrecht University, Utrecht, the Netherlands. Electronic address:

In response to changes in their environment bacteria need to change both their protein and phospholipid repertoire to match environmental requirements, but the dynamics of bacterial phospholipid composition under different growth conditions is still largely unknown. In the present study, we investigated the phospholipidome of the bacterial pathogen Campylobacter jejuni. Transcription profiling on logarithmic and stationary phase grown cells of the microaerophilic human pathogen C. jejuni using RNA-seq revealed differential expression of putative phospholipid biosynthesis genes. By applying high-performance liquid chromatography tandem-mass spectrometry, we identified 203 phospholipid species representing the first determination of the phospholipidome of this pathogen. We identified nine different phospholipid classes carrying between one and three acyl chains. Phospholipidome analysis on bacteria of different ages (0-5 days) showed rapid changes in the ratio of phospholipids containing ethanolamine, or glycerol as phospholipid head group and in the number of cyclopropane bond containing fatty acids. Oxygen concentration influenced the percentage of lysophospholipids, and cyclo-propane bonds containing acyl chains. We show that large amounts of the phospholipids are lysophospholipids (30-45%), which mutant studies reveal are needed for normal C. jejuni motility at low oxygen conditions. C. jejuni possesses an unusual phospholipidome that is highly dynamic in response to environmental changes.
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http://dx.doi.org/10.1016/j.jmb.2020.07.012DOI Listing
September 2020

The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation.

Nat Commun 2020 06 25;11(1):3210. Epub 2020 Jun 25.

Department of Molecular Biology and Biotechnology, the University of Sheffield, Sheffield, UK.

The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction.
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http://dx.doi.org/10.1038/s41467-020-16981-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316729PMC
June 2020

Extra Territorial Excursions by European badgers are not limited by age, sex or season.

Sci Rep 2020 06 15;10(1):9665. Epub 2020 Jun 15.

Department of Zoology, School of Natural Sciences, Trinity College Dublin, DO2 CX56, Dublin, Ireland.

European badgers (Meles meles) in medium and high density populations show strong territorial behaviour. Territories in these populations are contiguous, well-marked and often unchanging over many years. However, badgers do not always stay within their territorial boundaries. In our medium-density population, most individual badgers made extra-territorial excursions (ETEs) throughout the year. ETEs were most frequent between April and September and least frequent in December and January (the period of winter lethargy). Male badgers made longer and more frequent ETEs than females (especially between January and March, and in autumn). Breeding females made longer and more frequent ETEs than non-breeding females in November. While these peaks correspond with the main mating seasons, mating activity does not explain ETEs throughout the year. The shorter, but more frequent, ETEs in summer months may serve a monitoring purpose, rather than simply providing additional mating opportunities with badgers from outside the 'home' social group. We found that young badgers did not make regular ETEs until the summer of their second year. If badgers could be vaccinated as cubs, this would reduce any potential risk of TB spread during ETEs.
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http://dx.doi.org/10.1038/s41598-020-66809-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296015PMC
June 2020

An emended description of Sasi Jyothsna . 2013: genomic and phenotypic insights.

Int J Syst Evol Microbiol 2020 Jun;70(6):3921-3923

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium.

was originally described as the first obligate anaerobe in this genus by Sasi Jyothsna . 2013. The complete genome sequence of the type strain of this species was determined and analysed. Genes characteristic for organisms capable of aerobic growth were identified, and the ability of the organism to grow under microaerobic and aerobic conditions was confirmed in two independent laboratories. The description of is thus emended and the wider ramifications of these findings are discussed.
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http://dx.doi.org/10.1099/ijsem.0.004214DOI Listing
June 2020

Agricultural intensification and the evolution of host specialism in the enteric pathogen .

Proc Natl Acad Sci U S A 2020 05 4;117(20):11018-11028. Epub 2020 May 4.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7AY Bath, United Kingdom;

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen () in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
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http://dx.doi.org/10.1073/pnas.1917168117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245135PMC
May 2020

Caucasian Infants' Attentional Orienting to Own- and Other-Race Faces.

Brain Sci 2020 Jan 17;10(1). Epub 2020 Jan 17.

School of Psychology, Keynes College, University of Kent, Canterbury, Kent CT2 7NP, UK.

Infants show preferential attention toward faces and detect faces embedded within complex naturalistic scenes. Newborn infants are insensitive to race, but rapidly develop differential processing of own- and other-race faces. In the present study, we investigated the development of attentional orienting toward own- and other-race faces embedded within naturalistic scenes. Infants aged six-, nine- and twelve-months did not show differences in the speed of orienting to own- and other race faces, but other-race faces held infants' visual attention for longer. We also found a clear developmental progression in attentional capture and holding, with older infants orienting to faces faster and fixating them for longer. Results are interpreted within the context of the two-process model of face processing.
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http://dx.doi.org/10.3390/brainsci10010053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016870PMC
January 2020

Dispersal patterns in a medium-density Irish badger population: Implications for understanding the dynamics of tuberculosis transmission.

Ecol Evol 2019 Dec 13;9(23):13142-13152. Epub 2019 Nov 13.

Department of Zoology School of Natural Sciences Trinity College Dublin Dublin Ireland.

European badgers () are group-living mustelids implicated in the spread of bovine tuberculosis (TB) to cattle and act as a wildlife reservoir for the disease. In badgers, only a minority of individuals disperse from their natal social group. However, dispersal may be extremely important for the spread of TB, as dispersers could act as hubs for disease transmission. We monitored a population of 139 wild badgers over 7 years in a medium-density population (1.8 individuals/km). GPS tracking collars were applied to 80 different individuals. Of these, we identified 25 dispersers, 14 of which were wearing collars as they dispersed. This allowed us to record the process of dispersal in much greater detail than ever before. We show that dispersal is an extremely complex process, and measurements of straight-line distance between old and new social groups can severely underestimate how far dispersers travel. Assumptions of straight-line travel can also underestimate direct and indirect interactions and the potential for disease transmission. For example, one female disperser which eventually settled 1.5 km from her natal territory traveled 308 km and passed through 22 different territories during dispersal. Knowledge of badgers' ranging behavior during dispersal is crucial to understanding the dynamics of TB transmission, and for designing appropriate interventions, such as vaccination.
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http://dx.doi.org/10.1002/ece3.5753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912907PMC
December 2019

Domestication of Campylobacter jejuni NCTC 11168.

Microb Genom 2019 07 16;5(7). Epub 2019 Jul 16.

School of Veterinary Medicine, University of Surrey, Surrey, UK.

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.
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http://dx.doi.org/10.1099/mgen.0.000279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700657PMC
July 2019

Sodium Taurocholate Stimulates Outer Membrane Vesicle Production via Down-Regulation of the Maintenance of Lipid Asymmetry Pathway.

Front Cell Infect Microbiol 2019 29;9:177. Epub 2019 May 29.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.

outer membrane vesicles (OMVs) contain numerous virulence-associated proteins including the cytolethal distending toxin and three serine proteases. As lacks the classical virulence-associated secretion systems of other enteric pathogens that deliver effectors directly into target cells, OMVs may have a particularly important role in virulence. OMV production is stimulated by the presence of physiological concentrations of the bile salt sodium taurocholate (ST) through an unknown mechanism. The maintenance of lipid asymmetry (MLA) pathway has been implicated in a novel mechanism for OMV biogenesis, open to regulation by host signals. In this study we investigated the role of the MLA pathway in OMV biogenesis with ST as a potential regulator. OMV production was quantified by analyzing protein and lipid concentrations of OMV preparations and OMV particle counts produced by nanoparticle tracking analysis. Mutation of which encodes the outer membrane component of the MLA pathway significantly increased OMV production compared to the wild-type strain. Detergent sensitivity and membrane permeability assays confirmed the increased OMV production was not due to changes in membrane stability. The presence of 0.2% (w/v) ST increased wild-type OMV production and reduced OMV size, but did not further stimulate mutant OMV production or significantly alter mutant OMV size. qRT-PCR analysis demonstrated that the presence of ST decreased expression of both and in wild-type strains 11168 and 488. Collectively the data in this study suggests can regulate OMV production in response to host gut signals through changes in expression of the MLA pathway. As the gut bile composition is dependent on both diet and the microbiota, this study highlights the potential importance of diet and lifestyle factors on the varying disease presentations associated with gut pathogen infection.
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http://dx.doi.org/10.3389/fcimb.2019.00177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549495PMC
January 2020

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate.

mSystems 2019 Jun 11;4(4). Epub 2019 Jun 11.

Molecular Biology & Biotechnology, University of Sheffield, Sheffield, United Kingdom.

Productivity of bacterial cell factories is frequently compromised by stresses imposed by recombinant protein synthesis and carbon-to-product conversion, but little is known about these bioprocesses at a systems level. Production of the unnatural metabolite citramalate in requires the expression of a single gene coding for citramalate synthase. Multiomic analyses of a fermentation producing 25  g liter citramalate were undertaken to uncover the reasons for its productivity. Metabolite, transcript, protein, and lipid profiles of high-cell-density, fed-batch fermentations of expressing either citramalate synthase or an inactivated enzyme were similar. Both fermentations showed downregulation of flagellar genes and upregulation of chaperones IbpA and IbpB, indicating that these responses were due to recombinant protein synthesis and not citramalate production. Citramalate production did not perturb metabolite pools, except for an increased intracellular pyruvate pool. Gene expression changes in response to citramalate were limited; none of the general stress response regulons were activated. Modeling of transcription factor activities suggested that citramalate invoked a GadW-mediated acid response, and changes in GadY and RprA regulatory small RNA (sRNA) expression supported this. Although changes in membrane lipid composition were observed, none were unique to citramalate production. This systems analysis of the citramalate fermentation shows that has capacity to readily adjust to the redirection of resources toward recombinant protein and citramalate production, suggesting that it is an excellent chassis choice for manufacturing organic acids. Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the citramalate fermentation was undertaken to uncover the reasons underpinning its productivity. This showed that readily adjusts to the redirection of metabolic resources toward recombinant protein and citramalate production and suggests that is an excellent chassis for manufacturing similar small, polar, foreign molecules.
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http://dx.doi.org/10.1128/mSystems.00187-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561320PMC
June 2019

Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli.

mSystems 2019 Jun 11;4(4). Epub 2019 Jun 11.

Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom

Vanillin (4-hydroxy-3-methoxybenzaldehyde) is an economically important flavor compound that can be made in bacterial cell factories, but toxicity is a major problem for cells producing this aromatic aldehyde. Using (i) a global proteomic analysis supported by multiple physiological experiments, mutant analyses, and inferred transcription factor modeling and (ii) adaptive laboratory evolution (ALE) of vanillin tolerance combined with genome-wide analysis of the underlying mutations, mechanisms of vanillin toxicity in have been elucidated. We identified 147 proteins that exhibited a significant change in abundance in response to vanillin, giving the first detailed insight into the cellular response to this aldehyde. Vanillin caused accumulation of reactive oxygen species invoking adaptations coordinated by a MarA, OxyR, and SoxS regulatory network and increased RpoS/DksA-dependent gene expression. Differential fumarase C upregulation was found to prevent oxidative damage to FumA and FumB during growth with vanillin. Surprisingly, vanillin-dependent reduction pf copper (II) to copper (I) led to upregulation of the gene and growth in the presence of vanillin was shown to be hypersensitive to inhibition by copper ions. AcrD and AaeAB were identified as potential vanillin efflux systems. Vanillin-tolerant strains isolated by ALE had distinct nonsynonymous single nucleotide polymorphisms (SNPs) in that led to increased citrate synthase activity. Strain-specific mutations in , , and were also present. One strain had a large (∼10-kb) deletion that included the region. Our data provide new understanding of bacterial vanillin toxicity and identify novel gene targets for future engineering of vanillin-tolerant strains of A particular problem for the biotechnological production of many of the valuable chemicals that we are now able to manufacture in bacterial cells is that these products often poison the cells producing them. Solutions to improve product yields or alleviate such toxicity using the techniques of modern molecular biology first require a detailed understanding of the mechanisms of product toxicity. Here we have studied the economically important flavor compound vanillin, an aromatic aldehyde that exerts significant toxic effects on bacterial cells. We used high-resolution protein abundance analysis as a starting point to determine which proteins are upregulated and which are downregulated by growth with vanillin, followed by gene expression and mutant studies to understand the mechanism of the response. In a second approach, we evolved bacterial strains with higher vanillin tolerance. Their genome sequences have yielded novel insights into vanillin tolerance that are complementary to the proteomics data set.
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http://dx.doi.org/10.1128/mSystems.00163-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561319PMC
June 2019

The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen.

Adv Microb Physiol 2019 8;74:239-329. Epub 2019 Mar 8.

Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.

Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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http://dx.doi.org/10.1016/bs.ampbs.2019.02.003DOI Listing
February 2020

Infants' responses to interactive gaze-contingent faces in a novel and naturalistic eye-tracking paradigm.

Dev Psychol 2019 Jul 6;55(7):1362-1371. Epub 2019 May 6.

School of Psychology.

Face scanning is an important skill that takes place in a highly interactive context embedded within social interaction. However, previous research has studied face scanning using noninteractive stimuli. We aimed to study face scanning and social interaction in infancy in a more ecologically valid way by providing infants with a naturalistic and socially engaging experience. We developed a novel gaze-contingent eye-tracking paradigm in which infants could interact with face stimuli. Responses (socially engaging/socially disengaging) from faces were contingent on infants' eye movements. We collected eye-tracking and behavioral data of 162 (79 male, 83 female) 6-, 9- and 12-month-old infants. All infants showed a clear preference for looking at the eyes relative to the mouth. Contingency was learned implicitly, and infants were more likely to show behavioral responses (e.g., smiling, pointing) when receiving socially engaging responses. Infants' responses were also more often congruent with the actors' responses. Additionally, our large sample allowed us to look at the ranges of behavior on our task, and we identified a small number of infants who displayed deviant behaviors. We discuss these findings in relation to data collected from a small sample (N = 11) of infants considered to be at-risk for autism spectrum disorders. Our results demonstrate the versatility of the gaze-contingency eye-tracking paradigm, allowing for a more nuanced and complex investigation of face scanning as it happens in real-life interaction. As we provide additional measures of contingency learning and reciprocity, our task holds the potential to investigate atypical neurodevelopment within the first year of life. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
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http://dx.doi.org/10.1037/dev0000736DOI Listing
July 2019

Infants rapidly detect human faces in complex naturalistic visual scenes.

Dev Sci 2019 11 29;22(6):e12829. Epub 2019 Apr 29.

Universite Grenoble Alpes, Grenoble, France.

Infants respond preferentially to faces and face-like stimuli from birth, but past research has typically presented faces in isolation or amongst an artificial array of competing objects. In the current study infants aged 3- to 12-months viewed a series of complex visual scenes; half of the scenes contained a person, the other half did not. Infants rapidly detected and oriented to faces in scenes even when they were not visually salient. Although a clear developmental improvement was observed in face detection and interest, all infants displayed sensitivity to the presence of a person in a scene, by displaying eye movements that differed quantifiably across a range of measures when viewing scenes that either did or did not contain a person. We argue that infant's face detection capabilities are ostensibly "better" with naturalistic stimuli and artificial array presentations used in previous studies have underestimated performance.
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http://dx.doi.org/10.1111/desc.12829DOI Listing
November 2019
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