118 results on '"Campbell BJ"'
Search Results
2. MUCOSA-ASSOCIATED E. COLI ISOLATES FROM INFLAMMATORY BOWEL DISEASE AND COLORECTAL CANCER PATIENTS ACTIVATE WNT/BETA-CATENIN SIGNALLING IN VITRO AND IN VIVO
- Author
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Meehan, B, Campbell, BJ, and Rhodes, JM
- Published
- 2016
3. INFLUENCE OF IRON SUPPLEMENTATION ON THE NATURAL HISTORY OF COLITIS
- Author
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Mahalhal, A, Campbell, BJ, Pritchard, DM, and Probert, CS
- Published
- 2016
4. CROHN'S DISEASE MUCOSA-ASSOCIATED E. COLI SHOW BETTER TOLERANCE OF A SUPEROXIDATIVE STRESS ENVIRONMENT, THAT MIMICS CONDITIONS INSIDE MACROPHAGE PHAGOLYSOSOMES
- Author
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Tawfik, AT, Rhodes, JM, and Campbell, BJ
- Published
- 2016
5. Characterization of a novel simian immunodeficiency virus (SIV) from L'Hoest monkeys (Cercopithecus l'hoesti):Implications for the origins of SIVmnd and other primate lentiviruses
- Author
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Hirsch, VM, Campbell, BJ, Bailes, E, Goeken, R, Brown, C, Elkins, WR, Axthelm, M, Murphey-Corb, M, and Sharp, PM
- Subjects
PROVIRAL DNA ,SYKES MONKEYS ,SOOTY MANGABEYS ,animal diseases ,virus diseases ,GENETIC DIVERSITY ,AFRICAN-GREEN MONKEYS ,TANTALUS MONKEYS ,CROSS-SPECIES TRANSMISSION ,HIGHLY DIVERGENT ,SEQUENCE ,WILD-CAPTURED CHIMPANZEE - Abstract
The human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) appear to have originated by cross-species transmission of simian immunodeficiency virus (SN) from asymptomatically infected African primates. Few of the SIVs characterized to date efficiently infect human primary lymphocytes. Interesting, two of the three identified to infect such cultures (SIVsm and SIVcpz) have appeared in human populations as genetically related HIVs. In the present study, we characterized a novel SIV isolate from an East African monkey of the Cercopithecus genus, the l'hoest monkey (C. l'hoesti), which we designated SIVlhoest. This SN isolate efficiently infected both human and macaque lymphocytes and resulted in a persistent infection of macaques, characterized by high primary virus load and a progressive decline in circulating CD4 lymphocytes, consistent with progression to AIDS. Phylogenetic analyses showed that SIVIhoest is genetically distinct from other previously characterized primate lentiviruses but clusters in the same major lineage as SIV from mandrills (SIVmnd), a West African primate species. Given the geographic distance between the ranges of l'hoest monkeys and mandrills, this may indicate that SIVmnd arose through cross-species transmission from close relatives of l'hoest monkeys that are sympatric with mandrills. These observations lend support to the hypothesis that the primate lentiviruses originated and coevolved within monkeys of the Cercopithecus genus. Regarded in this light, lentivirus infections of primates not belonging to the Cercopithecus genus may have resulted from cross-species transmission in the not-too-distant past.
- Published
- 1999
6. Temporal changes in bacterial rRNA and rRNA genes in Delaware (USA) coastal waters
- Author
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Campbell, BJ, primary, Yu, L, additional, Straza, TRA, additional, and Kirchman, DL, additional
- Published
- 2009
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7. Identification of peanut lectin in peripheral venous blood after peanut ingestion
- Author
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Wang, Q, primary, Yu, LG, additional, Campbell, BJ, additional, Milton, JD, additional, and Rhodes, JM, additional
- Published
- 1998
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8. Regulated expression of GATA-6 transcription factor in gastric endocrine cells
- Author
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Dimaline, R, primary, Campbell, BJ, additional, Watson, F, additional, Sandvik, AK, additional, Struthers, J, additional, and Noble, PJ, additional
- Published
- 1997
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9. Characterising molecular mechanisms of Crohn���s disease-associated Escherichia coli that enable their survival and replication within macrophages
- Author
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Tawfik, AT, Campbell, BJ, and Rhodes, JM
- Abstract
Mucosa-associated adherent, invasive Escherichia coli (AIEC), found in increased number in Crohn���s disease (CD) ileal and colonic mucosae, can survive and replicate within underlying host immune competent cells (e.g. macrophages and dendritic cells) without triggering host cell death. The intra-macrophage environment plays an essential role in bacterial killing where engulfed bacteria are exposed to a hostile environment of low pH, high levels of proteolytic/lysosomal enzymes, high nitrosative and high oxidative stress, and the activation of a respiratory burst with generation of superoxide ions. Although a few stress response genes have been identified that likely support the paradigm ileal AIEC isolate LF82 to survive and replicate within the macrophage, the key molecular mechanisms involved in supporting Crohn���s disease (CD) mucosa-associated AIEC to resist killing by host mucosal macrophages within harsh environment of the phagolysosome still remains largely unclear. Here we aimed to compare the ability of a number of E. coli strains to survive and replicate inside macrophages, including a number of clinical isolates (from CD, colorectal cancer (CRC) and ulcerative colitis (UC) patients and other infective or non-inflamed sources), and this to toleration of growth in chemical-induced stress conditions mimicking the intra-phagolysosome environment. In addition, a focus was to further understand the molecular mechanisms responsible for acid tolerance of the paradigm CD isolates and examine their replication within macrophages defective in NF-��B pathway signalling. Finally, to also assess whether CD AIEC possess ability to alter host oxidative stress response gene expression in macrophages to support their survival/replication. Both ileal and colonic CD isolates (AIEC) were found to possess ability to either survive and/or replicate within murine macrophages (i.e. J774-A1 cell-line and wild-type (WT) C57BL/6 bone marrow derived macrophages [BMDM]) and to tolerate all stress conditions mimicking those within the phagolysosome, e.g. low nutrient, high acid, high nitrosative, high oxidative stress including exposure to superoxide ions. Interestingly pathogenic E. coli isolates from urinary tract infection (UTI) and some healthy-mucosa associated E. coli strains behaved similarly. Crohn���s AIEC were unable to survive and replicate inside Nf��b1-/- and Nf��b2-/- BMDM, whilst they survived/replicated within WT and c-Rel-/- BMDM. Thus Crohn���s AIEC survival and replication appears dependent on host NF��B signalling within the macrophage. Conversely, all CRC and UC isolates tested and the majority of laboratory E. coli strains studied were unable to survive inside murine J774-A1 macrophage phagolysosomes and they were also intolerant to most stress conditions, in particular superoxidative stress. Colonic CD AIEC isolate HM605 showed higher initial levels of expression of acid response genes gadA and gadB that may support adaptation to the intra-macrophage phagolysosome niche. Adaptation to an intra-macrophage lifestyle appeared not to be through any ability to alter host macrophage oxidative stress response to infection as no differential changes were observed in the expression of 84 host genes related to oxidative stress to that seen with non-replicating laboratory E. coli strain. Overall this study provides new insight into how CD mucosa-associated E. coli isolates resist killing by mucosal macrophages through adaptation to the acidic, high oxidative environment within the macrophage phagolysosome. The data may support future development of new therapeutic strategies that target the fundamental pathology of CD, in particular support a reduction in bacterial persistence/increased killing of intra-macrophage E. coli in CD patient mucosae.
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- 2017
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10. Bacteria-Macrophage interactions in the Pathogenesis of Crohn���s Disease
- Author
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Flanagan, PK, rhodes, JM, and campbell, BJ
- Published
- 2017
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11. Bacteria-induced Wnt signalling as a mechanism for malignant development in the intestinal epithelium
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Meehan, B, Campbell, BJ, Rhodes, J, and Winstanley, C
- Published
- 2017
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12. The Role of Soluble Plant Fibres (Non-Starch Polysaccharides, NSP) in the Maintenance of Intestinal Health and Prevention of Diarrhoeal Disease
- Author
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Simpson, H, Campbell, BJ, and Rhodes, JM
- Abstract
It has long been proposed that a high intake of dietary fibre promotes good intestinal health. Work performed previously by our research group suggests that soluble dietary fibre might have a particularly beneficial impact on intestinal health via its ability to inhibit potentially harmful interactions between bacterial pathogens and the gut epithelium. The aims of this thesis were to evaluate soluble plantain NSP for its ability to disrupt the epithelial interactions of diarrhoeal pathogens C. difficile and Enterotoxigenic Escherichia coli (ETEC), as well as other bacterial components implicated in diarrhoeal disease. Work was also performed to characterise the specific inhibitory fraction of plantain NSP, and in addition, to establish the molecular mechanism underlying its inhibitory activity. A range of soluble dietary fibres were shown to significantly inhibit the in vitro epithelial adhesion of C. difficile and ETEC, but out of all the fibres tested, soluble plantain NSP exhibited the highest efficacy. Plantain NSP also significantly inhibited the epithelial adhesion of eleven C. difficile clinical isolates, irrespective of their toxin expression or ribotype status. Furthermore, plantain NSP blocked the epithelial interactions of five purified C. difficile spore preparations. In addition to its anti-adhesive effects, soluble plantain NSP significantly down-regulated the pro-inflammatory, cytotoxicity and apoptotic response induced by C. difficile and its toxins. Similar effects were also found with respect to mucosally-associated E. coli isolated from ulcerative colitis (UC) patients, as well as bacterial components such as flagellin and LPS. Results demonstrated that the inhibitory activity of plantain NSP was mediated by its acidic polysaccharide fraction, which is mainly composed of pectic material. In addition, it was shown that soluble plantain disrupted bacterial-epithelial interactions via an interaction with the intestinal epithelium. Whilst plantain NSP induced increased cellular chloride secretion, this mechanism was not responsible for inhibitory activity. It was also hypothesised that plantain NSP might mimic intestinal MUC2 glycans by interacting with cell-surface galectin-3, with consequent nuclear localisation of β-catenin and down-regulation of inflammatory cytokines. Whilst plantain NSP was shown to induce activation of β-catenin, the knockdown of surface galectin-3 expression had no effect on inhibitory activity. Thus, the specific mechanism underlying the inhibitory activity of plantain NSP requires further investigation. This work supports the hypothesis that soluble plantain fibre can inhibit harmful interactions between bacteria and the human intestinal epithelium. Indeed, these studies provide convincing evidence to suggest that soluble plantain fibre, acting as a ‘contrabiotic’, could be developed as a potential prophylaxis or treatment against C. difficile and ETEC, which represent the main cause of antibiotic-associated diarrhoea and traveller’s diarrhoea, respectively. In addition, dietary supplementation with soluble plantain NSP may also confer a therapeutic benefit in inflammatory bowel disease (IBD).
- Published
- 2016
13. Guidelines for communicating commensurate magnetic structures. A report of the International Union of Crystallography Commission on Magnetic Structures.
- Author
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Perez-Mato JM, Campbell BJ, Garlea VO, Damay F, Aurelio G, Avdeev M, Fernández-Díaz MT, Henriques MS, Khalyavin D, Lee S, Pomjakushin V, Terada N, Zaharko O, Campo J, Fabelo O, Litvin DB, Petricek V, Rayaprol S, Rodriguez-Carvajal J, and Von Dreele R
- Abstract
A report from the International Union of Crystallography Commission on Magnetic Structures outlining the recommendations for communicating commensurate magnetic structures.
- Published
- 2024
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14. Chiral multiferroicity in two-dimensional hybrid organic-inorganic perovskites.
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Zheng H, Ghosh A, Swamynadhan MJ, Zhang Q, Wong WPD, Wu Z, Zhang R, Chen J, Cimpoesu F, Ghosh S, Campbell BJ, Wang K, Stroppa A, Mahendiran R, and Loh KP
- Abstract
Chiral multiferroics offer remarkable capabilities for controlling quantum devices at multiple levels. However, these materials are rare due to the competing requirements of long-range orders and strict symmetry constraints. In this study, we present experimental evidence that the coexistence of ferroelectric, magnetic orders, and crystallographic chirality is achievable in hybrid organic-inorganic perovskites [(R/S)-β-methylphenethylamine]
2 CuCl4 . By employing Landau symmetry mode analysis, we investigate the interplay between chirality and ferroic orders and propose a novel mechanism for chirality transfer in hybrid systems. This mechanism involves the coupling of non-chiral distortions, characterized by defining a pseudo-scalar quantity, ξ = p ⋅ r ( p represents the ferroelectric displacement vector and r denotes the ferro-rotational vector), which distinguishes between (R)- and (S)-chirality based on its sign. Moreover, the reversal of this descriptor's sign can be associated with coordinated transitions in ferroelectric distortions, Jahn-Teller antiferro-distortions, and Dzyaloshinskii-Moriya vectors, indicating the mediating role of crystallographic chirality in magnetoelectric correlations., (© 2024. The Author(s).)- Published
- 2024
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15. Gut bacteria of adult and larval Cotinis nitida Linnaeus (Coleoptera: Scarabaeidae) demonstrate community differences according to respective life stage and gut region.
- Author
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Kucuk RA, Campbell BJ, Lyon NJ, Shelby EA, and Caterino MS
- Abstract
The close association between bacteria and insect hosts has played an indispensable role in insect diversity and ecology. Thus, continued characterization of such insect-associated-microbial communities is imperative, especially those of saprophagous scarab beetles. The bacterial community of the digestive tract of adults and larvae of the cetoniine scarab species Cotinis nitida is characterized according to life stage, gut structure, and sex via high-throughput 16S rRNA gene amplicon sequencing. Through permutational ANOVAs of the resulting sequences, bacterial communities of the digestive system are shown to differ significantly between adults and larvae in taxon richness, evenness and relatedness. Significant bacterial community-level differences are also observed between the midgut and hindgut in adult beetles, while no significant host-sex differences are observed. The partitioning between bacterial communities in the larval digestive system is shown through significant differences in two distinct hindgut regions, the ileum and the expanded paunch, but not between the midgut and ileum portion of the hindgut region. These data further corroborate the hypothesis of strong community partitioning in the gut of members of the Scarabaeoidea, suggest hypotheses of physiological-digestive association, and also demonstrate the presence of a seemingly unusual non-scarab-associated taxon. These findings contribute to a general portrait of scarabaeoid digestive tract bacterial communities while illuminating the microbiome of a common new world cetoniine of the Gymnetini-a tribe largely neglected in scarab and beetle microbiome and symbiosis literature., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Kucuk, Campbell, Lyon, Shelby and Caterino.)
- Published
- 2023
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16. Effect of Probiotics in Breast Cancer: A Systematic Review and Meta-Analysis.
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Thu MS, Ondee T, Nopsopon T, Farzana IAK, Fothergill JL, Hirankarn N, Campbell BJ, and Pongpirul K
- Abstract
Probiotics may have the potential to protect against breast cancer, partly through systemic immunomodulatory action and active impact upon intestinal microbiota. Given a few clinical studies on their curative role, we conducted a systematic review of the potential effects of probiotics in breast cancer patients and survivors of breast cancer, aiming to support further clinical studies. A literature search was performed using PubMed, Embase, and the CENTRAL databases from inception through to March 2022. A total of eight randomized clinical trials were identified from thirteen articles published between 2004 and 2022. We evaluated quality-of-life measures, observed bacterial species and diversity indices, probiotic-related metabolites, inflammatory biomarkers, and other responses in breast cancer patients and survivors. Results were synthesized qualitatively and quantitatively using random-effects meta-analysis. Different probiotics supplements utilized included Lactobacillus species alone (Lacto), with or without estriol; probiotic combinations of Lactobacillus with Bifidobacterium (ProLB), with or without prebiotic fructooligosaccharides (FOS); ProLB plus Streptococcus and FOS (ProLBS + FOS); and ProLB plus Enterococcus (ProLBE). We found that use of ProLBS with FOS in breast cancer patients and use of ProLBE in survivors of breast cancer show potential benefits in countering obesity and dyslipidemia. ProLBS with FOS use decreases pro-inflammatory TNF-α in breast cancer survivors and improves quality of life in those with breast-cancer-associated lymphedema. Supplementing probiotics capsules (10
9 CFU) with a prebiotic and using an intake duration of 10 weeks could provide a better approach than probiotics alone., Competing Interests: The authors declare no conflict of interest.- Published
- 2023
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17. Interleukin-10 Deficiency Impacts on TNF-Induced NFκB Regulated Responses In Vivo.
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Papoutsopoulou S, Pollock L, Williams JM, Abdul-Mahdi MMLF, Dobbash R, Duckworth CA, and Campbell BJ
- Abstract
Interleukin-10 (IL-10) is an anti-inflammatory cytokine that has a major protective role against intestinal inflammation. We recently revealed that intestinal epithelial cells in vitro regulate NFκB-driven transcriptional responses to TNF via an autocrine mechanism dependent on IL-10 secretion. Here in this study, we investigated the impact of IL-10 deficiency on the NFκB pathway and its downstream targets in the small intestinal mucosa in vivo. We observed dysregulation of TNF, IκBα, and A20 gene and protein expression in the small intestine of steady-state or TNF-injected Il10
-/- mice, compared to wild-type C57BL6/J counterparts. Upon TNF injection, tissue from the small intestine showed upregulation of NFκB p65[RelA] activity, which was totally diminished in Il10-/- mice and correlated with reduced levels of TNF, IκBα, and A20 expression. In serum, whilst IgA levels were noted to be markedly downregulated in IL-10-deficient- mice, normal levels of mucosal IgA were seen in intestine mucosa. Importantly, dysregulated cytokine/chemokine levels were observed in both serum and intestinal tissue lysates from naïve, as well as TNF-injected Il10-/- mice. These data further support the importance of the IL-10-canonical NFκB signaling pathway axis in regulating intestinal mucosa homeostasis and response to inflammatory triggers in vivo.- Published
- 2022
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18. Cross-inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome.
- Author
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Zhang Z, Jatana BS, Campbell BJ, Gill J, Suseela V, and Tharayil N
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- Crops, Agricultural metabolism, Endoplasmic Reticulum-Associated Degradation, Proteome metabolism, Stress, Physiological, Droughts, Zea mays metabolism
- Abstract
Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross-inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon-inoculum), and rhizobiota from organic farm maintained under mesic condition (organic-inoculum). Across drought treatments (40% field capacity), maize that received andropogon-inoculum produced two-fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well-watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological-level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome-level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum-associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon-inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome-facilitated drought tolerance and demonstrates a better path to utilize plant-rhizobiome associations to enhance drought tolerance in crops., (© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
- Published
- 2022
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19. Root metabolome of plant-arbuscular mycorrhizal symbiosis mirrors the mutualistic or parasitic mycorrhizal phenotype.
- Author
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Kaur S, Campbell BJ, and Suseela V
- Subjects
- Metabolome, Phenotype, Plant Roots physiology, Symbiosis, Mycorrhizae physiology
- Abstract
The symbiosis of arbuscular mycorrhizal fungi (AMF) with plants, the most ancient and widespread association, exhibits phenotypes that range from mutualism to parasitism. However, we still lack an understanding of the cellular-level mechanisms that differentiate and regulate these phenotypes. We assessed the modulation in growth parameters and root metabolome of two sorghum accessions inoculated with two AMF species (Rhizophagus irregularis, Gigaspora gigantea), alone and in a mixture under phosphorus (P) limiting conditions. Rhizophagus irregularis exhibited a mutualistic phenotype with increased P uptake and plant growth. This positive outcome was associated with a facilitatory metabolic response including higher abundance of organic acids and specialized metabolites critical to maintaining a functional symbiosis. However, G. gigantea exhibited a parasitic phenotype that led to plant growth depression and resulted in inhibitory plant metabolic responses including the higher abundance of p-hydroxyphenylacetaldoxime with antifungal properties. These findings suggest that the differential outcome of plant-AMF symbiosis could be regulated by or reflected in changes in the root metabolome that arises from the interaction of the plant species with the specific AMF species. A mutualistic symbiotic association prevailed when the host plants were exposed to a mixture of AMF. Our results provide a metabolome-level landscape of plant-AMF symbiosis and highlight the importance of the identity of both AMF and crop genotypes in facilitating a mutualistic AMF symbiosis., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)
- Published
- 2022
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20. Effects of Human RelA Transgene on Murine Macrophage Inflammatory Responses.
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Papoutsopoulou S, Morris L, Bayliff A, Mair T, England H, Stagi M, Bergey F, Alam MT, Sheibani-Tezerji R, Rosenstiel P, Müller W, Martins Dos Santos VAP, and Campbell BJ
- Abstract
The NFκB transcription factors are major regulators of innate immune responses, and NFκB signal pathway dysregulation is linked to inflammatory disease. Here, we utilised bone marrow-derived macrophages from the p65-DsRedxp/IκBα-eGFP transgenic strain to study the functional implication of xenogeneic (human) RelA(p65) protein introduced into the mouse genome. Confocal imaging showed that human RelA is expressed in the cells and can translocate to the nucleus following activation of Toll-like receptor 4. RNA sequencing of lipid A-stimulated macrophages, revealed that human RelA impacts on murine gene transcription, affecting both non-NFκB and NFκB target genes, including immediate-early and late response genes, e.g., Fos and Cxcl10 . Validation experiments on NFκB targets revealed markedly reduced mRNA levels, but similar kinetic profiles in transgenic cells compared to wild-type. Enrichment pathway analysis of differentially expressed genes revealed interferon and cytokine signaling were affected. These immune response pathways were also affected in macrophages treated with tumor necrosis factor. Data suggests that the presence of xenogeneic RelA protein likely has inhibitory activity, altering specific transcriptional profiles of key molecules involved in immune responses. It is therefore essential that this information be taken into consideration when designing and interpreting future experiments using this transgenic strain.
- Published
- 2022
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21. Soluble Non-Starch Polysaccharides From Plantain ( Musa x paradisiaca L.) Diminish Epithelial Impact of Clostridioides difficile .
- Author
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Simpson HL, Roberts CL, Thompson LM, Leiper CR, Gittens N, Trotter E, Duckworth CA, Papoutsopoulou S, Miyajima F, Roberts P, O'Kennedy N, Rhodes JM, and Campbell BJ
- Abstract
Clostridioides difficile infection (CDI) is a leading cause of antibiotic-associated diarrhoea. Adhesion of this Gram-positive pathogen to the intestinal epithelium is a crucial step in CDI, with recurrence and relapse of disease dependent on epithelial interaction of its endospores. Close proximity, or adhesion of, hypervirulent strains to the intestinal mucosa are also likely to be necessary for the release of C. difficile toxins, which when internalized, result in intestinal epithelial cell rounding, damage, inflammation, loss of barrier function and diarrhoea. Interrupting these C. difficile -epithelium interactions could therefore represent a promising therapeutic strategy to prevent and treat CDI. Intake of dietary fibre is widely recognised as being beneficial for intestinal health, and we have previously shown that soluble non-starch polysaccharides (NSP) from plantain banana ( Musa spp.), can block epithelial adhesion and invasion of a number of gut pathogens, such as E. coli and Salmonellae. Here, we assessed the action of plantain NSP, and a range of alternative soluble plant fibres, for inhibitory action on epithelial interactions of C. difficile clinical isolates, purified endospore preparations and toxins. We found that plantain NSP possessed ability to disrupt epithelial adhesion of C. difficile vegetative cells and spores, with inhibitory activity against C. difficile found within the acidic (pectin-rich) polysaccharide component, through interaction with the intestinal epithelium. Similar activity was found with NSP purified from broccoli and leek, although seen to be less potent than NSP from plantain. Whilst plantain NSP could not block the interaction and intracellular action of purified C. difficile toxins, it significantly diminished the epithelial impact of C. difficile , reducing both bacteria and toxin induced inflammation, activation of caspase 3/7 and cytotoxicity in human intestinal cell-line and murine intestinal organoid cultures. Dietary supplementation with soluble NSP from plantain may therefore confer a protective effect in CDI patients by preventing adhesion of C. difficile to the mucosa, i.e. a "contrabiotic" effect, and diminishing its epithelial impact. This suggests that plantain soluble dietary fibre may be a therapeutically effective nutritional product for use in the prevention or treatment of CDI and antibiotic-associated diarrhoea., Competing Interests: NO’K is a present, and CR a past, employee of Provexis Plc. BC, HS and JR received additional funding support from the biotech partner Provexis Plc as part of the BBSRC Industrial CASE studentship (BB/I016783/1). JR is listed as inventor on patents held by Provexis Plc, in a licence agreement with the University of Liverpool, for use of complex oligosaccharides in the prevention or treatment of inflammatory bowel disease (US8945639B2), and for use of soluble fibres in antibiotic-associated diarrhoea (US20120165289A1). The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Simpson, Roberts, Thompson, Leiper, Gittens, Trotter, Duckworth, Papoutsopoulou, Miyajima, Roberts, O’Kennedy, Rhodes and Campbell.)
- Published
- 2021
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22. Quantitative trait loci controlling agronomic and biochemical traits in Cannabis sativa.
- Author
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Woods P, Campbell BJ, Nicodemus TJ, Cahoon EB, Mullen JL, and McKay JK
- Subjects
- Cannabis growth & development, Cannabis metabolism, Intramolecular Transferases genetics, Plant Proteins genetics, Quantitative Trait, Heritable, Cannabis genetics, Quantitative Trait Loci
- Abstract
Understanding the genetic basis of complex traits is a fundamental goal of evolutionary genetics. Yet, the genetics controlling complex traits in many important species such as hemp (Cannabis sativa) remain poorly investigated. Because hemp's change in legal status with the 2014 and 2018 U.S. Federal Farm Bills, interest in the genetics controlling its numerous agriculturally important traits has steadily increased. To better understand the genetics of agriculturally important traits in hemp, we developed an F2 population by crossing two phenotypically distinct hemp cultivars (Carmagnola and USO31). Using whole-genome sequencing, we mapped quantitative trait loci (QTL) associated with variation in numerous agronomic and biochemical traits. A total of 69 loci associated with agronomic (34) and biochemical (35) trait variation were identified. We found that most QTL co-localized, suggesting that the phenotypic distinctions between Carmagnola and USO31 are largely controlled by a small number of loci. We identified TINY and olivetol synthase as candidate genes underlying co-localized QTL clusters for agronomic and biochemical traits, respectively. We functionally validated the olivetol synthase candidate by expressing the alleles in yeast. Gas chromatography-mass spectrometry assays of extracts from these yeast colonies suggest that the USO31 olivetol synthase is functionally less active and potentially explains why USO31 produces lower cannabinoids compared to Carmagnola. Overall, our results help modernize the genomic understanding of complex traits in hemp., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)
- Published
- 2021
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23. The effects of protein supplementation and pasture maintenance on the growth, parasite burden, and economic return of pasture-raised lambs.
- Author
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Campbell BJ, Marsh AE, Parker EM, McCutcheon JS, Fluharty FL, and Parker AJ
- Abstract
The objective of this experiment was to evaluate the impact of protein supplementation and pasture contamination with gastrointestinal nematodes on the mitigation of parasitic infection in grazing lambs. We hypothesized that there would be no difference between protein supplementation and newly sown pasture in evaluating lamb growth and health parameters associated with parasitism. Furthermore, we questioned if there would be an interaction between protein supplementation and pasture type. A total of 192, 60-d-old lambs (28.3 ± 5.1 kg) were randomly assigned to one of four treatments: 1) new pasture without supplementation (NN); 2) new pasture with supplementation (NS); 3) established pasture without supplementation (EN); and 4) established pasture with supplementation (ES) and grazed for 112 d. Lambs were supplemented at a rate of 1% body weight/d. Supplemented lambs had greater body weight (BW) and average daily gain (ADG) when compared with non-supplemented lambs ( P < 0.04). Additionally, lambs on newly sown pasture demonstrated greater BW and ADG when compared with lambs grazing on established pasture ( P < 0.05). For lamb health, lambs in the EN treatment group had the greatest FAMACHA eye scores and lowest packed cell volume (PCV) over the course of the 112-d grazing period ( P < 0.05). Moreover, NS and ES treatment lambs demonstrated similar FAMACHA eye scores when compared with NN treatment lambs; however, NN treatment lambs showed lower PCV when compared with NS and ES treatment lambs ( P < 0.05). In evaluating fecal egg counts (FEC), lambs on new pasture or given supplement demonstrated lesser FEC when compared with those lambs on established pasture or not given supplement ( P < 0.05). Sixty-four lambs were harvested to evaluate total abomasum nematode counts which demonstrated that Haemonchus contortus represented approximately 80% of total nematodes. Furthermore, based upon gross margin analysis, lambs given a protein rich supplement on pasture had a 9.3 kg increase in lamb BW whereas newly sown pasture had a 1.3 kg increase in lamb BW. A protein rich supplement given to lambs grazing pastures contaminated primarily with H. contortus or placing lambs on newly sown pasture increases lamb BW and improves parasite resiliency. Selection of parasite management strategies may be influenced by cost of production and market opportunities., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science.)
- Published
- 2021
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24. Impact of Interleukin 10 Deficiency on Intestinal Epithelium Responses to Inflammatory Signals.
- Author
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Papoutsopoulou S, Pollock L, Walker C, Tench W, Samad SS, Bergey F, Lenzi L, Sheibani-Tezerji R, Rosenstiel P, Alam MT, Martins Dos Santos VAP, Müller W, and Campbell BJ
- Subjects
- Animals, Interleukin-10 deficiency, Interleukin-10 genetics, Mice, Inbred C57BL, Mice, Knockout, NF-kappa B immunology, Tumor Necrosis Factor-alpha immunology, Mice, Inflammation immunology, Interleukin-10 immunology, Intestinal Mucosa immunology
- Abstract
Interleukin 10 (IL-10) is a pleiotropic, anti-inflammatory cytokine that has a major protective role in the intestine. Although its production by cells of the innate and adaptive immune system has been extensively studied, its intrinsic role in intestinal epithelial cells is poorly understood. In this study, we utilised both ATAC sequencing and RNA sequencing to define the transcriptional response of murine enteroids to tumour necrosis factor (TNF). We identified that the key early phase drivers of the transcriptional response to TNF within intestinal epithelium were NF κ B transcription factor dependent. Using wild-type and Il10
-/- enteroid cultures, we showed an intrinsic, intestinal epithelium specific effect of IL-10 deficiency on TNF-induced gene transcription, with significant downregulation of identified NF κ B target genes Tnf , Ccl20 , and Cxcl10 , and delayed overexpression of NF κ B inhibitor encoding genes, Nfkbia and Tnfaip3 . IL-10 deficiency, or immunoblockade of IL-10 receptor, impacted on TNF-induced endogenous NF κ B activity and downstream NF κ B target gene transcription. Intestinal epithelium-derived IL-10 appears to play a crucial role as a positive regulator of the canonical NF κ B pathway, contributing to maintenance of intestinal homeostasis. This is particularly important in the context of an inflammatory environment and highlights the potential for future tissue-targeted IL-10 therapeutic intervention., Competing Interests: VMDS is a director and shareholder of LifeGlimmer GmbH. FB has received salary from LifeGlimmer GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Papoutsopoulou, Pollock, Walker, Tench, Samad, Bergey, Lenzi, Sheibani-Tezerji, Rosenstiel, Alam, Martins Dos Santos, Müller and Campbell.)- Published
- 2021
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25. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages.
- Author
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Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, and Anantharaman K
- Subjects
- Amino Acid Motifs, Bacteriophages classification, Bacteriophages genetics, Caudovirales classification, Caudovirales genetics, Caudovirales metabolism, Energy Metabolism, Environmental Microbiology, Genes, Viral genetics, Genetic Variation, Genome, Viral genetics, Metagenomics, Oxidation-Reduction, Phylogeny, Protein Domains, Thiosulfates metabolism, Viral Proteins chemistry, Viral Proteins genetics, Bacteriophages metabolism, Ecosystem, Sulfur metabolism
- Abstract
Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.
- Published
- 2021
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26. Metagenomes, Metatranscriptomes, and Metagenome-Assembled Genomes from Chesapeake and Delaware Bay (USA) Water Samples.
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Ahmed MA, Lim SJ, and Campbell BJ
- Abstract
Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries.
- Published
- 2021
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27. Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana.
- Author
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Lim SJ, Davis B, Gill D, Swetenburg J, Anderson LC, Engel AS, and Campbell BJ
- Subjects
- Animals, Bacteria, Gills, Phylogeny, Symbiosis, Bivalvia, Microbiota
- Abstract
Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes and their environment., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)
- Published
- 2021
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28. Long-Term Iron Deficiency and Dietary Iron Excess Exacerbate Acute Dextran Sodium Sulphate-Induced Colitis and Are Associated with Significant Dysbiosis.
- Author
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Mahalhal A, Burkitt MD, Duckworth CA, Hold GL, Campbell BJ, Pritchard DM, and Probert CS
- Subjects
- Anemia, Iron-Deficiency, Animals, Bacteria genetics, Colitis physiopathology, Colon pathology, Dextran Sulfate pharmacology, Diet, Dietary Supplements adverse effects, Disease Models, Animal, Dysbiosis etiology, Female, Gastrointestinal Microbiome drug effects, Gastrointestinal Microbiome genetics, Inflammation, Inflammatory Bowel Diseases pathology, Iron, Dietary adverse effects, Mice, Mice, Inbred C57BL, Microbiota, RNA, Ribosomal, 16S genetics, Colitis metabolism, Iron metabolism, Iron Overload physiopathology
- Abstract
Background: Oral iron supplementation causes gastrointestinal side effects. Short-term alterations in dietary iron exacerbate inflammation and alter the gut microbiota, in murine models of colitis. Patients typically take supplements for months. We investigated the impact of long-term changes in dietary iron on colitis and the microbiome in mice., Methods: We fed mice chow containing differing levels of iron, reflecting deficient (100 ppm), normal (200 ppm), and supplemented (400 ppm) intake for up to 9 weeks, both in absence and presence of dextran sodium sulphate (DSS)-induced chronic colitis. We also induced acute colitis in mice taking these diets for 8 weeks. Impact was assessed (i) clinically and histologically, and (ii) by sequencing the V4 region of 16S rRNA., Results: In mice with long-term changes, the iron-deficient diet was associated with greater weight loss and histological inflammation in the acute colitis model. Chronic colitis was not influenced by altering dietary iron however there was a change in the microbiome in DSS-treated mice consuming 100 ppm and 400 ppm iron diets, and control mice consuming the 400 ppm iron diet. Proteobacteria levels increased significantly, and Bacteroidetes levels decreased, in the 400 ppm iron DSS group at day-63 compared to baseline., Conclusions: Long-term dietary iron alterations affect gut microbiota signatures but do not exacerbate chronic colitis, however acute colitis is exacerbated by such dietary changes. More work is needed to understand the impact of iron supplementation on IBD. The change in the microbiome, in patients with colitis, may arise from the increased luminal iron and not simply from colitis.
- Published
- 2021
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29. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach.
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Frau A, Ijaz UZ, Slater R, Jonkers D, Penders J, Campbell BJ, Kenny JG, Hall N, Lenzi L, Burkitt MD, Pierik M, Darby AC, and Probert CSJ
- Subjects
- Adolescent, Adult, Aged, Bacteria classification, Bacteria genetics, Child, Cohort Studies, Dysbiosis microbiology, Feces microbiology, Female, Fungi classification, Fungi genetics, Humans, Male, Middle Aged, Young Adult, Bacteria isolation & purification, Crohn Disease microbiology, Fungi isolation & purification, Gastrointestinal Microbiome
- Abstract
The etiology of Crohn's disease (CD) is multifactorial. Bacterial and fungal microbiota are involved in the onset and/or progression of the disease. A bacterial dysbiosis in CD patients is accepted; however, less is known about the mycobiome and the relationships between the two communities. We investigated the interkingdom relationships, their metabolic consequences, and the changes in the fungal community during relapse and remission in CD.Two cohorts were evaluated: a British cohort (n = 63) comprising CD and ulcerative colitis patients, and controls. The fungal and bacterial communities of biopsy and fecal samples were analyzed, with the fecal volatiles; datasets were also integrated; and a Dutch cohort (n = 41) comprising CD patients and healthy controls was analyzed for stability of the gut mycobiome.A dysbiosis of the bacterial community was observed in biopsies and stool. Results suggest Bacteroides is likely key in CD and may modulate Candida colonization. A dysbiosis of the fungal community was observed only in the Dutch cohort; Malassezia and Candida were increased in patients taking immunosuppressants. Longitudinal analysis showed an increase in Cyberlindnera in relapse. Saccharomyces was dominant in all fecal samples, but not in biopsies, some of which did not yield fungal reads; amino acid degradation was the main metabolic change associated with CD and both bacteria and fungi might be implicated.We have shown that Bacteroides and yeasts may play a role in CD; understanding their role and relationship in the disease would shed new light on the development and treatment of CD.
- Published
- 2021
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30. Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease.
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Lloyd K, Papoutsopoulou S, Smith E, Stegmaier P, Bergey F, Morris L, Kittner M, England H, Spiller D, White MHR, Duckworth CA, Campbell BJ, Poroikov V, Martins Dos Santos VAP, Kel A, Muller W, Pritchard DM, Probert C, and Burkitt MD
- Subjects
- Animals, Cells, Cultured, Clarithromycin pharmacology, Clarithromycin therapeutic use, Colitis chemically induced, Colitis metabolism, Colitis pathology, DNA metabolism, Dextran Sulfate, Gene Regulatory Networks, Humans, Inflammatory Bowel Diseases metabolism, Lipopolysaccharides, Luciferases metabolism, Mice, Inbred C57BL, NF-kappa B metabolism, Organoids drug effects, Organoids metabolism, Protein Binding drug effects, Signal Transduction, Transcription Factors metabolism, Tumor Necrosis Factor-alpha metabolism, Drug Repositioning, Inflammatory Bowel Diseases drug therapy, Inflammatory Bowel Diseases pathology, Systems Analysis
- Abstract
Inflammatory bowel diseases (IBDs) cause significant morbidity and mortality. Aberrant NF-κB signalling is strongly associated with these conditions, and several established drugs influence the NF-κB signalling network to exert their effect. This study aimed to identify drugs that alter NF-κB signalling and could be repositioned for use in IBD. The SysmedIBD Consortium established a novel drug-repurposing pipeline based on a combination of in silico drug discovery and biological assays targeted at demonstrating an impact on NF-κB signalling, and a murine model of IBD. The drug discovery algorithm identified several drugs already established in IBD, including corticosteroids. The highest-ranked drug was the macrolide antibiotic clarithromycin, which has previously been reported to have anti-inflammatory effects in aseptic conditions. The effects of clarithromycin effects were validated in several experiments: it influenced NF-κB-mediated transcription in murine peritoneal macrophages and intestinal enteroids; it suppressed NF-κB protein shuttling in murine reporter enteroids; it suppressed NF-κB (p65) DNA binding in the small intestine of mice exposed to lipopolysaccharide; and it reduced the severity of dextran sulphate sodium-induced colitis in C57BL/6 mice. Clarithromycin also suppressed NF-κB (p65) nuclear translocation in human intestinal enteroids. These findings demonstrate that in silico drug repositioning algorithms can viably be allied to laboratory validation assays in the context of IBD, and that further clinical assessment of clarithromycin in the management of IBD is required.This article has an associated First Person interview with the joint first authors of the paper., Competing Interests: Competing interestsV.A.P.M.d.S. is a shareholder and director of GeneXplain GmbH. A.K. is a shareholder and director of LifeGlimmer GmbH., (© 2020. Published by The Company of Biologists Ltd.)
- Published
- 2020
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31. Review article: impact of cigarette smoking on intestinal inflammation-direct and indirect mechanisms.
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Papoutsopoulou S, Satsangi J, Campbell BJ, and Probert CS
- Subjects
- Cigarette Smoking epidemiology, Colitis, Ulcerative epidemiology, Colitis, Ulcerative etiology, Crohn Disease epidemiology, Crohn Disease etiology, Enteritis epidemiology, Humans, Inflammatory Bowel Diseases complications, Inflammatory Bowel Diseases epidemiology, Inflammatory Bowel Diseases etiology, Intestines pathology, Risk Factors, Signal Transduction physiology, Cigarette Smoking adverse effects, Enteritis etiology
- Abstract
Background: The inflammatory bowel diseases, Crohn's disease and ulcerative colitis are related multifactorial diseases. Their pathogenesis is influenced by each individual's immune system, the environmental factors within exposome and genetic predisposition. Smoking habit is the single best-established environmental factor that influences disease phenotype, behaviour and response to therapy., Aim: To assess current epidemiological, experimental and clinical evidence that may explain how smoking impacts on the pathogenesis of inflammatory bowel disease., Methods: A Medline search for 'cigarette smoking', in combination with terms including 'passive', 'second-hand', 'intestinal inflammation', 'Crohn's disease', 'ulcerative colitis', 'colitis'; 'intestinal epithelium', 'immune system', 'intestinal microbiota', 'tight junctions', 'mucus', 'goblet cells', 'Paneth cells', 'autophagy'; 'epigenetics', 'genes', 'DNA methylation', 'histones', 'short noncoding/long noncoding RNAs'; 'carbon monoxide/CO' and 'nitric oxide/NO' was performed., Results: Studies found evidence of direct and indirect effects of smoking on various parameters, including oxidative damage, impairment of intestinal barrier and immune cell function, epigenetic and microbiota composition changes, that contribute to the pathogenesis of inflammatory bowel disease., Conclusions: Cigarette smoking promotes intestinal inflammation by affecting the function and interactions among intestinal epithelium, immune system and microbiota/microbiome., (© 2020 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)
- Published
- 2020
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32. Correction: Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species.
- Author
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Lim SJ, Davis BG, Gill DE, Walton J, Nachman E, Engel AS, Anderson LC, and Campbell BJ
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2020
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33. High-pressure polymorphism in pyridine.
- Author
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Giordano N, Beavers CM, Campbell BJ, Eigner V, Gregoryanz E, Marshall WG, Peña-Álvarez M, Teat SJ, Vennari CE, and Parsons S
- Abstract
Single crystals of the high-pressure phases II and III of pyridine have been obtained by in situ crystallization at 1.09 and 1.69 GPa, revealing the crystal structure of phase III for the first time using X-ray diffraction. Phase II crystallizes in P 2
1 21 21 with Z ' = 1 and phase III in P 41 21 2 with Z ' = ½. Neutron powder diffraction experiments using pyridine-d5 establish approximate equations of state of both phases. The space group and unit-cell dimensions of phase III are similar to the structures of other simple compounds with C2v molecular symmetry, and the phase becomes stable at high pressure because it is topologically close-packed, resulting in a lower molar volume than the topologically body-centred cubic phase II. Phases II and III have been observed previously by Raman spectroscopy, but have been mis-identified or inconsistently named. Raman spectra collected on the same samples as used in the X-ray experiments establish the vibrational characteristics of both phases unambiguously. The pyridine molecules interact in both phases through CH⋯π and CH⋯N interactions. The nature of individual contacts is preserved through the phase transition between phases III and II, which occurs on decompression. A combination of rigid-body symmetry mode analysis and density functional theory calculations enables the soft vibrational lattice mode which governs the transformation to be identified., (© Nico Giordano et al. 2020.)- Published
- 2020
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34. NF-κB2 signalling in enteroids modulates enterocyte responses to secreted factors from bone marrow-derived dendritic cells.
- Author
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Jones LG, Vaida A, Thompson LM, Ikuomola FI, Caamaño JH, Burkitt MD, Miyajima F, Williams JM, Campbell BJ, Pritchard DM, and Duckworth CA
- Subjects
- Animals, Apoptosis drug effects, Bone Marrow Cells drug effects, Bone Marrow Cells metabolism, Cell Degranulation drug effects, Cell Proliferation drug effects, Culture Media, Conditioned pharmacology, Dendritic Cells drug effects, Enterocytes cytology, Enterocytes drug effects, Epithelial Cells drug effects, Epithelial Cells metabolism, Interferon-gamma pharmacology, Intestine, Small metabolism, Lipopolysaccharides pharmacology, Mice, Inbred C57BL, Paneth Cells drug effects, Paneth Cells metabolism, Reproducibility of Results, Tumor Necrosis Factor-alpha pharmacology, Bone Marrow Cells cytology, Dendritic Cells metabolism, Enterocytes metabolism, NF-kappa B p52 Subunit metabolism, Organoids metabolism, Signal Transduction
- Abstract
Alternative pathway NF-κB signalling regulates susceptibility towards developing inflammatory bowel disease (IBD), colitis-associated cancer and sepsis-associated intestinal epithelial cell apoptosis and shedding. However, the cell populations responsible for the perturbed alternative pathway NF-κB signalling in intestinal mucosal pathology remain unclear. In order to investigate the contribution of the epithelial compartment, we have tested whether NF-κB2 regulated transcription in intestinal epithelial cells controls the intestinal epithelial response to cytokines that are known to disrupt intestinal barrier permeability. Enteroids were generated from the proximal, middle and distal regions of small intestine (SI) from C57BL/6J wild-type mice and displayed region-specific morphology that was maintained during sub-culture. Enteroids treated with 100 ng/mL TNF were compared with corresponding regions of SI from C57BL/6J mice treated systemically with 0.33 mg/kg TNF for 1.5 h. TNF-induced apoptosis in all regions of the intestine in vitro and in vivo but resulted in Paneth cell degranulation only in proximal tissue-derived SI and enteroids. TNF also resulted in increased enteroid sphericity (quantified as circularity from two-dimensional bright field images). This response was dose and time-dependent and correlated with active caspase-3 immunopositivity. Proximal tissue-derived enteroids generated from Nfκb2
-/- mice showed a significantly blunted circularity response following the addition of TNF, IFNγ, lipopolysaccharide (LPS) activated C57BL/6J-derived bone marrow-derived dendritic cells (BMDC) and secreted factors from LPS-activated BMDCs. However, Nfκb1-/- mouse-derived enteroids showed no significant changes in response to these stimuli. In conclusion, the selection of SI region is important when designing enteroid studies as region-specific identity and response to stimuli such as TNF are maintained in culture. Intestinal epithelial cells are at least partially responsible for regulating their own fate by modulating NF-κB2 signalling in response to stimuli known to be involved in multiple intestinal and systemic diseases. Future studies are warranted to investigate the therapeutic potential of intestinal epithelial NF-κB2 inhibition.- Published
- 2019
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35. Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients.
- Author
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Papoutsopoulou S, Burkitt MD, Bergey F, England H, Hough R, Schmidt L, Spiller DG, White MHR, Paszek P, Jackson DA, Martins Dos Santos VAP, Sellge G, Pritchard DM, Campbell BJ, Müller W, and Probert CS
- Subjects
- Active Transport, Cell Nucleus genetics, Active Transport, Cell Nucleus immunology, Adult, Animals, Cell Nucleus genetics, Colitis, Ulcerative genetics, Colitis, Ulcerative pathology, Crohn Disease genetics, Crohn Disease pathology, Female, Humans, Macrophages pathology, Male, Mice, Mice, Knockout, Middle Aged, Signal Transduction genetics, Transcription Factor RelA genetics, Cell Nucleus immunology, Colitis, Ulcerative immunology, Crohn Disease immunology, Macrophages immunology, Signal Transduction immunology, Transcription Factor RelA immunology
- Abstract
The heterogeneous nature of inflammatory bowel disease (IBD) presents challenges, particularly when choosing therapy. Activation of the NF-κB transcription factor is a highly regulated, dynamic event in IBD pathogenesis. Using a lentivirus approach, NF-κB-regulated luciferase was expressed in patient macrophages, isolated from frozen peripheral blood mononuclear cell samples. Following activation, samples could be segregated into three clusters based on the NF-κB-regulated luciferase response. The ulcerative colitis (UC) samples appeared only in the hypo-responsive Cluster 1, and in Cluster 2. Conversely, Crohn's disease (CD) patients appeared in all Clusters with their percentage being higher in the hyper-responsive Cluster 3. A positive correlation was seen between NF-κB-induced luciferase activity and the concentrations of cytokines released into medium from stimulated macrophages, but not with serum or biopsy cytokine levels. Confocal imaging of lentivirally-expressed p65 activation revealed that a higher proportion of macrophages from CD patients responded to endotoxin lipid A compared to controls. In contrast, cells from UC patients exhibited a shorter duration of NF-κB p65 subunit nuclear localization compared to healthy controls, and CD donors. Analysis of macrophage cytokine responses and patient metadata revealed a strong correlation between CD patients who smoked and hyper-activation of p65. These in vitro dynamic assays of NF-κB activation in blood-derived macrophages have the potential to segregate IBD patients into groups with different phenotypes and may therefore help determine response to therapy., (Copyright © 2019 Papoutsopoulou, Burkitt, Bergey, England, Hough, Schmidt, Spiller, White, Paszek, Jackson, Martins Dos Santos, Sellge, Pritchard, Campbell, Müller and Probert.)
- Published
- 2019
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36. An Open-Format Enteroid Culture System for Interrogation of Interactions Between Toxoplasma gondii and the Intestinal Epithelium.
- Author
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Luu L, Johnston LJ, Derricott H, Armstrong SD, Randle N, Hartley CS, Duckworth CA, Campbell BJ, Wastling JM, and Coombes JL
- Subjects
- Animals, Cell Culture Techniques, Cholesterol, Collagen, Disease Models, Animal, Epithelial Cells parasitology, Epithelial Cells pathology, Humans, Intestinal Mucosa diagnostic imaging, Intestinal Mucosa pathology, Mice, Mice, Inbred C57BL, Host-Parasite Interactions physiology, Intestinal Mucosa metabolism, Intestinal Mucosa parasitology, Toxoplasma pathogenicity, Toxoplasma physiology
- Abstract
When transmitted through the oral route, Toxoplasma gondii first interacts with its host at the small intestinal epithelium. This interaction is crucial to controlling initial invasion and replication, as well as shaping the quality of the systemic immune response. It is therefore an attractive target for the design of novel vaccines and adjuvants. However, due to a lack of tractable infection models, we understand surprisingly little about the molecular pathways that govern this interaction. The in vitro culture of small intestinal epithelium as 3D enteroids shows great promise for modeling the epithelial response to infection. However, the enclosed luminal space makes the application of infectious agents to the apical epithelial surface challenging. Here, we have developed three novel enteroid-based techniques for modeling T. gondii infection. In particular, we have adapted enteroid culture protocols to generate collagen-supported epithelial sheets with an exposed apical surface. These cultures retain epithelial polarization, and the presence of fully differentiated epithelial cell populations. They are susceptible to infection with, and support replication of, T. gondii . Using quantitative label-free mass spectrometry, we show that T. gondii infection of the enteroid epithelium is associated with up-regulation of proteins associated with cholesterol metabolism, extracellular exosomes, intermicrovillar adhesion, and cell junctions. Inhibition of host cholesterol and isoprenoid biosynthesis with Atorvastatin resulted in a reduction in parasite load only at higher doses, indicating that de novo synthesis may support, but is not required for, parasite replication. These novel models therefore offer tractable tools for investigating how interactions between T. gondii and the host intestinal epithelium influence the course of infection.
- Published
- 2019
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37. Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition.
- Author
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Lim SJ, Alexander L, Engel AS, Paterson AT, Anderson LC, and Campbell BJ
- Abstract
Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data to resolve symbiont taxonomic, genetic, and functional diversity from Ctena orbiculata endosymbiont populations inhabiting carbonate-rich sediment at Sugarloaf Key, FL (USA). The sediment had mixed seagrass and calcareous green alga coverage and also was colonized by at least five other lucinid species. Four coexisting, thioautotrophic endosymbiont operational taxonomic units (OTUs), likely representing four strains from two different bacterial species, were identified from C. orbiculata Three of these OTUs also occurred at high relative abundances in the other sympatric lucinid species. Interspecies genetic differences averaged about 5% lower at both pairwise average nucleotide identity and amino acid identity than interstrain differences. Despite these genetic differences, C. orbiculata endosymbionts shared a high number of metabolic functions, including highly expressed thioautotrophy-related genes and a moderately to weakly expressed conserved one-carbon (C
1 ) oxidation gene cluster previously undescribed in lucinid symbionts. Few symbiont- and host-related genes, including those encoding symbiotic sulfurtransferase, host respiratory functions, and host sulfide oxidation functions, were differentially expressed between seagrass- and alga-covered sediment locations. In contrast to previous studies, the identification of multiple endosymbiont taxa within and across C. orbiculata individuals, which were also shared with other sympatric lucinid species, suggests that neither host nor endosymbiont displays strict taxonomic specificity. This necessitates further investigations into the nature and extent of specificity of lucinid hosts and their symbionts. IMPORTANCE Symbiont diversity and host/symbiont functions have been comprehensively profiled for only a few lucinid species. In this work, unprecedented thioautotrophic gill endosymbiont taxonomic diversity was characterized within a Ctena orbiculata population associated with both seagrass- and alga-covered sediments. Endosymbiont metabolisms included known chemosynthetic functions and an additional conserved, previously uncharacterized C1 oxidation pathway. Lucinid-symbiont associations were not species specific because this C. orbiculata population hosted multiple endosymbiont strains and species, and other sympatric lucinid species shared overlapping symbiont 16S rRNA gene diversity profiles with C. orbiculata Our results suggest that lucinid-symbiont association patterns within some host species could be more taxonomically diverse than previously thought. As such, this study highlights the importance of holistic analyses, at the population, community, and even ecosystem levels, in understanding host-microbe association patterns., (Copyright © 2019 Lim et al.)- Published
- 2019
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38. Topotactic, pressure-driven, diffusion-less phase transition of layered CsCoO 2 to a stuffed cristobalite-type configuration.
- Author
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Ali NZ, Campbell BJ, and Jansen M
- Abstract
CsCoO
2 , featuring a two-dimensional layered architecture of edge- and vertex-linked CoO4 tetrahedra, is subjected to a temperature-driven reversible second-order phase transformation (α → β) at 100 K, which corresponds to a structural relaxation with concurrent tilting and breathing modes of edge-sharing CoO4 tetrahedra. In the present investigation, it was found that pressure induces a phase transition, which encompasses a dramatic change in the connectivity of the tetrahedra. At 923 K and 2 GPa, β-CsCoO2 undergoes a first-order phase transition to a new quenchable high-pressure polymorph, γ-CsCoO2 . It is built up of a three-dimensional cristobalite-type network of vertex-sharing CoO4 tetrahedra. According to a Rietveld refinement of high-resolution powder diffraction data, the new high-pressure polymorph γ-CsCoO2 crystallizes in the tetragonal space group I41 /amd:2 (Z = 4) with the lattice constants a = 5.8711 (1) and c = 8.3214 (2) Å, corresponding to a shrinkage in volume by 5.7% compared with the ambient-temperature and atmospheric pressure β-CsCoO2 polymorph. The pressure-induced transition (β → γ) is reversible; γ-CsCoO2 stays metastable under ambient conditions, but transforms back to the β-CsCoO2 structure upon heating to 573 K. The transformation pathway revealed is remarkable in that it is topotactic, as is demonstrated through a clean displacive transformation track between the two phases that employs the symmetry of their common subgroup Pb21 a (alternative setting of space group No. 29 that matches the conventional β-phase cell).- Published
- 2019
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39. DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.
- Author
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Frau A, Kenny JG, Lenzi L, Campbell BJ, Ijaz UZ, Duckworth CA, Burkitt MD, Hall N, Anson J, Darby AC, and Probert CSJ
- Subjects
- DNA Primers genetics, DNA, Fungal genetics, Feces microbiology, Humans, RNA, Ribosomal, 18S genetics, DNA, Fungal isolation & purification, Gastrointestinal Microbiome genetics
- Abstract
Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.
- Published
- 2019
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40. Replication of Crohn's Disease Mucosal E. coli Isolates inside Macrophages Correlates with Resistance to Superoxide and Is Dependent on Macrophage NF-kappa B Activation.
- Author
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Tawfik A, Knight P, Duckworth CA, Pritchard DM, Rhodes JM, and Campbell BJ
- Abstract
Mucosa-associated Escherichia coli are increased in Crohn's disease (CD) and colorectal cancer (CRC). CD isolates replicate within macrophages but the specificity of this effect for CD and its mechanism are unclear. Gentamicin exclusion assay was used to assess E. coli replication within J774.A1 murine macrophages. E. coli growth was assessed following acid, low-nutrient, nitrosative, oxidative and superoxide stress, mimicking the phagolysosome. Twelve of 16 CD E. coli isolates replicated >2-fold within J774.A1 macrophages; likewise for isolates from 6/7 urinary tract infection (UTI), 8/9 from healthy subjects, compared with 2/6 ulcerative colitis, 2/7 colorectal cancer and 0/3 laboratory strains. CD mucosal E. coli were tolerant of acidic, low-nutrient, nitrosative and oxidative stress. Replication within macrophages correlated strongly with tolerance to superoxide stress (rho = 0.44, p = 0.0009). Exemplar CD E. coli HM605 and LF82 were unable to survive within Nfκb1
-/- murine bone marrow-derived macrophages. In keeping with this, pre-incubation of macrophages with hydrocortisone (0.6 µM for 24 h) caused 70.49 ± 12.11% inhibition of intra-macrophage replication. Thus, CD mucosal E. coli commonly replicate inside macrophages, but so do some UTI and healthy subject strains. Replication correlates with resistance to superoxide and is highly dependent on macrophage NF-κB signalling. This may therefore be a good therapeutic target.- Published
- 2019
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41. Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species.
- Author
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Lim SJ, Davis BG, Gill DE, Walton J, Nachman E, Engel AS, Anderson LC, and Campbell BJ
- Subjects
- Animals, Bacteria genetics, Gills microbiology, Microbiota, Phylogeny, RNA, Ribosomal, 16S genetics, Sulfides metabolism, Symbiosis, Wetlands, Bacteria classification, Bivalvia microbiology
- Abstract
Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid-bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies. The P. pectinatus thioautotrophic endosymbiont expressed metabolic gene variants for thioautotrophy, respiration, and nitrogen assimilation distinct from previously characterized lucinid thioautotrophic symbionts and other marine symbionts. At least two other bacterial species with different metabolisms were also consistently identified in the P. pectinatus gill microbiome, including a Kistimonas-like species and a Spirochaeta-like species. Bacterial transcripts involved in adhesion, growth, and virulence and mixotrophy were highly expressed, as were host-related hemoglobin and lysozyme transcripts indicative of sulfide/oxygen/CO
2 transport and bactericidal activity. This study suggests the potential roles of P. pectinatus and its gill microbiome species in mangrove sediment biogeochemistry and offers insights into host and microbe metabolisms in the habitat.- Published
- 2019
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42. Human TNF-Luc reporter mouse: A new model to quantify inflammatory responses.
- Author
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Minshawi F, White MRH, Muller W, Humphreys N, Jackson D, Campbell BJ, Adamson A, and Papoutsopoulou S
- Subjects
- Animals, Cells, Cultured, Chromosomes, Artificial, Bacterial, Disease Models, Animal, Humans, Inflammation metabolism, Inflammation pathology, Lipopolysaccharides pharmacology, Luciferases metabolism, Macrophages metabolism, Mice, Mice, Transgenic, NF-kappa B antagonists & inhibitors, Tumor Necrosis Factor-alpha antagonists & inhibitors, Tumor Necrosis Factor-alpha biosynthesis, Luciferases genetics, Tumor Necrosis Factor-alpha genetics
- Abstract
Tumour necrosis factor (TNF) is a key cytokine during inflammatory responses and its dysregulation is detrimental in many inflammatory diseases, such as rheumatoid arthritis and inflammatory bowel disease. Here, we used a bacterial artificial chromosome (BAC) construct that expresses luciferase under the control of the human TNF locus to generate a novel transgenic mouse, the hTNF.LucBAC strain. In vitro stimulation of hTNF.LucBAC cells of different origin revealed a cell specific response to stimuli demonstrating the integrated construct's ability as a proxy for inflammatory gene response. Lipopolysaccharide was the most potent luciferase inducer in macrophages, while TNF was a strong activator in intestinal organoids. Lipopolysaccharide-induced luciferase activity in macrophages was downregulated by inhibitors of NF-κB pathway, as well as by Interleukin-10, a known anti-inflammatory cytokine. Moreover, the transgene-dependent luciferase activity showed a positive correlation to the endogenous murine soluble TNF secreted to the culture medium. In conclusion, the hTNF.LucBAC strain is a valuable tool for studying and screening molecules that target TNF synthesis and will allow further functional studies of the regulatory elements of the TNF locus.
- Published
- 2019
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- View/download PDF
43. Oral iron exacerbates colitis and influences the intestinal microbiome.
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Mahalhal A, Williams JM, Johnson S, Ellaby N, Duckworth CA, Burkitt MD, Liu X, Hold GL, Campbell BJ, Pritchard DM, and Probert CS
- Subjects
- Administration, Oral, Anemia microbiology, Anemia pathology, Animals, Colitis chemically induced, Colitis metabolism, Dextran Sulfate toxicity, Disease Models, Animal, Feces microbiology, Gastrointestinal Microbiome drug effects, Humans, Inflammatory Bowel Diseases microbiology, Inflammatory Bowel Diseases pathology, Mice, RNA, Ribosomal, 16S genetics, Anemia drug therapy, Colitis diet therapy, Inflammatory Bowel Diseases drug therapy, Iron metabolism, Iron, Dietary administration & dosage
- Abstract
Inflammatory bowel disease (IBD) is associated with anaemia and oral iron replacement to correct this can be problematic, intensifying inflammation and tissue damage. The intestinal microbiota also plays a key role in the pathogenesis of IBD, and iron supplementation likely influences gut bacterial diversity in patients with IBD. Here, we assessed the impact of dietary iron, using chow diets containing either 100, 200 or 400 ppm, fed ad libitum to adult female C57BL/6 mice in the presence or absence of colitis induced using dextran sulfate sodium (DSS), on (i) clinical and histological severity of acute DSS-induced colitis, and (ii) faecal microbial diversity, as assessed by sequencing the V4 region of 16S rRNA. Increasing or decreasing dietary iron concentration from the standard 200 ppm exacerbated both clinical and histological severity of DSS-induced colitis. DSS-treated mice provided only half the standard levels of iron ad libitum (i.e. chow containing 100 ppm iron) lost more body weight than those receiving double the amount of standard iron (i.e. 400 ppm); p<0.01. Faecal calprotectin levels were significantly increased in the presence of colitis in those consuming 100 ppm iron at day 8 (5.94-fold) versus day-10 group (4.14-fold) (p<0.05), and for the 400 ppm day-8 group (8.17-fold) versus day-10 group (4.44-fold) (p<0.001). In the presence of colitis, dietary iron at 400 ppm resulted in a significant reduction in faecal abundance of Firmicutes and Bacteroidetes, and increase of Proteobacteria, changes which were not observed with lower dietary intake of iron at 100 ppm. Overall, altering dietary iron intake exacerbated DSS-induced colitis; increasing the iron content of the diet also led to changes in intestinal bacteria diversity and composition after colitis was induced with DSS., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2018
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44. Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay.
- Author
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Maresca JA, Miller KJ, Keffer JL, Sabanayagam CR, and Campbell BJ
- Subjects
- Actinobacteria genetics, Actinobacteria metabolism, Alphaproteobacteria genetics, Alphaproteobacteria metabolism, Bacteria classification, Bacterial Proteins genetics, Bacterial Proteins metabolism, Bacteroidetes genetics, Bacteroidetes metabolism, Carbon analysis, Chlorophyll A, Delaware, Environmental Microbiology, Estuaries, Genome, Bacterial, Heterotrophic Processes, Light, Metagenomics, Nitrogen analysis, Phylogeny, Rhodopsins, Microbial classification, Salinity, Transcriptome, Bacteria genetics, Bacteria metabolism, Bays microbiology, Rhodopsin biosynthesis, Rhodopsin genetics, Rhodopsins, Microbial genetics, Rhodopsins, Microbial metabolism
- Abstract
Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes , while those in the high-salinity samples are associated with SAR-11 type Alphaproteobacteria IMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers., (Copyright © 2018 American Society for Microbiology.)
- Published
- 2018
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45. Erratum: Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).
- Author
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, and Hugenholtz P
- Abstract
[This corrects the article on p. 682 in vol. 8, PMID: 28484436.].
- Published
- 2018
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46. Technical note: Instantaneous sampling intervals validated from continuous video observation for behavioral recording of feedlot lambs.
- Author
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Pullin AN, Pairis-Garcia MD, Campbell BJ, Campler MR, and Proudfoot KL
- Subjects
- Animals, Female, Linear Models, Male, Random Allocation, Behavior, Animal, Sheep physiology, Video Recording methods
- Abstract
When considering methodologies for collecting behavioral data, continuous sampling provides the most complete and accurate data set whereas instantaneous sampling can provide similar results and also increase the efficiency of data collection. However, instantaneous time intervals require validation to ensure accurate estimation of the data. Therefore, the objective of this study was to validate scan sampling intervals for lambs housed in a feedlot environment. Feeding, lying, standing, drinking, locomotion, and oral manipulation were measured on 18 crossbred lambs housed in an indoor feedlot facility for 14 h (0600-2000 h). Data from continuous sampling were compared with data from instantaneous scan sampling intervals of 5, 10, 15, and 20 min using a linear regression analysis. Three criteria determined if a time interval accurately estimated behaviors: 1) ≥ 0.90, 2) slope not statistically different from 1 ( > 0.05), and 3) intercept not statistically different from 0 ( > 0.05). Estimations for lying behavior were accurate up to 20-min intervals, whereas feeding and standing behaviors were accurate only at 5-min intervals (i.e., met all 3 regression criteria). Drinking, locomotion, and oral manipulation demonstrated poor associations () for all tested intervals. The results from this study suggest that a 5-min instantaneous sampling interval will accurately estimate lying, feeding, and standing behaviors for lambs housed in a feedlot, whereas continuous sampling is recommended for the remaining behaviors. This methodology will contribute toward the efficiency, accuracy, and transparency of future behavioral data collection in lamb behavior research.
- Published
- 2017
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47. Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H 2 -Oxidizing Cupriavidus necator .
- Author
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Campbell BJ, Sessions AL, Fox DN, Paul BG, Qin Q, Kellermann MY, and Valentine DL
- Abstract
Fatty acids produced by H
2 -metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H2 . Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H2 -consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δDwater values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H2 . Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H- ) ions, providing no direct mechanism to connect the isotopic composition of H2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+ ) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy.- Published
- 2017
- Full Text
- View/download PDF
48. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).
- Author
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, and Hugenholtz P
- Abstract
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria . Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales ( Deltaproteobacteria ) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
- Published
- 2017
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49. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
- Author
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Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, and Kyrpides NC
- Subjects
- Environmental Microbiology, Host-Pathogen Interactions, Metagenome, Sequence Analysis, DNA, DNA Viruses genetics, Databases, Genetic, Genome, Viral, Genomics methods, Metagenomics methods, Retroviridae genetics, Software
- Abstract
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2017
- Full Text
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50. Importance of the alternative NF-κB activation pathway in inflammation-associated gastrointestinal carcinogenesis.
- Author
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Merga YJ, O'Hara A, Burkitt MD, Duckworth CA, Probert CS, Campbell BJ, and Pritchard DM
- Subjects
- Animals, Gastrointestinal Neoplasms complications, Gastrointestinal Neoplasms epidemiology, Humans, Inflammatory Bowel Diseases complications, NF-kappa B genetics, Gastrointestinal Neoplasms metabolism, Inflammatory Bowel Diseases metabolism, NF-kappa B metabolism, Signal Transduction
- Abstract
Chronic inflammation is a common factor in the development of many gastrointestinal malignancies. Examples include inflammatory bowel disease predisposing to colorectal cancer, Barrett's esophagus as a precursor of esophageal adenocarcinoma, and Helicobacter pylori-induced gastric cancer. The classical activation pathway of NF-κB signaling has been identified as regulating several sporadic and inflammation-associated gastrointestinal tract malignancies. Emerging evidence suggests that the alternative NF-κB signaling pathway also exerts a distinct influence on these processes. This review brings together current knowledge of the role of the alternative NF-κB signaling pathway in the gastrointestinal tract, with a particular emphasis on inflammation-associated cancer development., (Copyright © 2016 the American Physiological Society.)
- Published
- 2016
- Full Text
- View/download PDF
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