Detection of Campylobacter concisus and other Campylobacter species in colonic biopsies from adults with ulcerative colitis

Introduction

The critical role of bacteria in the pathogenesis of ulcerative colitis (UC) is well recognized, but an individual causative microorganism has not been singled out so far. Campylobacter concisus and other non-jejuni species of Campylobacter have been implicated as putative aetiological agents in inflammatory bowel disease in children, but such studies have not been addressed in adults. This study investigated the prevalence of Campylobacter species in colonic biopsy samples from adults with UC and healthy controls.

Methods

Adult patients who were undergoing diagnostic colonoscopy were recruited for the study, which included 69 patients with histologically proven UC and 65 healthy controls. DNA was extracted from the biopsy samples and subjected to Campylobacter genus specific and Campylobacter concisus specific polymerase chain reaction and sequencing.

Results

Detection of all Campylobacter DNA utilising genus specific primers was significantly higher in cases of UC, with a prevalence of 73.9% (51/69) compared to 23.1% (15/65) in controls (p = 0.0001). Nested PCR for C. concisus DNA was positive in 33.3% (23/69) of biopsy samples from subjects with UC, which was significantly higher than the prevalence rate of 10.8% (7/65) from controls (p = 0.0019). Sequencing of the remaining Campylobacter positive samples revealed that Campylobacter ureolyticus was positive in 21.7% (15/69) of samples from UC subjects as opposed to 3.1% (2/65) in controls (p = 0.0013). Mixed Campylobacter species were more common in UC patients, 20.3% (14/69) as compared to controls 4.6% (3/65) (p = 0.0084).

Conclusion

The higher prevalence of Campylobacter genus and more specifically C. concisus and C. ureolyticus in biopsy samples from adults with UC suggests these genera of bacteria may be involved in the chronic inflammation that is characteristically seen in UC. To the best of our knowledge this is the first report of this association of C. concisus and C. ureolyticus with UC in adults.     

Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity

Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as 'hypothetical' in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.     

The relationship between biodiversity and ecosystem functioning in food webs

Recent theoretical and experimental work provides clear evidence that biodiversity loss can have profound impacts on functioning of natural and managed ecosystems and the ability of ecosystems to deliver ecological services to human societies. Work on simplified ecosystems in which the diversity of a single trophic level is manipulated shows that diversity can enhance ecosystem processes such as primary productivity and nutrient retention. Theory also strongly suggests that biodiversity can act as biological insurance against potential disruptions caused by environmental changes. However, these studies generally concern a single trophic level, primary producers for the most part. Changes in biodiversity also affect ecosystem functioning through trophic interactions. Here we review, through the analysis of a simple ecosystem model, several key aspects inherent in multitrophic systems that may strongly affect the relationship between diversity and ecosystem processes. Our analysis shows that trophic interactions have a strong impact on the relationships between diversity and ecosystem functioning, whether the ecosystem property considered is total biomass or temporal variability of biomass at the various trophic levels. In both cases, food-web structure and trade-offs that affect interaction strength have major effects on these relationships. Multitrophic interactions are expected to make biodiversity–ecosystem functioning relationships more complex and non-linear, in contrast to the monotonic changes predicted for simplified systems with a single trophic level.     

Echography of the stomach and duodenum in children in health and disease

The paper is concerned with the results of echography of the stomach and duodenum in 100 healthy children aged 1 month to 15 years and in 141 children with different types of gastritis, duodenitis and peptic ulcer. Echographic investigation of these hollow organs was made possible after their acoustic filling with 5% glucose solution. Echography permitted fast and reliable differentiation of the type and site of stomach and duodenal lesions, determining the presence of a gastroduodenal reflux and sizes of an ulcerative defect of the duodenal wall.     

Functional relationship between ammonia and gangliosides in brain

The functional significance of ammonia production in brain under physiological or pathological conditions is not clearly known. NH₄ ⁺ stimulates Na⁺, K⁺ activated ATPase causing stabilization of neuronal membranes of which gangliosides are major structural components. Moreover ammonia is known to inhibit lysosomal enzymes which include enzymes degrading gangliosides. Gangliosides have been shown to stimulate neuritogenesis in neuronal cultures and prevent the damage of the neurons from glutamate toxicity particularly in areas of brain ischemia. Hyperammonemia without any behavioural changes was induced in experimental rats by intraperitoneal administration of either a single dose (0.8 mmol/100 g wt.) or by six hourly doses (0.6 mmol/100 g wt.) of ammonium acetate. An increase in the content of gangliosides along with a rise in the content of GD_1A and GD_1B without any change in -galactosidase and N-acetylhexosaminidase was observed in cerebral cortex, cerebellum, and brain stem, following the administration of single dose of ammonium acetate. Gangliosides, after extraction from the different brain regions, were estimated by the thiobarbituric acid method and expressed in terms of sialic acid. Individual gangliosides were separated and estimated by thin layer chromatography using resorcinol as the staining agent. These results suggest that ammonia production in the neuronal pathways in brain either as a result of repeated stimulation under physiological conditions or as a result of focal ischemia or injury, may likewise cause an increase in the content of gangliosides which may help in neuritic growth (physiological conditions facilitating synaptic plasticity) and may exert a protective effect on the neurons in the ischemic area against glutamate toxicity.Former Professor of Biochemistry, OMC, Hyderabad.     

The role of the local microbial ecosystem in respiratory health and disease

Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form—together with harmless commensal bacteria, viruses and fungi—intricate ecological networks, collectively known as the ‘microbiome’. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.     

Functional relationship between Claspin and Rad17

Claspin was originally identified as a Check1 (Chk1)-interacting protein. Claspin and Rad17 are reportedly involved in the DNA damage-induced phosphorylation of Chk1, a hallmark of checkpoint activation. To understand the cellular functions of Claspin and the functional relationship between Claspin and Rad17, we generated Claspin^−/− and Claspin^−/−/RAD17⁻ cells using chicken DT40 cells, which contain an exogenously introduced Claspin that can be suppressed by the addition of doxycycline (Dox). In the presence of Dox, Claspin^−/− cells ceased growth within 2 days, leading to cell death. In addition, a remarkable reduction in the rate of DNA elongation was observed in Claspin-depleted cells, suggesting that Claspin plays a critical role in DNA replication in the absence of exogenous stress. When cells were exposed to methyl methanesulfonate (MMS), a DNA damaging agent, RAD17⁻ cells showed a greater defect in checkpoint activation than Claspin^−/− cells as monitored by progression of cell cycle and phosphorylation of Chk1. Knocking out RAD17 gene showed almost no additive effects on cell death and DNA elongation rates in Claspin-depleted cells.     

Functional interaction between transforming growth factor alpha and capsaicin-sensitive sensory neurons in the rat stomach

BACKGROUND AND AIMS: Transforming growth alpha (TGFalpha) and sensory neurons have been shown to promote gastric mucosal protection and healing. Aims were to examine in vitro interactions between gastric sensory neurons, the sensory neuropeptide calcitonin gene-related peptide (CGRP), and TGFalpha. METHODS: Gastric mucosal/submucosal tissue fragments from Sprague-Dawley (SD) rats were incubated in short-term (30 min) culture. Peptide release into media and TGFalpha tissue content were measured by radioimmunoassay. RESULTS: TGFalpha (1 x 10(-8) to 1 x 10(-6) M) caused dose-dependent stimulation of CGRP release. Maximal CGRP release (+87%) was observed with 1 x 10(-6) M TGFalpha: 28.6+/-3.8 vs. control of 15.5+/-2.7 pg/g tissue; P<0.05. Both CGRP (1 x 10(-7) to 1 x 10(-5) M) and capsaicin (1 x 10-(8) to 1 x 10(-6)M) significantly inhibited basal TGFalpha release in a dose-dependent fashion that ranged from -20% to -39%. In contrast, capsaicin-induced sensory denervation caused significant increases in both basal TGFalpha release and TGFalpha tissue content. CONCLUSION: Function interactions between TGFalpha and gastric sensory neurons are suggested by the observations that (1) TGFalpha stimulated CGRP release from gastric sensory neurons; (2) CGRP and acute capsaicin treatment inhibited TGFalpha release and; (3) capsaicin-induced sensory denervation caused significant increases in both gastric TGFalpha basal release and tissue content.     

Absence of a relationship between immunoreactive-gastrin and somatostatin-like immunoreactivity secretion in the perfused rat stomach

The possible interaction between somatostatin-like immunoreactivity (SLI) and immunoreactive-gastrin release was studied in an isolated perfused rat stomach preparation. Gastrin release was abolished by antrectomy but basal and gastric inhibitory polypeptide-stimulated SLI levels were unchanged from control experiments, implicating the corpus as the major source of SLI released into the vasculature. Perfused stomachs of vagotomized rats exhibited basal hypergastrinaemia with no alteration in basal or stimulated SLI release, suggesting an uncoupling of SLI and gastrin release. This study indicated that SLI released into the vasculature originated in the acid secretory region of the stomach and therefore may be involved in the regulation of acid secretion at the level of the parietal cell mass.     

Functional relationship between protein-bound and free factor F430 in Methanobacterium

Factor F430 is a nickel porphinoid present in all methanogenic bacteria. It is a component of methyl-CoM reductase to which it is tightly but not covalently bound. Evidence is presented that in Methanobacterium thermoautotrophicum grown on nickel sufficient medium only approximately 30% of total F430 is associated with methyl-CoM reductase and that 70% is present in a non-bound, free form. When such cells were transferred to a nickel deficient medium the bacteria continued to grow although synthesis of total F430 stopped. During growth in the absence of nickel the amount of total F430 per 1 culture remained constant and that per g cells decreased. The ratio of free F430 to bound F430, however, changed. Free F430 was converted into the protein-bound form until almost all of the free F430 had disappeared. The kinetics of labelling with ⁶³Ni of free and bound F430 agreed rather well with that calculated for a precursor-product relationship between free and bound F430.Dedicated to Professor H. G. Schlegel on the occasion of his 60th birthday     

Raising consciousness in ecosystem health

New knowledge and theory developed by physicists in the first half of the 20th century radically changed our concepts of the nature of reality and the place of the human species in it. This information has not yet penetrated the other natural sciences nor day-to-day life. This paper argues that it is essential that we leave behind the World as Machine world view, or paradigm, which has led us to global crisis. Instead we must more rapidly incorporate the information from the 20th century new physics, and shift the dominant social paradigm to a Systems view of the world, in our efforts towards defining and implementing ecosystem health and the closely-related sustainable development. Some of the key implications of new physics to ecosystem health are that the biosphere and the surrounding universe is an indivisible whole; that the human species, especially our consciousness, is integral to the biosphere; that nothing is static; and that dynamism and function are primary, whereas structure is secondary. It is suggested that the understanding of the connectedness of humans to the rest of the biosphere will alter the behaviour of the human species towards more ecologically sustainable actions.     

On the importance of the negative selection effect for the relationship between biodiversity and ecosystem functioning

Much of our knowledge on biodiversity and ecosystem functioning comes from studies examining the effects of biodiversity on biomass production within a trophic group. A large number of these studies have found that increasing biodiversity tends to increase biomass production, leading many ecologists to believe that there exists a general positive relationship between biodiversity and ecosystem functioning. Here we argue that such a positive relationship may not be general, particularly for ecosystem functions other than biomass. Our argument centers on the potential importance of the negative selection effect, which operates where competitively dominant species do not contribute significantly to the function of interest. We suggest that negative selection effects may be potentially common for non-biomass functions, for which species competitive ability may often be a poor indictor of its functional impact. We conclude that diverse (positive, negative, and neutral) BEF relationships are possible for non-biomass functions and that for a particular function, the exact form of the BEF relationship may depend on how species functional impacts relate to their competitive abilities in the community.     

Resource availability dominates and alters the relationship between species diversity and ecosystem productivity in experimental plant communities

Experimental evidence that plant species diversity has positive effects on biomass production appears to conflict with correlations of species diversity and standing biomass in natural communities. This may be due to the confounding effects of a third variable, resource availability, which has strong control over both diversity and productivity in natural systems and may conceal any positive effects of diversity on productivity. To test this hypothesis, I independently manipulated resource availability (soil fertility) and sown species diversity in a field experiment and measured their individual and interactive effects on productivity. Although fertility was a far stronger predictor of productivity than diversity, the effect of diversity on productivity significantly increased with fertility. Relative yield analyses indicated that plant mixtures of high fertility treatments significantly "overyielded," or were more productive than expected based on monoculture yields of component species. In contrast, plant mixtures of low fertility treatments had significantly lower-than-expected yields. The effect of diversity on productivity was also driven by sampling effects, where more species-rich mixtures were more likely to include particularly productive species. Unexpectedly, the strength of sampling effects was largely insensitive to fertility, although the particular species most responsible for sampling effects did change with fertility. These results suggest that positive effects of species diversity on ecosystem productivity in natural systems are likely to be masked by variation in environmental factors among habitats.     

肠道菌群代谢作用与人体健康关系的研究进展

人体肠道内寄居的大量共生微生物可以通过多方面作用影响人体健康,特别是肠道内菌群的代谢作用,及与人体自身代谢的交互作用在人类的健康促进与疾病的发生、发展中起着重要作用。本文从正反两面讨论了肠道菌群代谢作用对人体健康的影响,并进一步探讨了肠道菌群代谢在健康监测、疾病的预防与治疗,以及个体化医疗方面的运用。     

Dominant species can produce a negative relationship between species diversity and ecosystem function

Several studies have reported a positive relationship between species richness and ecosystem functioning. However, if much of a particular ecosystem function is performed by one species (i.e. a functionally dominant species) and this species is also a competitive dominant that excludes other taxa from a habitat, then it is possible to obtain a negative relationship between richness and ecosystem functioning. Results of a leaf pack breakdown experiment in a small stream suggested that the caddisfly Pycnopsyche gentilis , a common detritivorous insect in North American headwater streams, was both a functional and competitive dominant. In a second experiment we compared the effect of Pycnopsyche on leaf breakdown to that of other detritivore taxa by enclosing them with leaf packs in a section of headwater stream in which they were uncommon ( Pycnopsyche transplant experiment). Final leaf pack mass was significantly lower in the Pycnopsyche enclosure treatment; leaves exposed to a greater diversity of detritivores displayed little reduction in leaf mass. These results demonstrated that Pycnopsyche was a functionally dominant detritivore. In a third experiment ( Pycnopsyche density experiment) we found that Pycnopsyche was also a competitively dominant species. Leaf packs and large Pycnopsyche were placed in enclosures that were permeable to the majority of other detritivores but not Pycnopsyche . Leaf mass lost increased with increasing Pycnopsyche density. Leaf packs exposed to Pycnopsyche , however, contained fewer detritivore taxa which suggested that Pycnopsyche was also a competitive dominant. There was a negative relationship between three measures of diversity and leaf litter breakdown in the Pycnopsyche density experiment. Experiments conducted in natural communities that incorporate important species interactions may produce diversity-ecosystem function relationships other than the positive ones that are commonly reported.     

The relationship of the oral microbiotia to periodontal health and disease

The oral microbial community represents the best-characterized consortium associated with the human host. There are strong correlations between the qualitative composition of the oral microbiota and clinically healthy or diseased states. However, additional studies are needed to elucidate the mechanisms that define these microbial/host relationships.