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.     

试论生态系统与生物体之间的全息关系

提出生态系统与生物体之间存在全息关系的观点,并认为生态系统与生物体都具有保护、支撑、运动、同化、呼吸、循环、排泄、繁殖和调控功能,生态系统的次生演替与生物体的再生修复过程存在着共同点。根据全息胚重演过程中的滞育性、可简化性,可以对生态演替的多方向、多途径问题作出新的解释。     

生物多样性与生态系统多功能性的关系研究进展

生物多样性与生态系统功能关系是生态学研究的热点之一,以往研究多关注生物多样性与单一生态系统功能之间的关系,然而生态系统能够同时提供多种功能和服务即生态系统多功能性(ecosystem multifunctionality, EMF),仅考虑单一生态系统功能会低估生物多样性的重要性。近年来,EMF研究的重要性受到更多重视,生物多样性与生态系统多功能性(biodiversity and ecosystem multifunctionality, BEMF)关系成为生态学研究新的热点。梳理近15年的研究发现,不同维度、不同尺度的单一或多营养级生物多样性均会对EMF产生显著的影响,并且在全球变化的背景下,自然干扰与人为干扰均会影响生物多样性与生态系统多功能性从而改变BEMF关系,EMF测度方法的差异也可能导致BEMF关系的不一致。生物多样性维度(尺度)选择的局限、不同EMF测度方法的认知差异、BEMF时空数据库的缺乏以及BEMF关系研究方法的单一等问题阻碍了BEMF关系的深入探究。未来研究应对现有测度方法进行深入比较并发展通用的新方法,深入探究多维度、多尺度生物多样性对EMF影响的综合作用。此...     

生物多样性与生态系统服务关系研究进展

生物多样性与生态系统服务关系是当前生态学研究的热点之一,2005年千年生态系统评估之后如何将两者关系应用到生态系统管理和政策制定中逐渐受到重视。然而,从理论上的两者关系认知到应用上的管理实践仍面临着严峻挑战,梳理已有研究成果有利于更好地指导管理实践。本文基于近年生物多样性与生态系统服务关系的主要研究成果,从生物多样性对生态系统单种服务、多种服务、生态系统服务权衡的影响以及环境变化如何影响这些关系等方面,总结了两者关系的主要研究进展,概述了两者关系在自然保护区管理、森林生态系统管理、退化生态系统恢复和农业生态系统改善等领域中的应用,分析了两者关系研究中依然存在的不足之处,强调未来需加强的研究方向主要包括: 生物多样性不同组分相互作用和多营养级生物多样性相互关系对生态系统服务的影响、环境耦合变化对两者关系的复合效应以及生物多样性改善生态系统服务的实践途径。     

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.     

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.     

Trophic interactions and the relationship between species diversity and ecosystem stability

Several theoretical studies propose that biodiversity buffers ecosystem functioning against environmental fluctuations, but virtually all of these studies concern a single trophic level, the primary producers. Changes in biodiversity also affect ecosystem processes through trophic interactions. Therefore, it is important to understand how trophic interactions affect the relationship between biodiversity and the stability of ecosystem processes. Here we present two models to investigate this issue in ecosystems with two trophic levels. The first is an analytically tractable symmetrical plant-herbivore model under random environmental fluctuations, while the second is a mechanistic ecosystem model under periodic environmental fluctuations. Our analysis shows that when diversity affects net species interaction strength, species interactions--both competition among plants and plant-herbivore interactions--have a strong impact on the relationships between diversity and the temporal variability of total biomass of the various trophic levels. More intense plant competition leads to a stronger decrease or a lower increase in variability of total plant biomass, but plant-herbivore interactions always have a destabilizing effect on total plant biomass. Despite the complexity generated by trophic interactions, biodiversity should still act as biological insurance for ecosystem processes, except when mean trophic interaction strength increases strongly with diversity.     

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.     

西藏草地植物功能性状与多项生态系统服务关系

针对植被功能性状与生态系统服务功能之间的相互关系,构建了西藏草地株高和可食性两种功能性状的9项指标,并基于土壤和植物采样,分析了9项植物功能性状指标和5项生态系统服务指标间的相关性,探讨了4种机制(Mass ratio,Selection,Niche complementarity及Insurance)在西藏草地的适用性。结果表明,9项功能性状指标中,株高Rao和可食种与所有种株高CWM比分别与土壤有机碳、土壤全氮和土壤含水率3项生态系统服务指标呈显著负相关及显著正相关。说明群落植被对光能竞争的互补性及可食性状植株在群落中的光能资源相对竞争力,与土壤固碳、肥力供给及水源涵养有显著相关关系。而群落可食种、优势种、优势种与次优势种对光能资源竞争力水平,可食植株多样性、可食植株在群落中的优势度及其光能资源竞争力均值,对草地生态系统服务无显著影响。西藏草地植物功能性状对多项生态系统服务的影响机制从光能资源竞争角度更符合Niche complementarity和Insurance理论,而从可食功能性状角度更符合Mass ratio和Selection理论。     

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 relationship between the foot intrinsic and extrinsic muscles in walking

The intrinsic and extrinsic muscles are considered to stabilize the foot and contribute to propulsion during walking. This study aimed to clarify the functional relationship between intrinsic and extrinsic muscles during walking. Thirteen healthy men participated in this study. The muscle activities of the intrinsic muscles (quadratus plantae and abductor hallucis), and the extrinsic muscles (flexor hallucis longus, flexor digitorum longus, and tibialis posterior) were measured using fine-wire and surface electromyography during walking. The muscle onset timing after foot contact was calculated and compared among muscles using the one-way ANOVA. The stance phase was divided into early and late braking, and early and late propulsion phases. Muscle activity among phases was compared using repeated-measures ANOVA. The onset time of the abductor hallucis was significantly earlier than those of the flexor digitorum longus and tibialis posterior. The quadratus plantae demonstrated significantly earlier onset than that of the tibialis posterior. In the late propulsion phase, the activity of extrinsic muscles decreased, whereas intrinsic muscles were continuously active. Early activation of the intrinsic muscles may stabilize the foot for efficient torque production by the extrinsic muscles. Furthermore, the intrinsic muscles may contribute to the final push-off after the deactivation of extrinsic muscles.     

生态系统健康与相关概念的逻辑关系

生态系统健康是近年才发展起来的生态学上的一个研究热点。与可持续性一样,生态系统健康在生态学中也是很重要的新的研究领域。本文对生态系统健康及与之相关的概念进行了逻辑上的比较与推断。这些概念包括可持续性、稳定性、连续性和持久性。并得出了以下结论：①稳定性是健康、可持续性、连续性和持久性的必要条件而不是充分条件;②连续性是健康、可持续性、稳定性的充分条件而非必要条件,是持久性的充分必要条件;③持久性是可持续性和连续性的充分必要条件,是健康和稳定性的充分而非必要条件;④健康是可持续性、连续性和持久性的必要而非充分条件,是稳定性的充分而非必要条件;⑤可持续性是稳定性、健康的充分而非必要条件,是连续性的必要而非充分条件,是持久性的充分必要条件。     

Two approaches towards the relationship between plant species diversity and ecosystem functioning

Abstract. The main question to be dealt with in the papers published in this Special Feature is to which extent plant species richness can be applied as a parameter in restoration projects to qualify the ecosystem's state. Before considering this problem, it should be recognized that this approach illuminates only one side of the coin; the other side is touched by the opposite question, asking which plant species are essential components of an ecosystem. These two approaches towards the relationship between species richness and ecosystem functioning are not mutually exclusive, but should not be confused either. In view of ecosystem functioning certain species may be considered redundant, while in view of evolutionary processes certain ecosystem processes may be considered redundant. Where do the two approaches meet and when should they be separated? This paper touches upon this question by referring to the dual hierarchy of ecological systems.     

西南地区生态系统服务关系特征及其与植被覆盖的约束效应

西南地区是我国岩溶发育最强烈的生态脆弱区,同时也是植被恢复成效显著的生态修复区。尽管研究已证实了生态修复工程实施与生态系统服务功能提升之间的因果关系,但多个生态系统服务间的复杂关系、植被恢复对生态系统服务关系的约束效应却鲜有报道。研究在对西南地区的NPP、产水、粮食生产和土壤保持服务进行准确估算后,构建生态系统服务关系指数,对其时空变化特征及驱动因子进行剖析,并重点识别森林覆盖面积这一主导因子与生态系统服务关系的约束效应和影响阈值。结果显示：(1)2000到2018年,区域生态系统服务协同指数均值变化不明显,权衡指数呈减小趋势,综合指数略有上升,区域生态修复取得一定成效。(2)生态系统服务关系指数的空间分布差异明显,其中,协同指数的增长主要集中于研究区南部,权衡指数的减少主要位于四川中部和贵州东部,综合指数的增长主要分布在云南、贵州东部和四川南部。(3)生态系统服务关系变化受多种因素共同影响,其中森林覆盖面积的影响最突出,且各因素的作用具有明显的空间非平稳性。(4)森林覆盖面积与生态系统服务协同、权衡和综合关系间均存在一定约束关系,当影响阈值超过59%后,森林覆盖面积的扩大将不会带来生...