Mycobacterial proteomics: analysis of expressed proteomes and post-translational modifications to identify candidate virulence factors

The Mycobacterium tuberculosis bacillus has a number of unique features that make it a particularly effective human pathogen. Although genomic analysis has added to our current understanding of the molecular basis by which M. tuberculosis damages its host, proteomics may be better suited to describe the dynamic interactions between mycobacterial and host systems that underpin this disease. The M. tuberculosis proteome has been investigated using proteomics for over a decade, with increasingly sophisticated mass spectrometry technology and sensitive methods for comparative proteomic profiling. Deeper coverage of the M. tuberculosis proteome has led to the identification of hundreds of putative virulence determinants, as well as an unsurpassed coverage of post-translational modifications. Proteomics is therefore uniquely poised to contribute to our understanding of this pathogen, which may ultimately lead to better management of the disease.     

Evolutionary responses to environmental change: trophic interactions affect adaptation and persistence

According to recent reviews, the question of how trophic interactions may affect evolutionary responses to climate change remains unanswered. In this modelling study, we explore the evolutionary dynamics of thermal and plant–herbivore interaction traits in a warming environment. We find the herbivore usually reduces adaptation speed and persistence time of the plant by reducing biomass. However, if the plant interaction trait and thermal trait are correlated, herbivores can create different coevolutionary attractors. One attractor has a warmer plant thermal optimum, and the other a colder one compared with the environment. A warmer plant thermal strategy is given a head start under warming, the only case where herbivores can increase plant persistence under warming. Persistence time of the plant under warming is maximal at small or large thermal niche width. This study shows that considering trophic interactions is necessary and feasible for understanding how ecosystems respond to climate change.     

Gene duplication as a mechanism of genomic adaptation to a changing environment

A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.     

Plant adaptation to dynamically changing environment: the shade avoidance response

The success of competitive interactions between plants determines the chance of survival of individuals and eventually of whole plant species. Shade-tolerant plants have adapted their photosynthesis to function optimally under low-light conditions. These plants are therefore capable of long-term survival under a canopy shade. In contrast, shade-avoiding plants adapt their growth to perceive maximum sunlight and therefore rapidly dominate gaps in a canopy. Daylight contains roughly equal proportions of red and far-red light, but within vegetation that ratio is lowered as a result of red absorption by photosynthetic pigments. This light quality change is perceived through the phytochrome system as an unambiguous signal of the proximity of neighbors resulting in a suite of developmental responses (termed the shade avoidance response) that, when successful, result in the overgrowth of those neighbors. Shoot elongation induced by low red/far-red light may confer high relative fitness in natural dense communities. However, since elongation is often achieved at the expense of leaf and root growth, shade avoidance may lead to reduction in crop plant productivity. Over the past decade, major progresses have been achieved in the understanding of the molecular basis of shade avoidance. However, uncovering the mechanisms underpinning plant response and adaptation to changes in the ratio of red to far-red light is key to design new strategies to precise modulate shade avoidance in time and space without impairing the overall crop ability to compete for light.     

Lotic meiofaunal community dynamics: colonisation, resilience and persistence in a spatially and temporally heterogeneous environment

1.  The spatial and temporal dynamics of lotic meiofaunal communities were examined with a focus on colonisation, maintenance of populations in lotic environments and persistence of meiofaunal communities.
2.  Lotic meiofaunal colonisation of new habitats may take place via a number of mechanisms and is rapid at both the patch scale (within hours–days) and the drainage basin scale (within 20 years). Successional patterns in lotic meiofaunal communities are evident although data are extremely limited.
3.  Lotic meiofaunal communities appear to be resilient to high flow disturbances. Resilience is moderated by the availability of in-stream refugia and habitat hydrology. Lotic meiofauna may also adopt a 'refuge as habitat' approach to such disturbances.
4.  Lotic cyclopoid copepods possess a common suite of life history characteristics that confers resilience to disturbances. Compared to pelagic planktonic species they have short generation times, many descendants per reproductive cycle and long lifespans. Females in 'source' populations are likely to survive disturbances and so could continuously reproduce over a long period of time producing large numbers of offspring which develop rapidly and recolonise 'sink' areas of the stream.
5.  Persistence of lotic meiofaunal communities is highly variable. Meiofaunal persistence does not increase with increasing proportions of in-stream flow refugia.     

Technical Advance: a novel technique for the sensitive quantification of acyl CoA esters from plant tissues

We report a novel, highly sensitive and selective method for the extraction and quantification of acyl CoA esters from plant tissues. The method detects acyl CoA esters with acyl chain lengths from C4 to C20 down to concentrations as low as 6 fmol in extracts. Acyl CoA esters from standard solutions or plant extracts were derived to their fluorescent acyl etheno CoA esters in the presence of chloroacetaldehyde, separated by ion-paired reversed-phase high-performance liquid chromatography, and detected fluorometrically. This derivitization procedure circumvents the selectivity problems associated with previously published enzymatic methods, and methods that rely on acyl chain or thiol group modification for acyl CoA ester detection. The formation of acyl etheno CoA esters was verified by mass spectrometry, which was also used to identify unknown peaks from chromatograms of plant extracts. Using this method, we report the composition and concentration of the acyl CoA pool during lipid synthesis in maturing Brassica napus seeds and during storage lipid breakdown in 2-day-old Arabidopsis thaliana seedlings. The concentrations measured were in the 3--6 microM range for both tissue types. We also demonstrate the utility of acyl CoA profiling in a transgenic B. napus line that has high levels of lauric acid. To our knowledge, this is the first time that reliable estimates of acyl CoA ester concentrations have been made for higher plants, and the ability to profile these metabolites provides a valuable new tool for the investigation of gene function.     

Cell envelope phospholipid changes in a moderate halophile during phenotypic adaptation to altered salinity and osmotic stress

Abstract The increased content of negatively-charged phospholipids in membranes of Vibrio costicola grown at high salinities is mediated by increased phospholipid synthesis of phosphatidylglycerol relative to phosphatidylethanolamine. This phenomenon provides a system for investigating the factors involved in triggering and controlling haloadaptation in this moderately halophilic bacterium. We review recent experiments, which show that when subjected to sudden increases in external salinity, V. costicola senses both the absolute NaCl concentration and the magnitude of the salt shift. We show that the latter is sensed at least in part via osmotic pressure effects, since shift-up into sucrose-containing media triggers comparable changes in growth and in phospholipid composition and synthesis.     

肠道菌群改变与结核分枝杆菌感染相互作用的研究进展

人体内肠道菌群数量庞大,参与机体物质代谢以及免疫应答反应,成为目前众多研究的热点.肠道菌群对于维持呼吸系统稳态,特别是肺部的稳态发挥着重要作用.目前越来越多的结果证明肠道菌群对机体免疫系统具有诱导和调节作用,这种免疫反应的改变对于结核病的发病和治疗有着深远意义.本文梳理了近年来国内外发表的肠道菌群与结核病相关的文献,讨...     

Metabolic adaptation to the chronic loss of Ca2+ signaling induced by KO of IP3 receptors or the mitochondrial Ca2+ uniporter

Calcium signaling is essential for regulating many biological processes. Endoplasmic reticulum inositol trisphosphate receptors (IP₃Rs) and the mitochondrial Ca²⁺ uniporter (MCU) are key proteins that regulate intracellular Ca²⁺ concentration. Mitochondrial Ca²⁺ accumulation activates Ca²⁺-sensitive dehydrogenases of the tricarboxylic acid (TCA) cycle that maintain the biosynthetic and bioenergetic needs of both normal and cancer cells. However, the interplay between calcium signaling and metabolism is not well understood. In this study, we used human cancer cell lines (HEK293 and HeLa) with stable KOs of all three IP₃R isoforms (triple KO [TKO]) or MCU to examine metabolic and bioenergetic responses to the chronic loss of cytosolic and/or mitochondrial Ca²⁺ signaling. Our results show that TKO cells (exhibiting total loss of Ca²⁺ signaling) are viable, displaying a lower proliferation and oxygen consumption rate, with no significant changes in ATP levels, even when made to rely solely on the TCA cycle for energy production. MCU KO cells also maintained normal ATP levels but showed increased proliferation, oxygen consumption, and metabolism of both glucose and glutamine. However, MCU KO cells were unable to maintain ATP levels and died when relying solely on the TCA cycle for energy. We conclude that constitutive Ca²⁺ signaling is dispensable for the bioenergetic needs of both IP₃R TKO and MCU KO human cancer cells, likely because of adequate basal glycolytic and TCA cycle flux. However, in MCU KO cells, the higher energy expenditure associated with increased proliferation and oxygen consumption makes these cells more prone to bioenergetic failure under conditions of metabolic stress.     

A method for the direct evaluation of the fatty acid status in a drop of blood from a fingertip in humans: applicability to nutritional and epidemiological studies

Several studies have shown that the fatty acid composition of circulating lipids reflects dietary fat intake, in turn being related to health status. The fatty acid composition of plasma lipids is therefore an important parameter in studies on dietary interventions. The aim of our study was to develop a rapid and inexpensive method for the analysis of circulating fatty acids applicable to large population groups. Drops of blood collected from fingertips have been directly subjected to transmethylation for gas chromatography analysis. This new method, validated for reproducibility, has been compared with the conventional method, based on withdrawal of blood from the antecubital vein followed by lipid extraction, and identical data have been obtained with the two techniques. Observed and predicted differences between blood and plasma fatty acids are related to the contribution of circulating cell membranes in blood. Finally the application of the methods to samples from 100 healthy subjects and the assessed correlation between dietary habits and blood fatty acid profiles demonstrate the validity of the new method and its applicability to nutritional and epidemiological studies.     

Stromatolitic communities in Mediterranean streams: adaptations to a changing environment

A stromatolitic microbial mat extensively covers La Solana streambed, a calcareous Mediterranean stream. This stromatolite shows remarkable biological and physiological diversity. It is mainly composed by cyanobacteria, with Rivularia and Schizothrix as the most abundant taxa. The stromatolite is photosynthetically adaptated to the high irradiances reaching the streambed. Photosynthetically active chlorophyll is present even in the lowest layers of the stromatolite, indicating the presence of well-preserved cyanobacteria in that part. Diffusion of gases and nutrients within the stromatolite can be possible because of the high porosity of the crust. It has been experimentally established that the stromatolite recovers heterotrophic and autotrophic activities in a few hours, after being desiccated for long periods. Recovery after desiccation is indicative of the high resilience of this community to environmental extremes, which are common in Mediterranean climatic regimes. The stromatolitic community is adapted to nutrient limitation, both to low availability of inorganic phosphorus and nitrogen (that constrain growth of primary producers), and to low dissolved organic carbon (mainly affecting heterotrophs). Stromatolitic heterotrophs mainly rely on the organic carbon stored in the crust as the main organic carbon source. These strategies are the direct response of the stromatolite to oligotrophy, and justify the restricted occurrence in stream systems affected by organic pollution.     

The influence of glycerol on the binding of methotrexate to Mycobacterium tuberculosis dihydrofolate reductase: a molecular modelling study

The enzyme, dihydrofolate reductase (DHFR), from Mycobacterium tuberculosis (mt-DHFR) is believed to be a potential drug target for the treatment of tuberculosis. The co-crystal structure of mt-DHFR bound with glycerol (GOL), NAPDH and methotrexate (MTX) reveals a GOL binding site on the enzyme. This GOL binding site could be very important for the design of novel, selective mt-DHFR inhibitors, because this binding site is absent on human DHFR (h-DHFR). We have performed molecular dynamic simulations and free energy calculations to evaluate the binding affinity of GOL and its free energy contribution to the binding of MTX to mt-DHFR. The results showed that GOL does not bind tightly to mt-DHFR. Although GOL itself contributed free energy on MTX binding to mt-DHFR, GOL also increased the flexibilities of MTX, so that MTX cannot maintain strong electronic interactions with ARG32 and ARG60, which caused the total binding free energy to decrease. These data suggest that GOL binding is weak and it could be expelled from the binding site, to allow inhibitors containing appropriate side chains to bind. This observation can be used to inform future drug design studies, especially those aimed at improving drug selectivity against h-DHFR.     

Influence of feeding a fish oil-containing diet to young,lean, adult dogs: effects on lipid metabolites,postprandial glycaemia and body weight

The aim of this study was to determine the effect of feeding a fish oil (FO)-containing diet on lipid and protein metabolism, postprandial glycaemia and body weight in young, lean, adult dogs. Eight female Beagles were randomly assigned to one of two isonitrogenous and isoenergetic diets, Control or FO, in a crossover design. At the beginning of the experiment and at 30 and 60 d, a baseline blood sample was collected and the dogs then were fed their daily ration. Nitrogen balance began at 07:00 h on day 63 of each experimental period and ended at 07:00 h on day 69. On day 66 of each period, a single dose (7.5 mg/kg) of ¹⁵N-glycine was administered orally to each dog via gelatin capsule. Postprandial glycaemia did not differ between treatments or among sampling days within treatment. Cholesterol concentration was increased (p < 0.05) on the Control treatment throughout the experiment when compared to values of day 0. Dogs fed the FO treatment had higher plasma triglyceride and ghrelin concentrations than those fed the Control treatment. Body weight and food intake did not differ between dietary treatments. Faecal excretion was increased (p < 0.05) in the FO treatment. Dry matter digestibility was decreased (p < 0.05) and fat digestibility tended (p < 0.10) to decrease in the FO treatment. Overall, feeding a FO-containing diet showed a protective effect against the rise of plasma cholesterol and it increased plasma ghrelin concentration. However, FO supplementation did not appear to affect protein metabolism or postprandial glycaemia in adult lean dogs.     

Fueguian cranial morphology: The adaptation to a cold,harsh environment

Craniometric data from the three extinct tribes that inhabited Tierra del Fuego (Selk'nam, Yámana, and Kawéskar) were gathered following Howells's measurement technique. We studied 180 skulls preserved at thirteen different institutions. Analysis of variance (ANOVA) between groups showed that morphological similarities among Fueguian groups are far more important than some differences between marine (Yámana and Kawéskar) and terrestrial (Selk'nam) groups. A principal component analysis (PCA) generated from the correlation matrix shows that Fueguians fall as outliers with respect to the typical Mongoloid morphology. In addition, a UPGMA tree generated from a squared Euclidean distance matrix indicates that Fueguian groups have a morphological pattern that is very distinct from that of other present-day Amerindian groups, with the exception of the Eskimos. One of the variables that contributes substantially to the differentiation of Eskimos and Fueguians is the nasal height. This suggests that nasal morphology in both groups could be a response to adaptive pressures related to the cold environment. However, other morphological particularities of Fueguian skulls, such as craniofacial robustness and variables of craniofacial width, can be attributed to a large masticatory stress. As a whole, the morphological features of Fueguian groups can be regarded as a general adaptive response to a very harsh environment, along with the retention of some plesiomorphic features. Assuming that the initial entry in Tierra de Fuego took place around 10,000 years BP, before the disappearance of the last land bridges in the Magellan Straits, then this adaptation might have arisen in a relatively short period, hastened by the extreme environmental conditions. Am J Phys Anthropol 103:103–117, 1997. © 1997 Wiley-Liss, Inc.     

Dietary ratio of n-6 to n-3 polyunsaturated fatty acids and periodontal disease in community-based older Japanese: a 3-year follow-up study

The longitudinal relationship between dietary n-6 to n-3 PUFAs ratio and periodontal disease in 235 Japanese subjects for whom data were available for the years 2003-2006 was investigated. PUFAs intake was assessed at baseline with a brief-type self-administered diet history questionnaire. Full-mouth periodontal status, measured as the clinical attachment level (CAL), was recorded at baseline and once a year for 3 years. The number of teeth with a change in the loss of CAL ≥3 mm at any site over a year was calculated as ‘periodontal disease events’. Poisson regression analysis was conducted, with dietary n-6 to n-3 PUFAs ratio as the main predictor, to estimate its influence on periodontal disease events.A high dietary n-6 to n-3 PUFAs ratio was significantly associated with greater number of periodontal disease events. The findings suggest the dietary n-6 to n-3 PUFAs ratio is associated with periodontal disease among older Japanese.     

Reversed sexual size dimorphism in raptors: evaluation of the hypotheses in kestrels breeding in a temporally changing environment

Reversed sexual size dimorphism (RSD, females larger than males) is commonly found in birds of prey. We used kestrels (Falco tinnunculus), breeding in western Finland in a temporally varying environment of 3-year vole cycles, to assess current hypotheses for the evolution and maintenance of RSD. Our 12-year data showed only weak correlations between parental size and breeding parameters (laying date, clutch size and the number of fledglings produced). The degree of RSD per se was unrelated to breeding success, contrary to the prediction of the female dominance hypothesis. Females with small males produced larger clutches in low-vole years, independently of laying date, which supports the small male (or its equivalent inter-sexual selection) hypothesis. Small females tended to have more fledglings, particularly in low-vole years, which is inconsistent with the hypotheses for an advantage of large female size (the starvation, intra-sexual selection, reproductive effort, and supplementary feeding hypotheses). As for males, smaller females may be more efficient hunters, the importance of which should be most pronounced under harsh breeding conditions. Our results suggest that the directional selection on a particular size in kestrels may be under contrasting selection pressures by the environment, and, at least in breeding females, the advantages of large size can actually be counterbalanced during harsh environmental conditions. Received: 7 May 1999 / Accepted: 20 January 2000     

乳酸菌胆盐水解酶和共轭脂肪酸产生及对宿主脂代谢影响的研究进展

乳酸菌是一类影响宿主脂代谢的人体肠道益生菌。乳酸菌对脂代谢的影响作用与其产生胆盐水解酶(bile salt hydrolase,EC3.5.1.24,BSH)及共轭转化多不饱和脂肪酸(polyunsaturated fatty acids,PUFAs)关系密切。菌株差异、菌群分布和饮食差异是影响BSH及共轭脂肪酸产生的重要因素。本文重点阐述了两类物质对宿主脂代谢的影响机制,以期为后续研究提供借鉴。BSH能够降解肝脏分泌的胆汁酸(bile acids,BAs),降低脂类物质的吸收。BAs的降解产物胆汁酸脱氧胆酸(deoxycholic acid,DCA)和石胆酸(lithocholic acid,LCA)能够通过机体信号通路法尼类X受体(farnesoid X receptor,FXR)、小异二聚体伴侣(small heterodimer partner,SHP)及肝脏X受体(liver X receptor,LXR)等信号通路进行调控,促进胆固醇转运及向BAs转化。此外,BSH还能够通过下调固醇调节元件结合蛋白1c (sterol regulatory element binding protein 1c,SREBP-1c)、上调5ʹ-腺苷单磷酸激活蛋白激酶α(5ʹ-AMP activated protein kinase,AMPKα)和过氧化物酶体增殖物激活受体α (peroxisome proliferator-activated receptor α,PPARα)抑制脂质合成,促进脂质的分解。PUFAs可被乳酸菌转化产生共轭脂肪酸,如共轭亚油酸(conjugated linoleic acid,CLA)和共轭亚麻酸(conjugated linolenic acid,CLNA),CLA/CLNA能够促进机体产生瘦素(leptin,LP),抑制食欲、促进能量消耗;CLA/CLNA还可以通过激活PPARα进行调控,促进人体脂质的氧化分解。乳酸菌通过以上多种途径共同作用调节宿主的脂代谢,对深入理解乳酸菌调控脂代谢机制及临床应用有着重要意义。