IE-Kb: intron exon knowledge base

SUMMARY: IE-Kb (Intron Exon-Knowledge base) illustrates the intron-exon dynamics in eukaryotic genes. We have developed three different knowledge sets, namely 'Non-redundant ExInt', 'Non-redundant Pfam-ExInt complement' and 'Non-redundant GenBank eukaryotic subdivisional sets' to understand this phenomenon. Statistical analysis is performed on each knowledge set and the results are made available online. The entries in knowledge sets are ranked based on their intron length, exon length and protein length with relational hyper-links to the corresponding intron phase, intron position, intron sequence, gene definition and parent GenBank entry.     

Does experimental evolution reflect patterns in natural populations? E. coli strains from long-term studies compared with wild isolates

Our results show that experimental evolution mimics evolution in nature. In particular, only 1000 generations of periodic recombination with immigrant genotypes is enough for linkage disequilibrium values in experimental populations to change from a maximum linkage value to a value similar to the one observed in wild strains of E. coli. Our analysis suggests an analogy between the recombination experiment and the evolutionary history of E. coli; the E. coligenome is a patchwork of genes laterally inserted in a common backbone, and the experimental E. coli chromosome is a patchwork where some sites are highly prone to recombination and others are very clonal. In addition, we propose a population model for wild E. coli where gene flow (recombination and migration) are an important source of genetic variation, and where certain hosts act as selective sieves; i.e., the host digestive system allows only certain strains to adhere and prosper as resident strains generating a particular microbiota in each host. Therefore we suggest that the strains from a wide range of wild hosts from different regions of the world may present an ecotypic structure where adaptation to the host may play an important role in the population structure. This revised version was published online in August 2006 with corrections to the Cover Date.     

Species distribution and antifungal susceptibility patterns of <Emphasis Type="Italic">Candida</Emphasis> spp. bloodstream isolates from a Brazilian tertiary care hospital

In this work, we collect data from surveys of bloodstream Candida isolates performed in Brazil from 1996 to 2004. Besides, we analyzed the species distribution of bloodstream Candida isolates together with potential risk factors for candidemia and the susceptibility profile of these isolates in patients from Hospital das Clínicas in Goiania city, Brazil. Blood samples were collected in the admission day and on every 7 days, in the intensive care unit (ICU) of a tertiary hospital. Candida isolates were identified by standard protocols that included germ tube formation, chlamydoconidia production on cornmeal agar and sugar fermentation and assimilation tests. Data of patients were recorded and analyzed according to age at the time of diagnosis, gender and presence of potential risk factors. Statistical analysis was used to determine if the time of hospital permanence increased Candida colonization in ICU patients’ blood. The antifungal susceptibility testing was performed by broth microdilution method according to document NCCLS/CLSI M27–A2. Among the 345 blood samples cultured, candidemia was recovered in 33 patients, which were isolated 51.5% of Candida non-albicans. Fungemia was associated with long-term hospitalization. Fluconazole, itraconzole, voriconazole and amphotericin B exhibited a potent activity against all isolates of Candida. Voriconazole MICs were much low for all isolates tested. This work confirms data of increase of Candida non-albicans species in bloodstream in ICU and shows that voriconazole in vitro activity was higher than those of itraconazole, fluconazole and amphotericin B.     

Functional effects of alcohol withdrawal syndrome on peripheral sympathetic neurotransmission in vas deferens of adult rats

Aims

Alcohol withdrawal syndrome (AWS) is characterized by a set of physiological modifications triggered by abrupt withdrawal and/or decreasing consumption of ethanol (EtOH), which may manifest 16–48 h after ceasing consumption. The relationship between the effects of AWS and central and peripheral sympathetic neurotransmission is unknown. This study investigates the possible mechanisms on the sympathetic system during periods of AWS.

Main methods

Male Wistar rats were treated with EtOH (6–10 g/kg/day/v.o. 5 days). Subsequently, 1 h, 24 h, 48 h and 120 h after administration of the last dose of EtOH, the animals were sacrificed, and their vas deferens (VD) were removed to perform the following evaluations: (a) concentration–effect curves of sympathetic agonist; (b) activity of α₂-adrenoreceptor; (c) function of voltage-dependent calcium channels (Cav); and (d) release of endogenous catecholamines measured in real time coupled to HPLC.

Key findings

The results showed that the maximum effects of contraction were increased by agonists tested in at 24 h and 48 h EtOH withdrawal. The inhibitory affinity (pIC₅₀) of guanfacine was decreased 24 h EtOH withdrawal. The function of Cav was also decreased as pIC₅₀ values dropped 24 h and 48 h EtOH withdrawal. The release of catecholamines increased 48 h after EtOH withdrawal. It is suggested that AWS triggers hyperactivity in peripheral sympathetic neurotransmission.

Significance

The mechanisms underlying hyperactivity are possibly explained by a failure of autoregulation from catecholamines released by α₂-adrenoreceptors and/or an increase of Cav function, which may be potential targets to attenuate the symptoms of AWS at the peripheral level.     

Trichoderma asperelloides antagonism to nine Sclerotinia sclerotiorum strains and biological control of white mold disease in soybean plants

Sclerotinia sclerotiorum is an important plant pathogen with worldwide distribution that causes severe economic losses of various agricultural crops such as soybean. This fungus is normally controlled with synthetic chemical fungicides that pose risks to the environment, and can be harmful to human health, and they can also induce resistance in pests. The aim of this study was to investigate the potential of Trichoderma asperelloides as a biocontrol agent towards white mold disease on soybeans crops. The antagonism of two strains of T. asperelloides (T25 and T42) isolated from soil samples was determined in-vitro by dual-culture confrontation testing on nine S. sclerotiorum strains obtained from sclerotia collected on diseased soybean plants. The mycelial growth and inhibition of carpogenic and ascospore germination by T. asperelloides extracts, as well as the efficacy of these on white mold control in soybeans were evaluated. Both strains of T. asperelloides exhibited high potential of antagonism. Methanolic and ethyl acetate extracts of the two T. asperelloides strains showed excellent growth inhibition (60–100%) on all of the pathogens tested. The ethyl acetate extracts of both T. asperelloides strains exhibited the highest efficacy against carpogenic germination, decreasing by 20–30% the number of ascospores per apothecium. Strains of T. asperelloides tested were more efficient in controlling white mold than two commercial products made from Trichoderma harzianum. The new strains of T. asperelloides have potential for successful biological control of white mold disease of soybean crops in the field.     

Fatty acid composition of the tropical lichen Teloschistes flavicans and its cultivated symbionts

Fatty acid components, in both the free and combined form of the intact tropical lichen Teloschistes flavicans, and its isolated photobiont and mycobiont, were analyzed by GC-MS of derived methyl esters. Its rDNA analysis confirmed that the isolated cultured symbionts belong to the genera Trebouxia and Teloschistes, respectively. The fatty acid composition of the lichen did not correspond to those found in the isolated symbionts, suggesting that the fatty acid metabolism is markedly influenced by the symbiosis. Differences in the fatty acid composition in the lichen were observed during the summer (27 degrees C), when the main fatty acids were saturated and in the winter (22 degrees C) when an increase of unsaturated fatty acids occurred. Similar differences of composition were also observed for the cultured mycobiont at different temperatures. The increase in the unsaturation level at low temperatures would maintain the membrane fluidity. Our results are the first on the fatty acids of a tropical lichen and suggest that it is sensitive to small temperature variations, which influences its saturated and unsaturated fatty acid composition.     

Occurrence and relatedness of vancomycin-resistant enterococci in animals, humans, and the environment in different European regions

Vancomycin-resistant enterococci (VRE) in Europe are thought to have emerged partly due to the use of the glycopeptide avoparcin in animal husbandry. We compared the occurrence of VRE in geographical regions of Europe in which until 1997 large amounts of avoparcin were used (Spain, United Kingdom, and Denmark) with the occurrence of VRE in Sweden, where avoparcin was banned in 1986. We also studied the relatedness between VRE strains from different regions and habitats. In total, 2,580 samples were collected from humans, animals, and the environment (soil, sewage, recipient water). VRE resistant to 20 microg/ml vancomycin were identified in 8.2% of the samples and were found most frequently in raw and treated urban sewage samples (means, 71% and 36% of the samples, respectively), pig manure (17%), and hospital sewage (16%). The proportions of VRE-positive sewage samples were similar in Sweden, Spain, and the United Kingdom, whereas pig feces and manure were more often positive in Spain than in Sweden (30% versus 1%). Most VRE were Enterococcus faecium carrying vanA, and computerized biochemical phenotyping of the isolates of different ecological origins showed a high degree of polyclonality. In conclusion, it seems that animal-associated VRE probably reflect the former use of avoparcin in animal production, whereas VRE in human-associated samples may be a result of antibiotic use in hospitals. Since there seems to be a reservoir of the resistance genes in all countries studied, precautions must be taken to limit the use of antibiotics and antibiotic-like feed additives.     

Phenol oxidases from Rhodnius prolixus: Temporal and tissue expression pattern and regulation by ecdysone

Rhodnius prolixus 5th instar nymphs have significant PO enzymatic activity in the anterior midgut, fat body and hemolymph. The tissue with the major amount of PO activity is the anterior midgut while those with higher specific activities are the fat body and hemolymph. In this work the temporal pattern of PO enzymatic activity in different tissues was investigated. In fat body, PO peaks occur at 7, 12 and 16 days after a blood meal. In hemolymph, PO diminishes until day 7, and then recovers by day 14. In the anterior midgut tissue, PO peaks on day 9 and just before ecdysis; a similar pattern was observed in the anterior midgut contents. Some of these activities are dependent on the release of ecdysone, as feeding blood meal containing azadirachtin suppresses them and ecdysone treatment counteracts this effect. These results suggest that during the development of the 5th instar, the insect has natural regulating cycles of basal PO expression and activation, which could be related to the occurrence of natural infections. The differences in temporal patterns of activity and the effects of azadirachtin and ecdysone in each organ suggest that, at least in R. prolixus, different tissues are expressing different PO genes.     

A proteomic view of mycobacteria

Tuberculosis, the disease caused by Mycobacterium tuberculosis, remains a relevant public health issue. This is due mostly to the coepidemiology with HIV/AIDS, the appearance of multidrug-resistant strains globally, and failure of BCG (bacillus Calmette-Guerin) vaccination to confer complete protection. This bacterium was one of the first to have its genome sequenced, yet over a decade after the release of the genomic information, the characterization of its phylogenetic tree and of different strain variants inside this species revealed that much is still needed to be done for a full understanding of the M. tuberculosis genome and proteome. Current methods using LC-MS/MS and hybrid high-resolution mass spectrometers can identify 2400-2800 proteins of the 4000 predicted genes in M. tuberculosis. In this article, we review relevant details of this bacterium's pathology and immunology, describing articles where proteomics helped the community to tackle some of the organism biology, from understanding strain diversity, cellular structure composition, immunogenicity, and host-pathogen interactions. Finally, we will discuss the challenges yet to be fulfilled in order to better characterize M. tuberculosis by proteomics.