Evolutionary,structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales

Background  

Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes.     

Biochemical characterization of rat intestine development using high-resolution magic-angle-spinning 1H NMR spectroscopy and multivariate data analysis

We report details of metabolic profiles for small intestinal samples obtained using high-resolution magic-angle-spinning (HRMAS) (1)H NMR spectroscopy. Intact samples of jejunum and ileum from male Long Evans rats were analyzed on a 600 MHz spectrometer using standard one and two-dimensional (1)H NMR spectroscopic pulse sequences. The metabolic profiles of ileum and jejunum predominantly comprised a number of amino acids, lipids, glycerophosphocholine (GPC), choline, creatine, and ethanol, a number of carboxylic acids including acetate and lactate, and nucleoside bases including cytosine, isocytosine, and uracil. Principal component analysis (PCA) was applied to these NMR data to characterize the biochemical differences between jejunum and ileum tissues. Compared with ileum, jejunum contained higher levels of lipids, GPC, choline, lactate and creatinine, but lower levels of amino acids and acetate. In addition, the age dependence of the biochemical composition of intestinal tissues from young rats (15, 36 days and 3-4 months old) was studied. In general, levels of lipids, lactate, taurine and creatinine were positively correlated with age while amino acids and GPC decreased in the older age group. This study will provide a metabolic reference for further studies assessing the metabolic consequences of nutrition, stress and gut microbiota on intestinal composition.     

Changes in the glycosylation pattern of prion protein in murine scrapie. Implications for the mechanism of neurodegeneration in prion diseases

In prion diseases, the normal prion protein (PrP(c)) undergoes a conformational change that results in the abnormal form, named scrapie prion protein (PrP(sc)). The visual system of rodents provides a relatively simple neuronal model in which the cell bodies of neurons are confined to the retina and the axons constitute the optic nerve. We investigated by Western blot the profile of PrP(c) in the optic nerve and retina of normal hamsters and mice. We found that in the optic nerve the amount of PrP(c) is significantly higher than in the retina. A less abundant non-glycosylated band was observed in retinas compared with the optic nerve and brain. Similar results were found in the gray and white matter from normal mice and hamsters. After stereotaxic injection of ME7 or 139A in the superior colliculus, a visual target area, the proportion and glycopattern of PrP changed in the retina and optic nerve throughout the course of the disease. Similar results were found in the gray and white matter at terminal stage of scrapie after injection of ME7 and 139A in the dorsal hippocampus. This is the first time that changes in the distribution and glycopattern of PrP have been described in an in vivo model of prion diseases.     

Etiology of acute diarrheas in children from the Lodz region. I. Occurrence of etiologic agents

The aim of this study was determination of the etiologic agents (bacterial, fungal or viral) of acute diarrheas in children from the ?ód? region, suffering from acute diarrhoea during the period from October 1998 to February 2001. Rotaviruses were detected by the latex test. Other microorganisms belonging to the Enterobacteriaceae, Pseudomonadaceae and Vibrionaceae families, as well as the genera Listeria, Campylobacter, Candida, Staphylococcus were cultured on standard or selective culture media according to the NDH recommendations and identification by means of API system. Acute diarrhea in 155 small children below 6 years of age from the ?ód? region were caused by rotaviruses (n = 42; 27%). Enteropathogenic strains of Escherichia coli (n = 25; 16.1%) occupied the third place after Salmonella bacteria (n = 30; 19.3%--second place). Among bacterial etiologic factors of diarrhea Campylobacter bacteria showed high frequency of occurrence (n = 22; 14.1%). The investigations enabled identification both the mixed infections (n = 25; 16.1%) and more rare etiologic agents of diarrhea. CONCLUSIONS: 1. Acute diarrhea in children from the region ?ód? were most frequently caused by rotaviruses; 2. Modern microbiological diagnostics of acute diarrhea in children should be multilateral, taking account of the mixed infections and expanding the routine search for bacteria of the genus Campylobacter.     

Optical properties of the adaxial and abaxial faces of leaves. Chlorophyll fluorescence, absorption and scattering coefficients.

Emission fluorescence spectra were obtained for the adaxial and abaxial faces of dicotyledonous (Ficus benjamina L., Ficus elastica, Gardenia jasminoides and Hedera helix) and monocotyledonous leaves (Gladiolus spp. and Dracaena cincta bicolor). After correction by light-re-absorption processes, using a previously published physical model, the adaxial faces of dicotyledons showed a fluorescence ratio Fred/Ffar-red rather lower than the respective values for the abaxial faces. Monocotyledons and shade-adapted-plants showed similar values for the corrected fluorescence ratio for both faces. Even when differences in experimental fluorescence emission from adaxial and abaxial leaves in dicotyledons are mostly due to light re-absorption processes, the residual dissimilarity found after application of the correction model would point to the fact that fluorescence re-absorption is not the only responsible for the observed disparity. It was concluded that light re-absorption processes does not account entirely for the differences in the experimental emission spectra between adaxial and abaxial leaves. Differences that remains still present after correction might be interpreted in terms of a different photosystem ratio (PSII/PSI). Experiments at low temperature sustained this hypothesis. In dicotyledons, light reflectance for adaxial leaves was found to be lower than for the abaxial ones. It was mainly due to an increase in the scattering coefficient for the lower leaf-side. The absorption coefficient values were slightly higher for the upper leaf-side. During senescence of Ficus benjamina leaves, the scattering coefficient increased for both the upper and lower leaf-sides. With senescence time the absorption coefficient spectra broadened while the corrected fluorescence ratio (Fred/Ffar-red) decreased for both faces. The results pointed to a preferential destruction of photosystem II relative to photosystem I during senescence.     

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

Background  

In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques.     

Epigenetic Alterations in Fanconi Anaemia: Role in Pathophysiology and Therapeutic Potential

Fanconi anaemia (FA) is an inherited disorder characterized by chromosomal instability. The phenotype is variable, which raises the possibility that it may be affected by other factors, such as epigenetic modifications. These play an important role in oncogenesis and may be pharmacologically manipulated. Our aim was to explore whether the epigenetic profiles in FA differ from non-FA individuals and whether these could be manipulated to alter the disease phenotype. We compared expression of epigenetic genes and DNA methylation profile of tumour suppressor genes between FA and normal samples. FA samples exhibited decreased expression levels of genes involved in epigenetic regulation and hypomethylation in the promoter regions of tumour suppressor genes. Treatment of FA cells with histone deacetylase inhibitor Vorinostat increased the expression of DNM3Tβ and reduced the levels of CIITA and HDAC9, PAK1, USP16, all involved in different aspects of epigenetic and immune regulation. Given the ability of Vorinostat to modulate epigenetic genes in FA patients, we investigated its functional effects on the FA phenotype. This was assessed by incubating FA cells with Vorinostat and quantifying chromosomal breaks induced by DNA cross-linking agents. Treatment of FA cells with Vorinostat resulted in a significant reduction of aberrant cells (81% on average). Our results suggest that epigenetic mechanisms may play a role in oncogenesis in FA. Epigenetic agents may be helpful in improving the phenotype of FA patients, potentially reducing tumour incidence in this population.