Alternative splicing and protein function

Background  

Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.     

Feedback equilibrium control during human standing

Equilibrium maintenance during standing in humans was investigated with a 3-joint (ankle, knee and hip) sagittal model of body movement. The experimental paradigm consisted of sudden perturbations of humans in quiet stance by backward displacements of the support platform. Data analysis was performed using eigenvectors of motion equation. The results supported three conclusions. First, independent feedback control of movements along eigenvectors (eigenmovements) can adequately describe human postural responses to stance perturbations. This conclusion is consistent with previous observations (Alexandrov et al., 2001b) that these same eigenmovements are also independently controlled in a feed-forward manner during voluntary upper-trunk bending. Second, independent feedback control of each eigenmovement is sufficient to provide its stability. Third, the feedback loop in each eigenmovement can be modeled as a linear visco-elastic spring with delay. Visco-elastic parameters and time-delay values result from the combined contribution of passive visco-elastic mechanisms and sensory systems of different modalities     

The PINE study: rationale and design of a randomised comparison of epidural injection of local anaesthetics and steroids versus care-as-usual to prevent postherpetic neuralgia in the elderly [ISRCTN32866390]

BACKGROUND: Postherpetic neuralgia (PHN) is by far the most common complication of herpes zoster (HZ) and one of the most intractable pain disorders. Since PHN is seen most often in the elderly, the number of patients with this disorder is expected to increase in our ageing society. PHN may last for months to years and has a high impact on the quality of life. The results of PHN treatment are rather disappointing. Epidural injection of local anaesthetics and steroids in the acute phase of HZ is a promising therapy for the prevention of PHN. Since randomised trials on the effectiveness of this intervention are lacking, the PINE (Prevention by epidural Injection of postherpetic Neuralgia in the Elderly) study was set up. The PINE study compares the effectiveness and cost-effectiveness of a single epidural injection of local anaesthetics and steroids during the acute phase of HZ with that of care-as-usual (i.e. antivirals and analgesics) in preventing PHN in elderly patients. METHODS / DESIGN: The PINE study is an open, multicenter clinical trial in which 550 elderly (age >/= 50 yr.) patients who consult their general practitioner in the acute phase of HZ (rash < 7 days) are randomised to one of the treatment groups. The primary clinical endpoint is the presence of HZ-related pain one month after the onset of the rash. Secondary endpoints include duration and severity of pain, re-interventions aiming to treat the existing pain, side effects, quality of life, and cost-effectiveness. CONCLUSION: The PINE study is aimed to quantify the (cost-) effectiveness of a single epidural injection during the acute phase of HZ on the prevention of PHN.     

Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase

Fifteen bacterial strains containing 1-aminocyclopropane-1-carboxylate (ACC) deaminase were isolated from the rhizoplane of pea (Pisum sativum L.) and Indian mustard (Brassica juncea L.) grown in different soils and a long-standing sewage sludge contaminated with heavy metals. The isolated strains were characterized and assigned to various genera and species, such as Pseudomonas brassicacearum, Pseudomonas marginalis, Pseudomonas oryzihabitans, Pseudomonas putida, Pseudomonas sp., Alcaligenes xylosoxidans, Alcaligenes sp., Variovorax paradoxus, Bacillus pumilus, and Rhodococcus sp. by determination of 16S rRNA gene sequences. The root elongation of Indian mustard and rape (Brassica napus var. oleifera L.) germinating seedlings was stimulated by inoculation with 8 and 13 isolated strains, respectively. The bacteria were tolerant to cadmium toxicity and stimulated root elongation of rape seedlings in the presence of 300 microM CdCl2 in the nutrient solution. The effect of ACC-utilising bacteria on root elongation correlated with the impact of aminoethoxyvinylglycine and silver ions, chemical inhibitors of ethylene biosynthesis. A significant improvement in the growth of rape caused by inoculation with certain selected strains was also observed in pot experiments, when the plants were cultivated in cadmium-supplemented soil. The biomass of pea cv. Sparkle and its ethylene sensitive mutant E2 (sym5), in particular, was increased through inoculation with certain strains of ACC-utilising bacteria in pot experiments in quartz sand culture. The beneficial effect of the bacteria on plant growth varied significantly depending on individual bacterial strains, plant genotype, and growth conditions. The results suggest that plant growth promoting rhizobacteria containing ACC deaminase are present in various soils and offer promise as a bacterial inoculum for improvement of plant growth, particularly under unfavourable environmental conditions.     

Divergent Evolution of Symbiotic Bacteria: Rhizobia of the Relic Legume <Emphasis Type="Italic">Vavilovia formosa</Emphasis> Form an Isolated Group within <Emphasis Type="Italic">Rhizobium leguminosarum</Emphasis> bv. <Emphasis Type="Italic">viciae</Emphasis>

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype.     

Can the presence of curved forms of the diatom Aulacoseira ambigua in the Nile (Egypt) and Vaal (South Africa) Rivers be ascribed to similar water quality conditions?

Spiral colonies of the diatom Aulacoseira ambigua were assigned the rank of forma (Aulacoseira ambigua f. japonica). This spiral-shaped, colonial, centric diatom has limited geographical distribution and is currently reported to occur in only a few countries in the world. In Africa this species was described for the first time from the Vaal River, South Africa, but recent research on the Nile River also revealed its presence in Egypt. Physical and chemical data on water quality in these two river systems were compared to determine whether the presence of this uncommon ‘phenoecodeme’ could be ascribed to similar environmental conditions. Results indicate that the rivers are dissimilar with regard to many variables, but both rivers provide turbid, warm and eutrophic waters with medium to high mineral content and it was concluded that these factors favour and sustain the growth of this curved form.     

Laboratory evaluation of certain natural compounds against the melon ladybird beetle,Epilachna chrysomelina F. attacking cucurbit plants

Neem Azal-T/S, Neudosan and Spruzit flüssig at different concentrations were evaluated against the second and fourth instar larvae of E. chrysomelina under laboratory conditions. In case of acute effects, the highest mortality was recorded when larvae were offered squash leaves treated with the highest concentration (2%) of Neem Azal-T/S, and the lowest mortality was, however recorded after treating them with the lowest concentration (0.25%). On the other hand, the second instar larvae were more susceptible to any compound at any concentration than the fourth instar one. One per cent Neudosan formulation showed the highest toxicity to both the 2nd and 4th instar larvae. As the concentration of this compound decreased the mortality percentage of treated larvae decreased to reach the minimum at the lowest concentration (0.25%). The same trend could be applied for Spruzit flüssig compound. When Neem Azal-T/S was compared with Neudosan, the later at any concentration was more toxic than the former. Generally, Neudosan and Spruzit flüssig seemed to be active against E. chrysomelina during the first three days after treatment, then, deterioration occurred among this compound. In case of latent effects, the duration of the treated fourth instar larvae of E. chrysomelina with any tested compound, was prolonged. An increase in the concentration caused prolongation of this period to reach the longest at the highest concentration. This prolongation, was more pronounced after Neem Azal-T/S treatment followed by Neudosan and Spruzit flüssig. The same trend could be applied for the duration of the pupal stage as being affected by the different concentrations of the tested compounds which were applied to the fourth instar larvae. However, adults of E. Chrysomelina treated as fourth instar larvae with high concentrations of Neem Azal-T/S showed some adult malformations. The sex ratios of adults produced from fourth instar larvae treated with different concentrations of the tested natural compounds were about 1?:?1, except for two cases; 1% Neudosan where the number of females were double the number of males and 0.5% Spruzit flüssig where the number of males were double the number of females. An increase in the concentration of any tested compound caused an obvious decrease in the percentage of emerged adults. The least emergence percentage was recorded in the case of Spruzit flüssig, followed by Neudosan and Neem Azal-T/S. Treating the fourth instar larvae with the different concentrations of the tested natural compounds significantly shortened the longevity of produced adults and decreased the fecundity.     

Presence of a novel 16S-23S rRNA gene intergenic spacer insert in Bradyrhizobium canariense strains

Seven slow-growing bacterial strains isolated from root nodules of yellow serradella (Ornithopus compressus) that originated from Asinara Island on North Western Sardinia in Italy were characterized by partial 16S rRNA gene and intergenic spacer (ITS) sequencing as well as amplified fragment length polymorphism (AFLP) genomic fingerprinting. The results indicated that the O. compressus isolates belong to the Bradyrhizobium canariense species. The analysis of ITS sequences divided the branch of B. canariense strains into two statistically separated groups (ITS clusters I and II). All the strains in ITS cluster I showed the presence of unique oligonucleotide insert TTAGAGACTTAGGTTTCTK. This insert was neither found in other described species of the family Rhizobiaceae nor in any other bacterial families and can be used as a natural and high selective genetic marker for ITS cluster I of B. canariense strains. ITS grouping of O. compressus isolates was supported by the unweighted pair group method with arithmetic averages cluster analysis of their AFLP patterns, suggesting that the strains of ITS cluster II were genetically closer to each other than to isolates from the ITS cluster I. A taxonomic importance is supposed of the revealed 19 bp ITS insert for an intraspecific division within high heterogeneous B. canariense species.     

Intraspecific variability of cadmium tolerance in hydroponically grown Indian mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis> (L.) Czern.) seedlings

Indian mustard (Brassica juncea (L.) Czern.) is a promising plant species for phytoremediation of heavy metal polluted soils. However, genetic variability of metal tolerance in Indian mustard has not been studied. We evaluated intraspecific variation of Cd tolerance of this species by screening 64 varieties in hydroponics. The tolerance index (TI), calculated as percentage of root length of Cd-treated (7 μM CdCl₂) over untreated control seedlings, significantly varied from 34 to 79%, depending on the variety. Information about phenotypic and economic traits of the studied varieties was taken from the literature and subjected to a cluster analysis. The varieties were distributed into three clusters and most of the varieties characterized by the highest TI values (TI > 65%) were grouped together in one cluster. Moreover, TI negatively correlated with the following characteristics: yellow seed colour (R = −0.35, P = 0.005), total oil content (R = −0.33, P = 0.008), oleic acid (R = −0.25, P = 0.047) and linoleic acid (R = −0.36, P = 0.004) contents in seeds. The results showed the presence of significant variability for Cd tolerance in Indian mustard. The knowledge about correlations between Cd tolerance and phenotypic characteristics of plants might be utilized for rapid selection of cultivars to be used for phytoremediation of polluted soils.     

Impact of folic acid fortification on global DNA methylation and one-carbon biomarkers in the Women's Health Initiative Observational Study cohort

DNA methylation is an epigenetic mechanism that regulates gene expression and can be modified by one-carbon nutrients. The objective of this study was to investigate the impact of folic acid (FA) fortification of the US food supply on leukocyte global DNA methylation and the relationship between DNA methylation, red blood cell (RBC) folate, and other one-carbon biomarkers among postmenopausal women enrolled in the Women's Health Initiative Observational Study. We selected 408 women from the highest and lowest tertiles of RBC folate distribution matching on age and timing of the baseline blood draw, which spanned the pre- (1994–1995), peri- (1996–1997), or post-fortification (1998) periods. Global DNA methylation was assessed by liquid chromatography-tandem mass spectrometry and expressed as a percentage of total cytosine. We observed an interaction (P = 0.02) between fortification period and RBC folate in relation to DNA methylation. Women with higher (vs. lower) RBC folate had higher mean DNA methylation (5.12 vs. 4.99%; P = 0.05) in the pre-fortification period, but lower (4.95 vs. 5.16%; P = 0.03) DNA methylation in the post-fortification period. We also observed significant correlations between one-carbon biomarkers and DNA methylation in the pre-fortification period, but not in the peri- or post-fortification period. The correlation between plasma homocysteine and DNA methylation was reversed from an inverse relationship during the pre-fortification period to a positive relationship during the post-fortification period. Our data suggest that (1) during FA fortification, higher RBC folate status is associated with a reduction in leukocyte global DNA methylation among postmenopausal women and; (2) the relationship between one-carbon biomarkers and global DNA methylation is dependent on folate availability.