Strain-specific differences in <Emphasis Type="Italic">Neisseria gonorrhoeae</Emphasis> associated with the phase variable gene repertoire

Background  

There are several differences associated with the behaviour of the four main experimental Neisseria gonorrhoeae strains, FA1090, FA19, MS11, and F62. Although there is data concerning the gene complements of these strains, the reasons for the behavioural differences are currently unknown. Phase variation is a mechanism that occurs commonly within the Neisseria spp. and leads to switching of genes ON and OFF. This mechanism may provide a means for strains to express different combinations of genes, and differences in the strain-specific repertoire of phase variable genes may underlie the strain differences.     

Seed germination temperatures of eight Mexican Agave species with economic importance

The genetic diversity of Agave plants is threatened by clonal commercial reproduction and climatic change. Sexual reproduction is uncommon and research on seed germination is scarce. The present study evaluated the seed germination of Agave lechuguilla, Agave striata, Agave americana var. marginata, Agave asperrima, Agave cupreata, Agave duranguesis, Agave angustifolia ssp. tequilana and Agave salmiana at constant temperatures (10, 15, 20, 25, 30, 35 and 40°C). Initial imbibition (after the first 12 h) was significantly variable among species, positively correlated with seed weight (r = 0.6560, P < 0.001) and increased with temperature (from 35% at 10°C to 66% at 40°C). Temperature affected maximum imbibition (83–150%) for A. asperrima, A. lechuguilla, A. salmiana and A. striata; other species averaged 110%. Most germination kinetics best fitted a logistic model, whereas only a few treatments fit a Weibull model. The time to germination onset diminished (P < 0.05) from 125–173 h at 15°C to 68–84 h at 25°C, and then ascended to 84–196 h at 35°C. The mean germination rate and seed germination percentage after 312 h peaked at 25°C (0.50–0.95% seeds/h and 85–99%, respectively) and fell (P < 0.05) to near zero at 10 and 40°C. Temperatures of 10, 35 and 40°C were partially lethal to A. asperrima, A. duranguensis and A. salmiana seeds. The time to germination onset, seed germination percentage after 312 h and mean germination rate are best described by a Gaussian distribution, with its optimum at approximately 25°C. Thus, optimum temperatures are related to the ecological characteristics of each species area.     

Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements.

Background  

There are four widely used experimental strains of N. gonorrhoeae, one of which has been sequenced and used as the basis for the construction of a multi-strain, mutli-species pan-neisserial microarray. Although the N. gonorrhoeae population structure is thought to be less diverse than N. meningitidis, there are some recognized gene-complement differences between strains, including the 59 genes of the Gonococcal Genetic Island. In this study we have investigated the three experimental strains that have not been sequenced to determine the extent and nature of their similarities and differences.     

莱茵衣藻Nfr-4突变株中类胡萝卜素含量的变化及其对藻生长的影响

文章对相同条件下培养的莱茵衣藻野生型CC-137和八氢番茄红素脱氢酶(phytoene desaturase,PDS)基因突变株Nfr-4的生长进行分析;并用反相高效液相色谱分析总有色类胡萝卜素以及叶绿素含量变化,结果表明两者生长的差异明显;Nfr-4突变株的单细胞叶绿素和总有色类胡萝卜素含量高于野生型CC-137的。     

A high level interface to SCOP and ASTRAL implemented in Python

Background  

Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources.     

Genetic variability in the complete mitochondrial control region of the Eurasian otter (Lutra lutra) in the Iberian Peninsula

Sequencing of the complete mitochondrial DNA control region from 31 samples of the Eurasian otter, Lutra lutra , enabled us to establish the length and structure of this fragment, as well as to describe, for the first time, the RS3 repetitive region located at the 3' end. In addition, genetic variability of the 5' end was examined in 63 individuals, 57 of which were wild otters from the Iberian Peninsula and six captive reared otters. This analysis resulted in extremely low variability. All the samples from the Iberian Peninsula share a single haplotype, Lut 1, the most common haplotype in Europe. Captive otters showed two haplotypes: Lut 3, which has been described in wild otters from eastern Germany, and Lut 6, an haplotype not described to date. Higher variability was observed in the repetitive RS3 region. The tandem repeat was composed of an array of ten repeat units of 22 bp with differences in the repetitive motifs that differed in the arrays of different specimens. In total, 20 different haplotypes from 31 individuals were found. However, the geographical distribution of these haplotypes did not generate a phylogeographical signal. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 397–403.     

Phloem flow and sugar transport in Ricinus communis L. is inhibited under anoxic conditions of shoot or roots

Anoxic conditions should hamper the transport of sugar in the phloem, as this is an active process. The canopy is a carbohydrate source and the roots are carbohydrate sinks. By fumigating the shoot with N₂ or flooding the rhizosphere, anoxic conditions in the source or sink, respectively, were induced. Volume flow, velocity, conducting area and stationary water of the phloem were assessed by non‐invasive magnetic resonance imaging (MRI) flowmetry. Carbohydrates and δ¹³C in leaves, roots and phloem saps were determined. Following flooding, volume flow and conducting area of the phloem declined and sugar concentrations in leaves and in phloem saps slightly increased. Oligosaccharides appeared in phloem saps and after 3 d, carbon transport was reduced to 77%. Additionally, the xylem flow declined and showed finally no daily rhythm. Anoxia of the shoot resulted within minutes in a reduction of volume flow, conductive area and sucrose in the phloem sap decreased. Sugar transport dropped to below 40% by the end of the N₂ treatment. However, volume flow and phloem sap sugar tended to recover during the N₂ treatment. Both anoxia treatments hampered sugar transport. The flow velocity remained about constant, although phloem sap sugar concentration changed during treatments. Apparently, stored starch was remobilized under anoxia.     

Reduced glomerular filtration rate, inflammation and HDL cholesterol as main determinants of superoxide production in non-dialysis chronic kidney disease patients

Enhanced oxidative stress partly resulting from an over-production of superoxide anion (O(2)(?-)) represents a novel and particular risk factor in chronic kidney disease (CKD) patients. This study was therefore designed to evaluate O(2)(?-) determinants in this population. O(2)(?-) production was evaluated using chemiluminescence method in 136 CKD patients (79M/57F, median age: 69.5 [27.4-94.6]). Renal function (evaluated by the glomerular filtration rate using modification of diet in renal disease (MDRD)), inflammation, lipids, nutritional and bone mineral as well as clinical parameters were evaluated. Potential relationships between O(2)(?-) and these clinico-biological parameters were investigated to identify main determinants of such a pathological process. Enhanced O(2)(?-) production has been observed at the pre-dialysis phase: stages 4 and 5 of CKD (p = 0.0065). In multivariate analysis, low eGFR (MDRD <30 mL/min/1.73 m(2); p = 0.046), high fibrinogen (≥3.7 g/L; p = 0.044) and abnormal HDL cholesterol (<1.42 mmol/L and ≥ 1.75 mmol/L; p = 0.042) were the main determinants of O(2)(?-) production in CKD patients.     

Geographic variations of seasonality and coexistence in communities: The role of diversity and climate

One of the most conspicuous and widely analyzed patterns in ecology is the latitudinal gradient in species richness. Over the 200 years since its recognition, several hypotheses have accumulated in order to account for spatial variations in diversity. Geographic variations in seasonality have been repeatedly proposed as a determinant of community richness. However, the geographic structure of community seasonality has not yet been analyzed. In the present work we evaluated three hypotheses that account for variations in the temporal structuring of communities: first, environmental seasonality determines community seasonality; second, community richness determines its degree of structuring; and third, the presence of an increase in species segregation with latitude, reflected in a pattern of species negative co‐occurrence. The hypotheses were evaluated using path analysis on 29 amphibian communities from South America, connecting latitude, environmental conditions, diversity, seasonality, and coexistence structure – nestedness and negative co‐occurrence – within communities. Latitude positively affects community seasonality through an increase in temperature seasonality, but a weak negative direct effect suggests that other variables not considered in the model – such as the strength of biotic interactions – could also be involved. Both latitude and diversity (directly and indirectly) determine an increase in negative co‐occurrence and nestedness. This suggests that groups of species that are mutually nested in time are internally segregated. Further, the strength of this structure is determined by community diversity and latitude. Temporal structuring of a community is associated with latitude and diversity, pointing to the existence of a systematic change in community organization far beyond, but probably interrelated, with the recognized latitudinal trend in richness. The available information and analysis supported the three hypotheses evaluated.