A detailed thermodynamic analysis of ras/effector complex interfaces

Many cellular functions are based on the interaction and crosstalk of various signaling proteins. Among these, members of the Ras family of small GTP-binding proteins are important for communicating signals into different pathways. In order to answer the question of how binding affinity and specificity is achieved, we analyzed binding energetics on the molecular level, with reference to the available structural data. The interaction of two members of the Ras subfamily with two different effector proteins, namely Raf and RalGDS, were investigated using isothermal titration calorimetry and a fluorescence-based method. Experiments with alanine mutants, located in the complex interfaces, yielded an energy map for the contact areas of the Ras/effector complexes, which could be differentiated into enthalpy and entropy contributions. In addition, by using double mutant cycle analysis, we probed the energetic contribution of selected pairs of amino acid residues. The resulting energy landscapes of the Ras/effector interface areas show a highly different topology when comparing the two effectors, Raf and RalGDS, demonstrating the specificity of the respective interactions. Particularly, we observe a high degree of compensating effects between enthalpy and entropy; differences between these components are much greater than the overall free energy differences. This is observed also when using the software FOLD-X to predict the effect of point mutations on the crystal structures of the different complexes. Prediction of the free energy changes shows a very good correlation with the experimentally observed energies. Furthermore, in line with experimental data, energy decomposition indicates that many different components of large magnitude counteract each other to produce a smaller change in overall free energy, illustrating the importance of long-range electrostatic forces in complex formation.     

单链胰岛素前体在酵母中的分泌表达及其转变成人胰岛素

将化学合成的单链猪胰岛素前体(PIP)基因和用聚合酶链反应得到的α交配因子前导顺序(αMFL)基因插入质粒pVT102-U的醇脱氢酶基因ADH1的启动子和3’终止顺序之间而生成质粒pVT102-U/αMFL-PIP.被pVT102-U/αMFL-PIP转化的酵母(Saccharomyces cerevistae)可表达单链前体并分泌到培养基中.前体在纯化后可通过胰蛋白酶的转肽作用转变成人胰岛素.纯化的人胰岛素具有全部活力并可结晶.人胰岛素的总收率为每升培养液25mg.     

Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences

The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rodent species (representing seven families) were analyzed using phenetic, parsimony, and maximum-likelihood methods of phylogenetic inference; the rabbit, Oryctolagus cuniculus (Order Lagomorpha), and cow, Bos taurus (Order Artiodactyla), were used as outgroups. Investigation of 714 base pairs of the protein-coding cytochrome b gene indicate strong base bias at the third codon position with significant rate heterogeneity evident between the three structural domains of this gene. Similar analyses conducted on 816 base pairs of the 12S rRNA gene revealed a transversion bias in the loop sections of all taxa. The cytochrome b gene sequences proved useful in resolving associations between closely related species but failed to produce consistent tree topologies at the family level. In contrast, phylogenetic analysis of the 12S rRNA gene resulted in strong support for the clustering of Pedetidae/Heteromyidae/Geomyidae and Muridae in one clade to the exclusion of the Hystricidae/Thryonomyidae and Sciuridae, a finding which is concordant with studies of rodent fetal membranes as well as reproductive and other anatomical features.      

Nucleotide sequence of the Synechococcus sp. PCC7942 branching enzyme gene (glgB): expression in Bacillus subtilis

The nucleotide sequence of the Synechococcus sp. PCC7942 glgB gene has been determined. The gene contains a single open reading frame (ORF) of 2322 bp encoding a polypeptide of 774 amino acids (aa) with an Mr of 89,206. Extensive sequence similarity exists between the deduced aa sequence of the Synechococcus sp. glgB gene product and that of the Escherichia coli branching enzyme in the middle portions of the proteins (62% identical aa). In contrast, the N-terminal portions shared little homology. The sequenced region which follows glgB contains an ORF encoding 79 aa of the N terminus of a polypeptide that shares extensive sequence similarity (41% identical aa) with human and rat uroporphyrinogen decarboxylase. This suggests that the region downstream from glgB contains the hemE gene and, therefore, that the organization of genes involved in glycogen biosynthesis in Synechococcus sp. is different from that described for E. coli. A fusion gene was constructed between the 5' end of the Bacillus licheniformis penP gene and the Synechococcus sp. glgB gene. The fusion gene was efficiently expressed in the Gram+ micro-organism Bacillus subtilis and specified a branching enzyme with an optimal temperature for activity similar to the wild-type enzyme.     

The succinate dehydrogenase assembly factor,SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria

The activity of the respiratory enzyme fumarate reductase (FRD) is dependent on the covalent attachment of the redox cofactor flavin adenine dinucleotide (FAD). We demonstrate that the FAD assembly factor SdhE, which flavinylates and activates the respiratory enzyme succinate dehydrogenase (SDH), is also required for the complete activation and flavinylation of FRD. SdhE interacted with, and flavinylated, the flavoprotein subunit FrdA, whilst mutations in a conserved RGxxE motif impaired the complete flavinylation and activation of FRD. These results are of widespread relevance because SDH and FRD play an important role in cellular energetics and are required for virulence in many important bacterial pathogens.     

Using the salinity preferences of benthic macroinvertebrates to classify running waters in brackish marshes in Germany

Marshland streams along European coastlines are typically located in the transition zone from limnic to brackish conditions. They constitute a distinct and important stream type within the German stream typology, which is predominantly characterised by tidal influence and salinity. According to the Water Framework Directive (WFD) the basis for the abiotic classification of European transitional and coastal waters is the ‘Venice System’ (Weber, M., 2005. Ergebnisse der Bestandsaufnahme 2004 zur Umsetzung der europäischen Wasserrahmenrichtlinie (WRRL) in den Küstengewässern Mecklenburg-Vorpommerns. Rostocker Meeresbiol. Beitr. 14, 7–15). However, the extreme spatial and temporal variability in salinity and tidal influence determines and controls the macroinvertebrate communities of marshland river and stream ecosystems and hampers the application of the ‘Venice System’. Earlier, purely biotic classifications of brackish waters typically classify different brackish water zones, each with a specific macroinvertebrate community, and often yield unsatisfactory results due to the extensively dynamic abiotic factors found in marshland streams. In practice, the permanent impact of tidal charge means that stable salinity zones do not exist. This effect can than be intensified by freshwater discharges after heavy rainfall or high tides in combination with strong winds that hinder discharge into the open sea. To overcome the restricted applicability of abiotic and biotic classification systems, we present a scoring system for marshland streams that combines the abiotic salinity classes of the ‘Venice System’ with the salinity preferences of the macroinvertebrate community. This proposal is based on literature data for macroinvertebrate salinity tolerances and preferences. According to the 137 references that were evaluated, 151 macroinvertebrate taxa were classified into six salinity groups. In a second step, we applied this scoring scheme to empirical data from two official quality assessment surveys. These surveys had been carried out in ten estuary tributaries of German marshland areas in Lower Saxony and Schleswig-Holstein in order to implement the WFD. Applying the scoring system to these data revealed a clear (and expected) gradient that was not expressed in the abiotic data. Thus we conclude that the biotic salinity preferences of benthic macroinvertebrates are a useful baseline metric for the ecological assessment of marshland streams and other transitional waters. Regional revision and adaptation of taxonomic salinity preferences would broaden the applicability of this assessment to transitional waters worldwide.     

Tomato yellow leaf curl viruses: ménage à trois between the virus complex,the plant and the whitefly vector

Tomato yellow leaf curl disease (TYLCD) is one of the most devastating viral diseases affecting tomato crops in tropical, subtropical and temperate regions of the world. Here, we focus on the interactions through recombination between the different begomovirus species causing TYLCD, provide an overview of the interactions with the cellular genes involved in viral replication, and highlight recent progress on the relationships between these viruses and their vector, the whitefly Bemisia tabaci. Taxonomy: The tomato yellow leaf curl virus‐like viruses (TYLCVs) are a complex of begomoviruses (family Geminiviridae, genus Begomovirus) including 10 accepted species: Tomato yellow leaf curl Axarquia virus (TYLCAxV), Tomato yellow leaf curl China virus (TYLCCNV), Tomato yellow leaf curl Guangdong virus (TYLCGuV), Tomato yellow leaf curl Indonesia virus (TYLCIDV), Tomato yellow leaf curl Kanchanaburi virus (TYLVKaV), Tomato yellow leaf curl Malaga virus (TYLCMalV), Tomato yellow leaf curl Mali virus (TYLCMLV), Tomato yellow leaf curl Sardinia virus (TYLCSV), Tomato yellow leaf curl Thailand virus (TYLCTHV), Tomato yellow leaf curl Vietnam virus (TYLCVNV) and Tomato yellow leaf curl virus(TYLCV). We follow the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV), the most important of which is an 89% nucleotide identity threshold between full‐length DNA‐A component nucleotide sequences for begomovirus species. Strains of a species are defined by a 93% nucleotide identity threshold. Host range: The primary host of TYLCVs is tomato (Solanum lycopersicum), but they can also naturally infect other crops [common bean (Phaseolus vulgaris), sweet pepper (Capsicum annuum), chilli pepper (C. chinense) and tobacco (Nicotiana tabacum)], a number of ornamentals [petunia (Petunia×hybrida) and lisianthus (Eustoma grandiflora)], as well as common weeds (Solanum nigrum and Datura stramonium). TYLCVs also infect the experimental host Nicotiana benthamiana. Disease symptoms: Infected tomato plants are stunted or dwarfed, with leaflets rolled upwards and inwards; young leaves are slightly chlorotic; in recently infected plants, fruits might not be produced or, if produced, are small and unmarketable. In common bean, some TYLCVs produce the bean leaf crumple disease, with thickening, epinasty, crumpling, blade reduction and upward curling of leaves, as well as abnormal shoot proliferation and internode reduction; the very small leaves result in a bushy appearance.     

Pexophagy: autophagic degradation of peroxisomes

The abundance of peroxisomes within a cell can rapidly decrease by selective autophagic degradation (also designated pexophagy). Studies in yeast species have shown that at least two modes of peroxisome degradation are employed, namely macropexophagy and micropexophagy. During macropexophagy, peroxisomes are individually sequestered by membranes, thus forming a pexophagosome. This structure fuses with the vacuolar membrane, resulting in exposure of the incorporated peroxisome to vacuolar hydrolases. During micropexophagy, a cluster of peroxisomes is enclosed by vacuolar membrane protrusions and/or segmented vacuoles as well as a newly formed membrane structure, the micropexophagy-specific membrane apparatus (MIPA), which mediates the enclosement of the vacuolar membrane. Subsequently, the engulfed peroxisome cluster is degraded. This review discusses the current state of knowledge of pexophagy with emphasis on studies on methylotrophic yeast species.     

The co-distribution of Plasmodium falciparum and hookworm among African schoolchildren

Background

On the island of Bioko (Equatorial Guinea), insecticide-treated nets (ITNs) have been the main tool used to control malaria over the last 13 years. In 2004, started an indoor residual spraying (IRS) campaign to control malaria. The purpose of this study is to asses the impact of the two control strategies on the island of Bioko (Equatorial Guinea), with regards to Plasmodium infection and anaemia in the children under five years of age.

Methods

Two transversal studies, the first one prior to the start of the IRS campaign and the second one year later. Sampling was carried out by stratified clusters. Malaria infection was measured by means of thick and thin film, and the packed cell volume (PCV) percentage. Data related to ITN use and information regarding IRS were collected. The Pearson's chi-square and logistic regression statistical tests were used to calculate odds ratios (OR)

Results

In the first survey, 168 children were sampled and 433 children in the second one. The prevalence of infection was 40% in 2004, and significantly lower at 21.7% in 2005. PCV was 41% and 39%, respectively. 58% of the children surveyed in 2004 and 44.3% in 2005 had slept under an ITN. 78% of the dwellings studied in 2005 had been sprayed. In the 2005 survey, sleeping without a mosquito net meant a risk of infection 3 times greater than sleeping protected with a net hanged correctly and with no holes (p < 0.05).

Conclusion

IRS and ITNs have proven to be effective control strategies on the island of Bioko. The choice of one or other strategy is, above all, a question of operational feasibility and availability of local resources.