Analysis of the C-Terminal Membrane Anchor Domains of Hepatitis C Virus Glycoproteins E1 and E2: toward a Topological Model

The hepatitis C virus (HCV) glycoproteins E1 and E2 should be anchored in the viral membrane by their C-terminal domains. During synthesis, they are translocated to the endoplasmic reticulum (ER) lumen where they remain. The 31 C-terminal residues of the E1 protein and the 29 C-terminal residues of the E2 protein are implicated in the ER retention. Moreover, the E1 and E2 C termini are implicated in E1-E2 heterodimerization. We studied the E1 and E2 C-terminal sequences of 25 HCV strains in silico using molecular modeling techniques. We conclude that both C-terminal domains should adopt a similar and peculiar configuration: one amphipathic alpha-helix followed by a pair of transmembrane beta-strands. Several three-dimensional (3-D) models were generated. After energy minimization, their ability to interact with membranes was studied using the molecular hydrophobicity potentials calculation and the IMPALA procedure. The latter simulates interactions with a membrane by a Monte Carlo minimization of energy. These methods suggest that the beta-hairpins could anchor the glycoproteins in the ER membrane at least transiently. Anchoring could be stabilized by the adsorption of the nearby amphipathic alpha-helices at the membrane surface. The 3-D models correlate with experimental results which indicate that the E1-E2 transmembrane domains are involved in the heterodimerization and have ER retention properties.     

Determination of the biological diatom index (IBD NF T 90–354): results of an intercomparison exercise

A diatom intercomparison exercise on sampling, slide preparation, countsand identification has been carried out in September 1999 with 24French-speaking diatomists on the River Loup (Alpes Maritimes, France). Fewoperators strictly respected the standard, especially for the number ofindividuals to be counted. It has however been demonstrated this had a very lowimpact on the index value and that old counts can be used for indexcalculation,if there are at least 300 frustules or valves. Counts higher than 400 did notlead to a better precision. The total variability largely depended on theoperator and was distributed unevenly between sampling, which appears to be acritical stage, slide preparation and counting. For those who strictlyrespectedthe standard procedure, the natural variability can be estimated to about oneunit value of the Biological Diatom Index. This intra-operator variability canbe considered as very low, as the IBD scale is from 0 to 20, and notsignificantin assessing water quality. Despite this, the inter-operator variability isgreater. When comparing operators' results, after excluding those who did notrespect the standard requirements, the main source of variability is due tomisidentifications, especially for small Achnanthes(A. minutissima and A. biasolettiana)and Cocconeis (C. placentula var.placentula, var. euglypta and var.lineata). Intercomparison exercises, internet exchangesforchecking and reference material collections should be encouraged both tosatisfythe internal and external quality controls and to acquaint biologists with theimportance of field and laboratory protocols, as well as to allow progress indiatom identification.     

Distribution of phytoplankton pigments in nine European estuaries and implications for an estuarine typology

Phytoplankton pigments were studied by LiquidChromatography (HPLC) in nine West Europeanestuaries. Three estuaries, i.e. the Rhine,Scheldt and the Gironde were sampled four timesto cover the different seasons, whereas theother six estuaries were sampled once. Pigmentdistributions in estuaries reflect bothriverine inputs as well as autochthonousblooms. Fucoxanthin was the most commonaccessory photosynthetic pigment showing thatDiatoms were the most common group in thestudied estuaries and were particularlydominant during autumn and winter. In the veryturbid Gironde estuary, degradation processeswere predominant between salinities 1 and 20,while Diatoms, Dinoflagellates and Cryptophytesbloomed above 20 salinity during spring andsummer. This contrasted with the highlyeutrophic but less turbid Scheldt, wherephytoplanktonic blooms occurred at lowsalinities close to the city of Antwerp. In theScheldt, we observed both a tenfold fluctuationof phytoplankton biomass and a fluctuatingpigment diversity index. In contrast,chlorophyll a was always low in theGironde, but we observed large variations ofpigment diversity among samplings duringdifferent seasons. Distribution of pheopigmentsshowed that the maximum turbidity zone (MTZ)was a highly reactive region for heterotrophicphytoplankton degradation. The Scheldt and theThames were the most anthropogenic influencedestuaries contrasting with the Gironde estuarythat has a less urbanised watershed. Anestuarine typology is proposed based on threeclusters emerging from a correspondenceanalysis of pigment variables and variablescharacterising the anthropogenic impact andphysical forcing.     

Hemoglobin Porto Alegre forms a tetramer of tetramers superstructure

The effects of the mutation beta9(A6)Ser --> Cys on the interactions between the human hemoglobin molecules were investigated, and comparisons were made with other variants having an additional cysteine residue. In hemoglobin Porto Alegre (PA), the beta9 mutation induces polymerization by forming interchain disulfide bonds via the extra cysteine. The hemolysate from a heterozygote was separated by gel filtration into a tetrameric fraction and a higher-molecular-weight oligomeric fraction (30%). Reversed-phase high-performance liquid chromatography and electrospray ionization mass spectrometry (ESI-MS) under denaturing conditions showed that the tetrameric fraction contained only normal alpha- and beta-chains, whereas the oligomeric fraction contained only normal alpha-chain and disulfide-linked beta(PA) dimer. Under native conditions, ESI-MS of the oligomeric fraction revealed a principal complex of mass 258,400 Da corresponding to a tetramer of tetramers, and 10% of minor components. Transmission electron microscopy corroborated this structure by showing four spheres of 140 A diameter surrounding a central cavity. Equilibrium experiments on the oligomer at different concentrations, using gel filtration and dimer exchange experiments with metHbA-CN, showed that the tetramer of tetramers dissociates into smaller species, probably by breaking the dimer-dimer allosteric interface. None of the other variants investigated formed such a large oligomer.     

Scaling of Soaring Seabirds and Implications for Flight Abilities of Giant Pterosaurs

The flight ability of animals is restricted by the scaling effects imposed by physical and physiological factors. In comparisons of the power available from muscle and the mechanical power required to fly, it is predicted that the margin between the powers should decrease with body size and that flying animals have a maximum body size. However, predicting the absolute value of this upper limit has proven difficult because wing morphology and flight styles varies among species. Albatrosses and petrels have long, narrow, aerodynamically efficient wings and are considered soaring birds. Here, using animal-borne accelerometers, we show that soaring seabirds have two modes of flapping frequencies under natural conditions: vigorous flapping during takeoff and sporadic flapping during cruising flight. In these species, high and low flapping frequencies were found to scale with body mass (mass ^−0.30 and mass ^−0.18) in a manner similar to the predictions from biomechanical flight models (mass ^−1/3 and mass ^−1/6). These scaling relationships predicted that the maximum limits on the body size of soaring animals are a body mass of 41 kg and a wingspan of 5.1 m. Albatross-like animals larger than the limit will not be able to flap fast enough to stay aloft under unfavourable wind conditions. Our result therefore casts doubt on the flying ability of large, extinct pterosaurs. The largest extant soarer, the wandering albatross, weighs about 12 kg, which might be a pragmatic limit to maintain a safety margin for sustainable flight and to survive in a variable environment.     

Diversity and zoogeography of the fairy shrimps (Branchiopoda: Anostraca) on the Indian subcontinent

The Indian subcontinent has a specific biogeographical history, but has remained understudied with respect to invertebrates like the Anostraca. In this study, we discuss the anostracan diversity and zoogeography on the subcontinent. We collected all pertinent literature and considered nineteen bioclimatic variables along with altitude and its terrestrial ecoregions. The study area was overlaid with 10,000 km² grids, and five hundred random GIS data points per grid were extracted for analysis besides the species locality data. Species richness estimators predict at least 3–4 more species to the existing list of 19 species. The beta diversity measure βsim reveals two zoogeographic “zones,” viz., a Northern (NZ) zone and the rest of the subcontinent (RS) comprising the Central (CZ) and South (SZ) zones by Unweighted Pair-Group Method using arithmetic averages clustering and Analysis of Similarity. Complementarity index shows that no fauna is shared between NZ and RS, while CZ and SZ share 50% of the species. Principal Component analysis shows that NZ and RS differ somewhat from one another climatically. NZ and RS have different ecoregions with montane and temperate grasslands commonly observed in NZ while the latter comprising tropical forests, implying differences in soil geochemistry which is crucial for anostracan distribution.     

Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis

Super-enhancers are clusters of enhancers associated with cell lineage. They can be powerful gene-regulators and may be useful in cell-type specific viral-vector development. Here, we have screened for endothelial super-enhancers and identified an enhancer from within a cluster that conferred 5–70-fold increase in transgene expression. Importantly, CRISPR/Cas9 deletion of enhancers demonstrated regulation of ADAMTS18, corresponding to evidence of chromatin contacts between these genomic regions. Cell division-related pathways were primarily affected by the enhancer deletions, which correlated with significant reduction in cell proliferation. Furthermore, we observed changes in angiogenesis-related genes consistent with the endothelial specificity of this SE. Indeed, deletion of the enhancers affected tube formation, resulting in reduced or shortened sprouts. The super-enhancer angiogenic role is at least partly due to its regulation of ADAMTS18, as siRNA knockdown of ADAMTS18 resulted in significantly shortened endothelial sprouts. Hence, functional characterization of a novel endothelial super-enhancer has revealed substantial downstream effects from single enhancer deletions and led to the discovery of the cis-target gene ADAMTS18 and its role in endothelial function.     

Modelling facilitation or competition within a root system: importance of the overlap of root depletion and accumulation zones

Background and aims

Relevant soil properties and nutrient distributions influencing crop root growth might be different under no-till (NT) and mouldboard plough (MP) management. The possible different root systems within different managements might have key impact on crop nutrient uptake and consequently crop production. Our objective was to assess the long-term combined effects of tillage and phosphorus (P) fertilization on corn (Zea mays L.) root distribution and morphology.

Methods

Corn root and soil samples were collected during the silking stage at five depths (0–5, 5–10, 10–20, 20–30 and 30–40 cm) and three horizontal distances perpendicular to the corn row (5, 15 and 25 cm) under MP and NT with three P fertilizations (0, 17.5, and 35 kg P ha^?1) for a long-term (22 years) experiment in eastern Canada. Root morphology and soil properties were determined.

Results

NT practice decreased corn root biomass by ?26 % compared to MP, mainly by decreasing the primary and secondary roots. Additionally, corn roots in NT tend to be more expansive on the surface layer with higher root length and surface densities for the depth of 0–5 cm at two sampling distances of 15 and 25 cm. The 35 kg P ha^?1 rate increased the root biomass by 26 and 41 % compared to the 0 and 17.5 kg P ha^?1 rates.

Conclusions

No-tillage practice and low rates of P fertilization reduce corn roots. This is probably caused by the weed competition in NT and the continued downward P status with low P rates over 22 years.