Improving the quality of protein structure models by selecting from alignment alternatives

Background  

In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection.     

FRASS: the web-server for RNA structural comparison

Background  

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.     

Vegetation cover regulates the quantity,quality and temporal dynamics of dissolved organic carbon and nitrogen in Antarctic soils

Populations of the two native Antarctic vascular plant species (Deschampsia antarctica and Colobanthus quitensis) have expanded rapidly in recent decades, yet little is known about the effects of these expansions on soil nutrient cycling. We measured the concentrations of dissolved organic carbon (DOC) and nitrogen (DON), amino acids and inorganic N in soils under these two vascular plant species, and under mosses and lichens, over a growing season at Signy Island in the maritime Antarctic. We recorded higher concentrations of nitrate, total dissolved nitrogen, DOC, DON and free amino acids in soil under D. antarctica and C. quitensis than in lichen or moss dominated soils. Each vegetation cover gave a unique profile of individual free amino acids in soil solution. Significant interactions between soil type and time were found for free amino acid concentrations and C/N ratios, indicating that vascular plants significantly change the temporal dynamics of N mineralization and immobilization. We conclude that D. antarctica and C. quitensis exert a significant influence over C and N cycling in the maritime Antarctic, and that their recent population expansion will have led to significant changes in the amount, type and rate of organic C and N cycling in soil.     

Observations of the thermal environment on Red Sea platform reefs: a heat budget analysis

Hydrographic measurements were collected on nine offshore reef platforms in the eastern Red Sea shelf region, north of Jeddah, Saudi Arabia. The data were analyzed for spatial and temporal patterns of temperature variation, and a simple heat budget analysis was performed with the goal of advancing our understanding of the physical processes that control temperature variability on the reef. In 2009 and 2010, temperature variability on Red Sea reef platforms was dominated by diurnal variability. The daily temperature range on the reefs, at times, exceeded 5°C—as large as the annual range of water temperature on the shelf. Additionally, our observations reveal the proximity of distinct thermal microclimates within the bounds of one reef platform. Circulation on the reef flat is largely wave driven. The greatest diurnal variation in water temperature occurs in the center of larger reef flats and on reefs protected from direct wave forcing, while smaller knolls or sites on the edges of the reef flat tend to experience less diurnal temperature variability. We found that both the temporal and spatial variability in water temperature on the reef platforms is well predicted by a heat budget model that includes the transfer of heat at the air–water interface and the advection of heat by currents flowing over the reef. Using this simple model, we predicted the temperature across three different reefs to within 0.4°C on the outer shelf using only information about bathymetry, surface heat flux, and offshore wave conditions.     

CD4 receptor binding peptides that block HIV infectivity cause human monocyte chemotaxis. Relationship to vasoactive intestinal polypeptide

The octapeptide Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr (peptide T) and two structural analogs are potent agonists of human monocyte chemotaxis, evincing identical rank potency orders as was previously shown for their inhibition of human immunodeficiency virus (HIV) envelope binding and T cell infectivity. Chemotactic activity could be inhibited by anti-CD4 monoclonal antibodies (Mabs), but not other mononuclear cell Mabs. The core peptide required for chemotactic activity is a pentapeptide related to the sequence Thr-Thr-Asn-Tyr-Thr. Homologous pentapeptides, identified by computer search, were detected in several other non-HIV-related viruses as well as the neuropeptide vasoactive intestinal polypeptide (VIP). The CD4 molecule, therefore, appears to be a recognition molecule for a small signal peptide ligand whose active sequence is a homolog of peptide T and which may be the neuropeptide VIP.     

GEMMIFEROUS FERN GAMETOPHYTES—VITTARIACEAE

Approximately 10 % of all fern species reproduce vegetatively in the gametophytic stage by means of gemmae. Gametophyte morphologies in these species depart radically from the commonly figured heart-shaped type and expand considerably the opportunities for physiological and morphological studies utilizing fern gametophytes. Original observations on four species of vittarioid ferns are presented and compared with earlier observations on gametophytes of this family. Vittarioid gametophytes grow from a discontinuous marginal meristem which results in a much branched thallus of indeterminant growth. Aerial branches of the gametophytes terminate in gemma production, which proceeds by a regular and predictable sequence of events. The sequence may differ considerably among species but is remarkably constant within species. Archegonia are produced on short ventral branches, and antheridia are produced primarily on germinating gemmae. Ananthacorus angustifolius is the only known member of the Vittariaceae which does not produce gemmae and is considered to represent the primitive condition. In this species antheridia are scattered over the thallus, suggesting that a change in the mode of control of antheridium production may have evolved in the family along with gemma production.     

Evidence for the identification of lymphocyte activating factor as the adherent cell-derived mediator responsible for enhanced antibody synthesis by nude mouse spleen cells

Human adherent peripheral blood leukocytes spontaneously elaborate both a thymocyte proliferative factor and a factor which augments the in vitro anti-sheep erythrocyte (SRC) plaque-forming cell (PFC) response of nu/nu mouse spleen cells. Nonadherent leukocytes do not spontaneously elaborate either factor. The adherent cell-derived factors appear to have an identical molecular weight (approximately 14,500 Daltons) as determined by Sephadex gel filtration. The data support the hypothesis that the molecule(s) mediating both enhancing activities is identical to the previously described adherent leukocyte product, LAF.