Cascaded bidirectional recurrent neural networks for protein secondary structure prediction

Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of non-homologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system based on cascaded bidirectional recurrent neural network (BRNN). We compare the cascaded BRNN against another two BRNN architectures, namely the original BRNN architecture used for speech recognition as well as Pollastri's BRNN that was proposed for PSS prediction. Our cascaded BRNN achieves an overall three state accuracy Q3 of 74.38\%, and reaches a high Segment OVerlap (SOV) of 66.0455. It outperforms the original BRNN and Pollastri's BRNN in both Q3 and SOV. Specifically, it improves the SOV score by 4-6%.     

Field performance of bacterial inoculants to alleviate water stress effects in wheat (Triticum aestivum L.)

Plant and Soil - Plant growth promoting bacteria (PGPB) containing 1-aminocyclopropane-1-carboxylate (ACC) deaminase can play an important role in abiotic stress tolerance in plants, particularly...     

Hybrid vectors based on adeno-associated virus serotypes 2 and 5 for muscle-directed gene transfer

Vectors based on hybrids consisting of adeno-associated virus types 2 (ITRs and Rep) and 5 (Cap) were evaluated for muscle-directed gene transfer (called AAV2/5). Evaluation in immune-competent mice revealed greater transduction efficacy with AAV2/5 than with AAV2 and no cross-neutralization between AAV2/5 and AAV2. Interestingly, we saw no immunologic evidence of previous exposure to AAV5 capsids in a large population of healthy human subjects.     

Regulation of cell motility by tyrosine phosphorylated villin

Temporal and spatial regulation of the actin cytoskeleton is vital for cell migration. Here, we show that an epithelial cell actin-binding protein, villin, plays a crucial role in this process. Overexpression of villin in doxycyline-regulated HeLa cells enhanced cell migration. Villin-induced cell migration was modestly augmented by growth factors. In contrast, tyrosine phosphorylation of villin and villin-induced cell migration was significantly inhibited by the src kinase inhibitor 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP2) as well as by overexpression of a dominant negative mutant of c-src. These data suggest that phosphorylation of villin by c-src is involved in the actin cytoskeleton remodeling necessary for cell migration. We have previously shown that villin is tyrosine phosphorylated at four major sites. To further investigate the role of tyrosine phosphorylated villin in cell migration, we used phosphorylation site mutants (tyrosine to phenylalanine or tyrosine to glutamic acid) in HeLa cells. We determined that tyrosine phosphorylation at residues 60, 81, and 256 of human villin played an essential role in cell migration as well as in the reorganization of the actin cytoskeleton. Collectively, these studies define how biophysical events such as cell migration are actuated by biochemical signaling pathways involving tyrosine phosphorylation of actin binding proteins, in this case villin.     

High-performance liquid chromatographic method for the quantification of unbound evernimicin in human plasma ultrafiltrate

A rapid HPLC method was developed for quantification of unbound evernimicin in human plasma. Protein-free samples prepared by ultrafiltration were injected directly onto a polymeric reversed-phase column and the eluent monitored at 302 nm. Evernimicin that eluted within 3.5 min was well resolved from endogenous components. Linearity was established between peak height and evernimicin concentration from 25 to 2500 ng/ml. Assay precision (C.V.) was within 5% while bias was no greater than 3%. This method has been used for the ex vivo assessment of evernimicin protein binding in human plasma from safety and tolerance as well as liver dysfunction and renal insufficiency studies.     

Th2-dependent B cell responses in the absence of CD40-CD40 ligand interactions

CD40 is thought to play a central role in T cell-dependent humoral responses through two distinct mechanisms. CD4+ T helper cells are activated via CD40-dependent Ag presentation in which CD80/CD86 provides costimulation through CD28. In addition, engagement of CD40 on B cells provides a direct pathway for activation of humoral responses. We used a model of adenovirus-mediated gene transfer of beta-galactosidase (lacZ) into murine lung to evaluate the specific CD40-dependent pathways required for humoral immunity at mucosal surfaces of the lung. Animals deficient in CD40L failed to develop T and B cell responses to vector. Activation of Th2 cells, which normally requires CD40-dependent stimulation of APCs, was selectively reconstituted in CD40 ligand-deficient mice by systemic administration of an Ab that is agonistic to CD28. Surprisingly, this resulted in the development of a functional humoral response to vector as evidenced by formation of germinal centers and production of antiadenovirus IgG1 and IgA that neutralized and prevented effective readministration of vector. The CD28-dependent B cell response required CD4+ T cells and was mediated via IL-4. These studies indicate that CD40 signals to the B cells are not necessary for CD4+ Th2 cell-dependent humoral responses to be generated.     

Alkali‐catalyzed low temperature wet crosslinking of plant proteins using carboxylic acids

We report the development of a new method of alkali‐catalyzed low temperature wet crosslinking of plant proteins to improve their breaking tenacity without using high temperatures or phosphorus‐containing catalysts used in conventional poly(carboxylic acid) crosslinking of cellulose and proteins. Carboxylic acids are preferred over aldehyde‐containing crosslinkers for crosslinking proteins and cellulose because of their low toxicity and cost and ability to improve the desired properties of the materials. However, current knowledge in carboxylic acid crosslinking of proteins and cellulose requires the use of carboxylic acids with at least three carboxylic groups, toxic phosphorous‐containing catalysts and curing at high temperatures (150–185°C). The use of high temperatures and low pH in conventional carboxylic acid crosslinking has been reported to cause substantial strength loss and/or undesired changes in the properties of the crosslinked materials. In this research, gliadin, soyprotein, and zein fibers have been crosslinked with malic acid, citric acid, and butanetetracarboxylic acid to improve the tenacity of the fibers without using high temperatures and phosphorus‐containing catalysts. The new method of wet crosslinking using carboxylic acids containing two or more carboxylic groups will be useful to crosslink proteins for various industrial applications. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Potential of Mauritius Hemp (Furcraea gigantea Vent.) for the Remediation of Chromium Contaminated Soils

The present study was conducted to evaluate the ability of a high biomass producing, drought tolerant succulent plant Mauritius hemp (Furcraea gigantea Vent.) for its tolerance to different levels of Cr (0, 25, 50, 100 and 200 mg Cr kg soil^?1) and its potential for phytoremediation purposes. Based on the data on inhibition of the growth of plants with Cr, tolerance index and grade of growth inhibition, it was observed that the plant could tolerate up to 50 mg Cr kg ^?1 soil. Absorption of Cr from soil to plant and its translocation into plant tissues were discussed in terms of bio concentration factor (BCF), transfer factor (TF), and translocation efficiency (TE%). Cr was mainly accumulated in the roots and exclusion of Cr was found to be the principal physiological tolerance mechanism followed by a marked increase in proline, ascorbic acid, total free amino acids in the leaf tissue and malic acid in the rhizosphere samples to counter Cr stress. Based on the tissue concentration of Cr (< 300 μg g^?1 in the leaves and TF<1), it was concluded that, Furcraea gigantea could not be considered a hyperaccumulator and therefore unsuitable for phytoextraction of Cr. Nevertheless, Furcraea gigantea could be a suitable candidate for phytostablization of Cr contaminated soils.