Production of a fibronectin-associated lymphokine by cloned mouse T cells

Azobenzenearsonate-specific cloned mouse T cells able to transfer delayed hypersensitivity reactions in vivo produced macrophage agglutination factor (MaggF) after stimulation with mitogen or antigen in vitro. Mitogen (Con A) elicited MAggF production directly from T cells. Responses to Ag were Ag-specific, required syngeneic accessory cells in addition to T cells, and were independent of T cell fine specificity for azobenzenearsonate. Mouse MAggF shared a number of biochemical and immunochemical properties with the fibronectins (FN): 1) high Mr similar to that of plasma FN; 2) binding to gelatin, heparin, and polyclonal antibodies and mAb specific for cellular and plasma FN; 3) inhibition of activity in solution by monoclonal anti-human FN directed against plasma FN gelatin-binding domain; and 4) action on peritoneal exudate macrophages mediated through a FN-receptor cross reactive with one on human monocytes. MAggF production required active protein synthesis and was associated with significant increases in gelatin-binding immunoreactive FN (Mr 440 kDa on immunoblotting) in culture supernatants and T cell lysates. Metabolically labeled peptides could be precipitated by anti-FN from culture supernatants of activated T cells. Stimulated cultures contained significantly more cells with immunohistologically demonstrable cytoplasmic FN than unstimulated control cultures. We suggest that T cell FN is a distinct species of cellular FN which may play an important role in mediating delayed hypersensitivity inflammatory reactions in vivo.     

An efficient algorithm for protein structure comparison using elastic shape analysis

Background

Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have been proposed in literature for comparing protein structures but they have their own limitations in terms of accuracy and complexity with respect to computational time and space. There is a need to improve the computational complexity in comparison/alignment of proteins through incorporation of important biological and structural properties in the existing techniques.

Results

An efficient algorithm has been developed for comparing protein structures using elastic shape analysis in which the sequence of 3D coordinates atoms of protein structures supplemented by additional auxiliary information from side-chain properties are incorporated. The protein structure is represented by a special function called square-root velocity function. Furthermore, singular value decomposition and dynamic programming have been employed for optimal rotation and optimal matching of the proteins, respectively. Also, geodesic distance has been calculated and used as the dissimilarity score between two protein structures. The performance of the developed algorithm is tested and found to be more efficient, i.e., running time reduced by 80–90 % without compromising accuracy of comparison when compared with the existing methods. Source codes for different functions have been developed in R. Also, user friendly web-based application called ProtSComp has been developed using above algorithm for comparing protein 3D structures and is accessible free.

Conclusions

The methodology and algorithm developed in this study is taking considerably less computational time without loss of accuracy (Table 2). The proposed algorithm is considering different criteria of representing protein structures using 3D coordinates of atoms and inclusion of residue wise molecular properties as auxiliary information.

     

Real‐time PCR Detection of Sorghum Ergot Pathogens Claviceps africana,Claviceps sorghi and Claviceps sorghicola

Sorghum ergot is a serious disease that has caused major losses in sorghum growing regions worldwide. Claviceps africana, originally reported from Zimbabwe, is now the most widely distributed species causing ergot in many countries including the United States of America, whereas both C. africana and Claviceps sorghi exist in India. A third species (Claviceps sorghicola) has been described causing sorghum ergot in Japan. As the three species show morphological similarities, a DNA‐based assay is desirable for rapid identification in cases where ergot‐infected sorghum is found by regulatory authorities. We designed PCR primers and probes from the intron 3 region of the β‐tubulin gene (for C. africana and C. sorghi) and the intron 4 region of EF‐1α (for C. sorghicola) and tested them by real‐time PCR with purified DNA and ergot samples from the field and greenhouse. The primer and probe sets specifically amplified DNA from the respective species with a detection limit of c. 1 pg DNA. Genomic DNA from six other Claviceps species did not amplify in any of the three ergot species‐specific assays. The assays we describe will provide useful tools for detecting sorghum ergot pathogens in seed and grain shipments and for determining which species are present in the samples, thereby aiding in the regulatory decision‐making process.     

FuzzyART neural network for protein classification

One of the major research directions in bioinformatics is that of predicting the protein superfamily in large databases and classifying a given set of protein domains into superfamilies. The classification reflects the structural, evolutionary and functional relatedness. These relationships are embodied in hierarchical classification such as Structural Classification of Protein (SCOP), which is manually curated. Such classification is essential for the structural and functional analysis of proteins. Yet, a large number of proteins remain unclassified. We have proposed an unsupervised machine-learning FuzzyART neural network algorithm to classify a given set of proteins into SCOP superfamilies. The proposed method is fast learning and uses an atypical non-linear pattern recognition technique. In this approach, we have constructed a similarity matrix from p-values of BLAST all-against-all, trained the network with FuzzyART unsupervised learning algorithm using the similarity matrix as input vectors and finally the trained network offers SCOP superfamily level classification. In this experiment, we have evaluated the performance of our method with existing techniques on six different datasets. We have shown that the trained network is able to classify a given similarity matrix of a set of sequences into SCOP superfamilies at high classification accuracy.     

Entry of bovine viral diarrhea virus into ovine cells occurs through clathrin-dependent endocytosis and low pH-dependent fusion

Although mechanisms of bovine viral diarrhea virus (BVDV) entry into bovine cells have been elucidated, little is known concerning pestivirus entry and receptor usage in ovine cells. In this study, we determined the entry mechanisms of BVDV-1 and BVDV-2 in sheep fetal thymus cells. Both BVDV-1 and BVDV-2 infections were inhibited completely by chlorpromazine, β-methyl cyclodextrin, sucrose, bafilomycin A1, chloroquine, and ammonium chloride. Simultaneous presence of reducing agent and low pH resulted in marked loss of BVDV infectivity. Moreover, BVDV was unable to fuse with ovine cell membrane by the presence of reducing agent or low pH alone, while combination of both led to fusion at low efficiency. Furthermore, sheep fetal thymus cells acutely infected with BVDV-1 or BVDV-2 were found protected from heterologous BVDV infection. Taken together, our results showed for the first time that entry of both BVDV-1 and BVDV-2 into ovine cells occurred through clathrin-dependent endocytosis, endosomal acidification, and low pH-dependent fusion following an activation step, besides suggesting the involvement of a common ovine cellular receptor during attachment and entry.     

Micro-Raman spectroscopy of silver nanoparticle induced stress on optically-trapped stem cells

We report here results of a single-cell Raman spectroscopy study of stress effects induced by silver nanoparticles in human mesenchymal stem cells (hMSCs). A high-sensitivity, high-resolution Raman Tweezers set-up has been used to monitor nanoparticle-induced biochemical changes in optically-trapped single cells. Our micro-Raman spectroscopic study reveals that hMSCs treated with silver nanoparticles undergo oxidative stress at doping levels in excess of 2 μg/ml, with results of a statistical analysis of Raman spectra suggesting that the induced stress becomes more dominant at nanoparticle concentration levels above 3 μg/ml.     

IGF1 stimulates differentiation of primary follicles and their growth in ovarian explants of zebrafish (<Emphasis Type="Italic">Danio rerio)</Emphasis> cultured <Emphasis Type="Italic">in vitro</Emphasis>

The present study is an attempt to elucidate the involvement of insulin-like growth factor (IGF1) in the differentiation and growth of primary follicles in ovarian explant cultures of zebrafish. Ovaries from adult females were cultured in triplicate sets/treatment group for 15 days at 22°C in the laboratory. Culture medium was supplemented with either insulin (1 ng/mL) or IGF1 (1 ng/mL) or insulin + IGF1 (Experiment 1) or 0.1 or 1.0 or 10 ng/mL of IGF1 (Experiment 2). Ovaries cultured in medium alone served as controls and those fixed at the beginning of the culture as initial controls. Experiments were repeated. On the 16th day ovarian explants were fixed in Bouin’s fluid and processed for paraffin embedding, sections (3 µm) were cut and stained with hematoxylin-eosin. Follicles were classified into 6 stages and atretic follicles (AF). Previtellogenic, vitellogenic and total follicle number was calculated. At the start of the culture, ovaries contained all stages of growing and degenerating follicles. In in vitro cultured control ovaries, vitellogenic follicles underwent atresia, while, primary follicles remained unaffected. Insulin or insulin + IGF1 treated ovaries did not differ significantly while IGF1 exposed ovarian explants had greater (P < 0.05) number of primary follicles compared to controls. IGF1 also caused an increase in the number and growth of primary follicles in a dose dependent manner although; cultures were not supplemented with gonadotrophic hormones. Results suggest that locally derived intra-ovarian IGF1 may have a role in the differentiation and growth of primary follicles in zebrafish ovary.     

Nootropic activity of tuber extract of Pueraria tuberosa (Roxb)

Nootropic effect of alcoholic (ALE; 50, 75, 100 mg/kg) and aqueous (AQE; 100, 200, 400 mg/kg) extracts of P. tuberosa was evaluated by using Elevated Plus Maze (EPM), scopolamine-induced amnesia (SIA), diazepam-induced amnesia (DIA), clonidine-induced (NA-mediated) hypothermia (CIH), lithium-induced (5-HT mediated) head twitches (LIH) and haloperidol-induced (DA- mediated) catalepsy (HIC) models. Piracetam was used as the standard drug. A significant increase in inflexion ratio (IR) was recorded in EPM, SIA and DIA models. A significant reversal effect was observed on rectal temperature in CIH model, reduction of head twitches in LIH models. However no significant reduction in catalepsy scores in HIC models were observed with test extracts and standard piracetam. The results indicate that nootropic activity observed with ALE and AQE of tuber extracts of P. tuberosa could be through improved learning and memory either by augmenting the noradrenaline (NA) transmission or by interfering with 5-hydroxytryptamine (5-HT) release. Further, the extracts neither facilitated nor blocked release of the dopamine (DA). Thus ALE and AQE elicited significant nootropic effect in mice and rats by interacting with cholinergic, GABAnergic, adrenergic and serotonergic systems. Phytoconstituents like flavonoids have been reported for their nootropic effect and these are present in both ALE and AQE extracts of tubers of P. tuberosa (Roxb) and these active principles may be responsible for nootropic activity.