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.     

Relative contribution of caries and periodontal disease in adult tooth loss among patients reporting to the Institute of Dental Sciences,Belgaum, India

Objectives: To examine the reasons for tooth loss in an adult population. Methods: Patients who reported to the department of prosthodontics in Institute of Dental Sciences, Belgaum, located in the north‐western part of the state of Karnataka, in the southern region of India over a period of 2 months, with at least one missing tooth (excluding third molars) constituted the sample size. There were a total of 365 patients (185 females and 180 males) within the age group of 16–84 years (mean age 51.06 ± 16.47 years) who fulfilled this criterion. Socio‐demographic profile was recorded along with a clinical examination for assessing the number and pattern of tooth loss. The reasons for tooth loss were recorded according to the history reported by the patient. Results: In the present study of 365 patients, 58.9% of the patients were completely edentulous, 41% were partially dentate, of which 20.8% had lost their teeth from caries, 11% from periodontal disease and 9.3% from a combination of reasons. More females had lost their teeth because of dental caries whereas more males had lost their teeth because of periodontal disease, this being statistically significant. (χ² = 16.53, p = 0.001). Highly significant results were obtained for age and reasons for tooth loss. (χ² = 150.39, p < 0.001). Irrespective of the socio‐economic status, dental caries was the most common cause for tooth loss in partially dentate patients though it was not statistically significant (χ² = 13.62, p = 0.325). Mandibular first molars were the teeth most frequently lost due to dental caries. The maxillary left central incisor was most frequently lost due to periodontal disease, followed by the maxillary right central incisor. Conclusions: Since both dental caries and periodontal disease contributed to tooth loss at different ages, risk indicators need to be identified.     

Biometric ratio in estimating widths of maxillary anterior teeth derived after correlating anthropometric measurements with dental measurements

doi: 10.1111/j.1741‐2358.2012.00648.x Biometric ratio in estimating widths of maxillary anterior teeth derived after correlating anthropometric measurements with dental measurements Objective: To correlate dental measurements i.e. combined mesiodistal width of six maxillary anterior teeth with facial measurements i.e. inner canthal distance, interpupillary distance and intercommissural width and acquire a biometric ratio to serve as a preliminary guide in selection of the maxillary anterior teeth. Background: In the absence of pre‐extraction records, the resultant denture can lead to patient dissatisfaction towards the aesthetic appeal of their dentures. The maxillary anterior teeth play a pivotal role in denture aesthetics. Various techniques and biometric ratios have been described in literature for selection of the maxillary anteriors. This study derives a biometric ratio for the same, obtained after correlating anthropometric measurements with dental measurements. Materials and methods: Two standardized digital photographs of the face were generated; one, when the facial muscles were relaxed and the other, when the subject was smiling; thereby, revealing the maxillary anterior teeth upto the canine tip. Inner canthal distance, interpupillary distance, intercommissural distance, distance between the tips of the maxillary canines and distance between the distal surfaces of the canines were measured. On the cast, the distance between tips of maxillary canines and distance between distal surfaces of maxillary canines were noted. The data was analysed using Spearman’s rank correlation coefficient. Results: A high correlation was found between the intercommissural measurement with distance between the tips of the canines on the photograph and between the tips of the canines on the cast with the interpupillary distance, giving a biometric ratio of 1:1.35 and 1:1.41 respectively. The least correlation was between the inner canthal distance and the tips of the canines measured on the photograph. Conclusions: Extra oral anthropometric measurements of the interpupillary distances and the intercommissural distances with the help of standardised photographs can help us determine the combined widths of the anterior teeth accurately, thus aiding their selection in the absence of pre‐extraction records.     

Localization of macrophage agglutination factor activity to the gelatin-binding domain of fibronectin

We previously proposed that macrophage agglutination factor (MAggF, a T cell-derived guinea pig lymphokine) is a fibronectin (FN). We now show MAggF binding to gelatin and to peritoneal macrophages is mediated by domains similar to corresponding domains of plasma FN. MAggF activity in lymphokine concentrates prepared by two different methods differed nearly 10-fold in m.w. on gel filtration chromatography. Despite this difference, MAggF dose-activity curves of both preparations were parallel, and MAggF in both preparations bound reversibly to gelatin and to monoclonal anti-guinea pig FN immunoadsorbents. MAggF activity in one preparation was inhibited by the addition of soluble monoclonal antibody specific for the gelatin-binding domain of human FN; inhibitory activity of this antibody was blocked by purified guinea pig plasma FN or partially purified MAggF from the other preparation. Measured MAggF activity of both preparations was reduced in a dose-dependent manner by pretreatment of indicator macrophages with monoclonal anti-human monocyte FN receptor antibody or F(ab')2 fragments or with guinea pig plasma FN. Neither anti-FN receptor antibody nor plasma FN interacted directly with MAggF. Indirect immunofluorescence studies confirmed the presence of uncomplexed plasma membrane receptors for FN on indicator macrophages in MAggF-responsive populations that were able to bind added FN. Our identification of MAggF as lymphokine FN provides a basis for future biochemical analysis of delayed hypersensitivity inflammatory reactions.