An Analysis of the Amino Acid Clustering Pattern in (α/β)8 Barrel Proteins

The (/)₈ barrel proteins, in spite of having a common fold, do not show any sequence similarity. In order to understand the factors which are responsible for maintaining the common fold, the three-dimensional structures of 36 (/)₈ barrel proteins are analyzed for the presence of identical amino acid clusters or physicochemically similar clusters. The results reveal 14 identical amino acid clusters and a large number of physicochemically similar clusters. Further analysis of the similar clusters points to the conservation of secondary structures, the presence of pairs of residues occupying topologically equivalent secondary structures, and the presence of certain key residues which may play a vital role in directing and stabilizing the (/)₈ barrel fold.     

Leucine and spermidine enhance shoot differentiation in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Enhanced numbers of multiple shoots were induced from shoot tip explants of cucumber. The effects of amino acids (leucine, isoleucine, methionine, threonine, and tryptophan) and polyamines (spermidine, spermine, and putrescine) along with benzyladenine (BA) on multiple shoot induction were investigated. A Murashige and Skoog (MS) medium containing a combination of BA (4.44 μM), leucine (88 μM), and spermidine (68 μM) induced the maximum number of shoots (36.6 shoots per explant) compared to BA (4.44 μM) alone or BA (4.44 μM) with leucine (88 μM). The regenerated shoots were elongated on the same medium. Elongated shoots were transferred to the MS medium fortified with BA (4.44 μM), leucine (88 μM), and putrescine (62 μM) for root induction. Rooted plants were hardened and successfully established in soil with a 90% survival rate.     

Impact of d-pinitol on the attenuation of proinflammatory cytokines,hyperglycemia-mediated oxidative stress and protection of kidney tissue ultrastructure in streptozotocin-induced diabetic rats

Oxidative stress plays a crucial role in the progression and development of diabetes and its complications due to chronic hyperglycemia. The present study was aimed to investigate the kidney tissue protective nature of d-pinitol, a cyclitol present in soybean, by assessing the key markers of hyperglycemia-mediated oxidative stress, proinflammatory cytokines and ultrastructural alterations in streptozotocin-induced diabetic rats. Oral administration of d-pinitol (50 mg/kg body weight/day) for 30 days to diabetic group of rats showed a significant elevation in the level of total protein and significant decline in the levels of blood urea, serum uric acid, creatinine and advanced glycation endproducts (AGEs) and kidney proinflammatory cytokines such as TNF-α, IL-1β, IL-6, NF-κB p65 subunit and nitrite. Further, d-pinitol administration elicited a significant attenuation in the activities of kidney enzymatic antioxidants such as superoxide dismutase (SOD), catalase, glutathione peroxidase (GPx), glutathione-S-transferase (GST) and glutathione reductase (GR) and the levels of kidney non-enzymatic antioxidants such as vitamin E, vitamin C and reduced glutathione (GSH) in the diabetic group of rats, with a concomitant decline in the levels of kidney lipid peroxides, hydroperoxides and protein carbonyls. The histological and ultrastructural observations on the kidney tissues also confirmed the renoprotective nature of d-pinitol. Thus the present study demonstrated the renoprotective nature of d-pinitol by attenuating the hyperglycemia-mediated proinflammatory cytokines and antioxidant competence in kidney tissues of streptozotocin-induced diabetic rats.     

Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding

MaturaseK gene (MatK) of chloroplast is highly conserved in plant systematics which is involved in Group II intron splicing. The size of the gene is 1500 bp in length, located with in the intron of trnK. In the present study, matK gene from Zingiberaceae was taken for the analysis of variants, parsimony site, patterns, transition/tranversion rates and phylogeny. The family of Zingiberaceae comprises 47 genera with medicinal values. The matK gene sequence have been obtained from genbank and used for the analysis. The sequence alignments were performed by Clustal X, transition/transversion rates were predicted by MEGA and phylogenetic analyses were carried out by PHYLIP package. The result indicates that the Zingiberaceae genus Afromonum, Alpinia, Globba, Curcuma and Zingiber shows polyphylogeny. The overall variants between the species are 24% and transition/transversion rate is 1.54. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intera-generic relationships. From this study it could be concluded that the matK gene is a good candidate for DNA barcoding of plant family Zingiberaceae.     

A new approach for enhanced multiplication of arbuscular mycorrhizal fungi and isolation of ITS regions from Glomus deserticola and Laccaria fraterna

Rootlets induced from the petiole base of L. purpureus, using IAA and kinetin was used for enhanced multiplication of arbuscular mycorrhizal (AM) fungus, G. deserticula. Using conserved short arbitrary oligonucleotides, as specific primers, we amplified the ITS-region, a molecular marker for fungal identification, from the genomic DNA extracted from cultured spores of G. deserticola, and genomic DNA extracted from the mycelium of L. fraterna. The capacity of fungal colonization and subsequent spore formation of G. deserticola, compared with the natural root system was evaluated. This technology would provide a simple way to multiply AM fungi and to produce spores without microbial contamination useful for further molecular characterization.     

Concurrent and independent binding of Fcgamma receptors IIa and IIIb to surface-bound IgG

Fc receptor-antibody interactions are key mechanisms through which antibody effector functions are mediated. Neutrophils coexpress two low-affinity Fcgamma receptors, CD16b (FcgammaRIIIb) and CD32a (FcgammaRIIa), possessing overlapping ligand binding specificities but distinct membrane anchor and signaling capacities. Using K562 cell transfectants as a model, the kinetics of both separate and concurrent binding of CD16b and CD32a to surface-bound IgG ligands were studied. CD16b bound human IgG with 2-3 times higher affinity than did CD32a (A(c)K(a) = 4.1 and 1.6 x 10(-7) microm(4), respectively) and both FcgammaRs had similar reverse kinetic rates (k(r) = 0.5 and 0.4 s(-1), respectively). Because CD16b is expressed on neutrophils at a 4-5 times higher density than CD32a, our results suggest that CD16b plays the dominant role in binding of neutrophils to immobilized IgG. The question of possible cross-regulation of binding affinity between CD16b and CD32a was investigated using our multispecies concurrent binding model (Zhu and Williams, Biophys. J. 79:1850-1857, 2000). Because the model assumes independent binding (no cooperation among different species), the excellent agreement between the model predictions and the experimental data suggests that, when coexpressed on K562 cells, these two FcgammaRs do not interact in a manner that alters the kinetic rates of either molecule.     

Thermodynamic databases for proteins and protein-nucleic acid interactions

Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.     

Biosynthesis and function of LFA-3 in human mutant cells deficient in phosphatidylinositol-anchored proteins

Mutants that lack expression of phosphatidylinositol (PI)-anchored proteins were derived from the human B lymphoblastoid JY cell line. It was demonstrated that unlike wild-type cells, which normally express both a transmembrane and a PI-linked form of LFA-3 glycoprotein, the mutant cells expressed only the transmembrane form of LFA-3. [3H]Ethanolamine was not incorporated into LFA-3 of mutant cells, indicating that the anchor moiety was entirely missing. Blockade of normal biosynthesis of the PI-anchored form led to accumulation of two intermediates that may have intact and truncated polypeptide chains. The truncated LFA-3, which was not attached to the cell membrane, was secreted by mutant cells into culture supernatants. A possible division of adhesion function between the two forms of LFA-3 was studied by using the JY cell lines as targets for CTL. Wild-type and mutant JY cells formed conjugates with CTL and were subsequently lysed to a similar extent. In addition, wild-type and mutant JY cells stimulated CTL proliferation to the same extent. Antibody-blocking experiments demonstrated a predominant role for the CD2/LFA-3 pathway in interaction of both wild-type and mutant cells with CTL. Because E exclusively express only the PI-linked LFA-3 form, and this form is known to mediate cell adhesion, the present results indicate that the two distinct membrane-anchored LFA-3 forms are each capable of mediating adhesion. A possible division of signaling functions between the two forms of LFA-3 is under investigation.