Recombinant dengue virus type 3 envelope domain III protein from Escherichia coli

Dengue is a public health problem of global significance for which there is neither an effective antiviral therapy nor a preventive vaccine. The envelope protein of dengue virus is the major antigen to elicit neutralizing antibody response and protective immunity in hosts. Optimization of culture media was carried out for enhanced production of recombinant dengue virus type 3 envelope domain III (rDen 3 EDIII) protein in E. coli. Further, batch and fed-batch cultivation process were also developed in optimized medium. After fed-batch cultivation, the dry cell weight was about 22.80 g/L of culture. The rDen 3 EDIII protein was purified using immobilized metal affinity chromatography. This process produced ～649 mg of purified rDen 3 EDIII protein per liter of culture. The purity of the protein was determined by SDS-PAGE analysis and the reactivity was checked by Western blotting as well as ELISA. These results show that the purified protein may be used for the dengue diagnosis or further prophylactic studies for dengue infection.     

Patterns of tree phenological diversity in dry tropics

Recent phenological studies in tropical deciduous forests revealed a mosaic of vegetation composed of several pheno-phases that are evolved as an adaptation by the species to overcome seasonal drought in different ways. These pheno-phases represent extent of annual deciduousness (～leaflessness) and triggering factors for buds break (e.g. vegetative and flower). Thus, studying patterns of various pheno-phases (phonological diversity) in tropical forest have been thought to provide a potential tool to address critical questions related to climate change modeling and monitoring. In tropics, tree species represent a gradient of deciduousness (from leaf-exchanging species to >6 months deciduous species) and flowering initiation (breaking of flower buds in various part of annual cycle). Both processes are mostly triggered by variation in day length and/or temperature during late dry season/autumn, and/or first significant rain during rainy season. In addition, few factors like drought induced leaf fall and sporadic winter rains are supposed to affect these processes temporarily. Besides, the abundances of pheno-phases (i.e. leafing and flowering) also vary among tropical deciduous forest trees. Presence of such variations in tropical tree pheno-phases and their abundances are reported to vary due to micro-climatic variables and has specific implications in tropical forests. Present paper discusses the existing information on various pheno-phases and their abundances in tropical forests and role of climatic factors on tree phonological diversity. Further, we emphasized the need to develop predicting understanding of impending climatic change (i.e. precipitation and temperature) on diversity of pheno-phases by collecting long-term data on tree pheno-phases through a network of phonological stations in dry tropics.     

A novel dimer-tetramer transition captured by the crystal structure of the HIV-1 Nef

HIV-1 Nef modulates disease progression through interactions with over 30 host proteins. Individual chains fold into membrane-interacting N-terminal and C-terminal core (Nef_core) domains respectively. Nef exists as small oligomers near membranes and associates into higher oligomers such as tetramers or hexadecamers in the cytoplasm. Earlier structures of the Nef_core in apo and complexed forms with the Fyn-kinase SH3 domain revealed dimeric association details and the role of the conserved PXXP recognition motif (residues 72–78) of Nef in SH3-domain interactions. The crystal structure of the tetrameric Nef reported here corresponds to the elusive cytoplasmic stage. Comparative analyses show that subunits of Nef_core dimers (open conformation) swing out with a relative displacement of ∼22 Å and rotation of ∼174° to form the ‘closed’ tetrameric structure. The changes to the association are around Asp125, a conserved residue important for viral replication and the important XR motif (residues 107–108). The tetramer associates through C4 symmetry instead of the 222 symmetry expected when two dimers associate together. This novel dimer-tetramer transition agrees with earlier solution studies including small angle X-ray scattering, analytical ultracentrifugation, dynamic laser light scattering and our glutaraldehyde cross-linking experiments. Comparisons with the Nef_core—Fyn-SH3 domain complexes reveal that the PXXP motif that interacts with the SH3-domain in the dimeric form is sterically occluded in the tetramer. However the 151–180 loop that is distal to the PXXP motif and contains several protein interaction motifs remains accessible. The results suggest how changes to the oligomeric state of Nef can help it distinguish between protein partners.     

Aliphatic compounds from Curculigo orchioides rhizomes

21-Hydroxytetracontan-20-one and 4-methylheptadecanoic acid have been isolated from the rhizomes of Curculigo orchioides and characterized on the basis of chemical and spectroscopic evidence.     

Immunomodulatory role of native and heat denatured agglutinin from Abrus precatorius

Lectins are known as polyclonal activators of lymphocytes and work through the induction of battery of cytokines, which vary from lectin to lectin. Most widely used biological response modifier Mistletoe lectin (ML-1) in therapy stimulates lymphocytes, macrophages, and natural killer cells and induces both TH1 and TH2 type cytokines. Abrus agglutinin, similar to ML-1 with respect to carbohydrate specificity [gal (beta1-->3) gal/Nac], was studied both in native (NA) and heat denatured (HDA) condition for murine splenocyte proliferation, cytokine secretion, NK-cell activation, and thymocyte proliferation in vitro with a view to assess its potential as an immunomodulator. Both NA and HDA activate splenocytes and induce production of cytokines like IL-2, IFN-gamma and TNF-alphabeta indicating a TH1 type of immune response. Native agglutinin and HDA induced conditioned media of adherent splenocytes could stimulate non-adherent splenocytes and vice versa. Heat denatured agglutinin was able to induce NK-cell activation at much lower concentration than that of NA, but the extent of NK-cell activation was higher for NA. Proliferation of thymocytes by NA and HDA was also observed. This study indicates that Abrus agglutinin could be a potential immunomodulator both in native as well as in heat denatured form.     

NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors

DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents.     

Acanthocheilonema viteae: octopamine and its physiological role

Octopamine acts as an important neurotransmitter and neuromodulator in arthropods, mollusks, and nematodes. In mammals, however, no definite function for this amine has yet been described. By virtue of this difference in the neurophysiological requirement of the mammalian host and nematodes, octopamine offers good opportunity for exploring this area deeply with a view to identify a unique target for filarial chemotherapy. Results of the present study indicated that Acanthocheilonema viteae, the rodent filarial parasite, utilized tyrosine as a precursor for producing octopamine and some other biogenic amines. Octopamine exhibited specific saturable binding with the membrane prepared from the anterior portion of the filariid. This amine induced concentration dependent increase in the membrane potential which possibly caused tonic paralysis of the filariid. The rate of micro filarial release by the female worms also declined in the presence of this amine. The study thus provided preliminary evidences for the presence of an octopamine neurotransmitter system and also about some of the roles it plays in A. viteae.     

Effect of supplementary feeding of vitamin K1 on difethialone treated Indian gerbil, Tatera indica Hardwicke in laboratory

Two dosages (1 and 2 mg/kg) of vitamin K1 supplementation for 5 and 15 days were given to Indian gerbil T. indica fed on difethialone bait (0.0025%) for one day. The results indicated that the lower dosage could not reverse the anticoagulation process, however the period of mortality was considerably increased from 3-9 days (in control) to 5-14 days (5 days supplementation regime). Subsequently when the vitamin K1 dosage was doubled and given for 15 days, there was 100% reversal of anticoagulation process and all the test gerbils became normal within a month of poisoning with difethialone bait.     

Analysis of unigene derived microsatellite markers in family solanaceae

The family Solanaceae is the source of several economically important plants. The aim of this study was to trace and characterize simple sequence repeat (SSR) markers from unigene sequences of Solanum lycopersicum, an important member of family Solanaceae. 18,228 unigene sequences of Solanum lycopersicum was taken in order to develop SSR markers and analyzed for the in-silico design of PCR primers. A total of 12,090 (66.32 %) unigenes containing 17,524 SSRs (microsatellites) were identified. The average frequency of microsatellites in unigenes was one in every 1.3 kb of sequence. The analysis revealed that trinucleotide motifs, coding for Glutamic acid (GAA) and AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking sequences of the SSRs generated 877 primers with forward and reverse strands. Functional categorization of SSRs containing unigenes was done through gene ontology terms like Biological process, Cellular component and Molecular function.     

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase

Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H(2) molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O(2) molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.