In vitro analysis of synthetic peptides in blocking the entry of dengue virus.

Dengue fever is the most prevalent arthropod-borne viral disease, and no specific therapeutic or promising antiviral drug is available for its treatment. Peptide inhibitors are less toxic than synthetic compounds and have found proven effective against viral infections. Here, three peptides that mimic part of the E protein of the dengue virus (DENV) were synthesized and evaluated for their inhibitory activity against four serotypes of DENV in African green monkey kidney (Vero) and rhesus macaque (Macaca mulatta) monkey kidney (LLC-MK2) cell lines. The three peptides, Pep1, Pep2, and Pep3 are located in domains I, II, and III of the E protein respectively. All three peptides effectively reduced >80% of focus forming units in the virus treated mammalian cell lines than control and exhibited their IC50 in the range of 10-33 µM. Pep1 was found effective against DENV-2, DENV-3, and DENV-4 (IC80 below 50 µM). Pep2 showed the highest inhibitory activity against all four serotypes (IC50 below 20 µM). Pep3 reduced the 80% focus forming units in all serotypes at the concentration of 40 µM. Evaluation of peptides at different time points of viral infection in the mammalian cell lines revealed that the peptides inhibited viral infection by binding to the virus and not by binding to cellular receptors and blocking viral entry. The peptides assumedly exert their inhibitory effects by binding to the E protein and repressing its conformational changes; this prevents the virus from binding to cellular receptors, thereby inhibiting viral entry. Hence, these peptides might limit viral spread and reduce the virus's ability to infect.

A synthetic peptide derived from domain III envelope glycoprotein of Dengue virus induces neutralizing antibody.

Dengue virus (DENV) is an arthropod-borne human pathogen that represents a severe public health threat in both endemic and non-endemic regions. So far, there is no licensed vaccine or specific drugs available for dengue fever. A fifteen-amino-acid-long peptide that includes the NGR motif was chemically synthesized and conjugated with keyhole limpet hemocyanin. A standard immunization protocol was followed for the production of polyclonal antibodies by immunizing rabbits against the synthetic peptide. The immune response elicited high-titer polyclonal antibodies with the reactivity of the anti-peptide antibody against both synthetic peptide and four serotypes of DENV confirmed by DOT-ELISA. Neutralizing activity of anti-peptide antibody was found to be cross-reactive and effective resulting in 60% reduction of infectivity at 1:200 dilution in all four serotypes of DENV. Our findings have the potential to further improve our understanding of virus-host interactions and provide new insights into neutralizing antibodies and could also be used as a drug target.

Identification of sequence motifs involved in Dengue virus-host interactions.

Dengue fever is a rapidly spreading mosquito-borne virus infection, which remains a serious global public health problem. As there is no specific treatment or commercial vaccine available for effective control of the disease, the attempts on developing novel control strategies are underway. Viruses utilize the surface receptor proteins of host to enter into the cells. Though various proteins were said to be receptors of Dengue virus (DENV) using Virus Overlay Protein Binding Assay, the precise interaction between DENV and host is not explored. Understanding the structural features of domain III envelope glycoprotein would help in developing efficient antiviral inhibitors. Therefore, an attempt was made to identify the sequence motifs present in domain III envelope glycoprotein of Dengue virus. Computational analysis revealed that the NGR motif is present in the domain III envelope glycoprotein of DENV-1 and DENV-3. Similarly, DENV-1, DENV-2 and DENV-4 were found to contain Yxxphi motif which is a tyrosine-based sorting signal responsible for the interaction with a mu subunit of adaptor protein complex. High-throughput virtual screening resulted in five compounds as lead molecules based on glide score, which ranges from -4.664 to -6.52 kcal/Mol. This computational prediction provides an additional tool for understanding the virus-host interactions and helps to identify potential targets in the host. Further, experimental evidence is warranted to confirm the virus-host interactions and also inhibitory activity of reported lead compounds.

Statistical media design for efficient polyhydroxyalkanoate production in Pseudomonas sp. MNNG-S.

Polyhydroxyalkanoate (PHA) is a promising polymer for various biomedical applications. There is a high need to improve the production rate to achieve end use. When a cost-effective production was carried out with cheaper agricultural residues like molasses, traces of toxins were incorporated into the polymer, which makes it unfit for biomedical applications. On the other hand, there is an increase in the popularity of using chemically defined media for the production of compounds with biomedical applications. However, these media do not exhibit favorable characteristics such as efficient utilization at large scale compared to complex media. This article aims to determine the specific nutritional requirement of Pseudomonas sp. MNNG-S for efficient production of polyhydroxyalkanoate. Response surface methodology (RSM) was used in this study to statistically design for PHA production based on the interactive effect of five significant variables (sucrose; potassium dihydrogen phosphate; ammonium sulfate; magnesium sulfate; trace elements). The interactive effects of sucrose with ammonium sulfate, ammonium sulfate with combined potassium phosphate, and trace element with magnesium sulfate were found to be significant (p < .001). The optimization approach adapted in this study increased the PHA production more than fourfold (from 0.85 g L(-1) to 4.56 g L(-1)).

DENVirDB: a web portal of dengue virus sequence information on Asian isolates.

DENVirDB is a web portal that provides the sequence information and computationally curated information of dengue viral proteins. The advent of genomic technology has increased the sequences available in the public databases. In order to create relevant concise information on Dengue Virus (DENV), the genomic sequences were collected, analysed with the bioinformatics tools and presented as DENVirDB. It provides the comprehensive information of complete genome sequences of dengue virus isolates of Southeast Asia, viz. India, Bangladesh, Sri Lanka, East Timor, Philippines, Malaysia, Papua New Guinea, Brunei and China. DENVirDB also includes the structural and non-structural protein sequences of DENV. It intends to provide the integrated information on the physicochemical properties, topology, secondary structure, domain and structural properties for each protein sequences. It contains over 99 entries in complete genome sequences and 990 entries in protein sequences, respectively. Therefore, DENVirDB could serve as a user friendly database for researchers in acquiring sequences and proteomic information in one platform.

Indigenously produced polyhydroxyalkanoate based co-polymer as cellular supportive biomaterial.

The focus of this study was to evaluate the growth of the cells on a scaffold based on novel polyhydroxyalkanoate (PHA) (Polyhydroxy propionate copoly hydroxy ocatadecanoate copolymer), derived from a mutant strain of Pseudomonas sp. Naive PHA was also blended with several biodegradable polymeric materials (PEG, PLA, and MMT) to improve the scaffold properties. Protein adsorption study was done to evaluate the capability of scaffolds for cellular interaction. PHA:PEG blended scaffold showed better adsorption than others. 3T3 fibroblast cultures on various polymers were equally viable when compared with control culture except for the blend PHA:MMT by CCK 8 kit. MTT assay, performed with the continuous cultures HeLa, HEp-2, Vero, and McCoy on the polymer blends, supported the above finding. Among the blends PHA:PEG showed increased viability and was selected for further studies. Cell proliferation assay with colorimetric BrdU ELISA kit showed increase in cell proliferation over the matrix PHA:PEG than that of control. There were no observable morphological changes of continuous cells grown over matrix PHA:PEG when observed by phase contrast microscopy. HEp-2 cells were enclosed within the matrix when analyzed by SEM. The current study states that the scaffold prepared by using the indigenous PHA in combination with PEG supports cell growth better than the conventional plastic surface. PHA:PEG would be a promising material for tissue engineering.

Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus-host interaction.

Chikungunya fever is one of the reemerging vector-borne diseases. It has become a major global health problem especially in the developing countries. There are no vaccines or specific antiviral drugs available to date. This study reports small molecule inhibitors of envelope glycoprotein 2 (E2 glycoprotein) which are predicted based on Chikungunya virus-host interactions. E2 glycoprotein of Chikungunya virus interacts at 216 residue of the host receptor protein which plays a vital role in initiating infection. Understanding the structural aspects of E2 glycoprotein is crucial to develop specific inhibitors to prevent the virus binding from host receptors. In silico method was adopted to predict the sequence motifs of envelope protein, as the method like yeast two hybrid system is laborious, time consuming, and costly. The E2 glycoprotein structure of the Indian isolate was modeled using two templates (2XFC and 3JOC) and then validated. The class III PDZ domain binding motif was found to be identified at 213-216 amino acids. The corresponding peptide structures which recognize the PDZ domain binding motif were identified by the literature search and were used for generating five point pharmacophore model (ADDDR) containing acceptor, donor and aromatic ring features. Databases such as Asinex, TosLab and Maybridge were searched for the matches for the predicted pharmacophore model. Two compounds were identified as lead molecules as their glide score is > 5 kcal/mol. Since the pharmacophore model is developed based on Chikungunya virus-host interaction, it can be used for designing promising antiviral lead compounds for the treatment of Chikungunya fever.An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:21.

Quantification of intracellular polyhydroxyalkanoates by virtue of personalized flow cytometry protocol.

Polyhydroxyalkanoates (PHAs) are natural polyesters produced by microbes, a potential alternative to synthetic plastics. Various methods ranging from gravimetry to spectrophotometry are routinely used for qualitative analysis of extracted PHA. There is a great need for accurate quantification of intracellular PHA during bioprocess. Hence, the present study aims to improvise the existing Nile red-based flow cytometry protocol. It was achieved using respective cells in a non-PHA accumulating state as gating control to minimize non-specific staining. The optimal Nile red concentration required for PHA staining is 5 × 10(3) pg mL(-1), which is ~10(3)-fold less than that of earlier reports. Further, it was inferred that flow-based quantification was more accurate than the gravimetric method. The intracellular PHA content was highest in Pseudomonas sp. MNNG-S (52.06 %) among the Pseudomonas strains tested by the flow-based method. Both gravimetric and flow-based cell cycle analyses revealed that DNA synthesis (S phase) and PHA production (log phase) are synchronous at 24-48 h of culture. This study supports flow-based PHA quantification for real time online measurement of intracellular PHA for bioreactor monitoring, control and optimization enduing industrial applications.

Selenium levels in persons with HIV/tuberculosis in India, Madurai City.

BACKGROUND: Selenium plays a vital role in the immune status of the individual. The prospective observational study was conducted from September 2009 to March 2010. The aim of the present study is to investigate the association between serum selenium levels and pulmonary tuberculosis (PTB) patients with (n = 40) and without HIV (n = 40) in comparison to healthy controls (healthy family members; n = 20) who satisfied rigid selection criteria. METHODS: Standard methods were adopted to collect an early morning fasting blood sample for serum selenium concentrations, determined by atomic absorption spectrometry (AAS), and albumin, determined by the bro mocresol green method. RESULTS: The mean +/- SD for Body Mass Index (BMI), selenium, and albumin among the controls, HIV positive, and HIV negative patients were 19.6 +/- 0.6, 18 +/- 0.4 and 18.5 +/- 0.6 kg/m2; 113.1 +/- 4.1, 27.44 +/- 8, and 65.92 +/- 9, microg/dL; and 4.1 +/- 0.6, 2.9 +/- 0.4 and 3.6 +/- 0.7 g/dL, respectively. BMI, serum selenium, and albumin levels were found to be significantly lower (p < 0.004, p < 0.0321, and p < 0.002, respectively). CONCLUSIONS: Low serum selenium levels are associated with increased risk of pulmonary infection caused by mycobacteria.

Production and characterization of PHA from recombinant E. coli harbouring phaC1 gene of indigenous Pseudomonas sp. LDC-5 using molasses

Polyhydroxyalkanoates (PHA) are biodegradable and biocompatible green thermoplastics, synthesized by wide variety of bacteria as an intracellular carbon and energy storage intermediate. They are used as an alternative to nonrenewable petroleum derived plastics. The current interest in these biopolyesters is stimulated by the search for cost-effective capitalized production. This paper attempts to achieve maximized production rate from recombinant system using inexpensive substrate. Molasses from agro-industrial waste was used to produce PHA from recombinant E.coli in batch culture. PHA yield in molasses (3.06g/L ± 0.05-75.5 percent) was higher than that of sucrose (2.5g/L ± 0.05 - 65.1 percent). Properties of the polymer produced from molasses and sucrose were analyzed by DSC, TGA, DTA, GC/MS, TLC and optical rotation studies. The findings suggested that molasses enhanced PHA production in recombinant E.coli.

Production and characterization of PHA from recombinant E. coli harbouring phaC1 gene of indigenous Pseudomonas sp. LDC-5 using molasses.

Polyhydroxyalkanoates (PHA) are biodegradable and biocompatible green thermoplastics, synthesized by wide variety of bacteria as an intracellular carbon and energy storage intermediate. They are used as an alternative to nonrenewable petroleum derived plastics. The current interest in these biopolyesters is stimulated by the search for cost-effective capitalized production. This paper attempts to achieve maximized production rate from recombinant system using inexpensive substrate. Molasses from agro-industrial waste was used to produce PHA from recombinant E.coli in batch culture. PHA yield in molasses (3.06g/L ± 0.05‒75.5%) was higher than that of sucrose (2.5g/L ± 0.05 - 65.1%). Properties of the polymer produced from molasses and sucrose were analyzed by DSC, TGA, DTA, GC/MS, TLC and optical rotation studies. The findings suggested that molasses enhanced PHA production in recombinant E.coli.

Homology modeling of Cry10Aa toxin from B. thuringiensis israelensis and B. thuringiensis subsp. LDC-9.

A three dimensional model was developed for Cry10Aa protein sequence of B. thuringiensis LDC-9 and B. thuringiensis israelensis that has not been solved empirically by X-ray crystallography or NMR. Homology modeling was employed for the structure prediction using Cry2Aa as template protein, a high-resolution X-ray crystallography structure. The model predicted for the B. thuringiensis LDC-9 Cry10Aa protein reveals a partial N-terminal domain only due to its partial sequence of 104 amino acids. B. thuringiensis israelensis Cry10Aa model contains three domains such as domain I, a bundle of eight alpha helices with the central relatively hydrophobic helix surrounded by amphipathic helices while domain II and III contain mostly beta-sheets. Significant structural differences within domain II in this model among all Cry protein structures indicates that it is involved in recognition and binding to cell surfaces. Comparison of B. thuringiensis israelensis predicted structure with available experimentally determined Cry structures reveals identical folds. The distribution of electrostatic potential on the surface of the molecules in the model is non-uniform and identifies one side of the alpha-helical domain as negatively charged indicating orientation of toxic molecules toward the cell membrane during the initial binding with a cell surface receptor. The collective knowledge of Cry toxin structures will lead to a more critical understanding of the structural basis for receptor binding and pore formation, as well as allowing the scope of diversity to be better appreciated. This model will serve as a starting point for the design of mutagenesis experiments aimed to improve the toxicity and to provide a new tool for the elucidation of the mechanism of action of these mosquitocidal proteins.

Identification of native Bacillus thuringiensis strain from South India having specific cytocidal activity against cancer cells.

AIM: To identify the parasporin-producing, indigenous Bacillus thuringiensis strains that specifically targets human cancer cells in Madurai, Tamil Nadu, South India. METHODS AND RESULTS: Alkali-solubilized inclusion proteins from the 82 nonclonal indigenous isolates of B. thuringiensis were analysed for their cytotoxicity against two human cancer cell lines, U-937 (human histiocytic lymphoma) and HCT-15 [corrected] (adherent human colon cancer cells). Activated inclusion protein from one of the isolates, B. thuringiensis LDC-391, was found to be highly cytotoxic to HCT-15 [corrected] and moderately toxic to U-937, but nontoxic to normal lymphocytes. This strain did not show any insecticidal activity against the lepidopteran and dipteran larvae tested, as well as it was nonhaemolytic on human erythrocytes. The Western-blotting analysis showed that the putative 180 kDa cytotoxic protein from the isolate B. thuringiensis LDC-391 cross-reacted with the reference antisera of 81-kDa parasporin-1. CONCLUSIONS: Our observations imply that B. thuringiensis LDC-391 is different from the already reported parasporin producers, as it is showing variation in the target specificity. SIGNIFICANCE AND IMPACT OF THE STUDY: Characterizing these proteins can pave the way to alleviate problems associated with neoplastic transformation and cancer progression.

Molecular modeling and characterization of the B. thuringiensis and B. thuringiensis LDC-9 cytolytic proteins.

The Cyt toxins are able to lyse a wide range of cell types in vitro, unlike the Cry delta-endotoxins. It exerts its activity by the formation of pores within target cell membranes. The structural information available for Cyt2Aa (PDB id: 1CBY) consists of a single domain in which two outer layers of alpha-helix wrap around a mixed beta-sheet. Beta-barrel was suggested as a possible structure of the pores. Hence, this study seeks to investigate the structural properties of other Cytolytic proteins by predicting the three-dimensional (3D) model using Cyt2Aa as template. The predicted models are expected to be significantly more accurate as all the Cyt proteins showed significant similarity with the template (PDB id: 1CBY). The refined homology models revealed similar secondary structures (alpha-helices and beta-sheets) and tertiary features as Cyt2Aa. The variation in the loop regions of the tertiary structure accounts for the differential toxicity.

A study on medium chain length-polyhydroxyalkanoate accumulation in Escherichia coli harbouring phaC1 gene of indigenous Pseudomonas sp. LDC-5.

AIMS: This study is mainly focused on the heterologous expression and accumulation of polyhydroxyalkanoates (PHA) in Escherichia coli. METHODS AND RESULTS: PHA synthase gene (phaC1) from indigenous Pseudomonas sp. LDC-5 was amplified by PCR and cloned in E. coli (Qiagen EZ competent cells). The recombinant E. coli was analysed and confirmed for its expression of phaC1 gene by phase contrast microscopy, Western blot analysis and spectral studies (Fourier-transform infrared spectroscopy). It was further evaluated for its accumulation in different carbon and nitrogen sources. The accumulation of PHA (3.4 g l(-1)) was enhanced in the medium supplemented with glycerol and fish peptone compared to the other carbon and nitrogen sources used in this study. CONCLUSIONS: This study would enable the reduction of cost of PHA production. SIGNIFICANCE AND IMPACT OF THE STUDY: An important part of this study is that E. coli harbouring partial phaC1 gene could accumulate medium chain length PHA significantly. The results demonstrated that the E. coli strain could be a potential candidate for the large-scale production of polymer. The conditions for the higher yield and productivity will be optimized in the next phase using fermentation studies.

Identification of novel indigenous Bacillus thuringiensis isolates.

Internally Transcribed Spacers (ITS) characterization and distribution of Repetitive Extragenic Palindromic (REP) sequences were studied in the genome of 223 field isolates of Bacillus thuringiensis from Madurai, India. They were characterized by morphological, biochemical and molecular methods. One hundred and twenty four of a total 223 isolates fitted ITS characterization of B. thuringiensis varieties known. Significant genomic variation was observed among seven isolates using REP primers. The ITS PCR product (EMBL accession number AJ639659) exhibited 98% nucleotide sequence homology with B. thuringiensis and placed the origin of indigenous isolate LDC-7 closer to B. thuringiensis on the basis of phylogenetic analysis.

Introduction of a Lepidopteran-Specific Insecticidal Crystal Protein Gene of Bacillus thuringiensis subsp. kurstaki by Conjugal Transfer into a Bacillus megaterium Strain That Persists in the Cotton Phyllosphere.

A lepidopteran toxin gene of the entomopathogen Bacillus thuringiensis subsp. kurstaki HD-1 was introduced into a cotton leaf-colonizing Bacillus megaterium strain, RS1, by conjugal transfer. Rifampin- and nalidixic acid-resistant colonies obtained after cell mating were screened for crystal production by microscopy. A transcipient, B. megaterium RS1-43, was selected by this procedure. Southern blot hybridization with both total DNA and HindIII-digested DNA of the transcipient showed positive signals with a cryIA-specific probe, suggesting the transfer of the lepidopteran-specific cryIA(a) gene. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analysis confirmed the presence of the 134-kDa toxic crystal protein specific to lepidopteran larvae in the transcipient. Survival studies with cultures of the transcipient at both vegetative and postvegetative growth stages on cotton, under field conditions, suggested that the bacterium persisted on the leaf surfaces for more than 28 days, with a gradual decline in the population level with time, while the donor, B. thuringiensis subsp. kurstaki, disappeared completely after 7 days following inoculation. An in situ differential crystal-staining technique indicated the production of crystals by the transcipient on cotton leaf surfaces for about 30 days. Leaf bioassays of cotton plants inoculated with a single spray of the transcipient showed 75- to 96% mortality to the first-instar larvae of Heliothis armigera up to 21 days, and this single spray conferred total protection to the plants for about 30 days by causing an antifeeding effect on the remaining larvae.

Is the lactose-utilization ability ofRhizobium ofSesbania procumbens a vestigeal function?

Rhizobium SBS-R100, isolated from the stem nodules ofSesbania procumbens, synthesized ß-galactosidase constitutively. Transposon mutagenesis by Tn9 induced mutants defective in lactose utilization; the mutations did not interfere with growth, nodulation or N2 fixation. Mouse monoclonal antibody raised against ß-galactosidase ofEscherichia coli reacted with soluble proteins of wild typeRhizobium SBS-R100. Anin vivo constructed recombinant plasmid pSBS-4 complemented aRhizobium mutant defective in lactose utilization.