DNA-probe-target interaction based detection of Brucella melitensis by using surface plasmon resonance.

Surface plasmon resonance (SPR) immunosensor using 4-mercaptobenzoic acid (4-MBA) modified gold (4-MBA/Au) SPR chip was developed first time for the detection of Brucella melitensis (B. melitensis) based on the screening of its complementary DNA target by using two different newly designed DNA probes of IS711 gene. Herein, interaction between DNA probes and target molecule are also investigated and result revealed that the interaction is spontaneous. The kinetics and thermodynamic results derived from the experimental data showed that the interaction between complementary DNA targets and probe 1 is more effective than that of probe 2. Equilibrium dissociation constant (KD) and maximum binding capacity of analyte (Bmax) values for the interaction of complementary DNA target with the immobilized DNA probes were calculated by using kinetic evaluation software, and found to be 15.3 pM (KD) and 81.02m° (Bmax) with probe 1 and 54.9pM and 55.29m° (Bmax), respectively. Moreover, real serum samples analysis were also carried out using immobilized probe 1 and probe 2 with SPR which showed the applicability of this methodology and provides an alternative way for the detection of B. melitensis in less than 10min. This remarkable sensing response of present methodology offer a real time and label free detection of biological warfare agent and provide an opportunity to make miniaturized sensor, indicating considerable promise for diverse environmental, bio-defence, clinical diagnostics, food safety, water and security applications.

In Silico Structural, Virtual Screening and Docking Studies of Human Cytochrome P450 2A7 Protein.

Among CYPs, CYP2A sub-family is well known for its function to metabolise xenobiotics. CYP2A includes three members: CYP2A6, CYP2A7 and CYP2A13. Of these three proteins, structure and function of CYP2A6 and CYP2A13 are widely studied, whereas very little study has been carried out on CYP2A7. In the initial in vitro studies on CYP2A7, full protein in its active form could not be expressed. The exact structure and function of CYP2A7 is still not revealed. However, up-regulation of CYP2A7 has been reported in malignant oesophageal cells and colon cancer cells. In the present study, we generated the structure of CYP2A7 protein. The modelled proteins were validated and subjected to molecular docking analyses. The energy and RMSD calculations demonstrated that the protein is highly conserved in nature, i.e., the protein is not much flexible. Here the ligand molecules of NCI Diversity Set II from the ZINC database against the active site of the CYP2A7 protein were screened. Five compounds that possess good inhibitory activity against CYP2A7 active site were identified. The top ranking molecule (ZINC01572309) has a minimum energy score of -12.0 kcal/Mol. This compound is thus a good starting point for further development of strong inhibitors. Our in silico approach could help in better structural and functional analysis of CYP2A7. Apart from structural description of CYP2A7, elaboration of binding sites for inhibitors provides us with an opportunity to utilise binding pockets in targeted inactivation of this protein for further research.

In-silico structural, virtual screening and docking studies of Human Cytochrome P450 2A7 protein.

Among CYPs, CYP2A sub-family is well known for its function to metabolize xenobiotics. CYP2A includes three members: CYP2A6, CYP2A7 and CYP2A13. Of these three proteins, structure and function of CYP2A6 and CYP2A13 are widely studied whereas very little study has been carried out on CYP2A7. In the initial in vitro studies on CYP2A7, full protein in its active form could not be expressed. The exact structure and function of CYP2A7 is still not revealed. However, up-regulation of CYP2A7 has been reported in malignant oesophageal cells and colon cancer cells. In the present study, we generated the structure of CYP2A7 protein. The modelled proteins were validated and subjected to molecular docking analyses. The energy and RMSD calculations demonstrated that the protein is highly conserved in nature i.e. the protein is not much flexible. Here the ligand molecules of NCI Diversity Set II from the ZINC database against the active site of the CYP2A7 protein were screened. Five compounds that possess good inhibitory activity against CYP2A7 active site were identified. The top ranking molecule (ZINC01572309) has a minimum energy score of -12.0 Kcal/Mol. This compound is thus a good starting point for further development of strong inhibitors. Our in silico approach could help in better structural and functional analysis of CYP2A7. Apart from structural description of CYP2A7, elaboration of binding sites for inhibitors provides us with an opportunity to utilize binding pockets in targeted inactivation of this protein for further research.

Surface plasmon resonance characterization of monoclonal and polyclonal antibodies of malaria for biosensor applications.

Surface plasmon resonance (SPR) screening of monoclonal and polyclonal antibodies of Plasmodium falciparum (MoabPf and PoabPf) for recombinant Histidine rich protein-II antigen (Ag) of Pf (rHRP-II Ag) was conducted in a real-time and label-free manner to select an appropriate antibody (Ab) for biosensor applications. In this study 4-mercaptobenzoic acid (4-MBA) modified gold SPR chip was used for immobilizing the Ag and then Ab was interacted. SEM image showed modification of SPR chip with 4-MBA and EDAX confirmed the presence of 4-MBA on the SPR chip. Equilibrium constant (KD) and maximum binding capacity of analyte (Bmax) values for the interaction of MoabPf or PoabPf with the immobilized rHRP-II Ag were calculated and found to be 0.517 nM and 48.61 m° for MoabPf and 2.288 nM and 46.80 m° for PoabPf, respectively. In addition, thermodynamic parameters such as ΔG, ΔH and ΔS were determined for the interaction between rHRP-II Ag and MoabPf or PoabPf and the values revealed that the interaction is spontaneous, exothermic and driven by entropy. The kinetics and thermodymanic results of this study revealed that the interaction between MoabPf and rHRP-II Ag is more effective than that of PoabPf due to the fact that MoabPf was derived from a single epitope (single clone) whereas the PoabPf was from the mixture of a number of epitopes (polyclones). Finally, SPR methodology was developed for the sensing of malarial antibodies. The limit of detection was found to be 5.6 pg with MoabPf which was found to be the best in our study.

3D structure generation, virtual screening and docking of human Ras-associated binding (Rab3A) protein involved in tumourigenesis.

Rab3A is expressed predominantly in brain and synaptic vesicles. Rab3A is involved specifically in tethering and docking of synaptic vesicles prior to fusion which is a critical step in regulated release of neurotransmitters. The precise function of Rab3A is still not known. However, up-regulation of Rab3A has been reported in malignant neuroendocrine and breast cancer cells. In the present study, the structure of Rab3A protein was generated using MODELLER 9v8 software. The modeled protein structure was validated and subjected to molecular docking analyses. Docking with GTP was carried out on the binding site of Rab3A using GOLD software. The Rab3A-GTP complex has best GOLD fitness value of 77.73. Ligplot shows hydrogen bondings (S16, S17, V18, G19, K20, T21, S22, S31, T33, A35, S38, T39 and G65) and hydrophobic interacting residues (F25, F32, P34, F36, V37, D62 and A64) with the GTP ligands in the binding site of Rab3A protein. Here, the ligand molecules of NCI diversity set II from the ZINC database against the active site of the Rab3A protein were screened. For this purpose, the incremental construction algorithm of GLIDE and the genetic algorithm of GOLD were used. Docking results were analyzed for top ranking compounds using a consensus scoring function of X-Score to calculate the binding affinity and Ligplot was used to measure protein-ligand interactions. Five compounds which possess good inhibitory activity and may act as potential high affinity inhibitors against Rab3A active site were identified. The top ranking molecule (ZINC13152284) has a Glide score of -6.65 kcal/mol, X-Score of -3.02 kcal/mol and GOLD score of 64.54 with 03 hydrogen bonds and 09 hydrophobic contacts. This compound is thus a good starting point for further development of strong inhibitors.

A novel thermostable xylanase of Paenibacillus macerans IIPSP3 isolated from the termite gut.

Xylanase is an enzyme in high demand for various industrial applications, such as those in the biofuel and pulp and paper fields. In this study, xylanase-producing microbes were isolated from the gut of the wood-feeding termite at 50°C. The isolated microbe produced thermostable xylanase that was active over a broad range of temperatures (40-90°C) and pH (3.5-9.5), with optimum activity (4,170 ± 23.5 U mg⁻¹) at 60°C and pH 4.5. The enzyme was purified using a strong cation exchanger and gel filtration chromatography, revealing that the protein has a molecular mass of 205 kDa and calculated pI of 5.38. The half-life of xylanase was 6 h at 60°C and 2 h at 90°C. The isolated thermostable xylanase differed from other xylanases reported to date in terms of size, structure, and mode of action. The novelty of this enzyme lies in its high specific activity and stability at broad ranges of temperature and pH. These properties suggest that this enzyme could be utilized in bioethanol production as well as in the paper and pulp industry.

Health risk factors in different seasons of carpet industry in Kashmir, India.

Carpet workers are exposed to different types of health risk factors in different seasons of the year. As the environmental conditions become harsh, risk for developing various types of diseases increases. These problems are further aggravated when the environmental conditions at the workplace deteriorate. An attempt has been made to study the health risk factors in the carpet industry in different seasons of the year. It has been concluded that in winter weavers are affected by several types of health risk factors as compared to the other seasons.

A Mesorhizobium lipopolysaccharide (LPS) specific lectin (CRL) from the roots of nodulating host plant, Cicer arietinum.

A 30 kDa rabbit erythrocyte agglutinating glycoprotein isolated and characterized from the roots of Cicer arietinum and designated as cicer root lectin (CRL). Hemagglutination activity of CRL is strongly inhibited by cell surface LPS of nodulating cicer specific Rhizobium. CRL agglutinates mesorhizobial cells and not Escherichia coli or yeast cells. It binds to immobilized LPS of cicer specific Rhizobium only. The primary structure of CRL as predicted by peptide mass fingerprinting by MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) indicated ~54% amino acid sequence homology with C. arietinum seedling lectin (Accession no. gi/3204123) and ~26% with C. arietinum (Accession no. gi/110611256), and Pisum sativum (Accession nos. gi/230612, gi/6729956, gi/126148) lectins. These suggested CRL to be a member of vegetative tissue lectin. Circular dichroism analysis indicated that the secondary structure of CRL consists of 48% ß-sheets, 26% random coils, and 11% α-helix. CRL has six isoforms of closely associated molecular mass with differential acidic pI of 5.30, 5.20, 5.15, 5.05, 5.00, 4.80. Identity of these isoforms was confirmed from their binding with cicer specific Rhizobium LPS. All the isoforms of CRL are differentially glycosylated as identified by deglycosylation and monosaccharide analysis using high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD). All these results suggest that unlike other plant lectins CRL is a LPS-binding lectin.

Characterization of hyperthermostable alpha-amylase from Geobacillus sp. IIPTN.

A newly isolated Geobacillus sp. IIPTN (MTCC 5319) from the hot spring of Uttarakhand's Himalayan region produced a hyperthermostable alpha-amylase. The microorganism was characterized by biochemical tests and 16S rRNA gene sequencing. The optimal temperature and pH were 60 degrees C and 6.5, respectively, for growth and enzyme production. Although it was able to grow in temperature ranges from 50 to 80 degrees C and pH 5.5-8.5. Maximum enzyme production was in exponential phase with activity 135 U ml(-1) at 60 degrees C. Assayed with cassava as substrate, the enzyme displayed optimal activity 192 U ml(-1) at pH 5.0 and 80 degrees C. The enzyme was purified to homogeneity with purification fold 82 and specific activity 1,200 U mg(-1) protein. The molecular mass of the purified enzyme was 97 KDa. The values of K(m) and V(max) were 36 mg ml(-1) and 222 micromol mg(-1) protein min(-1), respectively. The amylase was stable over a broad range of temperature from 40 degrees C to 120 degrees C and pH ranges from 5 to 10. The enzyme was stimulated with Mn(2+), whereas it was inhibited by Hg(2+), Cu(2+), Zn(2+), Mg(2+), and EDTA, suggesting that it is a metalloenzyme. Besides hyperthermostability, the novelty of this enzyme is resistance against protease.

Lipopolysaccharide alters the vaginal electrical resistance in cycling and pregnant mice.

PROBLEM: Lipopolysaccharide (LPS) has been postulated to exert harmful biologic effects during pregnancy. The objective of present investigation is to measure the vaginal electrical resistance (VER) in LPS-treated normal cycling and pregnant female mice. METHOD OF STUDY: Minimum dose (MD) of LPS (250 microg/kg body weight) was injected in pregnant female mice through i.p. route on day 0.5 of pregnancy. VER was measured during different phases of reproductive cycle in female mice, which were pre-exposed to LPS and in untreated cycling female mice. VER was also measured in control pregnant female mice (saline-treated mice) through whole pregnancy and LPS-treated female mice in early stages of pregnancy. RESULTS: Vaginal electrical resistance was significantly higher during proestrous or early estrous stage as compared with any other stages of reproductive cycle in mouse. One peak of VER was observed during peri-implantation period of pregnancy in control female mice. The significant differences in the pattern of VER were found between LPS-treated and control female mice during peri-implantation period of pregnancy, and between cycling female mice, which were pre-exposed to LPS and untreated cycling female mice during proestrus. CONCLUSION: The presented results demonstrate, for the first time, that LPS exposure during pregnancy may be determined by measuring VER in mothers without any adverse effect on ongoing pregnancy and may help in refining the assisted reproduction techniques.

Modulation in the activity of lactate dehydrogenase and level of c-Myc and c-Fos by modified base queuine in cancer.

Cancer is characterized by uncontrolled cell growth, which results from unlimited proliferation and disturbs various cellular activities. Queuine is a highly modified base analogue of guanine found at first anti-codon position of specific tRNAs i.e. tRNA(Tyr), tRNA(His), tRNA(Asp) and tRNA(Asn). These tRNAs are known as Q-family of tRNA. The tRNAs of Q-family are completely modified to Q-tRNAs in terminally differentiated somatic cells, however hypomodification of Q-tRNA is closely associated with cell proliferation and malignancy. Queuosine modification of tRNAs may be essential for normal development, differentiation and cellular functions. Physiological role of queuine remains ill defined but direct or indirect evidences suggest that queuine or Q-tRNA participates in many cellular functions such as regulation of cell proliferation, control of glycolytic metabolism, alteration in expression of proto-oncogenes, modulation of signal transduction pathways but the mechanism is not well known. Increase in LDH-A expression regulated by c-myc is well documented in a variety of tumor cells. Overexpression of proto-oncogenes cause deregulated cellular responses which may lead to development of cancer. The cellular proto-oncogenes like c-myc and c-fos have important role in cell growth, proliferation and differentiation. The present study is aimed to investigate queuine mediated modulation in the activity of lactate dehydrogenase and expression of proto-oncogenes like c-myc and c-fos in T-cell lymphoma (DLAT) induced cancerous mouse. The results indicate that elevated lactate dehydrogenase activity is brought down by queuine treatments and the elevated levels of c-Myc and c-Fos in DLAT cancerous mouse are down-regulated, suggesting that queuine inhibits anaerobic metabolism and cell proliferation.

Queuine promotes antioxidant defence system by activating cellular antioxidant enzyme activities in cancer.

Constant generation of Reactive oxygen species (ROS) during normal cellular metabolism of an organism is generally balanced by similar rate of consumption by antioxidants. Imbalance between ROS production and antioxidant defense results in increased level of ROS causing oxidative stress which leads to promotion of malignancy. Queuine is a hyper modified base analogue of guanine, found at first anti-codon position of Q- family of tRNAs. These tRNAs are completely modified with respect to queuosine in terminally differentiated somatic cells, however hypomodification of Q-tRNAs is close association with cell proliferation. Q-tRNA modification is essential for normal development, differentiation and cellular functions. Queuine is a nutrient factor to eukaryotes. It is found to promote cellular antioxidant defense system and inhibit tumorigenesis. The activities of antioxidant enzymes like catalase, SOD, glutathione peroxidase and glutathione reductase are found to be low in Dalton's lymphoma ascites transplanted (DLAT) mouse liver compared to normal. However, exogenous administration of queuine to DLAT mouse improves the activities of antioxidant enzymes. The results suggest that queuine promotes antioxidant defense system by increasing antioxidant enzyme activities and in turn inhibits oxidative stress and tumorigenesis.

Queuine mediated inhibition in phosphorylation of tyrosine phosphoproteins in cancer.

Protein phosphorylation or dephosphorylation is the most important regulatory switch of signal transduction contributing to control of cell proliferation. The reversibility of phosphorylation and dephosphorylation is due to the activities of kinases and phosphatase, which determine protein phosphorylation level of cell under different physiological and pathological conditions. Receptor tyrosine kinase (RTK) mediated cellular signaling is precisely coordinated and tightly controlled in normal cells which ensures regulated mitosis. Deregulation of RTK signaling resulting in aberrant activation in RTKs leads to malignant transformation. Queuine is one of the modified base of tRNA which participates in down regulation of tyrosine kinase activity. The guanine analogue queuine is a nutrient factor to eukaryotes and occurs as free base or modified nucleoside queuosine into the first anticodon position of specific tRNAs. The tRNAs are often queuine deficient in cancer and fast proliferating tissues. The present study is aimed to investigate queuine mediated inhibition in phosphorylation of tyrosine phosphorylated proteins in lymphoma bearing mouse. The result shows high level of cytosolic and membrane associated tyrosine phosphoprotein in DLAT cancerous mouse liver compared to normal. Queuine treatments down regulate the level of tyrosine phosphoproteins, which suggests that queuine is involved in regulation of mitotic signaling pathways.

Possible involvement of queuine in regulation of cell proliferation.

An increase in cell number is one of the most prominent characteristics of cancer cells. This may be caused by an increase in cell proliferation or decrease in cell death. Queuine is one of the modified base which is found at first anticodon position of specific tRNAs. It is ubiquitously present throughout the living system except mycoplasma and yeast. The tRNAs of Q-family are completely modified to Q-tRNAs in terminally differentiated somatic cells, however hypomodification of Q-tRNA is closely associated with cell proliferation and malignancy. Queuine participates at various cellular functions such as regulation of cell proliferation, cell signaling and alteration in the expression of growth associated proto-oncogenes. Like other proto-oncogenes bcl2 is known to involve in cell survival by inhibiting apoptosis. Queuine or Q-tRNA is suggested to inhibit cell proliferation but the mechanism of regulation of cell proliferation by queuine or Q-tRNA is not well understood. Therefore, in the present study regulation in cell proliferation by queuine in vivo and in vitro as well as the expression of cell death regulatory protein Bcl2 are investigated. For this DLAT cancerous mouse, U87 cell line and HepG2 cell line are treated with different concentrations of queuine and the effect of queuine on cell proliferation and apoptosis are studied. The results indicate that queuine down regulates cell proliferation and expression of Bcl2 protein, suggesting that queuine promotes cell death and participates in the regulation of cell proliferation.

Hypomodification of transfer RNA in cancer with respect to queuosine.

Queuosine is a highly modified nucleoside analogue of guanosine. It is present only in the first position of anticodon loop of specific tRNA i.e., tRNA(his), tRNA(asp), tRNA(asn) and tRNA(tyr) and post transcriptionally modified with base-for-base exchange of guanine to queuine. The transfer RNA modifying enzyme transfer RNA guanine transglycosylase (TGTase) catalyzes the modification of tRNAs. Transfer RNA is completely modified with respect to queuosine in mature tissue, however modification is often incomplete in mitotically active cells. Hypomodification of transfer RNA is correlated with cell proliferation and malignancy. In the present study queuosine modification of transfer RNA and TGTase activity is compared in normal, Dalton's lymphoma ascites transplanted (DLAT) cancerous and queuine treated DLAT cancerous mouse liver. Transfer RNA of cancerous mouse is hypomodified in terms of queuosine modification. TGTase activity of cancerous mouse is found to decrease to less then half of enzyme activity of normal mouse; suggesting that the enzyme may be responsible for transfer RNA hypomodification. Exogenous treatment of queuine during development of cancer improves the queuosine modification of transfer RNA. The activators NaPP and ATP enhance TGTase activity of normal and DLAT cancerous mouse, where as 7mG inhibits the TGTase activity.

A 'minimum dose' of lipopolysaccharide required for implantation failure: assessment of its effect on the maternal reproductive organs and interleukin-1alpha expression in the mouse.

Genital tract infections caused by gram-negative bacteria induce abortion and are one of the most common complications of human pregnancy. This study was carried out to decipher the mechanism of gram-negative bacterial lipopolysaccharide (LPS)-induced pregnancy loss, using a mouse (Park strain) model. Since many of the biological effects of LPS are mediated by interleukin (IL)-1alpha, the role of IL-1alpha in LPS-induced pregnancy loss was studied. Pregnant female animals were injected intra-peritoneally (i.p.) with different doses (1 to 50 microg) of LPS from Salmonella minnesota Re-595, on day 0.5 of pregnancy. We found that 250 microg/kg body weight (i.e. 5 microg/female mouse) of LPS when given on day 0.5 of pregnancy was the 'minimum dose' (MD) required to completely inhibit the implantation of the blastocyst in the mouse. The effect of this dose on the pathophysiology of the various reproductive organs (i.e. uterus, ectoplacental cones, developing fetus, ovaries etc.) was assessed on day 14 of pregnancy. The effects of this dose on the level and pattern of expression of the proinflammatory cytokine IL-1alpha in the maternal uterine horns and preimplantation stage embryos were studied by RT-PCR. A single dose (100 ng/mouse) of recombinant mouse IL-1alpha was given i.p. to pregnant females on day 1 of pregnancy to study its effect on implantation. Our results show that treatment of the pregnant animals with LPS may alter cell proliferation and induce leukocyte infiltration, degeneration of luminal glandular epithelium, and hyperplasia in the various reproductive organs, and may also alter both embryonic and uterine IL-1alpha expression. IL-1alpha administration also caused implantation failure similar to that of LPS. The observations suggest that the determined MD of LPS may alter the expression of developmentally important proinflammatory cytokines such as IL-1alpha, which could, in turn, inhibit the normal processes of blastocyst implantation. Therefore, it is proposed that the LPS-induced histopathological alterations in the various reproductive organs of pregnant animals could be mediated by IL-1alpha and this may be one of the causes of failure of blastocyst implantation in the mouse.