Showing papers by "Kuvempu University published in 2014"

Plasma Proteome Database as a resource for proteomics research: 2014 update

Abstract: Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.

Metal oxide-coated anodes in wastewater treatment

Abstract: Electrochemical oxidation is an effective wastewater treatment method. Metal oxide-coated substrates are commonly used as anodes in this process. This article compiles the developments in the fabrication, application, and performance of metal oxide anodes in wastewater treatment. It summarizes the preparative methods and mechanism of oxidation of organics on the metal oxide anodes. The discussion is focused on the application of SnO2, PbO2, IrO2, and RuO2 metal oxide anodes and their effectiveness in wastewater treatment process.

Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients

Abstract: Rheumatoid arthritis and osteoarthritis are two common musculoskeletal disorders that affect the joints. Despite high prevalence rates, etiological factors involved in these disorders remain largely unknown. Dissecting the molecular aspects of these disorders will significantly contribute to improving their diagnosis and clinical management. In order to identify proteins that are differentially expressed between these two conditions, a quantitative proteomic profiling of synovial fluid obtained from rheumatoid arthritis and osteoarthritis patients was carried out by using iTRAQ labeling followed by high resolution mass spectrometry analysis. We have identified 575 proteins out of which 135 proteins were found to be differentially expressed by ≥3-fold in the synovial fluid of rheumatoid arthritis and osteoarthritis patients. Proteins not previously reported to be associated with rheumatoid arthritis including, coronin-1A (CORO1A), fibrinogen like-2 (FGL2), and macrophage capping protein (CAPG) were found to be upregulated in rheumatoid arthritis. Proteins such as CD5 molecule-like protein (CD5L), soluble scavenger receptor cysteine-rich domain-containing protein (SSC5D), and TTK protein kinase (TTK) were found to be upregulated in the synovial fluid of osteoarthritis patients. We confirmed the upregulation of CAPG in rheumatoid arthritis synovial fluid by multiple reaction monitoring assay as well as by Western blot. Pathway analysis of differentially expressed proteins revealed a significant enrichment of genes involved in glycolytic pathway in rheumatoid arthritis. We report here the largest identification of proteins from the synovial fluid of rheumatoid arthritis and osteoarthritis patients using a quantitative proteomics approach. The novel proteins identified from our study needs to be explored further for their role in the disease pathogenesis of rheumatoid arthritis and osteoarthritis. Sartaj Ahmad and Raja Sekhar Nirujogi contributed equally to this article.

Proteomic analysis of human osteoarthritis synovial fluid

Abstract: Osteoarthritis is a chronic musculoskeletal disorder characterized mainly by progressive degradation of the hyaline cartilage. Patients with osteoarthritis often postpone seeking medical help, which results in the diagnosis being made at an advanced stage of cartilage destruction. Sustained efforts are needed to identify specific markers that might help in early diagnosis, monitoring disease progression and in improving therapeutic outcomes. We employed a multipronged proteomic approach, which included multiple fractionation strategies followed by high resolution mass spectrometry analysis to explore the proteome of synovial fluid obtained from osteoarthritis patients. In addition to the total proteome, we also enriched glycoproteins from synovial fluid using lectin affinity chromatography. We identified 677 proteins from synovial fluid of patients with osteoarthritis of which 545 proteins have not been previously reported. These novel proteins included ADAM-like decysin 1 (ADAMDEC1), alanyl (membrane) aminopeptidase (ANPEP), CD84, fibulin 1 (FBLN1), matrix remodelling associated 5 (MXRA5), secreted phosphoprotein 2 (SPP2) and spondin 2 (SPON2). We identified 300 proteins using lectin affinity chromatography, including the glycoproteins afamin (AFM), attractin (ATRN), fibrillin 1 (FBN1), transferrin (TF), tissue inhibitor of metalloproteinase 1 (TIMP1) and vasorin (VSN). Gene ontology analysis confirmed that a majority of the identified proteins were extracellular and are mostly involved in cell communication and signaling. We also confirmed the expression of ANPEP, dickkopf WNT signaling pathway inhibitor 3 (DKK3) and osteoglycin (OGN) by multiple reaction monitoring (MRM) analysis of osteoarthritis synovial fluid samples. We present an in-depth analysis of the synovial fluid proteome from patients with osteoarthritis. We believe that the catalog of proteins generated in this study will further enhance our knowledge regarding the pathophysiology of osteoarthritis and should assist in identifying better biomarkers for early diagnosis.

Proteomic analysis of human vitreous humor

Abstract: Background The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry.

Ketosulfone Drug as a Green Corrosion Inhibitor for Mild Steel in Acidic Medium

Abstract: Ketosulfone has been evaluated as a green corrosion inhibitor for mild steel in 1 M HCl medium by chemical and electrochemical methods. The effect of Ketosulfone on the corrosion rate was determined at various concentrations and temperature. Polarization measurements reveal that Ketosulfone acts as a mixed-type inhibitor. The adsorption of the inhibitor on the mild steel surface in acid solution was found to obey the Langmuir adsorption isotherm. The activation and thermodynamic parameters of dissolution and adsorption were calculated and discussed. Quantum chemical calculations were calculated and discussed, and it supports the results. SEM images of inhibited strips reveal the likely formation of a protective film.

Genotypic variability for antioxidant and quality parameters among tomato cultivars, hybrids, cherry tomatoes and wild species

Abstract: BACKGROUND Wide germplasm diversity and transferability of antioxidant parameters is the primary requirement for the development of high-antioxidant tomato cultivars. The present study was conducted to screen tomato genotypes including hybrids, varieties, cherry tomatoes, wild species, elite germplasm lines, interspecific hybrids and backcross populations for antioxidant activity and other quality parameters to select high-antioxidant lines with good total soluble solids (TSS) for further usage in crop improvement programmes. RESULTS Wild species and interspecific hybrids between LA-1777 (Solanum habrochaites) and an elite genotype 15SBSB recorded very high antioxidant capacity (FRAP), DPPH radical-scavenging ability, and high phenols and flavonoids. Interspecific hybrids also recorded very high total soluble solids (TSS). Significantly higher total carotenoids, lycopene and vitamin C were observed in IIHR-249-1 with moderately higher TSS. Cherry tomato lines IIHR-2866, 2865 and 2864 recorded four to five times more β-carotene than commercial hybrids/varieties. CONCLUSION Tomato line IIHR-249-1 can be used for improving antioxidant capacity, total carotenoids and lycopene in tomato breeding programmes. Cherry tomato lines IIHR-2866, 2865 and 2864 can be used for improving β-carotene content. LA-1777 and interspecific hybrids could be used for developing tomato lines rich in antioxidants as well as TSS. © 2013 Society of Chemical Industry

Degradation of polyethylene by Trichoderma harzianum —SEM, FTIR, and NMR analyses

Abstract: Trichoderma harzianum was isolated from local dumpsites of Shivamogga District for use in the biodegradation of polyethylene. Soil sample of that dumpsite was used for isolation of T. harzianum. Degradation was carried out using autoclaved, UV-treated, and surface-sterilized polyethylene. Degradation was monitored by observing weight loss and changes in physical structure by scanning electron microscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. T. harzianum was able to degrade treated polyethylene (40 %) more efficiently than autoclaved (23 %) and surface-sterilized polyethylene (13 %). Enzymes responsible for polyethylene degradation were screened from T. harzianum and were identified as laccase and manganese peroxidase. These enzymes were produced in large amount, and their activity was calculated using spectrophotometric method and crude extraction of enzymes was carried out. Molecular weight of laccase was determined as 88 kDa and that of manganese peroxidase was 55 kDa. The capacity of crude enzymes to degrade polyethylene was also determined. By observing these results, we can conclude that this organism may act as solution for the problem caused by polyethylene in nature.

Phenology of a tropical dry deciduous forest of Bhadra wildlife sanctuary, southern India

Abstract: This paper describes the leafing, flowering and fruiting phenology of canopy trees in the dry deciduous forest of Bhadra wildlife sanctuary from June 2004 to May 2006. All the woody canopy individuals (> 20 cm girth at breast height) were identified and tagged with a unique number along a transect of approximately 2 Km comprising 157 individuals of 22 species. Observations were made at monthly intervals from June 2004 to May 2006 for leafing, flowering and fruiting phenophases. Leaf fall starts in September, with a peak in December and January. Leaf initiation begins in February, with a peak in April before the monsoon. Leaf expansion starts in February from pre-monsoon with a peak in May and July during the monsoon. Leaf senescence begins in September to November and peaks in January to March. Flower bud initiates in January with a peak in April and May, and pollination begins in April with a peak in May and July before the monsoon to onset of monsoon. Fruit bud initiates in May with a peak in September and October. Unripened fruit was observed in May with a peak in September and November. Fruit fall begins in November with a peak in March. Our results show that leafing and flowering activities occur in the summer or pre-monsoon. Fruiting patterns occur during the monsoon to post - monsoon season. Seasonality among various phenophases indicates that leaf senescence flower initiation and fruit fall have strong seasonality.

In vitro cytotoxicity of caralluma species by mtt and trypan blue dye exclusion

Abstract: Caralluma species have been reported for various traditional claims; the scientific data for possible activities have not yet been studied thoroughly. However the toxicity of a plant has to be studied for further exploration of various biological activities. Extracts were studied for their toxicity by MTT and trypan blue dye exclusion models against a panel of cancer, normal origin cell lines and EAC cells. The extracts found to be moderately toxic and showed dose dependent response.

Structural, dielectric and electromagnetic shielding properties of Ni–Cu nanoferrite/PVP composites

Abstract: Nickel–copper (Ni–Cu) nanoferrites were synthesized using solution combustion method. The XRD pattern of the as prepared and calcinated samples at 600 °C revealed the presence of both cubic NiFe2O4 and tetragonal CuFe2O4 phases. Frequency and temperature dependence of dielectric constant (ɛ′), dielectric loss (tan δ) and a.c. conductivity (σac) studies have been undertaken on the Ni–Cu nanoferrites blended with polyvinylpyrrolidone (PVP) in the range 100 Hz–5 MHz. Studies have shown increasing trend of ɛ′, tan δ and σac with the increase of temperature for Ni–Cu ferrite nanoparticles in the PVP matrix. Further, frequency and temperature dependence of electromagnetic interference (EMI) shielding effectiveness (SE) is studied. The SE is found to increase with the temperature and decrease with an increase in the frequency. Ni–Cu nanoferrite/PVP composites were demonstrated a promising efficient material for the absorbing of electromagnetic waves because of a large amount of dipole polarizations in the polymer backbone and the interfaces of the ferrite nanoparticles and PVP matrix.

Characterization, charge transport and magnetic properties of multi-walled carbon nanotube–polyvinyl chloride nanocomposites

Abstract: Multi-walled carbon nanotube (MWCNT)–polyvinyl chloride (PVC) nanocomposites, with MWCNT loading up to 44.4 weight percent (wt%), were prepared by the solvent mixing and casting method. Electron microscopy indicates high degree of dispersion of MWCNT in PVC matrix, achieved by ultrasonication without using any surfactants. Thermogravimetric analysis showed a significant monotonic enhancement in the thermal stability of nanocomposites by increasing the wt% of MWCNT. Electrical conductivity of nanocomposites followed the classical percolation theory and the conductivity prominently improved from 10 −7 to 9 S/cm as the MWCNT loading increased from 0.1 to 44.4 wt%. Low value of electrical percolation threshold ~0.2 wt% is achieved which is attributed to high aspect ratio and homogeneous dispersion of MWCNT in PVC. The analysis of the low temperature electrical resistivity data shows that sample of 1.9 wt% follows three dimensional variable range hopping model whereas higher wt% nanocomposite samples follow power law behavior. The magnetization versus applied field data for both bulk MWCNTs and nanocomposite of 44.4 wt% display ferromagnetic behavior with enhanced coercivities of 1.82 and 1.27 kOe at 10 K, respectively. The enhancement in coercivity is due to strong dipolar interaction and shape anisotropy of rod-shaped iron nanoparticles.

The L1 Family of Cell Adhesion Molecules: A Sickening Number of Mutations and Protein Functions

Abstract: L1-type proteins are transmembrane cell adhesion molecules with an evolutionary well-conserved protein domain structure of usually six immunoglobulin and five fibronectin type III domains. By engaging in many different protein–protein interactions they are involved in a multitude of molecular functions and are important players during the formation and maintenance of metazoan nervous systems. As a result, mutations in L1-type genes cause a great variety of phenotypes, most of which are neurological in nature. In humans, mutations in the L1CAM gene are responsible for L1 syndrome and other L1-type genes have been implicated in conditions as varied as mental retardation, autism, schizophrenia, multiple sclerosis, and other disorders. Equally, the overexpression of L1-type proteins appears to have deleterious effects in various types of human tumor cells, where they generally contribute to an increase in cell mobility and metastatic potential.

Synthesis, antimicrobial, and antioxidant activity of benzofuran barbitone and benzofuran thiobarbitone derivatives

Abstract: The synthesis of novel series of benzofuran derivatives, containing barbitone moiety, 5-[(2/4-substitutedphenyl)(5-substituted-1-benzofuran-2-yl) methylidene]pyrimidin-2,4,6(1H,3H,5H)-trione (4a–i) and thiobarbitone moiety, 5-[(2/4-substitutedphenyl)(5-substituted-1-benzofuran-2-yl)methylidene]-2-thioxodihydropyrimidin-4,6(1H, 5H)-dione (5a–i) have been reported. The target compounds (4a–i) and (5a–i) were synthesized by the Knoevenagel condensation of (5-substituted-1-benzofuran-2-yl)(2/4-substitutedphenyl) methanone (3a–i) with barbituric acid and thiobarbituric acid, respectively, in acid medium. These compounds were screened for the antimicrobial and antioxidant activities. From antimicrobial activity results it was found that compounds 4a, 5a, 4c, and 5c displayed good antibacterial and antifungal activity against all tested strains. Further, the synthesized compounds were studied for docking on the enzyme, Glucosamine-6-phosphate synthase and the compounds 4c and 5c have emerged has an active antimicrobial agent with least binding energy (−5.27 and −4.85 kJ mol−1). Compounds 4e, 4f, 5e, and 5f showed promising free radical scavenging activity and compounds 5a and 5b showed good chelating ability with Fe2+ ions.

Development of a simple bioelectrode for the electrochemical detection of hydrogen peroxide using Pichia pastoris catalase immobilized on gold nanoparticle nanotubes and polythiophene hybrid

Abstract: In this paper, a simple and innovative electrochemical hydrogen peroxide biosensor has been proposed using catalase (CATpp) derived from Pichia pastoris as bioelectrocatalyst. The model biocomponent was immobilized on gold nanoparticle nanotubes (AuNPNTs) and polythiophene composite using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide and N-hydroxysuccinimide (EDC–NHS) coupling reagent. In this present work, we have successfully synthesized gold nanoparticles (AuNPs) by ultrasonic irradiation. The tubular gold nanostructures containing coalesced AuNPs were obtained by sacrificial template synthesis. The assembly of AuNPNTs onto the graphite (Gr) electrode was achieved via S–Au chemisorption. The latter was pre-coated with electropolymerized thiophene (PTh) to enable S groups to bind AuNPNTs. The combination of AuNPNTs–PTh, i.e., an inorganic–organic hybrid, provides a stable enzyme immobilization platform. The physical morphology of the fabricated biosensor Gr/PTh/AuNPNTs/EDC–NHS/CATpp was investigated using scanning electron microscopy and energy-dispersive microscopy. The analytical performance of the bioelectrode was examined using cyclic voltammetry, differential pulse voltammetry and chronoamperometry. Operational parameters such as working potential, pH, and thermal stability of the modified electrode were examined. The beneficial analytical characteristics of the proposed electrode were demonstrated. Our results indicate that the Gr/PTh/AuNPNTs/EDC–NHS/CATpp bioelectrode exhibits a wide linear range from 0.05 mM to 18.5 mM of H2O2, fast response time of 7 s, excellent sensitivity of 26.2 mA mM−1 cm−2, good detection limit of 0.12 μM and good Michaelis–Menten constant of 1.4 mM. In addition, the bioelectrode displayed good repeatability, high stability and acceptable reproducibility, which can be attributed to the AuNPNTs–PTh composite that provides a biocompatible micro-environment.

Antioxidant and Prophylactic Effects of Delonix elata L., Stem Bark Extracts, and Flavonoid Isolated Quercetin against Carbon Tetrachloride-Induced Hepatotoxicity in Rats

Abstract: Delonix elata L. (Ceasalpinaceae), is widely used by the traditional medical practitioners of Karnataka, India, to cure jaundice, and bronchial and rheumatic problems. The objective of this study was to screen the in vitro antioxidant and hepatoprotective activity of the stem bark extracts against CCl4-induced liver damage in rats. Among different stem bark extracts tested, the ethanol extract (DSE) has shown significant in vitro antioxidant property in radicals scavenging, metal chelating, and lipid peroxidation inhibition assays. HPLC analysis of the DSE revealed the presence of known antioxidant molecules, namely, gallic acid, ellagic acid, coumaric acid, quercetin, and rutin. Bioassay-guided fractionation of DSE has resulted in the isolation and characterization of quercetin. DSE and quercetin have shown significant prophylactic effects by restoring the liver function markers (AST, ALT, ALP, serum bilirubin, and total protein) and antioxidant enzymes (SOD, CAT, GPx, and GST). These results were proved to be hepatoprotective at par with silymarin and well supported by the histological observations of liver sections with distinct hepatic cells, and mild degree of fatty change and necrosis. The results indicated that the DSE and quercetin were significant for prophylactic activity against CCl4-induced liver damage in rats. This activity could be attributed to the antioxidant constituents in the DSE and hence justified the ethnomedicinal claims.

DNA Barcoding and Elucidation of Cryptic Diversity in Thrips (Thysanoptera)

Abstract: Accurate and timely identification of invasive insect pests underpins most biological endeavors ranging from biodiversity estimation to insect pest management. In this regard, identification of thrips, an invasive insect pest is important and challenging due to their complex life cycles, parthenogenetic mode of reproduction, sex and color morphs. In the recent years, DNA barcoding employing 5′ region of the mitochondrial Cytochrome Oxidase I (CO-I) gene has become a popular tool for species identification. In this study, we employed CO-I gene sequences for discriminating 151 species of thrips for the first time. Analyses of the intraspecific and intrageneric distances of the CO-I sequences ranged from 0.0 to 7.91% and 8.65% to 31.15% respectively. This study has revealed the existence of cryptic species in Thrips hawaiiensis (Morgan) (Thysanoptera: Thripidae) and Scirtothrips perseae Nakahara (Thysanoptera: Thripidae) for the first time, along with previously reported cryptic species such as Thrips palmi Karny (Thysanoptera: Thripidae), T. tabaci Lindeman, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), Scirtothrips dorsalis Hood. We are proposing, the feasibility of hosting an independent integrated taxonomy library for thrips and indicate that it can serve as an effective system for species identification, this approach could potentially play a key role in formulating effective insect pest management strategies.