Studying the effects of correlation on protein selection in proteomics data

Recently, Efron (2007) provided methods for assessing the effect of correlation on false discovery rate (FDR) in large‐scale testing problems in the context of microarray data. Although FDR procedure does not require independence of the tests, existence of correlation grossly under‐ or overestimates the number of critical genes. Here, we briefly review Efron's method and apply it to a relatively smaller spectrometry proteomics data. We show that even here the correlation can affect the FDR values and the number of proteins declared as critical.     

Optimization of process for the production of fungal pectinases from deseeded sunflower head in submerged and solid-state conditions

Pectinase production studies were carried out in submerged and solid-state conditions from deseeded sunflower head employing Aspergillus niger. The two potential strains of A. niger, DMF 27 for submerged and DMF 45 for solid-state were isolated by multi-step screening technique based on coefficient of pectolysis and capability of pectinase production. Process variables such as size of inoculum, pH, temperature, particle size and moisture content were optimized with an aim to achieve the maximum production of pectinases. The increased level of pectinase production was recorded at pH 5.0 and temperature 34 degrees C in submerged and solid-state conditions. The optimum inoculum size was 1x10(5)ml(-1) for submerged and 1x10(7)g(-1) for solid-state conditions. Five hundred micrometer particle size and 65% moisture content of the substrate were optimum for the maximum production of pectinases in solid-state condition. Under optimum conditions, maximum production of exo-pectinase was 34.2U/g in SSF and endo-pectinase was 12.6U/ml in SmF.     

Production, characterization and application of keratinase from Streptomyces gulbargensis

A Streptomyces gulbargensis newly isolated, thermotolerant feather-degrading bacterial strain was investigated for its ability to produce keratinase enzyme. Maximum keratinolytic activity was observed at 45 degrees C and pH 9.0 at 120 h of incubation. Activity was completely stable (100%) between 30 and 45 degrees C and pH 7.0-9.0, respectively. Addition of starch to the growth medium affects the activity by means of increase in keratinase secretion. After seven days of cultivation, 10-fold increase (14.3 U ml(-1)) in keratinase activity was observed in the presence of 3g starch (per liter) of the medium. The enzyme was monomeric and had a molecular mass of 46 kDa. The enzyme activity was significantly inhibited by CaCl(2) and partly inhibited by EDTA, whereas, Na(2)SO(3) enhance the enzyme activity by 2.9 times more. In addition, native chicken feather was completely degraded at 96 h of incubation. The results obtained showed that newly isolated strain S. gulbargensis could be a useful in biotechnology in terms of valorization of keratin-containing wastes or in the leather industry.     

Production and partial purification of α-amylase from a novel isolate <Emphasis Type="Italic">Streptomyces gulbargensis</Emphasis>

Extracellular amylase production by a newly isolated alkali-thermotolerant strain Streptomyces gulbargensis DAS 131 was optimized and characterized. The highest amylase production was achieved by growing S. gulbargensis DAS 131 in media with 1% starch. Strain exhibited maximal activity at pH 9.0 and 45 degrees C and relatively stable in alkaline conditions (pH 11). Starch and peptone were found to be the good source of carbon and nitrogen with a yield of 2,216.6 and 2,156.1 U, respectively. Maltose and maltotriose were the main end products of starch hydrolysis, indicating alpha-amylase activity. SDS-PAGE analysis revealed a monomeric form with a molecular weight of 55 kDa.     

Activation of platelet-activating factor receptor-coupled G alpha q leads to stimulation of Src and focal adhesion kinase via two separate pathways in human umbilical vein endothelial cells

Platelet-activating factor (PAF), a phospholipid second messenger, has diverse physiological functions, including responses in differentiated endothelial cells to external stimuli. We used human umbilical vein endothelial cells (HUVECs) as a model system. We show that PAF activated pertussis toxin-insensitive G alpha(q) protein upon binding to its seven transmembrane receptor. Elevated cAMP levels were observed via activation of adenylate cyclase, which activated protein kinase A (PKA) and was attenuated by a PAF receptor antagonist, blocking downstream activity. Phosphorylation of Src by PAF required G alpha(q) protein and adenylate cyclase activation; there was an absolute requirement of PKA for PAF-induced Src phosphorylation. Immediate (1 min) PAF-induced STAT-3 phosphorylation required the activation of G alpha(q) protein, adenylate cyclase, and PKA, and was independent of these intermediates at delayed (30 min) and prolonged (60 min) PAF exposure. PAF activated PLC beta 3 through its G alpha(q) protein-coupled receptor, whereas activation of phospholipase C gamma 1 (PLC gamma 1) by PAF was independent of G proteins but required the involvement of Src at prolonged PAF exposure (60 min). We demonstrate for the first time in vascular endothelial cells: (i) the involvement of signaling intermediates in the PAF-PAF receptor system in the induction of TIMP2 and MT1-MMP expression, resulting in the coordinated proteolytic activation of MMP2, and (ii) a receptor-mediated signal transduction cascade for the tyrosine phosphorylation of FAK by PAF. PAF exposure induced binding of p130(Cas), Src, SHC, and paxillin to FAK. Clearly, PAF-mediated signaling in differentiated endothelial cells is critical to endothelial cell functions, including cell migration and proteolytic activation of MMP2.     

<Emphasis Type="Italic">Streptomyces gulbargensis</Emphasis> sp. nov., isolated from soil in Karnataka,India

During the course of screening for industrially important microorganisms, an alkali-tolerant and thermotolerant actinomycete, strain DAS 131T, was isolated from a soil sample collected from the Gulbarga region, Karnataka province, India. The strain was characterized by a polyphasic approach that showed that it belonged to the genus Streptomyces. Growth was observed over a wide pH range (pH 6-12) and at 45 degrees C. The 16S rRNA gene sequence of strain DAS 131T was deposited in the GenBank database under the accession number DQ317411. 16S rRNA gene sequence analysis revealed that strain DAS 131T was most closely related to Streptomyces venezuelae ISP 5230T (AY999739) with a sequence similarity of 99.5% (8 nucleotide differences out of 1,477). Despite this very high sequence similarity, strain DAS 131T was phenetically distinct from S. venezuelae. The DNA relatedness between these strains was 54%, indicating that strain DAS 131T is a distinct genomic species. On the basis of phenetic and genetic analyses, strain DAS 131T is classified as a new species in the genus Streptomyces, for which we propose the name Streptomyces gulbargensis sp. nov.     

<Emphasis Type="Italic">Streptomyces tritolerans</Emphasis> sp. nov., a novel actinomycete isolated from soil in Karnataka,India

A Gram-positive, nonmotile, moderately halophilic, alkali and thermotolerant strain designated DAS 165(T), was isolated from a dry land soil sample from the Gulbarga region, Karnataka province, India. The isolate produced yellow substrate mycelia and gray aerial mycelia on most tested media. Strain DAS 165(T) showed growth in the presence of 5 to 7% NaCl and at 45 degrees C. The DNA G + C content was 69.7%. 16S rRNA gene sequence analysis together with these characteristics consistently assigned strain DAS 165(T) to the genus Streptomyces. The 16S rRNA gene sequence analysis revealed that strain DAS 165(T) was most closely related to S. tendae ATCC 19812(T) (D 63873) with a sequence similarity of 99.6% (three nucleotide differences out of 1,517). Strain DAS 165(T) formed a distinct clade based on analysis of the almost complete sequence and 120-nucleotide variable gamma region of the 16S rRNA gene. Despite the high sequence similarity, strain DAS 165(T) was phenotypically different from S. tendae ATCC 19812(T). DNA-DNA hybridization between these strains was 47% showing that strain DAS 165(T) is a distinct genomic species. Phenetic and genetic results support the classification of strain DAS 165(T) as a new species, for which the name S. tritolerans is proposed, with strain DAS 165(T) as the type strain (=DSM 41899(T )= CCTCCAA 206013(T)).     

Bioremediation Perspective of Navy Blue Rx–Containing Textile Effluent by Bacterial Isolate

The aim of the present study was to investigate the textile effluent degrading potential of an isolated bacterium, Proteus sp. SUK7. The strain had the capacity to decolorize Navy Blue Rx–containing textile effluent up to 83% within 96 h. The maximum decolorization was observed under static conditions at pH 7.0 and 30°C. Reduction in the chemical oxygen demand (COD) and biological oxygen demand (BOD) of textile effluent was observed after treatment with Proteus sp. SUK7. Induction in the activities of laccase and aminopyrine N-demethylase was observed after decolorization, which indicates involvement of these enzymes in the decolorization process. The presence of various inducers was also found to have a modulatory effect on enzyme activities and the decolorization process. Biodegradation was confirmed using various analytical techniques, such as ultraviolet-visible (UV-Vis) spectroscopy, Fourier transform infrared (FTIR), gas chromatography–mass spectrometry (GC-MS), and high-performance liquid chromatography (HPLC). A phytotoxicity study was performed to confirm the nontoxic nature of the degradation metabolites.     

Malaria prevalence in Mangaluru city area in the southwestern coastal region of India

Background

Malaria is highly prevalent in many parts of India and the Indian subcontinent. Mangaluru, a city in the southwest coastal region of Karnataka state in India, and surrounding areas are malaria endemic with 10–12 annual parasite index. Despite high endemicity, to-date, very little has been reported on the epidemiology and burden of malaria in this area.

Methods

A cross-sectional surveillance of malaria cases was performed among 900 febrile symptomatic native people (long-time residents) and immigrant labourers (temporary residents) living in Mangaluru city area. During each of dry, rainy, and end of rainy season, blood samples from a group of 300 randomly selected symptomatic people were screened for malaria infection. Data on socio-demographic, literacy, knowledge of malaria, and treatment-seeking behaviour were collected to understand the socio-demographic contributions to malaria menace in this region.

Results

Malaria is prevalent in Mangaluru region throughout the year and Plasmodium vivax is predominant species compared to Plasmodium falciparum. The infection frequency was found to be high during rainy season. Infections were markedly higher in males than females, and in adults aged 16–45 years than both younger and older age groups. Also, malaria incidence was high among immigrants compared to native population. In both groups, infection rate was directly correlated with their literacy level, knowledge on malaria, dwelling environment, and protective measures used. There was also a significant difference in treatment-seeking behaviour between these two groups.

Conclusions

Malaria incidences in Mangaluru region are predominantly localized to certain hotspot areas within the city, where socioeconomically underprivileged and immigrant labourers are densely populated. These areas have inadequate sanitation and constant water stagnation, harbouring high vector density and contributing to high infection incidences. Additionally, people in these areas seldom practice preventive measures such as using bed nets. The high incidences of malaria in adults are due to minimal cloth wearing, and long working hours stretching to late evenings in places with high vector density. Instituting heightened preventive public measures by governments and creating awareness on using preventive protective and environmental hygienic measures through educational programmes may substantially reduce the risk of contracting infections in these areas and spreading to other areas.

     

Spiro Benzodiazepine Substituted Fluorocoumarins as Potent Anti-Anxiety Agents

Russian Journal of Bioorganic Chemistry - 1,5-Benzodiazepines are one of the important class of tranquilizers. The fusion of heterocyclic systems like coumarins and indolines with the...