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Nagaraj S.,Indian Central Food Technological Research Institute | Raghavan A.V.,Indian Central Food Technological Research Institute | Raghavan A.V.,Birla Institute of Technology and Science | Rao S.N.,Genotypic Technology Pvt Ltd. | Manjappara U.V.,Indian Central Food Technological Research Institute
International Journal of Biochemistry and Cell Biology | Year: 2014

Obestatin, its N-terminal fragment and the N-terminal fragment analog Nt8U were previously shown to reduce food intake, gain in body weight and triglyceride levels in albino mice. To establish their mode of action, mRNA profiling of the epididymal adipose tissue of mice treated with these peptides were performed. The differential expressions were markedly indicative of their involvement in lipid metabolism. Obestatin showed a significant upregulation of the genes patatin-like phospholipase domain containing 3, diacylglycerol O-acyltransferase 2, monoglyceride lipase, aldo-keto reductase family 1, member 7 which are involved in glycerolipid metabolism. It also upregulated peroxisome proliferator-activated receptor gamma, retinoid X receptor gamma, cluster of differentiation 36, adiponectin, C1Q and collagen domain containing, angiopoietin-like 4, lipoprotein lipase, stearoyl-coenzyme A and desaturase 3 involved in the peroxisome proliferator-activated receptor signaling pathway. Nt8U upregulated genes implicated in the same two pathways but with lesser significance and also upregulated APOL2. The N-terminal fragment though differentially regulated a small subset of the genes differentially regulated by obestatin and Nt8U, no conclusive evidence was obtained as to assign a specific pathway for its mode of action. We hypothesize that reduced food intake brought about by obestatin and Nt8U triggers lipid catabolism. The free fatty acids and lysophosphatidic acid thus produced in turn activates peroxisome proliferator-activated receptor gamma and the genes involved in peroxisome proliferator-activated receptor signaling. All of them together lead to reduction in gain in bodyweight, stored fat and circulating lipids. These results also correlate well with the observed efficacy of the peptides. © 2014 Elsevier Ltd. Source


Hickman O.J.,Kings College London | Smith R.A.,Kings College London | Dasgupta P.,Kings College London | Narayana Rao S.,Genotypic Technology Pvt Ltd. | And 6 more authors.
British Journal of Cancer | Year: 2016

Background: WFDC1/Prostate stromal 20 (ps20) is a small secreted protein highly expressed within the prostate stroma. WFDC1/ps20 expression is frequently downregulated or lost in prostate cancer (PCa) and ps20 has demonstrated growth-suppressive functions in numerous tumour model systems, although the mechanisms of this phenomenon are not understood.Methods:Ps20 was cloned and overexpressed in DU145, PC3, LNCaP and WPMY-1 cells. Cellular growth, cell cycle and apoptosis were characterised. WPMY-1 stromal cells expressing ps20 were characterised by transcriptome microarray and the function of WPMY-1 conditioned media on growth of PCa cell lines was assessed.Results:Prostrate stromal 20 expression enhanced the proliferation of LNCaP cells, whereas stromal WPMY-1 cells were inhibited and underwent increased apoptosis. Prostrate stromal 20-expressing WPMY-1 cells secrete a potently proapoptotic conditioned media. Prostrate stromal 20 overexpression upregulates expression of cyclooxygenase-2 (COX-2) in LNCaP and WPMY-1 cells, and induces expression of a growth-suppressive phenotype, which inhibits proliferation of PCa cells by ps20-expressing WPMY-1 conditioned media. This growth suppression was subsequently shown to be dependent on COX-2 function.Conclusions:This work posits that expression of ps20 in the prostate stroma can regulate growth of epithelial and other tissues through the prostaglandin synthase pathway, and thereby restricts development and progression of neoplasms. This provides a rational for selective pressure against ps20 expression in tumour- associated stroma. © 2016 Cancer Research UK. Source


Meir S.,Israel Agricultural Research Organization | Sundaresan S.,Israel Agricultural Research Organization | Sundaresan S.,Hebrew University of Jerusalem | Riov J.,Hebrew University of Jerusalem | And 2 more authors.
Stewart Postharvest Review | Year: 2015

Purpose of review: Abscission is a programmed developmental process initiated by auxin depletion. This review summarizes the mechanisms leading to auxin depletion in the abscission zone (AZ), evaluates the methods for estimation of the spatio-temporal auxin levels, demonstrates how auxin depletion occurs during natural, stressinduced, and artificially-induced organ abscission, and presents new evidence for early and late events resulting from auxin depletion which lead to organ abscission. Findings: Auxin depletion occurs during natural developmental processes which end in organ abscission (leaf and flower senescence, fruit ripening, and self-pruning) and stress-induced abscission, and following artificial organ removal in the tomato model system. Stress-induced auxin depletion is mediated by increased ethylene and reactive oxygen species (ROS) production and carbohydrate starvation. Similar changes in auxin-related genes occurred in both flower AZ (FAZ) and leaf AZ (LAZ) following flower or leaf removal, respectively, suggesting a similar regulation of the abscission process of these organs. Auxin depletion resulted from decreased indole-3- acetic acid (IAA) biosynthesis and transport, as well as from enhanced IAA transport autoinhibition (ATA), conjugation and oxidative IAA catabolism. Functional analyses of several target genes delaying abscission, such as Knotted- Like Homeobox Protein1 (KD1), Tomato Proline Rich Protein (TPRP), Ethylene Responsive Factor52 (ERF52), and Ribonuclease LX (LX), shed light on various events operating in response to auxin depletion in tomato FAZ and/or LAZ. The information gained allows a better understanding of the abscission process driven by auxin depletion, and might lead to development of improved methods for abscission control in horticultural crops. Direction for future research: A better understanding of abscission regulation as it pertains to auxin depletion will require advanced molecular tools such as microarrays, new generation sequencing (NGS), transcriptomic, functional, and proteomic analyses of target genes and proteins found to operate in the abscission process. © 2015 SPS (UK) Ltd. Source


Subudhi A.K.,Birla Institute of Technology and Science | Subudhi A.K.,King Abdullah University of Science and Technology | Boopathi P.A.,Birla Institute of Technology and Science | Boopathi P.A.,King Abdullah University of Science and Technology | And 8 more authors.
Genomics Data | Year: 2016

Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3 MB nuclear genome and encodes ~. 5600 transcripts. The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognostics. Here, we describe the strategy involved in designing a custom P. falciparum 15K array using the Agilent platform and Genotypic's Right Design methodology to study the transcriptome of Indian field isolates for which genome sequence information is limited. The array contains probes representing genome sequences of two distinct geographical isolates (i.e. 3D7 and HB3) and sub-telomeric var gene sequences of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts through a 244K array experimentation. Array performance for the 15K array, was evaluated and validated using RNA materials from P. falciparum clinical isolates. A large percentage (91%) of the represented transcripts was detected from Indian P. falciparum patient isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains. The 15K cross strain P. falciparum array has shown good efficiency in detecting transcripts from P. falciparum parasite samples isolated from patients. The low parasite loads and presence of host RNA makes arrays a preferred platform for gene expression studies over RNA-Seq. © 2016. Source


Boopathi P.A.,Birla Institute of Technology and Science | Subudhi A.K.,Birla Institute of Technology and Science | Garg S.,Birla Institute of Technology and Science | Middha S.,Sardar Patel Medical College | And 10 more authors.
Genomics Data | Year: 2014

Natural antisense transcripts (NATs) have been detected in many organisms and shown to regulate gene expression. Similarly, NATs have also been observed in malaria parasites with most studies focused on Plasmodium falciparum. There were no reports on the presence of NATs in Plasmodium vivax, which has also been shown to cause severe malaria like P. falciparum, until a recent study published by us. To identify in vivo prevalence of antisense transcripts in P. vivax clinical isolates, we performed whole genome expression profiling using a custom designed strand-specific microarray that contains probes for both sense and antisense strands. Here we describe the experimental methods and analysis of the microarray data available in Gene Expression Omnibus (GEO) under GSE45165. Our data provides a resource for exploring the presence of antisense transcripts in P. vivax isolated from patients showing varying clinical symptoms. Related information about the description and interpretation of the data can be found in a recent publication by Boopathi and colleagues in Infection, Genetics and Evolution 2013. © 2014. Source

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