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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Custer C. Deocaris
Research & Development Management Office, Technological Institute of the Philippines, Cubao, Quezon City, 1102 Philippines
Agriculture, Biological Sciences & Forestry Environmental Science

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Segmental Duplications: A Possible Mechanism of Hominid Uplift through MicroRNA Diversification Maria A. Endriga; Aldrich Ivan Lois D. Burog; Denise Lauren V. Dalmacion; Custer C. Deocaris
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Abstract

MicroRNAs (miRNA) are ~21 nucleotide-long gene silencers. Segmental duplications (SD) are among the driving forces in acquiring new genes. Both miRNA and SD are believed to have played a significant role in evolution, particularly in the divergence of humans (Homo sapiens) from the chimpanzee (Pan troglodytes). This study determines the distribution of miRNAs in humans and in chimpanzees, and presents a hypothesis on its significance in the occurrence of segmental duplications. MiRNA sequences from miRBASE were subjected to BLAT and BLAST to determine if miRNAs are located in SD regions or not. Homology between miRNAs was determined with ClustalW. BLAST was then used to determine whether the non-homologous human miRNA are homologous to any other part of the chimpanzee genome. We found that all 695 human miRNAs are found exclusively in SD regions, and that 67 are de novo miRNAs. Thirteen are homologues of chimpanzee miRNA, and 11 were possibly derived from non-miRNA regions in chimp. Of these, 6 were located in SD regions of the chimpanzee genome. Results indicate that miRNA evolution occurs within regions of segmental duplication and suggest that the presence of miRNA duplicates allows more exposure to mutations that could necessitate diversification, and possibly evolution, through sub- and neofunctionalization.Keywords:
HOX Gene Promoter Prediction and Inter-genomic Comparison: An Evo-Devo Study Maria A. Endriga; Victoria Karenina R. de la Paz; Jezreel Marie G. Sazon; Elisa L. Co; Custer C. Deocaris
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Abstract

Homeobox genes direct the anterior-posterior axis of the body plan in eukaryotic organisms. Promoter regions upstream of the Hox genes jumpstart the transcription process. CpG islands found within the promoter regions can cause silencing of these promoters. The locations of the promoter regions and the CpG islands of Homeo sapiens sapiens (human), Pan troglodytes (chimpanzee), Mus musculus (mouse), and Rattus norvegicus (brown rat) are compared and related to the possible influence on the specification of the mammalian body plan. The sequence of each gene in Hox clusters A-D of the mammals considered were retrieved from Ensembl and locations of promoter regions and CpG islands predicted using Exon Finder. The predicted promoter sequences were confirmed via BLAST and verified against the Eukaryotic Promoter Database. The significance of the locations was determined using the Kruskal-Wallis test. Among the four clusters, only promoter locations in cluster B showed significant difference. HOX B genes have been linked with the control of genes that direct the development of axial morphology, particularly of the vertebral column bones. The magnitude of variation among the body plans of closely-related species can thus be partially attributed to the promoter kind, location and number, and gene inactivation via CpG methylation.
Assessment of bio-activities of the crude extract and components of Withania somnifera leaves by bioinformatics Nashi Widodo; Didik Priyandoko; Custer C. Deocaris; Renu Wadhwa; Sunil C. Kaul
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Abstract

Traditional herbal medicines are now increasingly being appreciated with Western models of integrative health sciences and evidence-based approach both in the basic research and clinic scenario. Ashwagandha is a commonly used plant in Ayurvedic, Indian traditional medicine. Medicinal value of Ashwagandha (WithaniasomniferaDunal) extends from anti-inflammatory, anti-arthritic, anti-rheumatic, rejuvenation and anti-cancer. Based on the belief that holistic multi-site mechanism of action offers greater chance of success, the traditional Ayurvedicmedicine practices the use of whole herb or its crude extract. It opposes with the mainstream of pharmaceutical industry that uses single and purified molecules. In the present study, we used bioinformatics approach to reveal the mechanism of action of (i) crude extract of Ashwagandha leaf extract and its purified components, (ii) Withanone and (iii) Withaferin A. Whereas p53-p21 was identified as a common signaling pathway for the three kinds of reagents, specific signaling pathways for Withaferin-A and Withanone were identified. Whereas the crude extract and Withanone were selectively toxic to human cancer cells, Withaferin A showed cytotoxicity to the normal cells too. The study suggested that the crude extract or a combinational formulamay be a superior and safenatural reagent for cancer treatment.
Potential Anti-cancer and Anti-bacterial Activities of Philippine Echinoderm Extracts Rodyl J. Layson; Maria Criselda A. Rodil; Elmer-Rico E. Mojica; Custer C. Deocaris
Journal of Tropical Life Science Vol. 4 No. 3 (2014)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

In high-throughput search for bioactive compounds under resource-limited settings from Philippine echino­derms, the aqueous, methanol, chloroform and hexane extracts of seven Philippine echinoderms namely Holothuria nobilis (sea cucumber), Bohadscia marmorata (sea cucumber), Stichopus chloronatus (sea cucumber), Holothuria axiologa (sea cucumber), Linckia laevigata (starfish), Oreaster nodusus (starfish) and Ophiocoma ochoenleinii (brittle star) were screened for antitumor and antibacterial activity. Antitumor activity was deter­mined using brine shrimp lethality assay while antibacterial assay was performed using turbidimetric method. Both assays utilized 96-well microtiter plates to facilitate speed and ease in screening. The chloroform extract of H. nobilis gave a positive result on antitumor activity while almost all sample extracts showed antibacterial activity against E. coli.
Co-Authors Aldrich Ivan Lois D. Burog Denise Lauren V. Dalmacion Didik Priyandoko Elisa L. Co Elmer-Rico E. Mojica Jezreel Marie G. Sazon Maria A. Endriga Maria Criselda A. Rodil Nashi Widodo Renu Wadhwa Rodyl J. Layson Sunil C. Kaul Victoria Karenina R. de la Paz