A user's guide to the Encyclopedia of DNA elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments

Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide–Rich Environments

Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments

Phytochemical screening and Antibacterial activity of selected medicinal plants of Bayabas, Sablan, Benguet Province, Cordillera Administrative Region, Luzon, Philippines

580-585The traditional knowledge on medicinal plants, when confirmed by antimicrobial and phytochemical studies, can lead to the development of drugs and plant-based medicine. Twenty selected plants that are used for the treatment of various ailments by the Ibaloi tribe in Bayabas, Sablan were tested for antibacterial activity and analysed for phytochemical constituents. A modified Kirby-Bauer method was used to test the antibacterial potential of the plants against gram-positive and gram-negative bacteria such as <i style="mso-bidi-font-style: normal">Escherichia coli, Salmonella typhimurium, Staphylococcus aureus, and Pseudomonas aeruginosa. Results showed that out of the twenty plant samples, seven showed positive results in varying degrees. Methanol extracts from the same twenty plants were analysed for their secondary metabolites using standard methods. The extracts were macerated with 95% methanol and were tested for the presence or absence of saponins, alkaloids, glycosides, anthraquinones, steroids, flavonoids and tannins. Bidens pilosa gave positive results for all secondary metabolites while the other plants contained one or two metabolites. The presence of the secondary metabolites can contribute to the antibacterial potential of the plants. The information derived herein provides scientific basis for the ethno-botanical knowledge of the local community. The phytochemicals of the plants when developed further, can offer a less-expensive treatment for various ailments

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide–Rich Environments

Hydrogen sulfide (H(2)S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H(2)S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H(2)S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H(2)S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H(2)S detoxification and toxicity likely complement each other to mediate elevated H(2)S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments

Achiote (Bixa orellana L.) : a natural source of pigment and vitamin E

Commercialization of agricultural products, including seeds and its derived products, represents an important economic source for developing countries. Natural colorants obtained from the seeds of achiote plant (annatto) have been used since pre-Hispanic times. Also, production of this crop has been important for Mayan cuisine. Annual world production of achiote seeds is approximately 14,500 tons (dry weight). Two thirds of the production is commercialized as dried seeds and the rest as colorant. Latin America produces 60% of the total world production, followed by Africa (27%) and Asia (12%). The main producers in Latin America are Peru, Brazil and Mexico. The purpose of the present paper is to review the most recent literature on Bixa orellana L. focusing on bixin, norbixin, tocotrienols and tocopherols biosynthesis, use and industrial applications of annatto extracts, as well as its nutraceutical potential and its benefits for human health.Instituto de BiotecnologíaFil: Raddatz-Mota, Denise. Universidad Autónoma Metropolitana-Iztapalapa. Departamento de Ciencias de la Salud; MéxicoFil: Pérez Flores, Laura J. Universidad Autónoma Metropolitana-Iztapalapa. Departamento de Ciencias de la Salud; MéxicoFil: Carrari, Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Mendoza-Espinoza, José Alberto. Universidad Autónoma de la Ciudad de México. Departamento de Biología Humana; MéxicoFil: Díaz de León-Sánchez, Fernando. Universidad Autónoma Metropolitana-Iztapalapa. Departamento de Ciencias de la Salud; MéxicoFil: Pinzón-López, Luis L. Instituto Tecnológico de Conkal; MéxicoFil: Godoy-Hernández, Gregorio. Centro de Investigación Científica de Yucatán. Unidad de Bioquímica y Biología Molecular de Plantas; MéxicoFil: Rivera Cabrera, Fernando. Universidad Autónoma Metropolitana-Iztapalapa. Departamento de Ciencias de la Salud; Méxic

Vitamin E succinate inhibits survivin and induces apoptosis in pancreatic cancer cells

Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States. Identifying novel chemotherapeutic and chemopreventive approaches is critical in the prevention and treatment of cancers such as pancreatic cancer. Vitamin E succinate (VES) is a redox-silent analog of the fat-soluble vitamin alpha-tocopherol. In the present study, we explored the antiproliferative action of VES and its effects on inhibitor of apoptosis proteins in pancreatic cancer cells. We show that VES inhibits cell proliferation and induces apoptosis in pancreatic cancer cells. Further, we demonstrate that VES downregulates the expression of survivin and X-linked inhibitor of apoptosis proteins. The apoptosis induced by VES was augmented by siRNA-mediated inhibition of survivin in PANC-1 cells. In summary, our results suggest that VES targets survivin signaling and induces apoptosis in pancreatic cancer cells