WorldWideScience

Sample records for coffee genome project

  1. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

    NARCIS (Netherlands)

    Cornelis, M. C.; Byrne, E. M.; Esko, T.; Nalls, M. A.; Ganna, A.; Paynter, N.; Monda, K. L.; Amin, N.; Fischer, K.; Renstrom, F.; Ngwa, J. S.; Huikari, V.; Cavadino, A.; Nolte, I. M.; Teumer, A.; Yu, K.; Marques-Vidal, P.; Rawal, R.; Manichaikul, A.; Wojczynski, M. K.; Vink, J. M.; Zhao, J. H.; Burlutsky, G.; Lahti, J.; Mikkilä, V.; Lemaitre, R. N.; Eriksson, J.; Musani, S. K.; Tanaka, T.; Geller, F.; Luan, J.; Hui, J.; Mägi, R.; Dimitriou, M.; Garcia, M. E.; Ho, W.-K.; Wright, M. J.; Rose, L. M.; Magnusson, P. K. E.; Pedersen, N. L.; Couper, D.; Oostra, B. A.; Hofman, A.; Ikram, M. A.; Tiemeier, H. W.; Uitterlinden, A. G.; van Rooij, F. J. A.; Barroso, I.; Johansson, I.; Xue, L.; Kaakinen, M.; Milani, L.; Power, C.; Snieder, H.; Stolk, R. P.; Baumeister, S. E.; Biffar, R.; Gu, F.; Bastardot, F.; Kutalik, Z.; Jacobs, D. R.; Forouhi, N. G.; Mihailov, E.; Lind, L.; Lindgren, C.; Michaëlsson, K.; Morris, A.; Jensen, M.; Khaw, K.-T.; Luben, R. N.; Wang, J. J.; Männistö, S.; Perälä, M.-M.; Kähönen, M.; Lehtimäki, T.; Viikari, J.; Mozaffarian, D.; Mukamal, K.; Psaty, B. M.; Döring, A.; Heath, A. C.; Montgomery, G. W.; Dahmen, N.; Carithers, T.; Tucker, K. L.; Ferrucci, L.; Boyd, H. A.; Melbye, M.; Treur, J. L.; Mellström, D.; Hottenga, J. J.; Prokopenko, I.; Tönjes, A.; Deloukas, P.; Kanoni, S.; Lorentzon, M.; Houston, D. K.; Liu, Y.; Danesh, J.; Rasheed, A.; Mason, M. A.; Zonderman, A. B.; Franke, L.; Kristal, B. S.; Karjalainen, J.; Reed, D. R.; Westra, H.-J.; Evans, M. K.; Saleheen, D.; Harris, T. B.; Dedoussis, G.; Curhan, G.; Stumvoll, M.; Beilby, J.; Pasquale, L. R.; Feenstra, B.; Bandinelli, S.; Ordovas, J. M.; Chan, A. T.; Peters, U.; Ohlsson, C.; Gieger, C.; Martin, N. G.; Waldenberger, M.; Siscovick, D. S.; Raitakari, O.; Eriksson, J. G.; Mitchell, P.; Hunter, D. J.; Kraft, P.; Rimm, E. B.; Boomsma, D. I.; Borecki, I. B.; Loos, R. J. F.; Wareham, N. J.; Vollenweider, P.; Caporaso, N.; Grabe, H. J.; Neuhouser, M. L.; Wolffenbuttel, B. H. R.; Hu, F. B.; Hyppönen, E.; Järvelin, M.-R.; Cupples, L. A.; Franks, P. W.; Ridker, P. M.; van Duijn, C. M.; Heiss, G.; Metspalu, A.; North, K. E.; Ingelsson, E.; Nettleton, J. A.; van Dam, R. M.; Chasman, D. I.; Nalls, Michael A.; Plagnol, Vincent; Hernandez, Dena G.; Sharma, Manu; Sheerin, Una-Marie; Saad, Mohamad; Simón-Sánchez, Javier; Schulte, Claudia; Lesage, Suzanne; Sveinbjörnsdóttir, Sigurlaug; Arepalli, Sampath; Barker, Roger; Ben-Shlomo, Yoav; Berendse, Henk W.; Berg, Daniela; Bhatia, Kailash; de Bie, Rob M. A.; Biffi, Alessandro; Bloem, Bas; Bochdanovits, Zoltan; Bonin, Michael; Bras, M.; Brockmann, Kathrin; Brooks, Janet; Burn, David J.; Charlesworth, Gavin; Chen, Honglei; Chinnery, Patrick F.; Chong, Sean; Clarke, Carl E.; Cookson, Mark R.; Cooper, J. Mark; Corvol, Jean Christophe; Counsell, Carl; Damier, Philippe; Dartigues, Jean-François; Deloukas, Panos; Deuschl, Günther; Dexter, David T.; van Dijk, Karin D.; Dillman, Allissa; Durif, Frank; Dürr, Alexandra; Edkins, Sarah; Evans, Jonathan R.; Foltynie, Thomas; Dong, Jing; Gardner, Michelle; Gibbs, J. Raphael; Goate, Alison; Gray, Emma; Guerreiro, Rita; Harris, Clare; van Hilten, Jacobus J.; Hofman, Albert; Hollenbeck, Albert; Holton, Janice; Hu, Michele; Huang, Xuemei; Hershey, Milton S.; Wurster, Isabel; Mätzler, Walter; Hudson, Gavin; Hunt, Sarah E.; Huttenlocher, Johanna; Illig, Thomas; München, Helmholtz Zentrum; Jónsson, Pálmi V.; Lambert, Jean-Charles; Langford, Cordelia; Lees, Andrew; Lichtner, Peter; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw R.; Morrison, Karen E.; O' Sullivan, Sean S.; Pearson, Justin; Perlmutter, Joel S.; Pétursson, Hjörvar; Pollak, Pierre; Potter, Simon; Ravina, Bernard; Revesz, Tamas; Riess, Olaf; Rivadeneira, Fernando; Rizzu, Patrizia; Ryten, Mina; Sawcer, Stephen; Schapira, Anthony; Scheffer, Hans; Shaw, Karen; Sidransky, Ellen; Smith, Colin; Spencer, Chris C. A.; Stefánsson, Hreinn; Bettella, Francesco; Stockton, Joanna D.; Strange, Amy; Talbot, Kevin; Tanner, M.; Tashakkori-Ghanbaria, Avazeh; Tison, François; Trabzuni, Daniah; Traynor, Bryan J.; Uitterlinden, André G.; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H.; Winder-Rhodes, Sophie; Stefánsson, Kári; Martinez, Maria; Sabatier, Paul; Wood, Nicholas W.; Hardy, John; Heutink, Peter; Brice, Alexis; Gasser, Thomas; Singleton, Andrew B.; Singleton, Andrew; Cookson, Mark; Hernandez, Dena; Nalls, Michael; Zonderman, Alan; Ferrucci, Luigi; Johnson, Robert; Longo, Dan; O'Brien, Richard; Traynor, Bryan; Troncoso, Juan; van der Brug, Marcel; Zielke, Ronald; Weale, Michael; Ramasamy, Adaikalavan; Box, P. O.

    2015-01-01

    Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to

  2. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

    NARCIS (Netherlands)

    Cornelis, M. C.; Byrne, E. M.; Esko, T.; Nalls, M. A.; Ganna, A.; Paynter, N.; Monda, K. L.; Amin, N.; Fischer, K.; Renstrom, F.; Ngwa, J. S.; Huikari, V.; Cavadino, A.; Nolte, I. M.; Teumer, A.; Yu, K.; Marques-Vidal, P.; Rawal, R.; Manichaikul, A.; Wojczynski, M. K.; Vink, J. M.; Zhao, J. H.; Burlutsky, G.; Lahti, J.; Mikkila, V.; Lemaitre, R. N.; Eriksson, J.; Musani, S. K.; Tanaka, T.; Geller, F.; Luan, J.; Hui, J.; Maegi, R.; Dimitriou, M.; Garcia, M. E.; Ho, W-K; Wright, M. J.; Rose, L. M.; Magnusson, P. K. E.; Pedersen, N. L.; Couper, D.; Oostra, B. A.; Hofman, A.; Ikram, M. A.; Tiemeier, H. W.; Uitterlinden, A. G.; van Rooij, F. J. A.; Barroso, I.; Johansson, I.; Xue, L.; Kaakinen, M.; Milani, L.; Power, C.; Snieder, H.; Stolk, R. P.; Baumeister, S. E.; Biffar, R.; Gu, F.; Bastardot, F.; Kutalik, Z.; Jacobs, D. R.; Forouhi, N. G.; Mihailov, E.; Lind, L.; Lindgren, C.; Michaelsson, K.; Morris, A.; Jensen, M.; Khaw, K-T; Luben, R. N.; Wang, J. J.; Mannisto, S.; Perala, M-M; Kahonen, M.; Lehtimaki, T.; Viikari, J.; Mozaffarian, D.; Mukamal, K.; Psaty, B. M.; Doering, A.; Heath, A. C.; Montgomery, G. W.; Dahmen, N.; Carithers, T.; Tucker, K. L.; Ferrucci, L.; Boyd, H. A.; Melbye, M.; Treur, J. L.; Mellstrom, D.; Hottenga, J. J.; Prokopenko, I.; Toenjes, A.; Deloukas, P.; Kanoni, S.; Lorentzon, M.; Houston, D. K.; Liu, Y.; Danesh, J.; Rasheed, A.; Mason, M. A.; Zonderman, A. B.; Franke, L.; Kristal, B. S.; Karjalainen, J.; Reed, D. R.; Westra, H-J; Evans, M. K.; Saleheen, D.; Harris, T. B.; Dedoussis, G.; Curhan, G.; Stumvoll, M.; Beilby, J.; Pasquale, L. R.; Feenstra, B.; Bandinelli, S.; Ordovas, J. M.; Chan, A. T.; Peters, U.; Ohlsson, C.; Gieger, C.; Martin, N. G.; Waldenberger, M.; Siscovick, D. S.; Raitakari, O.; Eriksson, J. G.; Mitchell, P.; Hunter, D. J.; Kraft, P.; Rimm, E. B.; Boomsma, D. I.; Borecki, I. B.; Loos, R. J. F.; Wareham, N. J.; Vollenweider, P.; Caporaso, N.; Grabe, H. J.; Neuhouser, M. L.; Wolffenbuttel, B. H. R.; Hu, F. B.; Hyppoenen, E.; Jarvelin, M-R; Cupples, L. A.; Franks, P. W.; Ridker, P. M.; van Duijn, C. M.; Heiss, G.; Metspalu, A.; North, K. E.; Ingelsson, E.; Nettleton, J. A.; van Dam, R. M.; Chasman, D. I.

    Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to

  3. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

    NARCIS (Netherlands)

    M. Cornelis (Marilyn); E.M. Byrne; T. Esko (Tõnu); M.A. Nalls (Michael); A. Ganna (Andrea); N.P. Paynter (Nina); K.L. Monda (Keri); N. Amin (Najaf); K. Fischer (Krista); F. Renström (Frida); J.S. Ngwa; V. Huikari (Ville); A. Cavadino (Alana); I.M. Nolte (Ilja M.); A. Teumer (Alexander); K. Yu; P. Marques-Vidal; R. Rawal; A. Manichaikul (Ani); M.K. Wojczynski (Mary ); J.M. Vink; J.H. Zhao (Jing Hua); G. Burlutsky (George); J. Lahti (Jari); V. Mikkilä (Vera); R.N. Lemaitre (Rozenn ); J. Eriksson; S. Musani (Solomon); T. Tanaka; F. Geller (Frank); J. Luan; J. Hui; R. Mägi (Reedik); M. Dimitriou (Maria); M. Garcia (Melissa); W.-K. Ho; M.J. Wright (Margaret); L.M. Rose (Lynda M.); P.K.E. Magnusson (Patrik K. E.); N.L. Pedersen (Nancy L.); D.J. Couper (David); B.A. Oostra (Ben); A. Hofman (Albert); M.A. Ikram (Arfan); H.W. Tiemeier (Henning); A.G. Uitterlinden (André); F.J.A. van Rooij (Frank); I. Barroso; I. Johansson (Ingegerd); L. Xue (Luting); M. Kaakinen (Marika); L. Milani (Lili); C. Power (Christine); H. Snieder (Harold); R.P. Stolk; S.E. Baumeister (Sebastian); R. Biffar; F. Gu; F. Bastardot (Francois); Z. Kutalik; D.R. Jacobs (David); N.G. Forouhi (Nita G.); E. Mihailov (Evelin); L. Lind (Lars); C. Lindgren; K. Michaëlsson; A.P. Morris (Andrew); M.K. Jensen (Majken K.); K.T. Khaw; R.N. Luben (Robert); J.J. Wang; S. Männistö (Satu); M.-M. Perälä; M. Kähönen (Mika); T. Lehtimäki (Terho); J. Viikari (Jorma); D. Mozaffarian; K. Mukamal (Kenneth); B.M. Psaty (Bruce); A. Döring; A.C. Heath (Andrew C.); G.W. Montgomery (Grant W.); N. Dahmen (N.); T. Carithers; K.L. Tucker; L. Ferrucci (Luigi); H.A. Boyd; M. Melbye (Mads); J.L. Treur; D. Mellström (Dan); J.J. Hottenga (Jouke Jan); I. Prokopenko (Inga); A. Tönjes (Anke); P. Deloukas (Panagiotis); S. Kanoni (Stavroula); M. Lorentzon (Mattias); D.K. Houston; Y. Liu; J. Danesh (John); A. Rasheed; M.A. Mason; A.B. Zonderman; L. Franke (Lude); B.S. Kristal; J. Karjalainen (Juha); D.R. Reed; H.-J. Westra; M.K. Evans; D. Saleheen; T.B. Harris (Tamara); G.V. Dedoussis (George V.); G.C. Curhan (Gary); M. Stumvoll (Michael); J. Beilby (John); L.R. Pasquale; B. Feenstra; S. Bandinelli; J.M. Ordovas; A.T. Chan; U. Peters (Ulrike); C. Ohlsson (Claes); C. Gieger (Christian); N.G. Martin (Nicholas); M. Waldenberger (Melanie); D.S. Siscovick (David); O. Raitakari (Olli); J.G. Eriksson (Johan G.); P. Mitchell (Paul); D. Hunter (David); P. Kraft (Peter); E.B. Rimm (Eric B.); D.I. Boomsma (Dorret); I.B. Borecki (Ingrid); R.J.F. Loos (Ruth); N.J. Wareham (Nick); P.K. Vollenweider (Peter K.); N. Caporaso; H.J. Grabe (Hans Jörgen); M.L. Neuhouser (Marian L.); B.H.R. Wolffenbuttel (Bruce H. R.); F.B. Hu (Frank); E. Hypponen (Elina); M.-R. Jarvelin (Marjo-Riitta); L.A. Cupples (Adrienne); P.W. Franks; P.M. Ridker (Paul); C.M. van Duijn (Cornelia); G. Heiss (Gerardo); A. Metspalu (Andres); K.E. North (Kari); E. Ingelsson (Erik); J.A. Nettleton; R.M. van Dam (Rob); D.I. Chasman (Daniel)

    2015-01-01

    textabstractCoffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day)

  4. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

    KAUST Repository

    Vega, Fernando E.

    2015-07-31

    The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.

  5. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

    KAUST Repository

    Vega, Fernando E.; Brown, Stuart M.; Chen, Hao; Shen, Eric; Nair, Mridul B.; Ceja-Navarro, Javier A.; Brodie, Eoin L.; Infante, Francisco; Dowd, Patrick F.; Pain, Arnab

    2015-01-01

    The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.

  6. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  7. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  8. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  9. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  10. The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

    Science.gov (United States)

    Privat, Isabelle; Bardil, Amélie; Gomez, Aureliano Bombarely; Severac, Dany; Dantec, Christelle; Fuentes, Ivanna; Mueller, Lukas; Joët, Thierry; Pot, David; Foucrier, Séverine; Dussert, Stéphane; Leroy, Thierry; Journot, Laurent; de Kochko, Alexandre; Campa, Claudine; Combes, Marie-Christine; Lashermes, Philippe; Bertrand, Benoit

    2011-01-05

    Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

  11. The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

    Directory of Open Access Journals (Sweden)

    Leroy Thierry

    2011-01-01

    Full Text Available Abstract Background Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta. Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica. Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics. This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid, drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

  12. The Ensembl genome database project.

    Science.gov (United States)

    Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

    2002-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

  13. Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.

    Science.gov (United States)

    Tran, Hue T M; Ramaraj, Thiruvarangan; Furtado, Agnelo; Lee, Leonard Slade; Henry, Robert J

    2018-03-07

    Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high- or low-caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long-read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway-based analysis, 65 caffeine-associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  14. Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil.

    Science.gov (United States)

    Barbosa, Deibs; Alencar, Valquíria Campos; Santos, Daiene Souza; de Freitas Oliveira, Ana Cláudia; de Souza, Alessandra A; Coletta-Filho, Helvecio D; de Oliveira, Regina Souza; Nunes, Luiz R

    2015-05-01

    Strains of Xylella fastidiosa constitute a complex group of bacteria that develop within the xylem of many plant hosts, causing diseases of significant economic importance, such as Pierce's disease in North American grapevines and citrus variegated chlorosis in Brazil. X. fastidiosa has also been obtained from other host plants, in direct correlation with the development of diseases, as in the case of coffee leaf scorch (CLS)--a disease with potential to cause severe economic losses to the Brazilian coffee industry. This paper describes a thorough genomic characterization of coffee-infecting X. fastidiosa strains, initially performed through a microarray-based approach, which demonstrated that CLS strains could be subdivided in two phylogenetically distinct subgroups. Whole-genomic sequencing of two of these bacteria (one from each subgroup) allowed identification of ORFs and horizontally transferred elements (HTEs) that were specific to CLS-related X. fastidiosa strains. Such analyses confirmed the size and importance of HTEs as major mediators of chromosomal evolution amongst these bacteria, and allowed identification of differences in gene content, after comparisons were made with previously sequenced X. fastidiosa strains, isolated from alternative hosts. Although direct experimentation still needs to be performed to elucidate the biological consequences associated with such differences, it was interesting to verify that CLS-related bacteria display variations in genes that produce toxins, as well as surface-related factors (such as fimbrial adhesins and LPS) that have been shown to be involved with recognition of specific host factors in different pathogenic bacteria. © 2015 The Authors.

  15. The Pediatric Cancer Genome Project

    Science.gov (United States)

    Downing, James R; Wilson, Richard K; Zhang, Jinghui; Mardis, Elaine R; Pui, Ching-Hon; Ding, Li; Ley, Timothy J; Evans, William E

    2013-01-01

    The St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project (PCGP) is participating in the international effort to identify somatic mutations that drive cancer. These cancer genome sequencing efforts will not only yield an unparalleled view of the altered signaling pathways in cancer but should also identify new targets against which novel therapeutics can be developed. Although these projects are still deep in the phase of generating primary DNA sequence data, important results are emerging and valuable community resources are being generated that should catalyze future cancer research. We describe here the rationale for conducting the PCGP, present some of the early results of this project and discuss the major lessons learned and how these will affect the application of genomic sequencing in the clinic. PMID:22641210

  16. Identification and chromosomal distribution of copia-like retrotransposon sequences in the coffee (Coffea L. genome

    Directory of Open Access Journals (Sweden)

    Juan-Carlos Herrera

    2013-12-01

    Full Text Available The presence of copia-like transposable elements in seven coffee (Coffea sp. species, including the cultivated Coffea arabica, was investigated. The highly conserved domains of the reverse transcriptase (RT present in the copia retrotransposons were amplified by PCR using degenerated primers. Fragments of roughly 300 bp were obtained and the nucleotide sequence was determined for 36 clones, 19 of which showed good quality. The deduced amino acid sequences were compared by multiple alignment analysis. The data suggested two distinct coffee RT groups, designated as CRTG1 and CRTG2. The sequence identities among the groups ranged from 52 to 60% for CRTG1 and 74 to 85% for CRTG2. The multiple alignment analysis revealed that some of the clones in CRTG1 were closely related to the representative elements present in other plant species such as Brassica napus, Populus ciliata and Picea abis. Furthermore, the chromosomal localization of the RT domains in C. arabica and their putative ancestors was investigated by fluorescence in situ hybridization (FISH analysis. FISH signals were observed throughout the chromosomes following a similar dispersed pattern with some localized regions exhibiting higher concentrations of those elements, providing new evidence of their relative conservation and stability in the coffee genome

  17. The 1000 bull genome project

    Science.gov (United States)

    To meet growing global demands for high value protein from milk and meat, rates of genetic gain in domestic cattle must be accelerated. At the same time, animal health and welfare must be considered. The 1000 bull genomes project supports these goals by providing annotated sequence variants and ge...

  18. The Human Genome Diversity Project

    Energy Technology Data Exchange (ETDEWEB)

    Cavalli-Sforza, L. [Stanford Univ., CA (United States)

    1994-12-31

    The Human Genome Diversity Project (HGD Project) is an international anthropology project that seeks to study the genetic richness of the entire human species. This kind of genetic information can add a unique thread to the tapestry knowledge of humanity. Culture, environment, history, and other factors are often more important, but humanity`s genetic heritage, when analyzed with recent technology, brings another type of evidence for understanding species` past and present. The Project will deepen the understanding of this genetic richness and show both humanity`s diversity and its deep and underlying unity. The HGD Project is still largely in its planning stages, seeking the best ways to reach its goals. The continuing discussions of the Project, throughout the world, should improve the plans for the Project and their implementation. The Project is as global as humanity itself; its implementation will require the kinds of partnerships among different nations and cultures that make the involvement of UNESCO and other international organizations particularly appropriate. The author will briefly discuss the Project`s history, describe the Project, set out the core principles of the Project, and demonstrate how the Project will help combat the scourge of racism.

  19. All about the Human Genome Project (HGP)

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  20. Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee.

    OpenAIRE

    Taye H Hamza; Honglei Chen; Erin M Hill-Burns; Shannon L Rhodes; Jennifer Montimurro; Denise M Kay; Albert Tenesa; Victoria I Kusel; Patricia Sheehan; Muthukrishnan Eaaswarkhanth; Dora Yearout; Ali Samii; John W Roberts; Pinky Agarwal; Yvette Bordelon

    2011-01-01

    Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal compo...

  1. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Directory of Open Access Journals (Sweden)

    Wim Degrave

    1997-11-01

    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  2. Genomics and the human genome project: implications for psychiatry

    OpenAIRE

    Kelsoe, J R

    2004-01-01

    In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project h...

  3. Turning Farmers into Business Partners through Value Co-Creation Projects. Insights from the Coffee Supply Chain

    Directory of Open Access Journals (Sweden)

    Elena Candelo

    2018-03-01

    Full Text Available This study examines the empowerment of low-power, vulnerable stakeholders of global, complex supply chains as one effective strategy to increase value co-creation and to moderate the vulnerabilities that threaten supply chain resilience. Previous scholars have indicated the necessity of investigating the concept of value co-creation further by including various stakeholder perspectives and suggesting systems of evaluation. This research thus focuses on low-power smallholder farmers within the coffee supply chain by qualitatively evaluating the effectiveness of value co-creation projects. The study also analyzes the extent of development and the nature of empowerment initiatives designed conjointly by nongovernmental organizations (NGOs and coffee roasters that are addressed to farmers. The mixed qualitative methodology includes a literature review, interviews, focus groups, and content analysis of 20 value co-creation projects conducted in various developing and emerging coffee-producing countries. The research proposes a theoretical framework employed to conduct focus groups with Brazilian coffee farmers. This framework empirically demonstrates that these farmers are in the process of becoming business partners of the coffee supply chain thanks to various empowerment initiatives, common to most of the analyzed projects, that appear to moderate specific vulnerabilities of the coffee supply chain and therefore benefit supply chain resilience.

  4. The Chlamydomonas genome project: a decade on

    Science.gov (United States)

    Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

    2014-01-01

    The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

  5. Helminth genome projects: all or nothing

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; Horák, Aleš; Scholz, Tomáš

    2005-01-01

    Roč. 21, č. 6 (2005), s. 265-266 ISSN 1471-4922 Institutional research plan: CEZ:AV0Z60220518 Keywords : genome project * helminth * Dracunculus Subject RIV: EG - Zoology Impact factor: 4.526, year: 2005

  6. Origins of the Human Genome Project.

    Science.gov (United States)

    Watson, J D; Cook-Deegan, R M

    1991-01-01

    The Human Genome Project has become a reality. Building on a debate that dates back to 1985, several genome projects are now in full stride around the world, and more are likely to form in the next several years. Italy began its genome program in 1987, and the United Kingdom and U.S.S.R. in 1988. The European communities mounted several genome projects on yeast, bacteria, Drosophila, and Arabidospis thaliana (a rapidly growing plant with a small genome) in 1988, and in 1990 commenced a new 2-year program on the human genome. In the United States, we have completed the first year of operation of the National Center for Human Genome Research at the National Institutes of Health (NIH), now the largest single funding source for genome research in the world. There have been dedicated budgets focused on genome-scale research at NIH, the U.S. Department of Energy, and the Howard Hughes Medical Institute for several years, and results are beginning to accumulate. There were three annual meetings on genome mapping and sequencing at Cold Spring Harbor, New York, in the spring of 1988, 1989, and 1990; the talks have shifted from a discussion about how to approach problems to presenting results from experiments already performed. We have finally begun to work rather than merely talk. The purpose of genome projects is to assemble data on the structure of DNA in human chromosomes and those of other organisms. A second goal is to develop new technologies to perform mapping and sequencing. There have been impressive technical advances in the past 5 years since the debate about the human genome project began. We are on the verge of beginning pilot projects to test several approaches to sequencing long stretches of DNA, using both automation and manual methods. Ordered sets of yeast artificial chromosome and cosmid clones have been assembled to span more than 2 million base pairs of several human chromosomes, and a region of 10 million base pairs has been assembled for

  7. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

    Science.gov (United States)

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

  8. Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee.

    Science.gov (United States)

    Hamza, Taye H; Chen, Honglei; Hill-Burns, Erin M; Rhodes, Shannon L; Montimurro, Jennifer; Kay, Denise M; Tenesa, Albert; Kusel, Victoria I; Sheehan, Patricia; Eaaswarkhanth, Muthukrishnan; Yearout, Dora; Samii, Ali; Roberts, John W; Agarwal, Pinky; Bordelon, Yvette; Park, Yikyung; Wang, Liyong; Gao, Jianjun; Vance, Jeffery M; Kendler, Kenneth S; Bacanu, Silviu-Alin; Scott, William K; Ritz, Beate; Nutt, John; Factor, Stewart A; Zabetian, Cyrus P; Payami, Haydeh

    2011-08-01

    Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P(2df) = 10(-6), GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10(-7)) but not in light coffee-drinkers. The a priori Replication hypothesis that "Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers" was confirmed: OR(Replication) = 0.59, P(Replication) = 10(-3); OR(Pooled) = 0.51, P(Pooled) = 7×10(-8). Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10(-3)), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10(-13)). Imputation revealed a block of SNPs that achieved P(2df)coffee-drinkers. This study is proof of concept that inclusion of environmental factors can help identify

  9. Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee.

    Directory of Open Access Journals (Sweden)

    Taye H Hamza

    2011-08-01

    Full Text Available Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD. We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC, and we performed a genome-wide association and interaction study (GWAIS, testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P(2df = 10(-6, GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10(-7 but not in light coffee-drinkers. The a priori Replication hypothesis that "Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers" was confirmed: OR(Replication = 0.59, P(Replication = 10(-3; OR(Pooled = 0.51, P(Pooled = 7×10(-8. Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10(-3, whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10(-13. Imputation revealed a block of SNPs that achieved P(2df<5×10(-8 in GWAIS, and OR = 0.41, P = 3×10(-8 in heavy coffee-drinkers. This study is proof of

  10. Annotation of a hybrid partial genome of the Coffee Rust (Hemileia vastatrix contributes to the gene repertoire catalogue of the Pucciniales

    Directory of Open Access Journals (Sweden)

    Marco Aurelio Cristancho

    2014-10-01

    Full Text Available Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333Mb was built based on the 8 isolates; this assembly was used for subsequent analyses.Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3,921 families were uncovered; a considerable proportion of the predicted proteins (73.8% were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish

  11. Attitudes towards the Human Genome Project.

    Science.gov (United States)

    Shahroudi, Julie; Shaw, Geraldine

    Attitudes concerning the Human Genome Project were reported by faculty (N=40) and students (N=66) from a liberal arts college. Positive attitudes toward the project involved privacy, insurance and health, economic purposes, reproductive purposes, genetic counseling, religion and overall opinions. Negative attitudes were expressed regarding…

  12. Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee

    Science.gov (United States)

    Hamza, Taye H.; Chen, Honglei; Hill-Burns, Erin M.; Rhodes, Shannon L.; Montimurro, Jennifer; Kay, Denise M.; Tenesa, Albert; Kusel, Victoria I.; Sheehan, Patricia; Eaaswarkhanth, Muthukrishnan; Yearout, Dora; Samii, Ali; Roberts, John W.; Agarwal, Pinky; Bordelon, Yvette; Park, Yikyung; Wang, Liyong; Gao, Jianjun; Vance, Jeffery M.; Kendler, Kenneth S.; Bacanu, Silviu-Alin; Scott, William K.; Ritz, Beate; Nutt, John; Factor, Stewart A.; Zabetian, Cyrus P.; Payami, Haydeh

    2011-01-01

    Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P2df = 10−6, GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10−7) but not in light coffee-drinkers. The a priori Replication hypothesis that “Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers” was confirmed: ORReplication = 0.59, PReplication = 10−3; ORPooled = 0.51, PPooled = 7×10−8. Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10−3), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10−13). Imputation revealed a block of SNPs that achieved P2dfcoffee-drinkers. This study is proof of concept that inclusion of environmental factors can help identify genes that

  13. Human genomics projects and precision medicine.

    Science.gov (United States)

    Carrasco-Ramiro, F; Peiró-Pastor, R; Aguado, B

    2017-09-01

    The completion of the Human Genome Project (HGP) in 2001 opened the floodgates to a deeper understanding of medicine. There are dozens of HGP-like projects which involve from a few tens to several million genomes currently in progress, which vary from having specialized goals or a more general approach. However, data generation, storage, management and analysis in public and private cloud computing platforms have raised concerns about privacy and security. The knowledge gained from further research has changed the field of genomics and is now slowly permeating into clinical medicine. The new precision (personalized) medicine, where genome sequencing and data analysis are essential components, allows tailored diagnosis and treatment according to the information from the patient's own genome and specific environmental factors. P4 (predictive, preventive, personalized and participatory) medicine is introducing new concepts, challenges and opportunities. This review summarizes current sequencing technologies, concentrates on ongoing human genomics projects, and provides some examples in which precision medicine has already demonstrated clinical impact in diagnosis and/or treatment.

  14. Genome projects and the functional-genomic era.

    Science.gov (United States)

    Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

    2005-12-01

    The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

  15. Drinking Coffee

    DEFF Research Database (Denmark)

    Strøbæk, Pernille Solveig

    2015-01-01

    The chapter explores how coffee is an integral part of our daily life. Focusing on coffee drinking at home, at work, and on the go I show that coffee consumption is a social practice. The chapter illustrates through everyday examples that coffee is more than a caffeine drug. Coffee, with or without...... caffeine, is a social lubricant. We talk to each other and share emotions with one another as we share a cup of coffee. Coffee makes conversation and we embrace coffee, to stay or to go, in the daily rhythm of our busy and global social existence. The practice and sociality of coffee consumption provide...... the coffee industry with the opportunity to make money on our coffee preferences – indeed, also for those of us who actually dislike the taste of coffee. Would you prefer coffee mixed and stirred with non-coffee products such as salt, caramel and licorice? Then you are one of us in the modern age of coffee...

  16. Justice and the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, T.F.; Lappe, M. (eds.)

    1992-01-01

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  17. Justice and the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, T.F.; Lappe, M. [eds.

    1992-12-31

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  18. Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

    DEFF Research Database (Denmark)

    Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

    Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

  19. The Human Genome Project and Biology Education.

    Science.gov (United States)

    McInerney, Joseph D.

    1996-01-01

    Highlights the importance of the Human Genome Project in educating the public about genetics. Discusses four challenges that science educators must address: teaching for conceptual understanding, the nature of science, the personal and social impact of science and technology, and the principles of technology. Contains 45 references. (JRH)

  20. Implications of the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Kitcher, P.

    1998-11-01

    The Human Genome Project (HGP), launched in 1991, aims to map and sequence the human genome by 2006. During the fifteen-year life of the project, it is projected that $3 billion in federal funds will be allocated to it. The ultimate aims of spending this money are to analyze the structure of human DNA, to identify all human genes, to recognize the functions of those genes, and to prepare for the biology and medicine of the twenty-first century. The following summary examines some of the implications of the program, concentrating on its scientific import and on the ethical and social problems that it raises. Its aim is to expose principles that might be used in applying the information which the HGP will generate. There is no attempt here to translate the principles into detailed proposals for legislation. Arguments and discussion can be found in the full report, but, like this summary, that report does not contain any legislative proposals.

  1. Origins of the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, Robert

    1993-07-01

    The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

  2. Origins of the Human Genome Project

    Science.gov (United States)

    Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)

    1993-07-01

    The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

  3. A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

    Science.gov (United States)

    Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

    2007-06-29

    In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

  4. An overview of the human genome project

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.

    1994-01-01

    The human genome project is one of the most ambitious scientific projects to date, with the ultimate goal being a nucleotide sequence for all four billion bases of human DNA. In the process of determining the nucleotide sequence for each base, the location, function, and regulatory regions from the estimated 100,000 human genes will be identified. The genome project itself relies upon maps of the human genetic code derived from several different levels of resolution. Genetic linkage analysis provides a low resolution genome map. The information for genetic linkage maps is derived from the analysis of chromosome specific markers such as Sequence Tagged Sites (STSs), Variable Number of Tandem Repeats (VNTRs) or other polymorphic (highly informative) loci in a number of different-families. Using this information the location of an unknown disease gene can be limited to a region comprised of one million base pairs of DNA or less. After this point, one must construct or have access to a physical map of the region of interest. Physical mapping involves the construction of an ordered overlapping (contiguous) set of recombinant DNA clones. These clones may be derived from a number of different vectors including cosmids, Bacterial Artificial Chromosomes (BACs), P1 derived Artificial Chromosomes (PACs), somatic cell hybrids, or Yeast Artificial Chromosomes (YACs). The ultimate goal for physical mapping is to establish a completely overlapping (contiguous) set of clones for the entire genome. After a gene or region of interest has been localized using physical mapping the nucleotide sequence is determined. The overlap between genetic mapping, physical mapping and DNA sequencing has proven to be a powerful tool for the isolation of disease genes through positional cloning.

  5. The Human Genome Project (HGP): dividends and challenges: a ...

    African Journals Online (AJOL)

    The Human Genome Project (HGP): dividends and challenges: a review. ... Genomic studies have given profound insights into the genetic organization of ... with it will be an essential part of modern medicine and biology for years to come.

  6. Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.

    Directory of Open Access Journals (Sweden)

    Philippe Lashermes

    2016-09-01

    Full Text Available Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.

  7. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

    OpenAIRE

    Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

    2015-01-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

  8. A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms.

    Directory of Open Access Journals (Sweden)

    Christiane Noronha Fernandes-Brum

    Full Text Available microRNAs (miRNAs are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs are derived from double-stranded RNA (dsRNA or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL in processing the smallRNAs (sRNAs and ARGONAUTE (AGO as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR, Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated, and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.

  9. The modest beginnings of one genome project.

    Science.gov (United States)

    Kaback, David B

    2013-06-01

    One of the top things on a geneticist's wish list has to be a set of mutants for every gene in their particular organism. Such a set was produced for the yeast, Saccharomyces cerevisiae near the end of the 20th century by a consortium of yeast geneticists. However, the functional genomic analysis of one chromosome, its smallest, had already begun more than 25 years earlier as a project that was designed to define most or all of that chromosome's essential genes by temperature-sensitive lethal mutations. When far fewer than expected genes were uncovered, the relatively new field of molecular cloning enabled us and indeed, the entire community of yeast researchers to approach this problem more definitively. These studies ultimately led to cloning, genomic sequencing, and the production and phenotypic analysis of the entire set of knockout mutations for this model organism as well as a better concept of what defines an essential function, a wish fulfilled that enables this model eukaryote to continue at the forefront of research in modern biology.

  10. Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM.

    Science.gov (United States)

    Amin, N; Byrne, E; Johnson, J; Chenevix-Trench, G; Walter, S; Nolte, I M; Vink, J M; Rawal, R; Mangino, M; Teumer, A; Keers, J C; Verwoert, G; Baumeister, S; Biffar, R; Petersmann, A; Dahmen, N; Doering, A; Isaacs, A; Broer, L; Wray, N R; Montgomery, G W; Levy, D; Psaty, B M; Gudnason, V; Chakravarti, A; Sulem, P; Gudbjartsson, D F; Kiemeney, L A; Thorsteinsdottir, U; Stefansson, K; van Rooij, F J A; Aulchenko, Y S; Hottenga, J J; Rivadeneira, F R; Hofman, A; Uitterlinden, A G; Hammond, C J; Shin, S-Y; Ikram, A; Witteman, J C M; Janssens, A C J W; Snieder, H; Tiemeier, H; Wolfenbuttel, B H R; Oostra, B A; Heath, A C; Wichmann, E; Spector, T D; Grabe, H J; Boomsma, D I; Martin, N G; van Duijn, C M

    2012-11-01

    Coffee consumption is a model for addictive behavior. We performed a meta-analysis of genome-wide association studies (GWASs) on coffee intake from 8 Caucasian cohorts (N=18 176) and sought replication of our top findings in a further 7929 individuals. We also performed a gene expression analysis treating different cell lines with caffeine. Genome-wide significant association was observed for two single-nucleotide polymorphisms (SNPs) in the 15q24 region. The two SNPs rs2470893 and rs2472297 (P-values=1.6 × 10(-11) and 2.7 × 10(-11)), which were also in strong linkage disequilibrium (r(2)=0.7) with each other, lie in the 23-kb long commonly shared 5' flanking region between CYP1A1 and CYP1A2 genes. CYP1A1 was found to be downregulated in lymphoblastoid cell lines treated with caffeine. CYP1A1 is known to metabolize polycyclic aromatic hydrocarbons, which are important constituents of coffee, whereas CYP1A2 is involved in the primary metabolism of caffeine. Significant evidence of association was also detected at rs382140 (P-value=3.9 × 10(-09)) near NRCAM-a gene implicated in vulnerability to addiction, and at another independent hit rs6495122 (P-value=7.1 × 10(-09))-an SNP associated with blood pressure-in the 15q24 region near the gene ULK3, in the meta-analysis of discovery and replication cohorts. Our results from GWASs and expression analysis also strongly implicate CAB39L in coffee drinking. Pathway analysis of differentially expressed genes revealed significantly enriched ubiquitin proteasome (P-value=2.2 × 10(-05)) and Parkinson's disease pathways (P-value=3.6 × 10(-05)).

  11. Green Coffee

    Science.gov (United States)

    ... coffee product Coffee Slender (Med-Eq Ltd., Tonsberg, Norway), lose an average of 2.5 to 3. ... might increase the risk of experiencing serious or life-threatening side effects such as high blood pressure, ...

  12. Suitability Analysis and Projected Climate Change Impact on Banana and Coffee Production Zones in Nepal

    Science.gov (United States)

    Sujakhu, Nani M.; Merz, Juerg; Kindt, Roeland; Xu, Jianchu; Matin, Mir A.; Ali, Mostafa; Zomer, Robert J.

    2016-01-01

    The Government of Nepal has identified opportunities in agricultural commercialization, responding to a growing internal demand and expansion of export markets to reduce the immense trade deficit. Several cash crops, including coffee and bananas, have been identified in the recently approved Agriculture Development Strategy. Both of these crops have encouraged smallholder farmers to convert their subsistence farming practices to more commercial cultivation. Identification of suitable agro-ecological zones and understanding climate-related issues are important for improved production and livelihoods of smallholder farmers. Here, the suitability of coffee and banana crops is analyzed for different agro-ecological zones represented by Global Environmental Stratification (GEnS). Future shifts in these suitability zones are also predicted. Plantation sites in Nepal were geo-referenced and used as input in species distribution modelling. The multi-model ensemble model suggests that climate change will reduce the suitable growing area for coffee by about 72% across the selected emission scenarios from now to 2050. Impacts are low for banana growing, with a reduction in suitability by about 16% by 2050. Bananas show a lot of potential for playing an important role in Nepal as a sustainable crop in the context of climate change, as this study indicates that the amount of area suited to banana growing will grow by 40% by 2050. Based on our analysis we recommend possible new locations for coffee plantations and one method for mitigating climate change-related problems on existing plantations. These findings are expected to support planning and policy dialogue for mitigation and support better informed and scientifically based decision-making relating to these two crops. PMID:27689354

  13. A 1000 Arab genome project to study the Emirati population.

    Science.gov (United States)

    Al-Ali, Mariam; Osman, Wael; Tay, Guan K; AlSafar, Habiba S

    2018-04-01

    Discoveries from the human genome, HapMap, and 1000 genome projects have collectively contributed toward the creation of a catalog of human genetic variations that has improved our understanding of human diversity. Despite the collegial nature of many of these genome study consortiums, which has led to the cataloging of genetic variations of different ethnic groups from around the world, genome data on the Arab population remains overwhelmingly underrepresented. The National Arab Genome project in the United Arab Emirates (UAE) aims to address this deficiency by using Next Generation Sequencing (NGS) technology to provide data to improve our understanding of the Arab genome and catalog variants that are unique to the Arab population of the UAE. The project was conceived to shed light on the similarities and differences between the Arab genome and those of the other ethnic groups.

  14. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  15. The Human Genome Project: how do we protect Australians?

    Science.gov (United States)

    Stott Despoja, N

    It is the moon landing of the nineties: the ambitious Human Genome Project--identifying the up to 100,000 genes that make up human DNA and the sequences of the three billion base-pairs that comprise the human genome. However, unlike the moon landing, the effects of the genome project will have a fundamental impact on the way we see ourselves and each other.

  16. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    Science.gov (United States)

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Coffee intake.

    Science.gov (United States)

    Cornelis, Marilyn C

    2012-01-01

    Coffee is one of the most widely consumed beverages in the world. Its widespread popularity and availability has fostered public health concerns of the potential health consequences of regular coffee consumption. Epidemiological studies of coffee intake and certain health outcomes have been inconsistent. The precise component of coffee potentially contributing to development of these conditions also remains unclear. One step toward addressing the challenges in studying the impact coffee has on health is a better understanding of the factors contributing to its consumption and physiological effects. This chapter focuses on those factors that are genetically determined and briefly summarizes progress in applying this knowledge to epidemiological studies of coffee and disease. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Comparative genomic data of the Avian Phylogenomics Project.

    Science.gov (United States)

    Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun

    2014-01-01

    genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

  19. A computational genomics pipeline for prokaryotic sequencing projects.

    Science.gov (United States)

    Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

    2010-08-01

    New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

  20. The Human Genome Project: big science transforms biology and medicine.

    Science.gov (United States)

    Hood, Leroy; Rowen, Lee

    2013-01-01

    The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called 'big science' - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project.

  1. The Human Genome Project: An Imperative for International Collaboration.

    Science.gov (United States)

    Allende, J. E.

    1989-01-01

    Discussed is the Human Genome Project which aims to decipher the totality of the human genetic information. The historical background, the objectives, international cooperation, ethical discussion, and the role of UNESCO are included. (KR)

  2. The Human Genome Project: big science transforms biology and medicine

    OpenAIRE

    Hood, Leroy; Rowen, Lee

    2013-01-01

    The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called ‘big science’ - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and a...

  3. National human genome projects: an update and an agenda.

    Science.gov (United States)

    An, Joon Yong

    2017-01-01

    Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions in defined population. This perspective summarizes national genome projects conducted in the past 10 years and introduces case studies to utilize genomic data in genetic research.

  4. The Genome 10K Project: a way forward.

    Science.gov (United States)

    Koepfli, Klaus-Peter; Paten, Benedict; O'Brien, Stephen J

    2015-01-01

    The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

  5. Toward systems epidemiology of coffee and health.

    Science.gov (United States)

    Cornelis, Marilyn C

    2015-02-01

    Coffee is one of the most widely consumed beverages in the world and has been associated with many health conditions. This review examines the limitations of the classic epidemiological approach to studies of coffee and health, and describes the progress in systems epidemiology of coffee and its correlated constituent, caffeine. Implications and applications of this growing body of knowledge are also discussed. Population-based metabolomic studies of coffee replicate coffee-metabolite correlations observed in clinical settings but have also identified novel metabolites of coffee response, such as specific sphingomyelin derivatives and acylcarnitines. Genome-wide analyses of self-reported coffee and caffeine intake and serum levels of caffeine support an overwhelming role for caffeine in modulating the coffee consumption behavior. Interindividual variation in the physiological exposure or response to any of the many chemicals present in coffee may alter the persistence and magnitude of their effects. It is thus imperative that future studies of coffee and health account for this variation. Systems epidemiological approaches promise to inform causality, parse the constituents of coffee responsible for health effects, and identify the subgroups most likely to benefit from increasing or decreasing coffee consumption.

  6. Los Alamos Science: The Human Genome Project. Number 20, 1992

    Science.gov (United States)

    Cooper, N. G.; Shea, N. eds.

    1992-01-01

    This document provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.

  7. Los Alamos Science: The Human Genome Project. Number 20, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, N G; Shea, N [eds.

    1992-01-01

    This article provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.

  8. A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

    Science.gov (United States)

    Moraes, Fernanda; Góes, Andréa

    2016-05-06

    The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  9. Human genome project: revolutionizing biology through leveraging technology

    Science.gov (United States)

    Dahl, Carol A.; Strausberg, Robert L.

    1996-04-01

    The Human Genome Project (HGP) is an international project to develop genetic, physical, and sequence-based maps of the human genome. Since the inception of the HGP it has been clear that substantially improved technology would be required to meet the scientific goals, particularly in order to acquire the complete sequence of the human genome, and that these technologies coupled with the information forthcoming from the project would have a dramatic effect on the way biomedical research is performed in the future. In this paper, we discuss the state-of-the-art for genomic DNA sequencing, technological challenges that remain, and the potential technological paths that could yield substantially improved genomic sequencing technology. The impact of the technology developed from the HGP is broad-reaching and a discussion of other research and medical applications that are leveraging HGP-derived DNA analysis technologies is included. The multidisciplinary approach to the development of new technologies that has been successful for the HGP provides a paradigm for facilitating new genomic approaches toward understanding the biological role of functional elements and systems within the cell, including those encoded within genomic DNA and their molecular products.

  10. The human genome project and the future of medical practice ...

    African Journals Online (AJOL)

    Contrary to the scepticism that characterised the planning stages of the human genome project, the technology and sequence data resulting from the project are set to revolutionise medical practice for good. The expected benefits include: enhanced discovery of disease genes, which will lead to improved knowledge on the ...

  11. COFFEE - Coherent Optical System Field Trial for Spectral Efficiency Enhancement

    DEFF Research Database (Denmark)

    Imran, Muhammad; Fresi, Francesco; Rommel, Simon

    2016-01-01

    The scope, aims, and contributions of the COFFEE project for spectral efficiency enhancement and market exposure are presented.......The scope, aims, and contributions of the COFFEE project for spectral efficiency enhancement and market exposure are presented....

  12. The Pocket-4-Life project, bioavailability and beneficial properties of the bioactive compounds of espresso coffee and cocoa-based confectionery containing coffee: study protocol for a randomized cross-over trial

    OpenAIRE

    Mena, Pedro; Tassotti, Michele; Martini, Daniela; Rosi, Alice; Brighenti, Furio; Del Rio, Daniele

    2017-01-01

    Background Coffee is an important source of bioactive compounds, including caffeine, phenolic compounds (mainly chlorogenic acids), trigonelline, and diterpenes. Several studies have highlighted the preventive effects of coffee consumption on major cardiometabolic diseases, but the impact of coffee dosage on markers of cardiometabolic risk is not well understood. Moreover, the pool of coffee-derived circulating metabolites and the contribution of each metabolite to disease prevention still ne...

  13. Harvard Personal Genome Project: lessons from participatory public research

    Science.gov (United States)

    2014-01-01

    Background Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants. PMID:24713084

  14. Harvard Personal Genome Project: lessons from participatory public research.

    Science.gov (United States)

    Ball, Madeleine P; Bobe, Jason R; Chou, Michael F; Clegg, Tom; Estep, Preston W; Lunshof, Jeantine E; Vandewege, Ward; Zaranek, Alexander; Church, George M

    2014-02-28

    Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an 'open consent' framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants.

  15. The human Genome project and the future of oncology

    International Nuclear Information System (INIS)

    Collins, Francis S.

    1996-01-01

    The Human Genome Project is an ambitious 15-year effort to devise maps and sequence of the 3-billion base pair human genome, including all 100,000 genes. The project is running ahead of schedule and under budget. Already the effects on progress in disease gene discovery have been dramatic, especially for cancer. The most appropriate uses of susceptibility testing for breast, ovarian, and colon cancer are being investigated in research protocols, and the need to prevent genetic discrimination in employment and health insurance is becoming more urgent. In the longer term, these gene discoveries are likely to usher in a new era of therapeutic molecular medicine

  16. Sequencing of a new target genome: the Pediculus humanus humanus (Phthiraptera: Pediculidae) genome project.

    Science.gov (United States)

    Pittendrigh, B R; Clark, J M; Johnston, J S; Lee, S H; Romero-Severson, J; Dasch, G A

    2006-11-01

    The human body louse, Pediculus humanus humanus (L.), and the human head louse, Pediculus humanus capitis, belong to the hemimetabolous order Phthiraptera. The body louse is the primary vector that transmits the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. The genomes of the bacterial causative agents of several of these aforementioned diseases have been sequenced. Thus, determining the body louse genome will enhance studies of host-vector-pathogen interactions. Although not important as a major disease vector, head lice are of major social concern. Resistance to traditional pesticides used to control head and body lice have developed. It is imperative that new molecular targets be discovered for the development of novel compounds to control these insects. No complete genome sequence exists for a hemimetabolous insect species primarily because hemimetabolous insects often have large (2000 Mb) to very large (up to 16,300 Mb) genomes. Fortuitously, we determined that the human body louse has one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome in which many genes have been eliminated during its adaptation to human parasitism. Because many louse species infest birds and mammals, the body louse genome-sequencing project will facilitate studies of their comparative genomics. A 6-8X coverage of the body louse genome, plus sequenced expressed sequence tags, should provide the entomological, evolutionary biology, medical, and public health communities with useful genetic information.

  17. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

    Science.gov (United States)

    Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

    2015-08-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

  18. Reconsidering democracy. History of the Human Genome Project.

    NARCIS (Netherlands)

    Marli Huijer

    2003-01-01

    What options are open for people—citizens, politicians, and other nonscientists—to become actively involved in and anticipate new directions in the life sciences? In addressing this question, this article focuses on the start of the Human Genome Project (1985-1990). By contrasting various models of

  19. The Human Genome Project: Biology, Computers, and Privacy.

    Science.gov (United States)

    Cutter, Mary Ann G.; Drexler, Edward; Gottesman, Kay S.; Goulding, Philip G.; McCullough, Laurence B.; McInerney, Joseph D.; Micikas, Lynda B.; Mural, Richard J.; Murray, Jeffrey C.; Zola, John

    This module, for high school teachers, is the second of two modules about the Human Genome Project (HGP) produced by the Biological Sciences Curriculum Study (BSCS). The first section of this module provides background information for teachers about the structure and objectives of the HGP, aspects of the science and technology that underlie the…

  20. Reconsidering democracy - History of the human genome project

    NARCIS (Netherlands)

    Huijer, M

    What options are open for people-citizens, politicians, and other nonscientists-to become actively involved in and anticipate new directions in the life sciences? In addressing this question, this article focuses on the start of the Human Genome Project (1985-1990). By contrasting various models of

  1. Enhancing Biology Instruction with the Human Genome Project

    Science.gov (United States)

    Buxeda, Rosa J.; Moore-Russo, Deborah A.

    2003-01-01

    The Human Genome Project (HGP) is a recent scientific milestone that has received notable attention. This article shows how a biology course is using the HGP to enhance students' experiences by providing awareness of cutting edge research, with information on new emerging career options, and with opportunities to consider ethical questions raised…

  2. Comparing genetic variants detected in the 1000 genomes project ...

    Indian Academy of Sciences (India)

    Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide ...

  3. Mapping our genes: The genome projects: How big, how fast

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1988-04-01

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

  4. Mapping Our Genes: The Genome Projects: How Big, How Fast

    Science.gov (United States)

    1988-04-01

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for ?writing the rules? of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. The Office of Technology Assessment (OTA) prepared this report with the assistance of several hundred experts throughout the world.

  5. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

    NARCIS (Netherlands)

    Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

    2015-01-01

    We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

  6. The African Genome Variation Project shapes medical genetics in Africa.

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  7. The African Genome Variation Project shapes medical genetics in Africa

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  8. The Pocket-4-Life project, bioavailability and beneficial properties of the bioactive compounds of espresso coffee and cocoa-based confectionery containing coffee: study protocol for a randomized cross-over trial.

    Science.gov (United States)

    Mena, Pedro; Tassotti, Michele; Martini, Daniela; Rosi, Alice; Brighenti, Furio; Del Rio, Daniele

    2017-11-09

    Coffee is an important source of bioactive compounds, including caffeine, phenolic compounds (mainly chlorogenic acids), trigonelline, and diterpenes. Several studies have highlighted the preventive effects of coffee consumption on major cardiometabolic diseases, but the impact of coffee dosage on markers of cardiometabolic risk is not well understood. Moreover, the pool of coffee-derived circulating metabolites and the contribution of each metabolite to disease prevention still need to be evaluated in real-life settings. The aim of this study will be to define the bioavailability and beneficial properties of coffee bioactive compounds on the basis of different levels of consumption, by using an innovative experimental design. The contribution of cocoa-based products containing coffee to the pool of circulating metabolites and their putative bioactivity will also be investigated. A three-arm, crossover, randomized trial will be conducted. Twenty-one volunteers will be randomly assigned to consume three treatments in a random order for 1 month: 1 cup of espresso coffee/day, 3 cups of espresso coffee/day, and 1 cup of espresso coffee plus 2 cocoa-based products containing coffee twice per day. The last day of each treatment, blood and urine samples will be collected at specific time points, up to 24 hours following the consumption of the first product. At the end of each treatment the same protocol will be repeated, switching the allocation group. Besides the bioavailability of the coffee/cocoa bioactive compounds, the effect of the coffee/cocoa consumption on several cardiometabolic risk factors (anthropometric measures, blood pressure, inflammatory markers, trimethylamine N-oxide, nitric oxide, blood lipids, fasting indices of glucose/insulin metabolism, DNA damage, eicosanoids, and nutri-metabolomics) will be investigated. Results will provide information on the bioavailability of the main groups of phytochemicals in coffee and on their modulation by the level

  9. The Qatar genome project: translation of whole-genome sequencing into clinical practice.

    Science.gov (United States)

    Zayed, Hatem

    2016-10-01

    Qatar Genome Project was launched in 2013 with the intent to sequence the genome of each Qatari citizen in an effort to protect Qataris from the high rate of indigenous genetic diseases by allowing the mapping of disease-causing variants/rare variants and establishing a Qatari reference genome. Indeed, this project is expected to have numerous global benefits because the elevated homogeneity of the Qatari population, that will make Qatar an excellent genetic laboratory that will generate a wealth of data that will allow us to make sense of the genotype-phenotype correlations of many diseases, especially the complex multifactorial diseases, and will pave the way for changing the traditional medical practice of looking first at the phenotype rather than the genotype. © 2016 John Wiley & Sons Ltd.

  10. The African Genome Variation Project shapes medical genetics in Africa

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2014-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible. PMID:25470054

  11. nGASP - the nematode genome annotation assessment project

    Energy Technology Data Exchange (ETDEWEB)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

  12. The Human Genome Diversity (HGD) Project. Summary document

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1993-12-31

    In 1991 a group of human geneticists and molecular biologists proposed to the scientific community that a world wide survey be undertaken of variation in the human genome. To aid their considerations, the committee therefore decided to hold a small series of international workshops to explore the major scientific issues involved. The intention was to define a framework for the project which could provide a basis for much wider and more detailed discussion and planning--it was recognized that the successful implementation of the proposed project, which has come to be known as the Human Genome Diversity (HGD) Project, would not only involve scientists but also various national and international non-scientific groups all of which should contribute to the project`s development. The international HGD workshop held in Sardinia in September 1993 was the last in the initial series of planning workshops. As such it not only explored new ground but also pulled together into a more coherent form much of the formal and informal discussion that had taken place in the preceding two years. This report presents the deliberations of the Sardinia workshop within a consideration of the overall development of the HGD Project to date.

  13. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

    Science.gov (United States)

    Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

    2017-01-04

    The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Climate Change Impacts on Worldwide Coffee Production

    Science.gov (United States)

    Foreman, T.; Rising, J. A.

    2015-12-01

    Coffee (Coffea arabica and Coffea canephora) plays a vital role in many countries' economies, providing necessary income to 25 million members of tropical countries, and supporting a $81 billion industry, making it one of the most valuable commodities in the world. At the same time, coffee is at the center of many issues of sustainability. It is vulnerable to climate change, with disease outbreaks becoming more common and suitable regions beginning to shift. We develop a statistical production model for coffee which incorporates temperature, precipitation, frost, and humidity effects using a new database of worldwide coffee production. We then use this model to project coffee yields and production into the future based on a variety of climate forecasts. This model can then be used together with a market model to forecast the locations of future coffee production as well as future prices, supply, and demand.

  15. The Genome of the Netherlands: design, and project goals

    Science.gov (United States)

    Boomsma, Dorret I; Wijmenga, Cisca; Slagboom, Eline P; Swertz, Morris A; Karssen, Lennart C; Abdellaoui, Abdel; Ye, Kai; Guryev, Victor; Vermaat, Martijn; van Dijk, Freerk; Francioli, Laurent C; Hottenga, Jouke Jan; Laros, Jeroen F J; Li, Qibin; Li, Yingrui; Cao, Hongzhi; Chen, Ruoyan; Du, Yuanping; Li, Ning; Cao, Sujie; van Setten, Jessica; Menelaou, Androniki; Pulit, Sara L; Hehir-Kwa, Jayne Y; Beekman, Marian; Elbers, Clara C; Byelas, Heorhiy; de Craen, Anton J M; Deelen, Patrick; Dijkstra, Martijn; den Dunnen, Johan T; de Knijff, Peter; Houwing-Duistermaat, Jeanine; Koval, Vyacheslav; Estrada, Karol; Hofman, Albert; Kanterakis, Alexandros; Enckevort, David van; Mai, Hailiang; Kattenberg, Mathijs; van Leeuwen, Elisabeth M; Neerincx, Pieter B T; Oostra, Ben; Rivadeneira, Fernanodo; Suchiman, Eka H D; Uitterlinden, Andre G; Willemsen, Gonneke; Wolffenbuttel, Bruce H; Wang, Jun; de Bakker, Paul I W; van Ommen, Gert-Jan; van Duijn, Cornelia M

    2014-01-01

    Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent–offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910–1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14–15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project. PMID:23714750

  16. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

    Science.gov (United States)

    Holt, Carson; Yandell, Mark

    2011-12-22

    Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

  17. The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

    Science.gov (United States)

    Reuter, Miriam S; Walker, Susan; Thiruvahindrapuram, Bhooma; Whitney, Joe; Cohn, Iris; Sondheimer, Neal; Yuen, Ryan K C; Trost, Brett; Paton, Tara A; Pereira, Sergio L; Herbrick, Jo-Anne; Wintle, Richard F; Merico, Daniele; Howe, Jennifer; MacDonald, Jeffrey R; Lu, Chao; Nalpathamkalam, Thomas; Sung, Wilson W L; Wang, Zhuozhi; Patel, Rohan V; Pellecchia, Giovanna; Wei, John; Strug, Lisa J; Bell, Sherilyn; Kellam, Barbara; Mahtani, Melanie M; Bassett, Anne S; Bombard, Yvonne; Weksberg, Rosanna; Shuman, Cheryl; Cohn, Ronald D; Stavropoulos, Dimitri J; Bowdin, Sarah; Hildebrandt, Matthew R; Wei, Wei; Romm, Asli; Pasceri, Peter; Ellis, James; Ray, Peter; Meyn, M Stephen; Monfared, Nasim; Hosseini, S Mohsen; Joseph-George, Ann M; Keeley, Fred W; Cook, Ryan A; Fiume, Marc; Lee, Hin C; Marshall, Christian R; Davies, Jill; Hazell, Allison; Buchanan, Janet A; Szego, Michael J; Scherer, Stephen W

    2018-02-05

    The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set ( n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care. © 2018 Joule Inc. or its licensors.

  18. Documenting genomics: Applying archival theory to preserving the records of the Human Genome Project.

    Science.gov (United States)

    Shaw, Jennifer

    2016-02-01

    The Human Genome Archive Project (HGAP) aimed to preserve the documentary heritage of the UK's contribution to the Human Genome Project (HGP) by using archival theory to develop a suitable methodology for capturing the results of modern, collaborative science. After assessing past projects and different archival theories, the HGAP used an approach based on the theory of documentation strategy to try to capture the records of a scientific project that had an influence beyond the purely scientific sphere. The HGAP was an archival survey that ran for two years. It led to ninety scientists being contacted and has, so far, led to six collections being deposited in the Wellcome Library, with additional collections being deposited in other UK repositories. In applying documentation strategy the HGAP was attempting to move away from traditional archival approaches to science, which have generally focused on retired Nobel Prize winners. It has been partially successful in this aim, having managed to secure collections from people who are not 'big names', but who made an important contribution to the HGP. However, the attempt to redress the gender imbalance in scientific collections and to improve record-keeping in scientific organisations has continued to be difficult to achieve. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

  19. Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

    Science.gov (United States)

    Pemberton, Trevor J; Szpiech, Zachary A

    2018-04-05

    Genomic regions of autozygosity (ROAs) represent segments of individual genomes that are homozygous for haplotypes inherited identical-by-descent (IBD) from a common ancestor. ROAs are nonuniformly distributed across the genome, and increased ROA levels are a reported risk factor for numerous complex diseases. Previously, we hypothesized that long ROAs are enriched for deleterious homozygotes as a result of young haplotypes with recent deleterious mutations-relatively untouched by purifying selection-being paired IBD as a consequence of recent parental relatedness, a pattern supported by ROA and whole-exome sequence data on 27 individuals. Here, we significantly bolster support for our hypothesis and expand upon our original analyses using ROA and whole-genome sequence data on 2,436 individuals from The 1000 Genomes Project. Considering CADD deleteriousness scores, we reaffirm our previous observation that long ROAs are enriched for damaging homozygotes worldwide. We show that strongly damaging homozygotes experience greater enrichment than weaker damaging homozygotes, while overall enrichment varies appreciably among populations. Mendelian disease genes and those encoding FDA-approved drug targets have significantly increased rates of gain in damaging homozygotes with increasing ROA coverage relative to all other genes. In genes implicated in eight complex phenotypes for which ROA levels have been identified as a risk factor, rates of gain in damaging homozygotes vary across phenotypes and populations but frequently differ significantly from non-disease genes. These findings highlight the potential confounding effects of population background in the assessment of associations between ROA levels and complex disease risk, which might underlie reported inconsistencies in ROA-phenotype associations. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  20. Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

    OpenAIRE

    Spradling, A C; Stern, D M; Kiss, I; Roote, J; Laverty, T; Rubin, G M

    1995-01-01

    Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and a...

  1. Genomes to life project quarterly report June 2004.

    Energy Technology Data Exchange (ETDEWEB)

    Heffelfinger, Grant S.

    2005-01-01

    This SAND report provides the technical progress through June 2004 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO{sub 2} are important terms in the global environmental response to anthropogenic atmospheric inputs of CO{sub 2} and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes

  2. The GenABEL Project for statistical genomics.

    Science.gov (United States)

    Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

    2016-01-01

    Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

  3. The human genome project and the Catholic Church (1)

    Science.gov (United States)

    Moraczewski, Albert S

    1991-12-01

    The Cathlic Church has not made any formal statements about the Human Genome Project as such. But the present Pope, John Paul II, has commented, albeit very briefly, on various aspects of genetic manipulation. Genetic interventions which are therapeutic (e.g. gene therapy), namely, directed to the correction or amelioration of a disorder are acceptable, in principle, provided they promote the personal well being of the individual being so treated. Genetic interventions which are not therapeutic for the specific individual involved but are experimental and directed primarily to improving humans as biological entities are of dubious moral probity, but are not necessarily to be totally rejected out of hand. To be morally acceptable such genetic intervention should meet certain conditions which include due respect for the given psychological nature of each individual human being. In addition, no harm should be inflicted on the process of human generation, and its fundamental design should not be altered. Any genetic manipulation which results in, or tends to, the creation of groups with different qualities such that there would result a fresh marginalization of these people must be avoided. It has been also suggested by a few that because the Son of God took on a human nature in Jesus Christ, one may not so alter the human genome that a new distinct species would be created....

  4. The UK Human Genome Mapping Project online computing service.

    Science.gov (United States)

    Rysavy, F R; Bishop, M J; Gibbs, G P; Williams, G W

    1992-04-01

    This paper presents an overview of computing and networking facilities developed by the Medical Research Council to provide online computing support to the Human Genome Mapping Project (HGMP) in the UK. The facility is connected to a number of other computing facilities in various centres of genetics and molecular biology research excellence, either directly via high-speed links or through national and international wide-area networks. The paper describes the design and implementation of the current system, a 'client/server' network of Sun, IBM, DEC and Apple servers, gateways and workstations. A short outline of online computing services currently delivered by this system to the UK human genetics research community is also provided. More information about the services and their availability could be obtained by a direct approach to the UK HGMP-RC.

  5. The impact of the human genome project on risk assessment

    International Nuclear Information System (INIS)

    Katarzyna Doerffer; Paul Unrau.

    1996-01-01

    The radiation protection approach to risk assessment assumes that cancer induction following radiation exposure is purely random. Present risk assessment methods derive risk from cancer incidence frequencies in exposed populations and associate disease outcomes totally with the level of exposure to ionizing red aeon. Exposure defines a risk factor that affects the probability of the disease outcome. But cancer risk can be affected by other risk factors such as underlying genetic factors (predisposition) of the exposed organism. These genetic risk factors are now becoming available for incorporation into ionizing radiation risk assessment Progress in the Human Genome Project (HOP) will lead to direct assays to measure the effects of genetic risk determinants in disease outcomes. When all genetic risk determinants are known and incorporated into risk assessment it will be possible to reevaluate the role of ionizing radiation in the causation of cancer. (author)

  6. Genomes to Life Project Quartely Report October 2004.

    Energy Technology Data Exchange (ETDEWEB)

    Heffelfinger, Grant S.; Martino, Anthony; Rintoul, Mark Daniel; Geist, Al; Gorin, Andrey; Xu, Ying; Palenik, Brian

    2005-02-01

    This SAND report provides the technical progress through October 2004 of the Sandia-led project, %22Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,%22 funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop

  7. Smashing CoffeeScript

    CERN Document Server

    Hudson, Alex

    2013-01-01

    Brew the perfect code with CoffeeScript If you're familiar with JavaScript and the often-frustrating process of creating complex applications, a nice cup of CoffeeScript can help. CoffeeScript is a programming language that compiles into JavaScript and simplifies the entire development process. Now you can tap the full power of CoffeeScript with Smashing CoffeeScript. This full-color, practical book explains CoffeeScript language, syntax, and processes, and will soon have you producing concise and quality code. Ultimately, you'll create RIAs and mobile apps faster, with less

  8. The Epilepsy Phenome/Genome Project (EPGP) informatics platform.

    Science.gov (United States)

    Nesbitt, Gerry; McKenna, Kevin; Mays, Vickie; Carpenter, Alan; Miller, Kevin; Williams, Michael

    2013-04-01

    The Epilepsy Phenome/Genome Project (EPGP) is a large-scale, multi-institutional, collaborative network of 27 epilepsy centers throughout the U.S., Australia, and Argentina, with the objective of collecting detailed phenotypic and genetic data on a large number of epilepsy participants. The goals of EPGP are (1) to perform detailed phenotyping on 3750 participants with specific forms of non-acquired epilepsy and 1500 parents without epilepsy, (2) to obtain DNA samples on these individuals, and (3) to ultimately genotype the samples in order to discover novel genes that cause epilepsy. To carry out the project, a reliable and robust informatics platform was needed for standardized electronic data collection and storage, data quality review, and phenotypic analysis involving cases from multiple sites. EPGP developed its own suite of web-based informatics applications for participant tracking, electronic data collection (using electronic case report forms/surveys), data management, phenotypic data review and validation, specimen tracking, electroencephalograph and neuroimaging storage, and issue tracking. We implemented procedures to train and support end-users at each clinical site. Thus far, 3780 study participants have been enrolled and 20,957 web-based study activities have been completed using this informatics platform. Over 95% of respondents to an end-user satisfaction survey felt that the informatics platform was successful almost always or most of the time. The EPGP informatics platform has successfully and effectively allowed study management and efficient and reliable collection of phenotypic data. Our novel informatics platform met the requirements of a large, multicenter research project. The platform has had a high level of end-user acceptance by principal investigators and study coordinators, and can serve as a model for new tools to support future large scale, collaborative research projects collecting extensive phenotypic data. Copyright © 2012

  9. Ethical considerations of research policy for personal genome analysis: the approach of the Genome Science Project in Japan.

    Science.gov (United States)

    Minari, Jusaku; Shirai, Tetsuya; Kato, Kazuto

    2014-12-01

    As evidenced by high-throughput sequencers, genomic technologies have recently undergone radical advances. These technologies enable comprehensive sequencing of personal genomes considerably more efficiently and less expensively than heretofore. These developments present a challenge to the conventional framework of biomedical ethics; under these changing circumstances, each research project has to develop a pragmatic research policy. Based on the experience with a new large-scale project-the Genome Science Project-this article presents a novel approach to conducting a specific policy for personal genome research in the Japanese context. In creating an original informed-consent form template for the project, we present a two-tiered process: making the draft of the template following an analysis of national and international policies; refining the draft template in conjunction with genome project researchers for practical application. Through practical use of the template, we have gained valuable experience in addressing challenges in the ethical review process, such as the importance of sharing details of the latest developments in genomics with members of research ethics committees. We discuss certain limitations of the conventional concept of informed consent and its governance system and suggest the potential of an alternative process using information technology.

  10. Human Genome Teacher Networking Project, Final Report, April 1, 1992 - March 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Debra

    1999-10-01

    Project to provide education regarding ethical legal and social implications of Human Genome Project to high school science teachers through two consecutive summer workshops, in class activities, and peer teaching workshops.

  11. The lawful uses of knowledge from the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Grad, F.P.

    1994-04-15

    Part I of this study deals with the right to know or not to know personal genetic information, and examines available legal protections of the right of privacy and the adverse effect of the disclosure of genetic information both on employment and insurance interests and on self esteem and protection of personal integrity. The study examines the rationale for the legal protection of privacy as the protection of a public interest. It examines the very limited protections currently available for privacy interests, including genetic privacy interests, and concludes that there is a need for broader, more far-reaching legal protections. The second part of the study is based on the assumption that as major a project as the Human Genome Project, spending billions of dollars on science which is health related, will indeed be applied for preventive and therapeutic public health purposes, as it has been in the past. It also addresses the recurring fear that public health initiatives in the genetic area must evolve a new eugenic agenda, that we must not repeat the miserable discriminatory experiences of the past.

  12. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

    OpenAIRE

    Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

  13. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

    Science.gov (United States)

    Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

    2010-01-01

    The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

  14. Bat biology, genomes, and the Bat1K project

    DEFF Research Database (Denmark)

    Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M

    2018-01-01

    and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any...

  15. Coffee seed physiology

    NARCIS (Netherlands)

    Eira, M.T.S.; Silva, da E.A.A.; Castro, de R.D.; Dussert, S.; Walters, C.; Bewley, J.D.; Hilhorst, H.W.M.

    2006-01-01

    Coffee is a member of the Rubiaceae family and the genus Coffea. There are more than 70 species of coffee but only two are economically important: Coffea arabica L. and Coffea canephora Pierre; 70 % of the coffee traded in the world is arabica and 30 % is robusta (C. canephora). Other species such

  16. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

    Science.gov (United States)

    Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A.; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M.; Kyrpides, Nikos C.

    2012-01-01

    The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond. PMID:22135293

  17. Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

    Science.gov (United States)

    The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

  18. Coffee and Liver Disease.

    Science.gov (United States)

    Wadhawan, Manav; Anand, Anil C

    2016-03-01

    Coffee is the most popular beverage in the world. Consumption of coffee has been shown to benefit health in general, and liver health in particular. This article reviews the effects of coffee intake on development and progression of liver disease due to various causes. We also describe the putative mechanisms by which coffee exerts the protective effect. The clinical evidence of benefit of coffee consumption in Hepatitis B and C, as well as nonalcoholic fatty liver disease and alcoholic liver disease, has also been presented. Coffee consumption is associated with improvement in liver enzymes (ALT, AST, and GGTP), especially in individuals with risk for liver disease. Coffee intake more than 2 cups per day in patients with preexisting liver disease has been shown to be associated with lower incidence of fibrosis and cirrhosis, lower hepatocellular carcinoma rates, as well as decreased mortality.

  19. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

    Science.gov (United States)

    Cai, Binghuang; Li, Biao; Kiga, Nikki; Thusberg, Janita; Bergquist, Timothy; Chen, Yun-Ching; Niknafs, Noushin; Carter, Hannah; Tokheim, Collin; Beleva-Guthrie, Violeta; Douville, Christopher; Bhattacharya, Rohit; Yeo, Hui Ting Grace; Fan, Jean; Sengupta, Sohini; Kim, Dewey; Cline, Melissa; Turner, Tychele; Diekhans, Mark; Zaucha, Jan; Pal, Lipika R; Cao, Chen; Yu, Chen-Hsin; Yin, Yizhou; Carraro, Marco; Giollo, Manuel; Ferrari, Carlo; Leonardi, Emanuela; Tosatto, Silvio C E; Bobe, Jason; Ball, Madeleine; Hoskins, Roger A; Repo, Susanna; Church, George; Brenner, Steven E; Moult, John; Gough, Julian; Stanke, Mario; Karchin, Rachel; Mooney, Sean D

    2017-09-01

    The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features. © 2017 Wiley Periodicals, Inc.

  20. The pig genome project has plenty to squeal about.

    Science.gov (United States)

    Fan, B; Gorbach, D M; Rothschild, M F

    2011-01-01

    Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed. Copyright © 2011 S. Karger AG, Basel.

  1. Understanding the Human Genome Project — A Fact Sheet | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... The Human Genome Project spurred a revolution in biotechnology innovation around the world and played a key ... the U.S. the global leader in the new biotechnology sector. In April 2003, researchers successfully completed the ...

  2. National human genome projects: an update and an agenda

    OpenAIRE

    An, Joon Yong

    2017-01-01

    Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions...

  3. The Human Genome Project: Information access, management, and regulation. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, J.D.; Micikas, L.B.

    1996-08-31

    The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

  4. Coffee and pregnancy

    DEFF Research Database (Denmark)

    Bech, Bodil Hammer

    Background: Coffee consumption in Denmark is high also among pregnant women and it is presumably their main source of caffeine intake. Coffee or caffeine intake during pregnancy has been linked to adverse pregnancy outcomes such as spontaneous abortion, stillbirth and reduced fetal growth. However...... a review of the literature indicates that further studies are needed to test the hypothesis of an effect of coffee or caffeine on the risk of adverse pregnancy outcomes.The aim of the thesis was to study the relation between coffee and the risk of fetal death and the relation between caffeine intake...

  5. [Coffee in Cancer Chemoprevention].

    Science.gov (United States)

    Neuwirthová, J; Gál, B; Smilek, P; Urbánková, P

    Coffee consumption is associated with a reduced risk of several diseases including cancer. Its chemopreventive effect has been studied in vitro, in animal models, and more recently in humans. Several modes of action have been proposed, namely, inhibition of oxidative stress and damage, activation of metabolizing liver enzymes involved in carcinogen detoxification processes, and anti-inflammatory effects. The antioxidant activity of coffee relies partly on its chlorogenic acid content and is increased during the roasting process. Maximum antioxidant activity is observed for medium-roasted coffee. The roasting process leads to the formation of several components, e.g., melanoidins, which have antioxidant and anti-inflammatory properties. Coffee also contains two specific diterpenes, cafestol and kahweol, which have anticarcinogenic properties. Roasted coffee is a complex mixture of various chemicals. Previous studies have reported that the chemopreventive components present in coffee induce apoptosis, inhibit growth and metastasis of tumor cells, and elicit antiangiogenic effects. A meta-analysis of epidemiological studies showed that coffee consumption is associated with a lower risk of developing various malignant tumors. This review summarizes the molecular mechanisms and the experimental and epidemiological evidence supporting the chemopreventive effect of coffee.Key words: coffee - chemoprevention - antioxidative enzyme - detoxification enzyme - anti-inflammatory effect The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 11. 9. 2016Accepted: 24. 11. 2016.

  6. Too much coffee

    DEFF Research Database (Denmark)

    Nordentoft, Helle Merete; Olesen, Birgitte Ravn

    coffee can be motivated to drink less coffee. The ethnomethodological perspective reveals how the participants’ different common-sense and hierarchical perceptions of a normative theory and its meaning in practice appears to guide the talk about how to motivate the patient to drink less coffee....... The negotiation between the researchers’ and practitioners’ approach to the coffee drinking patient facilitate a more profound understanding of how different knowledge forms can be at play in other ways than expected. In conclusion the findings show that dialogue and interplay between different knowledge forms...

  7. The Human Genome Project: applications in the diagnosis and treatment of neurologic disease.

    Science.gov (United States)

    Evans, G A

    1998-10-01

    The Human Genome Project (HGP), an international program to decode the entire DNA sequence of the human genome in 15 years, represents the largest biological experiment ever conducted. This set of information will contain the blueprint for the construction and operation of a human being. While the primary driving force behind the genome project is the potential to vastly expand the amount of genetic information available for biomedical research, the ramifications for other fields of study in biological research, the biotechnology and pharmaceutical industry, our understanding of evolution, effects on agriculture, and implications for bioethics are likely to be profound.

  8. Exposure to lead from intake of coffee

    DEFF Research Database (Denmark)

    Hansen, Max; Sloth, Jens Jørgen; Rasmussen, Rie Romme

    Food and beverages is one of the primary sources of intake of and exposure to lead, with beverages accounting for almost 50%. Previous studies from Denmark have estimated that the intake of lead from coffee is very high and may contribute to up to 20% of the total lead intake from food and bevera......Food and beverages is one of the primary sources of intake of and exposure to lead, with beverages accounting for almost 50%. Previous studies from Denmark have estimated that the intake of lead from coffee is very high and may contribute to up to 20% of the total lead intake from food...... and beverages. This estimate is, however, based on older, non-published data. In the current project extensive chemical analyses of coffee beans, drinking water and ready-to-drink coffee have been performed. The results hereof have been compared to calculations of the total intake of lead from food...... and beverages. The results show that the intake of lead from coffee is considerably lower than previously estimated and account for 4.2% and 3.3% of the total lead intake from food and beverages for Danish men and women, respectively. It can generally be concluded that the intake of lead from coffee is low...

  9. Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection

    Directory of Open Access Journals (Sweden)

    Pedro eTalhinhas

    2014-03-01

    Full Text Available Hemileia vastatrix is the causal agent of coffee leaf rust, the most important disease of coffee (Coffea arabica. In this work, a 454-pyrosequencing transcriptome analysis of H. vastatrix germinating urediniospores (gU and appressoria (Ap was performed and compared to previously published in planta haustoria-rich (H data. A total of 9234 transcripts were identified and annotated. Ca. 50% of these transcripts showed no significant homology to international databases. Only 784 sequences were shared by the three conditions, and 75% were exclusive of either gU (2146, Ap (1479 or H (3270. Relative transcript abundance and RT-qPCR analyses for a selection of genes indicated a particularly active metabolism, translational activity and production of new structures in the appressoria and intense signalling, transport, secretory activity and cellular multiplication in the germinating urediniospores, suggesting the onset of a plant-fungus dialogue as early as at the germ tube stage. Gene expression related to the production of carbohydrate-active enzymes and accumulation of glycerol in germinating urediniospores and appressoria suggests that combined lytic and physical mechanisms are involved in appressoria-mediated penetration. Besides contributing to the characterisation of molecular processes leading to appressoria-mediated infection by rust fungi, these results point towards the identification of new H. vastatrix candidate virulence factors, with 516 genes predicted to encode secreted proteins.

  10. Complementary Coffee Cups

    Science.gov (United States)

    Banchoff, Thomas

    2006-01-01

    What may have been the birth of a new calculus problem took place when the author noticed that two coffee cups, one convex and one concave, fit nicely together, and he wondered which held more coffee. The fact that their volumes were about equal led to the topic of this article: complementary surfaces of revolution with equal volumes.

  11. Mainstreaming sustainable coffee

    NARCIS (Netherlands)

    Kolk, A.

    2013-01-01

    This overview article examines the various dimensions of sustainable coffee as well as the actors involved and their perceptions of how to advance the market from niche to mainstream. The issues at hand are very complex, with different types of coffee producers, manufacturing/roasting companies and

  12. Can good coffee prices increase smallholder revenue?

    OpenAIRE

    Pinard, Fabrice; Aithal, Anand

    2011-01-01

    The global coffee market is currently plagued by 2 paradoxes, a coffee boom in consuming countries, and a coffee crisis in producing countries (over supply of low quality coffee and shortage of high quality coffee) which is actually driving the coffee market (Daviron and Ponte, 2005). After the termination of the International Coffee Agreement between producing and consuming countries in 1989, the coffee market has been in a flux, with market forces and over supply bringing down the coffee pr...

  13. Human genome education model project. Ethical, legal, and social implications of the human genome project: Education of interdisciplinary professionals

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, J.O. [Alliance of Genetic Support Groups, Chevy Chase, MD (United States); Lapham, E.V. [Georgetown Univ., Washington, DC (United States). Child Development Center

    1996-12-31

    This meeting was held June 10, 1996 at Georgetown University. The purpose of this meeting was to provide a multidisciplinary forum for exchange of state-of-the-art information on the human genome education model. Topics of discussion include the following: psychosocial issues; ethical issues for professionals; legislative issues and update; and education issues.

  14. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

    Science.gov (United States)

    Dunlap, Jay C; Borkovich, Katherine A; Henn, Matthew R; Turner, Gloria E; Sachs, Matthew S; Glass, N Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E; Birren, Bruce W; Weiss, Richard L; Townsend, Jeffrey P; Loros, Jennifer J; Nelson, Mary Anne; Lambreghts, Randy; Colot, Hildur V; Park, Gyungsoon; Collopy, Patrick; Ringelberg, Carol; Crew, Christopher; Litvinkova, Liubov; DeCaprio, Dave; Hood, Heather M; Curilla, Susan; Shi, Mi; Crawford, Matthew; Koerhsen, Michael; Montgomery, Phil; Larson, Lisa; Pearson, Matthew; Kasuga, Takao; Tian, Chaoguang; Baştürkmen, Meray; Altamirano, Lorena; Xu, Junhuan

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to accomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of non yeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.

  15. Competence development organizations in project management on the basis of genomic model methodologies

    OpenAIRE

    Бушуев, Сергей Дмитриевич; Рогозина, Виктория Борисовна; Ярошенко, Юрий Федерович

    2013-01-01

    The matrix technology for identification of organisational competencies in project management is presented in the article. Matrix elements are the components of organizational competence in the field of project management and project management methodology represented in the structure of the genome. The matrix model of competence in the framework of the adopted methodologies and scanning method for identifying organizational competences formalised. Proposed methods for building effective proj...

  16. Genomics England's implementation of its public engagement strategy: Blurred boundaries between engagement for the United Kingdom's 100,000 Genomes project and the need for public support.

    Science.gov (United States)

    Samuel, Gabrielle Natalie; Farsides, Bobbie

    2018-04-01

    The United Kingdom's 100,000 Genomes Project has the aim of sequencing 100,000 genomes from National Health Service patients such that whole genome sequencing becomes routine clinical practice. It also has a research-focused goal to provide data for scientific discovery. Genomics England is the limited company established by the Department of Health to deliver the project. As an innovative scientific/clinical venture, it is interesting to consider how Genomics England positions itself in relation to public engagement activities. We set out to explore how individuals working at, or associated with, Genomics England enacted public engagement in practice. Our findings show that individuals offered a narrative in which public engagement performed more than one function. On one side, public engagement was seen as 'good practice'. On the other, public engagement was presented as core to the project's success - needed to encourage involvement and ultimately recruitment. We discuss the implications of this in this article.

  17. Crowdfunding the Azolla fern genome project: a grassroots approach.

    Science.gov (United States)

    Li, Fay-Wei; Pryer, Kathleen M

    2014-01-01

    Much of science progresses within the tight boundaries of what is often seen as a "black box". Though familiar to funding agencies, researchers and the academic journals they publish in, it is an entity that outsiders rarely get to peek into. Crowdfunding is a novel means that allows the public to participate in, as well as to support and witness advancements in science. Here we describe our recent crowdfunding efforts to sequence the Azolla genome, a little fern with massive green potential. Crowdfunding is a worthy platform not only for obtaining seed money for exploratory research, but also for engaging directly with the general public as a rewarding form of outreach.

  18. [Coffee as hepatoprotective factor].

    Science.gov (United States)

    Szántová, Mária; Ďurkovičová, Zuzana

    The mind about the coffee did change upon the recent studies and metaanalysis of the last years. Consensual protective effect of coffee on the progression of chronic liver diseases (NASH, viral hepatitis, liver cirrhosis, hepatocelullar carcinoma) was detected in experimental, clinical and large population studies together with decrease of mortality. Antioxidant, antifibrotic, insulinsensitizing and anticarcinogenic effect of coffee were detected. Modulation of genetic expression of key enzymes of fatty acid synthesis, modulation of mRNA included in autophagia, reduction of stress of endoplasmatic reticulum together with decrease of proinflammatory cytokines and decrease of fibrogenesis are main mechanisms. Chlorogenic acids, diterpens (cafestol, kahweol), caffein, polyfenols and melanoidins are key protective components of coffee. Inverse dose-dependent correlation of coffee consumption with liver diseases was found in clinical and population studies. Coffee is non-pharmacological tool of primary and secondary prevention of chronic liver diseases. Review of published data together with supposed mechanisms of hepatoprotection are given.Key words: coffee - hepatoprotective effect - metaanalysis.

  19. Coffee and liver health.

    Science.gov (United States)

    Morisco, Filomena; Lembo, Vincenzo; Mazzone, Giovanna; Camera, Silvia; Caporaso, Nicola

    2014-01-01

    Coffee is one of the most widely used beverages in the world. It includes a wide array of components that can have potential implications for health. Several epidemiological studies associate coffee consumption with a reduced incidence of various chronic diseases such as diabetes, cardiovascular diseases, and neurodegenerative diseases. Over the past 20 years, an increasing number of epidemiological and experimental studies have demonstrated the positive effects of coffee on chronic liver diseases. Coffee consumption has been inversely associated with the activity of liver enzymes in subjects at risk, including heavy drinkers. Coffee favours an improvement in hepatic steatosis and fibrosis, and a reduction in cirrhosis and the risk of hepatocellular carcinoma. The mechanisms of action through which it exerts its beneficial effects are not fully understood. Experimental studies show that coffee consumption reduces fat accumulation and collagen deposition in the liver and promotes antioxidant capacity through an increase in glutathione as well as modulation of the gene and protein expression of several inflammatory mediators. Animal and in vitro studies indicate that cafestol and kahweol, 2 diterpens, can operate by modulating multiple enzymes involved in the detoxification process of carcinogens causing hepatocellular carcinoma. It is unclear whether the benefits are significant enough to "treat" patients with chronic liver disease. While we await clarification, moderate daily unsweetened coffee use is a reasonable adjuvant to therapy for these patients.

  20. Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project.

    Science.gov (United States)

    Santpere, Gabriel; Darre, Fleur; Blanco, Soledad; Alcami, Antonio; Villoslada, Pablo; Mar Albà, M; Navarro, Arcadi

    2014-04-01

    Most people in the world (∼90%) are infected by the Epstein-Barr virus (EBV), which establishes itself permanently in B cells. Infection by EBV is related to a number of diseases including infectious mononucleosis, multiple sclerosis, and different types of cancer. So far, only seven complete EBV strains have been described, all of them coming from donors presenting EBV-related diseases. To perform a detailed comparative genomic analysis of EBV including, for the first time, EBV strains derived from healthy individuals, we reconstructed EBV sequences infecting lymphoblastoid cell lines (LCLs) from the 1000 Genomes Project. As strain B95-8 was used to transform B cells to obtain LCLs, it is always present, but a specific deletion in its genome sets it apart from natural EBV strains. After studying hundreds of individuals, we determined the presence of natural EBV in at least 10 of them and obtained a set of variants specific to wild-type EBV. By mapping the natural EBV reads into the EBV reference genome (NC007605), we constructed nearly complete wild-type viral genomes from three individuals. Adding them to the five disease-derived EBV genomic sequences available in the literature, we performed an in-depth comparative genomic analysis. We found that latency genes harbor more nucleotide diversity than lytic genes and that six out of nine latency-related genes, as well as other genes involved in viral attachment and entry into host cells, packaging, and the capsid, present the molecular signature of accelerated protein evolution rates, suggesting rapid host-parasite coevolution.

  1. Ion beam analysis of ground coffee and roasted coffee beans

    International Nuclear Information System (INIS)

    Debastiani, R.; Santos, C.E.I. dos; Yoneama, M.L.; Amaral, L.; Dias, J.F.

    2014-01-01

    The way that coffee is prepared (using roasted ground coffee or roasted coffee beans) may influence the quality of beverage. Therefore, the aim of this work is to use ion beam techniques to perform a full elemental analysis of packed roasted ground coffee and packed roasted coffee beans, as well as green coffee beans. The samples were analyzed by PIXE (particle-induced X-ray emission). Light elements were measured through RBS (Rutherford backscattering spectrometry) experiments. Micro-PIXE experiments were carried out in order to check the elemental distribution in the roasted and green coffee beans. In general, the elements found in ground coffee were Mg, P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Rb and Sr. A comparison between ground coffee and grinded roasted beans shows significant differences for several elements. Elemental maps reveal that P and K are correlated and practically homogeneously distributed over the beans

  2. Ion beam analysis of ground coffee and roasted coffee beans

    Energy Technology Data Exchange (ETDEWEB)

    Debastiani, R., E-mail: rafa_debas@yahoo.com.br; Santos, C.E.I. dos; Yoneama, M.L.; Amaral, L.; Dias, J.F.

    2014-01-01

    The way that coffee is prepared (using roasted ground coffee or roasted coffee beans) may influence the quality of beverage. Therefore, the aim of this work is to use ion beam techniques to perform a full elemental analysis of packed roasted ground coffee and packed roasted coffee beans, as well as green coffee beans. The samples were analyzed by PIXE (particle-induced X-ray emission). Light elements were measured through RBS (Rutherford backscattering spectrometry) experiments. Micro-PIXE experiments were carried out in order to check the elemental distribution in the roasted and green coffee beans. In general, the elements found in ground coffee were Mg, P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Rb and Sr. A comparison between ground coffee and grinded roasted beans shows significant differences for several elements. Elemental maps reveal that P and K are correlated and practically homogeneously distributed over the beans.

  3. The Human Genome Project and the social contract: a law policy approach.

    Science.gov (United States)

    Byk, C

    1992-08-01

    For the first time in history, genetics will enable science to completely identify each human as genetically unique. Will this knowledge reinforce the trend for more individual liberties or will it create a 'brave new world'? A law policy approach to the problems raised by the human genome project shows how far our democratic institutions are from being the proper forum to discuss such issues. Because of the fears and anxiety raised in the population, and also because of its wide implications on the everyday life, the human genome analysis more than any other project needs to succeed in setting up such a social assessment.

  4. Apple Coffee Cake

    Science.gov (United States)

    ... this page: https://medlineplus.gov/recipe/applecoffeecake.html Apple Coffee Cake To use the sharing features on ... time: 50 minutes Number of Servings: 20 Tart apples and raisins make for a moist, delicious cake. ...

  5. Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

    Science.gov (United States)

    Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

    2017-07-01

    The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

  6. Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels

    Directory of Open Access Journals (Sweden)

    Xiaoyi eGao

    2012-06-01

    Full Text Available Genotype imputation is a vital tool in genome-wide association studies (GWAS and meta-analyses of multiple GWAS results. Imputation enables researchers to increase genomic coverage and to pool data generated using different genotyping platforms. HapMap samples are often employed as the reference panel. More recently, the 1000 Genomes Project resource is becoming the primary source for reference panels. Multiple GWAS and meta-analyses are targeting Latinos, the most populous and fastest growing minority group in the US. However, genotype imputation resources for Latinos are rather limited compared to individuals of European ancestry at present, largely because of the lack of good reference data. One choice of reference panel for Latinos is one derived from the population of Mexican individuals in Los Angeles contained in the HapMap Phase 3 project and the 1000 Genomes Project. However, a detailed evaluation of the quality of the imputed genotypes derived from the public reference panels has not yet been reported. Using simulation studies, the Illumina OmniExpress GWAS data from the Los Angles Latino Eye Study and the MACH software package, we evaluated the accuracy of genotype imputation in Latinos. Our results show that the 1000 Genomes Project AMR+CEU+YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1000 Genomes Project panel for Latinos. Our results serve as a guide to future imputation-based analysis in Latinos.

  7. Spent coffee grounds as a versatile source of green energy.

    Science.gov (United States)

    Kondamudi, Narasimharao; Mohapatra, Susanta K; Misra, Mano

    2008-12-24

    The production of energy from renewable and waste materials is an attractive alternative to the conventional agricultural feed stocks such as corn and soybean. This paper describes an approach to extract oil from spent coffee grounds and to further transesterify the processed oil to convert it into biodiesel. This process yields 10-15% oil depending on the coffee species (Arabica or Robusta). The biodiesel derived from the coffee grounds (100% conversion of oil to biodiesel) was found to be stable for more than 1 month under ambient conditions. It is projected that 340 million gallons of biodiesel can be produced from the waste coffee grounds around the world. The coffee grounds after oil extraction are ideal materials for garden fertilizer, feedstock for ethanol, and as fuel pellets.

  8. The 1000 Genomes Project: new opportunities for research and social challenges

    Science.gov (United States)

    2010-01-01

    The 1000 Genomes Project, an international collaboration, is sequencing the whole genome of approximately 2,000 individuals from different worldwide populations. The central goal of this project is to describe most of the genetic variation that occurs at a population frequency greater than 1%. The results of this project will allow scientists to identify genetic variation at an unprecedented degree of resolution and will also help improve the imputation methods for determining unobserved genetic variants that are not represented on current genotyping arrays. By identifying novel or rare functional genetic variants, researchers will be able to pinpoint disease-causing genes in genomic regions initially identified by association studies. This level of detailed sequence information will also improve our knowledge of the evolutionary processes and the genomic patterns that have shaped the human species as we know it today. The new data will also lay the foundation for future clinical applications, such as prediction of disease susceptibility and drug response. However, the forthcoming availability of whole genome sequences at affordable prices will raise ethical concerns and pose potential threats to individual privacy. Nevertheless, we believe that these potential risks are outweighed by the benefits in terms of diagnosis and research, so long as rigorous safeguards are kept in place through legislation that prevents discrimination on the basis of the results of genetic testing. PMID:20193048

  9. Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health

    NARCIS (Netherlands)

    Stierum, R.; Burgemeister, R.; Helvoort, van A.; Peijnenburg, A.; Schütze, K.; Seidelin, M.; Vang, O.; Ommen, van B.

    2001-01-01

    Functional Food Ingredients Against Colorectal Cancer is one of the first European Union funded Research Projects at the cross-road of functional genomics [comprising transcriptomics, the measurement of the expression of all messengers RNA (mRNAs) and proteomics, the measurement of expression/state

  10. The Human Genome Project and Eugenics: Identifying the Impact on Individuals with Mental Retardation.

    Science.gov (United States)

    Kuna, Jason

    2001-01-01

    This article explores the impact of the mapping work of the Human Genome Project on individuals with mental retardation and the negative effects of genetic testing. The potential to identify disabilities and the concept of eugenics are discussed, along with ethical issues surrounding potential genetic therapies. (Contains references.) (CR)

  11. Reflections on Mental Retardation and Eugenics, Old and New: Mensa and the Human Genome Project.

    Science.gov (United States)

    Smith, J. David

    1994-01-01

    This article addresses the moral and ethical issues of mental retardation and a continuing legacy of belief in eugenics. It discusses the involuntary sterilization of Carrie Buck in 1927, support for legalized killing of subnormal infants by 47% of respondents to a Mensa survey, and implications of the Human Genome Project for the field of mental…

  12. Democratizing Human Genome Project Information: A Model Program for Education, Information and Debate in Public Libraries.

    Science.gov (United States)

    Pollack, Miriam

    The "Mapping the Human Genome" project demonstrated that librarians can help whomever they serve in accessing information resources in the areas of biological and health information, whether it is the scientists who are developing the information or a member of the public who is using the information. Public libraries can guide library…

  13. From Mendel to the Human Genome Project: The Implications for Nurse Education.

    Science.gov (United States)

    Burton, Hilary; Stewart, Alison

    2003-01-01

    The Human Genome Project is brining new opportunities to predict and prevent diseases. Although pediatric nurses are the closest to these developments, most nurses will encounter genetic aspects of practice and must understand the basic science and its ethical, legal, and social dimensions. (Includes commentary by Peter Birchenall.) (SK)

  14. Getting the Word Out on the Human Genome Project: A Course for Physicians

    Energy Technology Data Exchange (ETDEWEB)

    Sara L. Tobin

    2004-09-29

    Our project, ''Getting the Word Out on the Human Genome Project: A Course for Physicians,'' presented educational goals to convey the power and promise of the Human Genome Program to a variety of professional, educational, and public audiences. Our initial goal was to provide practicing physicians with a comprehensive multimedia tool to update their skills in the genomic era. We therefore created the multimedia courseware, ''The New Genetics: Courseware for Physicians. Molecular Concepts, Applications, and Ramifications.'' However, as the project moved forward, several unanticipated audiences found the courseware to be useful for instruction and for self-education, so an additional edition of the courseware ''The New Genetics: Medicine and the Human Genome. Molecular Concepts, Applications, and Ramifications'' was published simultaneously with the physician version. At the time that both versions of the courseware were being completed, Stanford's Office of Technology Licensing opted not to commercialize the courseware and offered a license-back agreement if the authors founded a commercial business. The authors thus became closely involved in marketing and sales, and several thousand copies of the courseware have been sold. Surprisingly, the non-physician version has turned out to be more in demand, and this has led us in several new directions, most of which involve undergraduate education. These are discussed in detail in the Report.

  15. Thrips (Thysanoptera) of coffee flowers

    Science.gov (United States)

    A survey of thrips (Thysanoptera) associated with coffee flowers was conducted in coffee plantations in Chiapas, Mexico. The main objectives were to identify them and to determine whether they were carrying coffee pollen grains. A total of 40 thrips species in 22 genera were identified. The most com...

  16. Growing Coffee in the Shade

    NARCIS (Netherlands)

    Thapa, Sushil; Lantinga, Egbert A.

    2017-01-01

    Coffee white stem borer, Xylotrechus quadripes Chevrolat (Coleoptera: Cerambycidae) is a major coffee pest in parts of Asia and Africa. In recent years, the pest has also been found in American countries. This study in Gulmi District, Nepal, aimed to determine the infestation by coffee white stem

  17. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

    Science.gov (United States)

    Dong, Zirui; Wang, Huilin; Chen, Haixiao; Jiang, Hui; Yuan, Jianying; Yang, Zhenjun; Wang, Wen-Jing; Xu, Fengping; Guo, Xiaosen; Cao, Ye; Zhu, Zhenzhen; Geng, Chunyu; Cheung, Wan Chee; Kwok, Yvonne K; Yang, Huanming; Leung, Tak Yeung; Morton, Cynthia C; Cheung, Sau Wai; Choy, Kwong Wai

    2017-11-02

    PurposeRecent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.MethodsThe 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold).ResultsWith this approach, we detected four reciprocal balanced translocations and four inversions, ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and polymerase chain reaction studies. One of these DNAs has a subtle translocation that is not readily identified by chromosome analysis because of the similarity of the banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene.ConclusionOur study demonstrates the extension of utilizing low-pass whole-genome sequencing for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.GENETICS in MEDICINE advance online publication, 2 November 2017; doi:10.1038/gim.2017.170.

  18. Earth BioGenome Project: Sequencing life for the future of life.

    Science.gov (United States)

    Lewin, Harris A; Robinson, Gene E; Kress, W John; Baker, William J; Coddington, Jonathan; Crandall, Keith A; Durbin, Richard; Edwards, Scott V; Forest, Félix; Gilbert, M Thomas P; Goldstein, Melissa M; Grigoriev, Igor V; Hackett, Kevin J; Haussler, David; Jarvis, Erich D; Johnson, Warren E; Patrinos, Aristides; Richards, Stephen; Castilla-Rubio, Juan Carlos; van Sluys, Marie-Anne; Soltis, Pamela S; Xu, Xun; Yang, Huanming; Zhang, Guojie

    2018-04-24

    Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

  19. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    Science.gov (United States)

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  20. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

    Science.gov (United States)

    Konkel, Miriam K; Walker, Jerilyn A; Hotard, Ashley B; Ranck, Megan C; Fontenot, Catherine C; Storer, Jessica; Stewart, Chip; Marth, Gabor T; Batzer, Mark A

    2015-08-29

    The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

    Science.gov (United States)

    Jarvis, Erich D

    2016-01-01

    The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.

  2. Field of genes: the politics of science and identity in the Estonian Genome Project.

    Science.gov (United States)

    Fletcher, Amy L

    2004-04-01

    This case study of the Estonian Genome Project (EGP) analyses the Estonian policy decision to construct a national human gene bank. Drawing upon qualitative data from newspaper articles and public policy documents, it focuses on how proponents use discourse to link the EGP to the broader political goal of securing Estonia's position within the Western/European scientific and cultural space. This dominant narrative is then situated within the analytical notion of the "brand state", which raises potentially negative political consequences for this type of market-driven genomic research. Considered against the increasing number of countries engaging in gene bank and/or gene database projects, this analysis of Estonia elucidates issues that cross national boundaries, while also illuminating factors specific to this small, post-Soviet state as it enters the global biocybernetic economy.

  3. The Human Genome Project and Mental Retardation: An Educational Program. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Sharon

    1999-05-03

    The Arc, a national organization on mental retardation, conducted an educational program for members, many of whom have a family member with a genetic condition causing mental retardation. The project informed members about the Human Genome scientific efforts, conducted training regarding ethical, legal and social implications and involved members in issue discussions. Short reports and fact sheets on genetic and ELSI topics were disseminated to 2,200 of the Arc's leaders across the country and to other interested individuals. Materials produced by the project can e found on the Arc's web site, TheArc.org.

  4. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.

    Science.gov (United States)

    Vassy, Jason L; Lautenbach, Denise M; McLaughlin, Heather M; Kong, Sek Won; Christensen, Kurt D; Krier, Joel; Kohane, Isaac S; Feuerman, Lindsay Z; Blumenthal-Barby, Jennifer; Roberts, J Scott; Lehmann, Lisa Soleymani; Ho, Carolyn Y; Ubel, Peter A; MacRae, Calum A; Seidman, Christine E; Murray, Michael F; McGuire, Amy L; Rehm, Heidi L; Green, Robert C

    2014-03-20

    Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients' genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only

  5. Public trust and 'ethics review' as a commodity: the case of Genomics England Limited and the UK's 100,000 genomes project.

    Science.gov (United States)

    Samuel, Gabrielle Natalie; Farsides, Bobbie

    2018-06-01

    The UK Chief Medical Officer's 2016 Annual Report, Generation Genome, focused on a vision to fully integrate genomics into all aspects of the UK's National Health Service (NHS). This process of integration, which has now already begun, raises a wide range of social and ethical concerns, many of which were discussed in the final Chapter of the report. This paper explores how the UK's 100,000 Genomes Project (100 kGP)-the catalyst for Generation Genome, and for bringing genomics into the NHS-is negotiating these ethical concerns. The UK's 100 kGP, promoted and delivered by Genomics England Limited (GEL), is an innovative venture aiming to sequence 100,000 genomes from NHS patients who have a rare disease, cancer, or an infectious disease. GEL has emphasised the importance of ethical governance and decision-making. However, some sociological critique argues that biomedical/technological organisations presenting themselves as 'ethical' entities do not necessarily reflect a space within which moral thinking occurs. Rather, the 'ethical work' conducted (and displayed) by organisations is more strategic, relating to the politics of the organisation and the need to build public confidence. We set out to explore whether GEL's ethical framework was reflective of this critique, and what this tells us more broadly about how genomics is being integrated into the NHS in response to the ethical and social concerns raised in Generation Genome. We do this by drawing on a series of 20 interviews with individuals associated with or working at GEL.

  6. Coffee and Cigarettes

    DEFF Research Database (Denmark)

    Fahnøe, Kristian

    , I analyze how the informal and supposedly non-therapeutic interactions (e.g. coffee breaks, lunch or fieldtrips) between clients and social workers are scenes of subtle acts of governing and resistance. I employ Susie Scott’s (2010) notions of performative regulation and reinventive institutions...

  7. Ethical challenges and innovations in the dissemination of genomic data: the experience of the PERSPECTIVE project

    Directory of Open Access Journals (Sweden)

    Lévesque E

    2015-08-01

    Full Text Available Emmanuelle Lévesque,1 Bartha Maria Knoppers,1 Jacques Simard,2 1Department of Human Genetics, Centre for Genomics and Policy, McGill University, Montréal, 2Genomics Centre, CHU de Québec Research Center, Department of Molecular Medicine, Laval University, Québec City, QC, Canada Abstract: The importance of making genomic data available for future research is now widely recognized among the scientific community and policymakers. In this era of shared responsibility for data dissemination, improved patient care through research depends on the development of powerful and secure data-sharing systems. As part of the concerted effort to share research resources, the project entitled Personalized Risk Stratification for Prevention and Early Detection of Breast Cancer (PERSPECTIVE makes effective data sharing through the development of a data-sharing framework, one of its goals. The secondary uses of data from PERSPECTIVE for future research promise to enhance our knowledge of breast cancer etiologies without duplicating data-gathering efforts. Despite its benefit for research, we recognize the ethical challenges of data sharing on the local, national, and international levels. The effective management of ethical approvals for projects spanning across jurisdictions, the return of results to research participants, and research incentives and recognition for data production, are but a few pressing issues that need to be properly addressed. We discuss how we managed these issues and suggest how ongoing innovations might help to facilitate data sharing in future genomic research projects. Keywords: data sharing, research ethics, cancer

  8. Coffee, hunger, and peptide YY.

    Science.gov (United States)

    Greenberg, James A; Geliebter, Allan

    2012-06-01

    There is evidence from several empirical studies suggesting that coffee may help people control body weight. Our objective was to assess the effects of caffeine, caffeinated coffee, and decaffeinated coffee, both alone and in combination with 75 g of glucose, on perceived hunger and satiety and related peptides. We conducted a placebo-controlled single-blinded randomized 4-way crossover trial. Eleven healthy male volunteers (mean age, 23.5 ± 5.7 years; mean BMI, 23.6 ± 4.2 kg/m(2)) ingested 1 of 3 test beverages (caffeine in water, caffeinated coffee, or decaffeinated coffee) or placebo (water), and 60 minutes later they ingested the glucose. Eight times during each laboratory visit, hunger and satiety were assessed by visual analog scales, and blood samples were drawn to measure 3 endogenous peptides associated with hunger and satiety: ghrelin, peptide YY (PYY), and leptin. Compared to placebo, decaffeinated coffee yielded significantly lower hunger during the whole 180-minute study period and higher plasma PYY for the first 90 minutes (p hunger or PYY. Caffeinated coffee showed a pattern between that of decaffeinated coffee and caffeine in water. These findings suggest that one or more noncaffeine ingredients in coffee may have the potential to decrease body weight. Glucose ingestion did not change the effects of the beverages. Our randomized human trial showed that decaffeinated coffee can acutely decrease hunger and increase the satiety hormone PYY.

  9. The human genome project: Information management, access, and regulation. Technical progress report, 1 April--31 August 1993

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, J.D.; Micikas, L.B.

    1993-09-10

    Efforts are described to prepare educational materials including computer based as well as conventional type teaching materials for training interested high school and elementary students in aspects of Human Genome Project.

  10. Hunting for genes for hypertension: the Millennium Genome Project for Hypertension.

    Science.gov (United States)

    Tabara, Yasuharu; Kohara, Katsuhiko; Miki, Tetsuro

    2012-06-01

    The Millennium Genome Project for Hypertension was started in 2000 to identify genetic variants conferring susceptibility to hypertension, with the aim of furthering the understanding of the pathogenesis of this condition and realizing genome-based personalized medical care. Two different approaches were launched, genome-wide association analysis using single-nucleotide polymorphisms (SNPs) and microsatellite markers, and systematic candidate gene analysis, under the hypothesis that common variants have an important role in the etiology of common diseases. These multilateral approaches identified ATP2B1 as a gene responsible for hypertension in not only Japanese but also Caucasians. The high blood pressure susceptibility conferred by certain alleles of ATP2B1 has been widely replicated in various populations. Ex vivo mRNA expression analysis in umbilical artery smooth muscle cells indicated that reduced expression of this gene associated with the risk allele may be an underlying mechanism relating the ATP2B1 variant to hypertension. However, the effect size of a SNP was too small to clarify the entire picture of the genetic basis of hypertension. Further, dense genome analysis with accurate phenotype data may be required.

  11. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project.

    Science.gov (United States)

    Higgins, Anne W; Alkuraya, Fowzan S; Bosco, Amy F; Brown, Kerry K; Bruns, Gail A P; Donovan, Diana J; Eisenman, Robert; Fan, Yanli; Farra, Chantal G; Ferguson, Heather L; Gusella, James F; Harris, David J; Herrick, Steven R; Kelly, Chantal; Kim, Hyung-Goo; Kishikawa, Shotaro; Korf, Bruce R; Kulkarni, Shashikant; Lally, Eric; Leach, Natalia T; Lemyre, Emma; Lewis, Janine; Ligon, Azra H; Lu, Weining; Maas, Richard L; MacDonald, Marcy E; Moore, Steven D P; Peters, Roxanna E; Quade, Bradley J; Quintero-Rivera, Fabiola; Saadi, Irfan; Shen, Yiping; Shendure, Jay; Williamson, Robin E; Morton, Cynthia C

    2008-03-01

    Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.

  12. The coffee agroforestry system. Its importance for the agro-alimentary and nutritional security in Ecuador

    Directory of Open Access Journals (Sweden)

    Luciano Abelardo Ponce Vaca

    2018-01-01

    Full Text Available In the context of coffee growing, Ecuador is characterized by planting two main commercial species of Coffea arabica L. (Arabica coffee, and Coffea canephora Pierre ex Froehner (Robusta coffee, where small production units and agroforestry systems predominate. To overcome the low national production, which constitutes the central problem of coffee growing in the country, the Ministry of Agriculture and Livestock of Ecuador, promoted the project «Reactivation of the Ecuadorian coffee industry», which contributes to food security and nutrition with integral approach. In these circumstances, the objective of this paper is to analyze the importance of coffee agroforestry systems for agro-alimentary and nutritional security in Ecuador. The proposal is born from the agro-economic diagnosis «case study», from the situation of the Coffee Production Units, from the Association of Peasants «Juntos Lucharemos» from the La Unión parish of the Jipijapa county, province of Manabí, in which they settled Main contributions to the agro-alimentary and nutritional security coming from the coffee agroforestry systems, this allowed to analyze characteristics related to the object of study. Based on the research results, gaps in national consumption needs were detected. This proposal contributed to articulate and promote the reactivation of coffee growing on agroecological bases, in harmony with the dimensions of sustainability in order to protect and conserve biodiversity and the coffee forest.

  13. Evaluation of the International coffee market conditions

    OpenAIRE

    FISAKOVA O.S.

    2014-01-01

    This article includes analysis of coffee market and its conditions for coffee companies. Also, coffee export amounts and prices are compared and analyzed. Statistics were collected over few last years to present accurate research

  14. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

    Science.gov (United States)

    Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

    2015-01-01

    The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

  15. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Tatiparthi B. K. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Thomas, Alex D. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Stamatis, Dimitri [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bertsch, Jon [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Isbandi, Michelle [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Jansson, Jakob [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Mallajosyula, Jyothi [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pagani, Ioanna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lobos, Elizabeth A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

    2014-10-27

    The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

  16. Radioactivity in coffee

    International Nuclear Information System (INIS)

    Roselli, C.; Desideri, D.; Feduzi, L.; Rongoni, A.; Saetta, D.

    2013-01-01

    This research was dedicated to the study of the background levels of 210 Po and natural gamma emitters as 40 K, 214 Pb, 214 Bi, 228 Ac, 212 Pb and 212 Bi in coffee powder and in coffee beverage; also the artificial 137 Cs was determined. In the coffee powder the mean 210 Po activity resulted 7.25 ± 2.25 x 10 -2 Bq kg -1 . 40 K showed a mean activity of 907.4 ± 115.6 Bq kg -1 . The mean activity concentration of 214 Pb and 214 Bi, indicators of 226 Ra, given as mean value of the two radionuclides, resulted 10.61 ± 4.02 Bq kg -1 . 228 Ac, 228 Ra indicator, showed a mean activity concentration of 13.73 ± 3.20 Bq kg -1 . The mean activity concentration of 212 Pb, 224 Ra indicator, was 8.28 ± 2.88 Bq kg -1 . 208 Tl, 224 Ra indicator, presented a mean activity concentration of 11.03 ± 4.34 Bq kg -1 . In all samples, the artificial 137 Cs resulted below the detection limit (2.0 Bq kg -1 ). The arithmetical mean value of percentage of 210 Po extraction in coffee beverage resulted 20.5 ± 6.9. The percentage of transfer of gamma emitters, 40 K, 214 Pb, 214 Bi, 228 Ac, 212 Pb, 208 Tl resulted of 80.0, 33.5, 24.7, 30.0, 35.1 and 53.5 % for 40 K, 214 Pb, 214 Bi, 228 Ac, 212 Pb and 208 Tl respectively. (author)

  17. Cloning, production, and purification of proteins for a medium-scale structural genomics project.

    Science.gov (United States)

    Quevillon-Cheruel, Sophie; Collinet, Bruno; Trésaugues, Lionel; Minard, Philippe; Henckes, Gilles; Aufrère, Robert; Blondeau, Karine; Zhou, Cong-Zhao; Liger, Dominique; Bettache, Nabila; Poupon, Anne; Aboulfath, Ilham; Leulliot, Nicolas; Janin, Joël; van Tilbeurgh, Herman

    2007-01-01

    The South-Paris Yeast Structural Genomics Pilot Project (http://www.genomics.eu.org) aims at systematically expressing, purifying, and determining the three-dimensional structures of Saccharomyces cerevisiae proteins. We have already cloned 240 yeast open reading frames in the Escherichia coli pET system. Eighty-two percent of the targets can be expressed in E. coli, and 61% yield soluble protein. We have currently purified 58 proteins. Twelve X-ray structures have been solved, six are in progress, and six other proteins gave crystals. In this chapter, we present the general experimental flowchart applied for this project. One of the main difficulties encountered in this pilot project was the low solubility of a great number of target proteins. We have developed parallel strategies to recover these proteins from inclusion bodies, including refolding, coexpression with chaperones, and an in vitro expression system. A limited proteolysis protocol, developed to localize flexible regions in proteins that could hinder crystallization, is also described.

  18. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

    Science.gov (United States)

    Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

  19. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  20. Shaded Coffee: A way to Increase Sustainability in Brazilian Organic Coffee plantations

    OpenAIRE

    Moreira, Cassio Franco; De Nadai Fernandes, Elisabete A.; Tagliaferro, Fábio Sileno

    2008-01-01

    Consumption of specialty coffee, mainly organic coffee, increases worldwide following the tendency of consuming social and ecological sustainable products. Brazil is the world largest coffee producer, with an average of 2,300,000 tons of green coffee in the last 5 years. Cultivation of organic coffee and shaded coffee are common in Central America, while in Brazil both conventional and organic coffee are cultivated in the full sun system. The full sun system is criticized due to the lack of b...

  1. 75 FR 7471 - Chandra Coffee and Rabun Boatworks, Complainants v. Georgia Power Company, Respondent; Notice of...

    Science.gov (United States)

    2010-02-19

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 2354-10] Chandra Coffee and Rabun Boatworks, Complainants v. Georgia Power Company, Respondent; Notice of Complaint February 3, 2010. Take notice that on December 14, 2009, as amended on January 8, 2010, Chandra Coffee and Rabun...

  2. Consortium biology in immunology: the perspective from the Immunological Genome Project.

    Science.gov (United States)

    Benoist, Christophe; Lanier, Lewis; Merad, Miriam; Mathis, Diane

    2012-10-01

    Although the field has a long collaborative tradition, immunology has made less use than genetics of 'consortium biology', wherein groups of investigators together tackle large integrated questions or problems. However, immunology is naturally suited to large-scale integrative and systems-level approaches, owing to the multicellular and adaptive nature of the cells it encompasses. Here, we discuss the value and drawbacks of this organization of research, in the context of the long-running 'big science' debate, and consider the opportunities that may exist for the immunology community. We position this analysis in light of our own experience, both positive and negative, as participants of the Immunological Genome Project.

  3. ELSI Bibliography: Ethical legal and social implications of the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Yesley, M.S. [comp.

    1993-11-01

    This second edition of the ELSI Bibliography provides a current and comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. Since the first edition of the ELSI Bibliography was printed last year, new publications and earlier ones identified by additional searching have doubled our computer database of ELSI publications to over 5600 entries. The second edition of the ELSI Bibliography reflects this growth of the underlying computer database. Researchers should note that an extensive collection of publications in the database is available for public use at the General Law Library of Los Alamos National Laboratory (LANL).

  4. Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project

    Directory of Open Access Journals (Sweden)

    McDonagh Paul D

    2003-06-01

    Full Text Available Abstract Background Seattle Biomedical Research Institute (SBRI as part of the Leishmania Genome Network (LGN is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. Results Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. Conclusion An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

  5. Human Genome Project discoveries: Dialectics and rhetoric in the science of genetics

    Science.gov (United States)

    Robidoux, Charlotte A.

    The Human Genome Project (HGP), a $437 million effort that began in 1990 to chart the chemical sequence of our three billion base pairs of DNA, was completed in 2003, marking the 50th anniversary that proved the definitive structure of the molecule. This study considered how dialectical and rhetorical arguments functioned in the science, political, and public forums over a 20-year period, from 1980 to 2000, to advance human genome research and to establish the official project. I argue that Aristotle's continuum of knowledge--which ranges from the probable on one end to certified or demonstrated knowledge on the other--provides useful distinctions for analyzing scientific reasoning. While contemporary scientific research seeks to discover certified knowledge, investigators generally employ the hypothetico-deductive or scientific method, which often yields probable rather than certain findings, making these dialectical in nature. Analysis of the discourse describing human genome research revealed the use of numerous rhetorical figures and topics. Persuasive and probable reasoning were necessary for scientists to characterize unknown genetic phenomena, to secure interest in and funding for large-scale human genome research, to solve scientific problems, to issue probable findings, to convince colleagues and government officials that the findings were sound and to disseminate information to the public. Both government and private venture scientists drew on these tools of reasoning to promote their methods of mapping and sequencing the genome. The debate over how to carry out sequencing was rooted in conflicting values. Scientists representing the academic tradition valued a more conservative method that would establish high quality results, and those supporting private industry valued an unconventional approach that would yield products and profits more quickly. Values in turn influenced political and public forum arguments. Agency representatives and investors sided

  6. Commentary: The Materials Project: A materials genome approach to accelerating materials innovation

    Directory of Open Access Journals (Sweden)

    Anubhav Jain

    2013-07-01

    Full Text Available Accelerating the discovery of advanced materials is essential for human welfare and sustainable, clean energy. In this paper, we introduce the Materials Project (www.materialsproject.org, a core program of the Materials Genome Initiative that uses high-throughput computing to uncover the properties of all known inorganic materials. This open dataset can be accessed through multiple channels for both interactive exploration and data mining. The Materials Project also seeks to create open-source platforms for developing robust, sophisticated materials analyses. Future efforts will enable users to perform ‘‘rapid-prototyping’’ of new materials in silico, and provide researchers with new avenues for cost-effective, data-driven materials design.

  7. A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

    International Nuclear Information System (INIS)

    Lakhssassi, K.; González-Recio, O.

    2017-01-01

    Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

  8. A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

    Energy Technology Data Exchange (ETDEWEB)

    Lakhssassi, K.; González-Recio, O.

    2017-07-01

    Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

  9. The analysis of APOL1 genetic variation and haplotype diversity provided by 1000 Genomes project.

    Science.gov (United States)

    Peng, Ting; Wang, Li; Li, Guisen

    2017-08-11

    The APOL1 gene variants has been shown to be associated with an increased risk of multiple kinds of diseases, particularly in African Americans, but not in Caucasians and Asians. In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. Variants of APOL1 gene in 1000 Genome Project were obtained and SNPs located in the regulatory region or coding region were selected for genetic variation analysis. Total 2504 individuals from 26 populations were classified as four groups that included Africa, Europe, Asia and Admixed populations. Tag SNPs were selected to evaluate the haplotype diversities in the four populations by HaploStats software. APOL1 gene was surrounded by some of the most polymorphic genes in the human genome, variation of APOL1 gene was common, with up to 613 SNP (1000 Genome Project reported) and 99 of them (16.2%) with MAF ≥ 1%. There were 79 SNPs in the URR and 92 SNPs in 3'UTR. Total 12 SNPs in URR and 24 SNPs in 3'UTR were considered as common variants with MAF ≥ 1%. It is worth noting that URR-1 was presents lower frequencies in European populations, while other three haplotypes taken an opposite pattern; 3'UTR presents several high-frequency variation sites in a short segment, and the differences of its haplotypes among different population were significant (P < 0.01), UTR-1 and UTR-5 presented much higher frequency in African population, while UTR-2, UTR-3 and UTR-4 were much lower. APOL1 coding region showed that two SNP of G1 with higher frequency are actually pull down the haplotype H-1 frequency when considering all populations pooled together, and the diversity among the four populations be widen by the G1 two mutation (P 1  = 3.33E-4 vs P 2  = 3.61E-30). The distributions of APOL1 gene variants and haplotypes were significantly different among the different populations, in either regulatory or coding regions. It could provide

  10. COFFEE GROWING AREAS OF ETHIOPIA"

    African Journals Online (AJOL)

    accelerated economic growth, part of which is hoped to be achieved via increased ... at the Fifth International Conference on the Ethiopian Economy held at the United ... Samuel and Ludi: Agricultural commercialisation in coffee growing areas. ... Ethiopia produces and exports one of the best fighland coffees in the world.

  11. TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Degrave Wim

    1997-01-01

    Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

  12. Turkish cultural heritage: a cup of coffee

    Directory of Open Access Journals (Sweden)

    Birsen Yılmaz

    2017-12-01

    Full Text Available Setting out a fabulous journey from a tiny bean, coffee is the stimulant of the heart and mind and a mysterious plant that strengthens friendship and also takes your tiredness away during the day. Although information on how and where the coffee came from is not clear, Sheikh Şazeli is regarded as the “father” by coffee makers. The word coffee originates from “Kaffa”, a primary coffee production center in Abyssinia, Africa, which can be considered the homeland of coffee. According to this consideration, in Abyssinia, coffee was consumed with bread; it was then pulped and brought to Yemen, and Yemeni people started to cultivate coffee. The word “kahve” in Turkish does not mean the coffee plant like its synonym in Arabic but means the beverage made by boiling. Turkish coffee is a blend of high-quality Arabic-type coffee beans, originating from Brazil and Central America and moderately roasted and ground finely. The way it is prepared differentiates Turkish coffee from others. This coffee was called Turkish coffee because of a new method of preparation invented by Turkish people where it is boiled in copper coffee pots. Turkish coffee that has spread around the world with this name has been an indispensable part of the cultural and social history of Turks.

  13. Sensitivity to coffee and subjective health

    NARCIS (Netherlands)

    Snel, J.; Koppes, L.L.J.; Twisk, J.W.

    2009-01-01

    The question was whether health complaints are associated with coffee consumption and self reported sensitivity to coffee. Participants were 89 men and 107 women, all coffee drinkers. Questionnaires were used at 2 points of time with an interval of 3.7 years. The correlations among coffee

  14. Evaluation of physiological changes in coffee seedlings ...

    African Journals Online (AJOL)

    Field experiments were carried out at three locations with different vegetation in Nigeria between 1996 and 1998 to determine the physiological changes in coffee intercropped with maize, cassava and plantain. There were four intercropping treatments comprising coffee/maize, coffee/cassava, coffee/plantain and ...

  15. Have coffee reforms and coffee supply chains affected farmers' income? The case of coffee growers in Rwanda

    OpenAIRE

    Murekezi, Abdoul Karim; Loveridge, Scott

    2009-01-01

    Low prices in the international coffee markets have worsened the economic well-being among coffee farmers. In the face of this situation, the Government of Rwanda has introduced coffee sector reforms that aimed to transform the sector in a way that targets the high quality market and moves away from the bulk coffee market. The high quality coffee market has shown consistent growth over time and exhibits price premiums in international market. If these high prices are passed on to farmers who ...

  16. My Morning Coffee: The Effect of Climate Change on the Economies of Coffee-Producing Countries

    Science.gov (United States)

    Shilling, K.; Brauman, K. A.

    2012-12-01

    Through its effect on export crops, climate change will have important effects on economic systems and government capacity in sub-Saharan Africa. We show that climate change effects on three important export crops - coffee, cocoa and cotton - will undermine large portions of the economy, not just the rural farmers who grow these crops. Our analysis is based high-resolution data on crop location, temperature, and water requirements in conjunction with new projections for temperature increases and precipitation changes in sub-Saharan Africa. Our focus on export crops is distinct from most work on the effects of climate change on agriculture, which often focuses on subsistence and food crops. We posit that substantial and important effects on the economy and political systems will come from negative impacts on cash crops, which underpin many economies in sub-Saharan Africa. For instance, 3% of cropland in Uganda (and 2% in Ethiopia) is used for coffee production and over 3.5 million households are involved in the sector; by contrast, 7% of cropland in Uganda (and 11% in Ethiopia) is used for maize, which contributes much less to the formal economy. The relationship between the value of coffee exported and government revenue illustrates the importance of coffee to political and economic stability. A drop in the export value of coffee by 10% in Uganda will drive government revenue down by 20%, and while there is uncertainty around the exact impact of climate change, it is likely that production will take a turn for the worse. We use these factors to assess reliance of select country's economy on these crops, from the farmer to the exporter; the sensitivity of the crops to variation in the climate; and the subsequent impact on government capacity. Our research illustrates how strongly the impacts of climate change are linked to economic and political structures.

  17. Understanding our genetic inheritance: The US Human Genome Project, The first five years FY 1991--1995

    Energy Technology Data Exchange (ETDEWEB)

    None

    1990-04-01

    The Human Genome Initiative is a worldwide research effort with the goal of analyzing the structure of human DNA and determining the location of the estimated 100,000 human genes. In parallel with this effort, the DNA of a set of model organisms will be studied to provide the comparative information necessary for understanding the functioning of the human genome. The information generated by the human genome project is expected to be the source book for biomedical science in the 21st century and will by of immense benefit to the field of medicine. It will help us to understand and eventually treat many of the more than 4000 genetic diseases that affect mankind, as well as the many multifactorial diseases in which genetic predisposition plays an important role. A centrally coordinated project focused on specific objectives is believed to be the most efficient and least expensive way of obtaining this information. The basic data produced will be collected in electronic databases that will make the information readily accessible on convenient form to all who need it. This report describes the plans for the U.S. human genome project and updates those originally prepared by the Office of Technology Assessment (OTA) and the National Research Council (NRC) in 1988. In the intervening two years, improvements in technology for almost every aspect of genomics research have taken place. As a result, more specific goals can now be set for the project.

  18. Buying cannabis in 'coffee shops'.

    Science.gov (United States)

    Monshouwer, Karin; Van Laar, Margriet; Vollebergh, Wilma A

    2011-03-01

    The key objective of Dutch cannabis policy is to prevent and limit the risks of cannabis consumption for users, their direct environment and society ('harm reduction'). This paper will focus on the tolerated sale of cannabis in 'coffee shops'. We give a brief overview of Dutch policy on coffee shops, its history and recent developments. Furthermore, we present epidemiological data that may be indicative of the effects of the coffee shop policy on cannabis and other drug use. Dutch coffee shop policy has become more restrictive in recent years and the number of coffee shops has decreased. Cannabis prevalence rates in the adult population are somewhat below the European average; the rate is relatively high among adolescents; and age of first use appears to be low. On a European level, the use of hard drugs in both the Dutch adult and adolescent population is average to low (except for ecstasy among adults). International comparisons do not suggest a strong, upward effect of the coffee shop system on levels of cannabis use, although prevalence rates among Dutch adolescents give rise to concern. Furthermore, the coffee shop system appears to be successful in separating the hard and soft drugs markets. Nevertheless, in recent years, issues concerning the involvement of organised crime and the public nuisance related to drug tourism have given rise to several restrictive measures on the local level and have sparked a political debate on the reform of Dutch drug policy. © 2011 Trimbos Institute.

  19. O admirável Projeto Genoma Humano The brave New Human Genome Project

    Directory of Open Access Journals (Sweden)

    Marilena V. Corrêa

    2002-12-01

    Full Text Available Este artigo apresenta um panorama das implicações sociais, éticas e legais do Projeto Genoma Humano. Os benefícios desse megaprojeto, traduzidos em promessas de uma revolução terapêutica na medicina, não se realizarão sem conflitos. O processo de inovação tecnológica na genética traz problemas de ordens diversas: por um lado, pesquisas em consórcio, patenteamento de genes e produtos da genômica apontam interesses comerciais e dificuldades de gerenciamento dos resultados dessas pesquisas. Esses problemas colocam desafios em termos de uma possível desigualdade no acesso aos benefícios das pesquisas. Por outro lado, temos a questão da informação genética e da proteção de dados individuais sobre riscos e suscetibilidades a doenças e atributos humanos. O problema da definição de homens e mulheres em função de traços genéticos traz uma ameaça discriminatória clara, e se torna agudo em função do reducionismo genético que a mídia ajuda a propagar. As respostas a esses problemas não podem ser esperadas apenas da bioética. A abordagem bioética deve poder combinar-se a análises políticas da reprodução, da sexualidade, da saúde e da medicina. Um vastíssimo espectro de problemas como estes não pode ser discutido em profundidade em um artigo. Optou-se por mapeá-los no sentido de enfatizar em que medida, na reflexão sobre o projeto genoma, a genômica e a pós-genômica, enfrenta-se o desafio de articular aspectos tão diferenciados.This article presents an overview of the social, ethical, and legal implications of the Human Genome Project. The benefits of this mega-project, expressed as promises of a therapeutic revolution in medicine, will not be achieved without conflict. The process of technological innovation in genetics poses problems of various orders: on the one hand, consortium-based research, gene patenting, and genomic products tend to feature commercial interests and management of the results of such

  20. Caffeine content of decaffeinated coffee.

    Science.gov (United States)

    McCusker, Rachel R; Fuehrlein, Brian; Goldberger, Bruce A; Gold, Mark S; Cone, Edward J

    2006-10-01

    Caffeine is the most widely consumed drug in the world with coffee representing a major source of intake. Despite widespread availability, various medical conditions necessitate caffeine-restricted diets. Patients on certain prescription medications are advised to discontinue caffeine intake. Such admonition has implications for certain psychiatric patients because of pharmacokinetic interactions between caffeine and certain anti-anxiety drugs. In an effort to abstain from caffeine, patients may substitute decaffeinated for caffeinated coffee. However, decaffeinated beverages are known to contain caffeine in varying amounts. The present study determined the caffeine content in a variety of decaffeinated coffee drinks. In phase 1 of the study, 10 decaffeinated samples were collected from different coffee establishments. In phase 2 of the study, Starbucks espresso decaffeinated (N=6) and Starbucks brewed decaffeinated coffee (N=6) samples were collected from the same outlet to evaluate variability of caffeine content of the same drink. The 10 decaffeinated coffee samples from different outlets contained caffeine in the range of 0-13.9 mg/16-oz serving. The caffeine content for the Starbucks espresso and the Starbucks brewed samples collected from the same outlet were 3.0-15.8 mg/shot and 12.0-13.4 mg/16-oz serving, respectively. Patients vulnerable to caffeine effects should be advised that caffeine may be present in coffees purported to be decaffeinated. Further research is warranted on the potential deleterious effects of consumption of "decaffeinated" coffee that contains caffeine on caffeine-restricted patients. Additionally, further exploration is merited for the possible physical dependence potential of low doses of caffeine such as those concentrations found in decaffeinated coffee.

  1. The GenABEL Project for statistical genomics [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Lennart C. Karssen

    2016-05-01

    Full Text Available Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination.

  2. Human Genome Diversity Project. Summary of planning workshop 3(B): Ethical and human-rights implications

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1993-12-31

    The third planning workshop of the Human Genome Diversity Project was held on the campus of the US National Institutes of Health in Bethesda, Maryland, from February 16 through February 18, 1993. The second day of the workshop was devoted to an exploration of the ethical and human-rights implications of the Project. This open meeting centered on three roundtables, involving 12 invited participants, and the resulting discussions among all those present. Attendees and their affiliations are listed in the attached Appendix A. The discussion was guided by a schedule and list of possible issues, distributed to all present and attached as Appendix B. This is a relatively complete, and thus lengthy, summary of the comments at the meeting. The beginning of the summary sets out as conclusions some issues on which there appeared to be widespread agreement, but those conclusions are not intended to serve as a set of detailed recommendations. The meeting organizer is distributing his recommendations in a separate memorandum; recommendations from others who attended the meeting are welcome and will be distributed by the meeting organizer to the participants and to the Project committee.

  3. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

    Science.gov (United States)

    Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

    2005-06-01

    Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

  4. BIOETHICS METHODS IN THE ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS OF THE HUMAN GENOME PROJECT LITERATURE

    Science.gov (United States)

    Walker, Rebecca; Morrissey, Clair

    2013-01-01

    While bioethics as a field has concerned itself with methodological issues since the early years, there has been no systematic examination of how ethics is incorporated into research on the Ethical, Legal and Social Implications (ELSI) of the Human Genome Project. Yet ELSI research may bear a particular burden of investigating and substantiating its methods given public funding, an explicitly cross-disciplinary approach, and the perceived significance of adequate responsiveness to advances in genomics. We undertook a qualitative content analysis of a sample of ELSI publications appearing between 2003-2008 with the aim of better understanding the methods, aims, and approaches to ethics that ELSI researchers employ. We found that the aims of ethics within ELSI are largely prescriptive and address multiple groups. We also found that the bioethics methods used in the ELSI literature are both diverse between publications and multiple within publications, but are usually not themselves discussed or employed as suggested by bioethics method proponents. Ethics in ELSI is also sometimes undistinguished from related inquiries (such as social, legal, or political investigations). PMID:23796275

  5. The human genome project and novel aspects of cytochrome P450 research

    International Nuclear Information System (INIS)

    Ingelman-Sundberg, Magnus

    2005-01-01

    Currently, 57 active cytochrome P450 (CYP) genes and 58 pseudogenes are known to be present in the human genome. Among the genes discovered by initiatives in the human genome project are CYP2R1, CYP2W1, CYP2S1, CYP2U1 and CYP3A43, the latter apparently encoding a pseudoenzyme. The function, polymorphism and regulation of these genes are still to be discovered to a great extent. The polymorphism of drug metabolizing CYPs is extensive and influences the outcome of drug therapy causing lack of response or adverse drug reactions. The basis for the differences in the global distribution of the polymorphic variants is inactivating gene mutations and subsequent genetic drift. However, polymorphic alleles carrying multiple active gene copies also exist and are suggested in case of CYP2D6 to be caused by positive selection due to development of alkaloid resistance in North East Africa about 10,000-5000 BC. The knowledge about the CYP genes and their polymorphisms is of fundamental importance for effective drug therapy and for drug development as well as for understanding metabolic activation of carcinogens and other xenobiotics. Here, a short review of the current knowledge is given

  6. Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans.

    Directory of Open Access Journals (Sweden)

    Alberto Gómez-Carballa

    Full Text Available Genetic analyses have recently been carried out on present-day Tuscans (Central Italy in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000 and partial control region sequences (>180,000.Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%. Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

  7. [Coffee can protect against disease].

    Science.gov (United States)

    Hermansen, Kjeld; Krogholm, Kirstine Suszkiewicz; Bech, Bodil Hammer; Dragsted, Lars Ove; Hyldstrup, Lars; Jørgensen, Kasper; Larsen, Mogens Lytken; Tjønneland, Anne Marie

    2012-09-24

    A moderate daily intake of 3-4 cups of coffee has convincing protective effects against development of type 2 diabetes and Parkinson's disease. The literature also indicates that moderate coffee intake reduces the risk of stroke, the overall risk of cancer, Alzheimer's disease, suicide and depression. However, pregnant women, people suffering from anxiety disorder and persons with a low calcium intake should restrain from moderate or high intake of coffee due to uncertainty regarding potential negative effects on pregnancy, anxiety and risk of osteoporosis, respectively.

  8. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.

    Science.gov (United States)

    Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M; Ray, David A; Gilbert, M Thomas P; Myers, Eugene

    2018-02-15

    Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

  9. Climate and Pest-Driven Geographic Shifts in Global Coffee Production: Implications for Forest Cover, Biodiversity and Carbon Storage

    Science.gov (United States)

    Magrach, Ainhoa; Ghazoul, Jaboury

    2015-01-01

    Coffee is highly sensitive to temperature and rainfall, making its cultivation vulnerable to geographic shifts in response to a changing climate. This could lead to the establishment of coffee plantations in new areas and potential conflicts with other land covers including natural forest, with consequent implications for biodiversity and ecosystem services. We project areas suitable for future coffee cultivation based on several climate scenarios and expected responses of the coffee berry borer, a principle pest of coffee crops. We show that the global climatically-suitable area will suffer marked shifts from some current major centres of cultivation. Most areas will be suited to Robusta coffee, demand for which could be met without incurring forest encroachment. The cultivation of Arabica, which represents 70% of consumed coffee, can also be accommodated in the future, but only by incurring some natural forest loss. This has corresponding implications for carbon storage, and is likely to affect areas currently designated as priority areas for biodiversity. Where Arabica coffee does encroach on natural forests, we project average local losses of 35% of threatened vertebrate species. The interaction of climate and coffee berry borer greatly influences projected outcomes. PMID:26177201

  10. Coffee Shop Youth Lifestyle

    Directory of Open Access Journals (Sweden)

    Vahid Shalchi

    2008-04-01

    Full Text Available This article has a review on the third zone coffee shop youth life style and looks forward to note the features of this group’s life style. Some of the other objective of this article are notifying the importance of different elements in life, consumption norms and the types of leisure. The results of this research shows that in this social atmosphere, post modern lifestyle features are seen as fashion, hybrid taste, interaction among local and global affairs, the importance of hobbies, consumption and the necessity of leisure. The study on this group of Iranian youth foretells how difficult. Complicated and fragile cultural policy is. Therefore, cultural affecting on the youth generation is not possible only through addrssing the values in surface.

  11. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

    DEFF Research Database (Denmark)

    Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya

    2007-01-01

    We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses...

  12. Turkish cultural heritage: a cup of coffee

    OpenAIRE

    Birsen Yılmaz; Nilüfer Acar-Tek; Saniye Sözlü

    2017-01-01

    Setting out a fabulous journey from a tiny bean, coffee is the stimulant of the heart and mind and a mysterious plant that strengthens friendship and also takes your tiredness away during the day. Although information on how and where the coffee came from is not clear, Sheikh Şazeli is regarded as the “father” by coffee makers. The word coffee originates from “Kaffa”, a primary coffee production center in Abyssinia, Africa, which can be considered the homeland of coffee. According to this con...

  13. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

    Directory of Open Access Journals (Sweden)

    Claire eBertelli

    2015-02-01

    Full Text Available With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by embedded bioinformaticians, i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the Sequence a genome class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2,233 putative proteins. Estrella also possesses a 9,136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

  14. Athlome Project Consortium: a concerted effort to discover genomic and other "omic" markers of athletic performance.

    Science.gov (United States)

    Pitsiladis, Yannis P; Tanaka, Masashi; Eynon, Nir; Bouchard, Claude; North, Kathryn N; Williams, Alun G; Collins, Malcolm; Moran, Colin N; Britton, Steven L; Fuku, Noriyuki; Ashley, Euan A; Klissouras, Vassilis; Lucia, Alejandro; Ahmetov, Ildus I; de Geus, Eco; Alsayrafi, Mohammed

    2016-03-01

    Despite numerous attempts to discover genetic variants associated with elite athletic performance, injury predisposition, and elite/world-class athletic status, there has been limited progress to date. Past reliance on candidate gene studies predominantly focusing on genotyping a limited number of single nucleotide polymorphisms or the insertion/deletion variants in small, often heterogeneous cohorts (i.e., made up of athletes of quite different sport specialties) have not generated the kind of results that could offer solid opportunities to bridge the gap between basic research in exercise sciences and deliverables in biomedicine. A retrospective view of genetic association studies with complex disease traits indicates that transition to hypothesis-free genome-wide approaches will be more fruitful. In studies of complex disease, it is well recognized that the magnitude of genetic association is often smaller than initially anticipated, and, as such, large sample sizes are required to identify the gene effects robustly. A symposium was held in Athens and on the Greek island of Santorini from 14-17 May 2015 to review the main findings in exercise genetics and genomics and to explore promising trends and possibilities. The symposium also offered a forum for the development of a position stand (the Santorini Declaration). Among the participants, many were involved in ongoing collaborative studies (e.g., ELITE, GAMES, Gene SMART, GENESIS, and POWERGENE). A consensus emerged among participants that it would be advantageous to bring together all current studies and those recently launched into one new large collaborative initiative, which was subsequently named the Athlome Project Consortium. Copyright © 2016 the American Physiological Society.

  15. Deep brain stimulation, brain maps and personalized medicine: lessons from the human genome project.

    Science.gov (United States)

    Fins, Joseph J; Shapiro, Zachary E

    2014-01-01

    Although the appellation of personalized medicine is generally attributed to advanced therapeutics in molecular medicine, deep brain stimulation (DBS) can also be so categorized. Like its medical counterpart, DBS is a highly personalized intervention that needs to be tailored to a patient's individual anatomy. And because of this, DBS like more conventional personalized medicine, can be highly specific where the object of care is an N = 1. But that is where the similarities end. Besides their differing medical and surgical provenances, these two varieties of personalized medicine have had strikingly different impacts. The molecular variant, though of a more recent vintage has thrived and is experiencing explosive growth, while DBS still struggles to find a sustainable therapeutic niche. Despite its promise, and success as a vetted treatment for drug resistant Parkinson's Disease, DBS has lagged in broadening its development, often encountering regulatory hurdles and financial barriers necessary to mount an adequate number of quality trials. In this paper we will consider why DBS-or better yet neuromodulation-has encountered these challenges and contrast this experience with the more successful advance of personalized medicine. We will suggest that personalized medicine and DBS's differential performance can be explained as a matter of timing and complexity. We believe that DBS has struggled because it has been a journey of scientific exploration conducted without a map. In contrast to molecular personalized medicine which followed the mapping of the human genome and the Human Genome Project, DBS preceded plans for the mapping of the human brain. We believe that this sequence has given personalized medicine a distinct advantage and that the fullest potential of DBS will be realized both as a cartographical or electrophysiological probe and as a modality of personalized medicine.

  16. Rhipicephalus microplus strain Deutsch, whole genome shotgun sequencing project Version 2

    Science.gov (United States)

    The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. Cot filtration/selection techniques were used ...

  17. lon beam analysis of Brazilian coffee

    Energy Technology Data Exchange (ETDEWEB)

    Debastiani, R.; Santos, C.E.I. dos; Ramos, M.M.; Souza, V.S.; Yoneama, M.L.; Amaral, L.; Dias, J.F. [Universidade Federal do Rio Grande so Sul (UFRGS), Porto Alegre, RS (Brazil). Instituto de Fisica

    2013-07-01

    Full text: Coffee is one of the most popular and consumed beverages worldwide. Consumers can make the beverage from different types of coffee such as ground coffee, instant coffee or grinding roasted coffee beans. Each type of coffee leads to different characteristics in flavor and scent. The aim of this work is to perform an elemental analysis of ground coffee and roasted coffee beans. To that end, eight popular Brazilian ground coffee brands have been chosen to make a comparative study among brands. One of these brands was selected for a complete study of the beverage preparation process. This same brand offers packages of roasted coffee beans, which allowed the elemental comparison between ground coffee and roasted coffee beans. Roasted coffee beans were ground with a pestle and mortar. The beverage was prepared using a typical coffee pot. The spent and liquid coffees were submitted to a heat treatment and subsequently homogenized and pressed into pellets. The filters used in the coffee pot were analyzed as well. For micro-PIXE studies, coffee beans were cut in different parts for analysis. Samples of ground coffee and roasted coffee beans (grind) were analyzed by PIXE, while light elements like C, O and N were analyzed by RBS (Rutherford Backscattering Spectrometry). The roasted coffee beans were analyzed by micro-PIXE to check the elemental distribution in the beans. The elements found in powder coffee were Mg, AI, Si, P, S, CI, K, Ca, Ti, Mn, Fe, Cu, Zn and Rb. Potassium is the element with higher concentration, while Ti and Zn are trace elements. AI, Si and Ti showed the same concentration for all brands. Potassium and chlorine have high solubility, and about 80% of their concentration is transferred from the powder to the beverage during the infusion. Mg, P, CI, K, Mn, Fe, Zn and Rb showed significant variation between ground coffee and roasted coffee beans. The elemental maps show that potassium and phosphorus are correlated, and iron appears in particular

  18. lon beam analysis of Brazilian coffee

    International Nuclear Information System (INIS)

    Debastiani, R.; Santos, C.E.I. dos; Ramos, M.M.; Souza, V.S.; Yoneama, M.L.; Amaral, L.; Dias, J.F.

    2013-01-01

    Full text: Coffee is one of the most popular and consumed beverages worldwide. Consumers can make the beverage from different types of coffee such as ground coffee, instant coffee or grinding roasted coffee beans. Each type of coffee leads to different characteristics in flavor and scent. The aim of this work is to perform an elemental analysis of ground coffee and roasted coffee beans. To that end, eight popular Brazilian ground coffee brands have been chosen to make a comparative study among brands. One of these brands was selected for a complete study of the beverage preparation process. This same brand offers packages of roasted coffee beans, which allowed the elemental comparison between ground coffee and roasted coffee beans. Roasted coffee beans were ground with a pestle and mortar. The beverage was prepared using a typical coffee pot. The spent and liquid coffees were submitted to a heat treatment and subsequently homogenized and pressed into pellets. The filters used in the coffee pot were analyzed as well. For micro-PIXE studies, coffee beans were cut in different parts for analysis. Samples of ground coffee and roasted coffee beans (grind) were analyzed by PIXE, while light elements like C, O and N were analyzed by RBS (Rutherford Backscattering Spectrometry). The roasted coffee beans were analyzed by micro-PIXE to check the elemental distribution in the beans. The elements found in powder coffee were Mg, AI, Si, P, S, CI, K, Ca, Ti, Mn, Fe, Cu, Zn and Rb. Potassium is the element with higher concentration, while Ti and Zn are trace elements. AI, Si and Ti showed the same concentration for all brands. Potassium and chlorine have high solubility, and about 80% of their concentration is transferred from the powder to the beverage during the infusion. Mg, P, CI, K, Mn, Fe, Zn and Rb showed significant variation between ground coffee and roasted coffee beans. The elemental maps show that potassium and phosphorus are correlated, and iron appears in particular

  19. Genomics: The Science and Technology Behind the Human Genome Project (by Charles R. Cantor and Cassandra L. Smith)

    Science.gov (United States)

    Serra, Reviewed By Martin J.

    2000-01-01

    Genomics is one of the most rapidly expanding areas of science. This book is an outgrowth of a series of lectures given by one of the former heads (CRC) of the Human Genome Initiative. The book is designed to reach a wide audience, from biologists with little chemical or physical science background through engineers, computer scientists, and physicists with little current exposure to the chemical or biological principles of genetics. The text starts with a basic review of the chemical and biological properties of DNA. However, without either a biochemistry background or a supplemental biochemistry text, this chapter and much of the rest of the text would be difficult to digest. The second chapter is designed to put DNA into the context of the larger chromosomal unit. Specialized chromosomal structures and sequences (centromeres, telomeres) are introduced, leading to a section on chromosome organization and purification. The next 4 chapters cover the physical (hybridization, electrophoresis), chemical (polymerase chain reaction), and biological (genetic) techniques that provide the backbone of genomic analysis. These chapters cover in significant detail the fundamental principles underlying each technique and provide a firm background for the remainder of the text. Chapters 7­9 consider the need and methods for the development of physical maps. Chapter 7 primarily discusses chromosomal localization techniques, including in situ hybridization, FISH, and chromosome paintings. The next two chapters focus on the development of libraries and clones. In particular, Chapter 9 considers the limitations of current mapping and clone production. The current state and future of DNA sequencing is covered in the next three chapters. The first considers the current methods of DNA sequencing - especially gel-based methods of analysis, although other possible approaches (mass spectrometry) are introduced. Much of the chapter addresses the limitations of current methods, including

  20. The effect of dewaxing of green coffee on the coffee brew

    NARCIS (Netherlands)

    Stegen, G.H.D. van der

    1979-01-01

    The two commercially most important mild treatments for green coffee are the steam treatment and the dewaxing process. In the former treatment the green coffee is just steamed. In the dewaxing process the waxy layer is extracted from the green coffee with an organic solvent, after which this coffee

  1. DEVELOPMENT OF COFFEE MARKET AND CHANGES IN COFFEE CONSUMPTION AMONG POLES

    Directory of Open Access Journals (Sweden)

    Sylwia Chudy

    2014-12-01

    Full Text Available The paper presents results of a survey concerning coffee consumption together with results of visual and instrumental coffee analyses. The investigations focused on the type of additives used when preparing coffee. Based on the survey it was found that 58.3% respondents use sweeteners and 92.7% coffee whiteners (mainly milk with 3.2% fat content.

  2. The RadGenomics project. Prediction for radio-susceptibility of individuals with genetic predisposition

    International Nuclear Information System (INIS)

    Imai, Takashi

    2003-01-01

    The ultimate goal of our project, named RadGenomics, is to elucidate the heterogeneity of the response to ionizing radiation arising from genetic variation among individuals, for the purpose of developing personalized radiation therapy regimens for cancer patients. Cancer patients exhibit patient-to-patient variability in normal tissue reactions after radiotherapy. Several observations support the hypothesis that the radiosensitivity of normal tissue is influenced by genetic factors. The rapid progression of human genome sequencing and the recent development of new technologies in molecular biology are providing new opportunities for elucidating the genetic basis of individual differences in susceptibility to radiation exposure. The development of a sufficiently robust, predictive assay enabling individual dose adjustment would improve the outcome of radiation therapy in patients. Our strategy for identification of DNA polymorphisms that contribute to the individual radiosensitivity is as follows. First, we have been categorizing DNA samples obtained from cancer patients, who have been kindly introduced to us through many collaborators, according to their clinical characteristics including the method and effect of treatment and side effects as scored by toxicity criteria, and also the result of an in vitro radiosensitivity assay, e.g., the micronuclei assay of their lymphocytes. Second, we have identified candidate genes for genotyping mainly by using our custom-designed oligonucleotide array with RNA samples, in which the probes were obtained from more than 40 cancer and 3 fibroblast cell lines whose radiosensitivity level was quite heterogeneous. We have also been studying the modification of proteins after irradiation of cells which may be caused by mainly phosphorylation or dephosphorylation, using mass spectrometry. Genes encoding the modified proteins and/or other proteins with which they interact such as specific protein kinases and phosphatases are also

  3. Lawrence Livermore National Laboratory- Completing the Human Genome Project and Triggering Nearly $1 Trillion in U.S. Economic Activity

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Jeffrey S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-07-28

    The success of the Human Genome project is already nearing $1 Trillion dollars of U.S. economic activity. Lawrence Livermore National Laboratory (LLNL) was a co-leader in one of the biggest biological research effort in history, sequencing the Human Genome Project. This ambitious research effort set out to sequence the approximately 3 billion nucleotides in the human genome, an effort many thought was nearly impossible. Deoxyribonucleic acid (DNA) was discovered in 1869, and by 1943 came the discovery that DNA was a molecule that encodes the genetic instructions used in the development and functioning of living organisms and many viruses. To make full use of the information, scientists needed to first sequence the billions of nucleotides to begin linking them to genetic traits and illnesses, and eventually more effective treatments. New medical discoveries and improved agriculture productivity were some of the expected benefits. While the potential benefits were vast, the timeline (over a decade) and cost ($3.8 Billion) exceeded what the private sector would normally attempt, especially when this would only be the first phase toward the path to new discoveries and market opportunities. The Department of Energy believed its best research laboratories could meet this Grand Challenge and soon convinced the National Institute of Health to formally propose the Human Genome project to the federal government. The U.S. government accepted the risk and challenge to potentially create new healthcare and food discoveries that could benefit the world and the U.S. Industry.

  4. Evidence from The Rwandan Coffee Sector.

    African Journals Online (AJOL)

    the coffee value chain and to promote the production of speciality coffee. A research team ... exporters and the installation of several parchment mills by companies ..... use a Simple linear regression model was used to explain the total quantity.

  5. Some like it hot: the influence and implications of climate change on coffee berry borer (Hypothenemus hampei and coffee production in East Africa.

    Directory of Open Access Journals (Sweden)

    Juliana Jaramillo

    Full Text Available The negative effects of climate change are already evident for many of the 25 million coffee farmers across the tropics and the 90 billion dollar (US coffee industry. The coffee berry borer (Hypothenemus hampei, the most important pest of coffee worldwide, has already benefited from the temperature rise in East Africa: increased damage to coffee crops and expansion in its distribution range have been reported. In order to anticipate threats and prioritize management actions for H. hampei we present here, maps on future distributions of H. hampei in coffee producing areas of East Africa. Using the CLIMEX model we relate present-day insect distributions to current climate and then project the fitted climatic envelopes under future scenarios A2A and B2B (for HADCM3 model. In both scenarios, the situation with H. hampei is forecasted to worsen in the current Coffea arabica producing areas of Ethiopia, the Ugandan part of the Lake Victoria and Mt. Elgon regions, Mt. Kenya and the Kenyan side of Mt. Elgon, and most of Rwanda and Burundi. The calculated hypothetical number of generations per year of H. hampei is predicted to increase in all C. arabica-producing areas from five to ten. These outcomes will have serious implications for C. arabica production and livelihoods in East Africa. We suggest that the best way to adapt to a rise of temperatures in coffee plantations could be via the introduction of shade trees in sun grown plantations. The aims of this study are to fill knowledge gaps existing in the coffee industry, and to draft an outline for the development of an adaptation strategy package for climate change on coffee production. An abstract in Spanish is provided as Abstract S1.

  6. Markkinointiviestintäsuunnitelma : Classic Coffee Oy

    OpenAIRE

    Eerola, Laura

    2015-01-01

    Opinnäytetyön aiheena oli laatia markkinointiviestintäsuunnitelma kalenterivuodelle 2016 vuosikellon muodossa, toimintansa jo vakiinnuttaneelle Classic Coffee Oy:lle. Classic Coffee Oy on vuonna 2011 perustettu, Tampereella toimiva kahvila-alan yritys joka tarjoaa lounaskahvilatoiminnan lisäksi laadukkaita konditoria-palveluita, yritys- ja kokoustarjoiluja sekä tilavuokrausta. Classic Coffee Oy:llä on yksi kahvila, Classic Coffee Tampella. Kahvila sijaitsee Tampellassa, Tampereen keskustan vä...

  7. Structural analysis of a set of proteins resulting from a bacterial genomics project.

    Science.gov (United States)

    Badger, J; Sauder, J M; Adams, J M; Antonysamy, S; Bain, K; Bergseid, M G; Buchanan, S G; Buchanan, M D; Batiyenko, Y; Christopher, J A; Emtage, S; Eroshkina, A; Feil, I; Furlong, E B; Gajiwala, K S; Gao, X; He, D; Hendle, J; Huber, A; Hoda, K; Kearins, P; Kissinger, C; Laubert, B; Lewis, H A; Lin, J; Loomis, K; Lorimer, D; Louie, G; Maletic, M; Marsh, C D; Miller, I; Molinari, J; Muller-Dieckmann, H J; Newman, J M; Noland, B W; Pagarigan, B; Park, F; Peat, T S; Post, K W; Radojicic, S; Ramos, A; Romero, R; Rutter, M E; Sanderson, W E; Schwinn, K D; Tresser, J; Winhoven, J; Wright, T A; Wu, L; Xu, J; Harris, T J R

    2005-09-01

    The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Copyright 2005 Wiley-Liss, Inc.

  8. Brain Genomics Superstruct Project initial data release with structural, functional, and behavioral measures.

    Science.gov (United States)

    Holmes, Avram J; Hollinshead, Marisa O; O'Keefe, Timothy M; Petrov, Victor I; Fariello, Gabriele R; Wald, Lawrence L; Fischl, Bruce; Rosen, Bruce R; Mair, Ross W; Roffman, Joshua L; Smoller, Jordan W; Buckner, Randy L

    2015-01-01

    The goal of the Brain Genomics Superstruct Project (GSP) is to enable large-scale exploration of the links between brain function, behavior, and ultimately genetic variation. To provide the broader scientific community data to probe these associations, a repository of structural and functional magnetic resonance imaging (MRI) scans linked to genetic information was constructed from a sample of healthy individuals. The initial release, detailed in the present manuscript, encompasses quality screened cross-sectional data from 1,570 participants ages 18 to 35 years who were scanned with MRI and completed demographic and health questionnaires. Personality and cognitive measures were obtained on a subset of participants. Each dataset contains a T1-weighted structural MRI scan and either one (n=1,570) or two (n=1,139) resting state functional MRI scans. Test-retest reliability datasets are included from 69 participants scanned within six months of their initial visit. For the majority of participants self-report behavioral and cognitive measures are included (n=926 and n=892 respectively). Analyses of data quality, structure, function, personality, and cognition are presented to demonstrate the dataset's utility.

  9. The post-Human Genome Project mindset: race, reliability, and health care.

    Science.gov (United States)

    Kimmelman, J

    2006-11-01

    The following essay reports on the first session of a 2-day workshop on genetic diversity and science communication, organized by the Institute of Genetics. I argue that the four talks in this session reflected two different facets of a 'post-Human Genome Project (HGP)' view of human genetics. The first is characterized by an increasing interest in genetic differences. Two speakers - Troy Duster and Jasber Singh - expressed skepticism about one aspect of this trend: an emphasis on race in medicine and genetics. The other two speakers - Kenneth Weiss and Gustavo Turecki - spoke to a second facet of the post-HGP view: a recognition of the difficulty in translating genetic discovery into medical or public health applications. Though both sets of talks were highly critical of current trends in genetic research, they pulled in opposite directions: one warned about the role of genetics in stabilizing racial categories, while the other lamented the failure of any genetic claims or categories to stabilize at all. I argue that the use of racial categories in medicine seems likely to encounter scientific, medical, and social challenges.

  10. ELSI Bibliography: Ethical, legal and social implications of the Human Genome Project. 1994 Supplement

    Energy Technology Data Exchange (ETDEWEB)

    Yesley, M.S.; Ossorio, P.N. [comps.

    1994-09-01

    This report updates and expands the second edition of the ELSI Bibliography, published in 1993. The Bibliography and Supplement provides a comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. The Bibliography and Supplement are extracted from a database compiled at Los Alamos National Laboratory with the support of the Office of Energy Research, US Department of Energy. The second edition of the ELSI Bibliography was dated May 1993 but included publications added to the database until fall 1993. This Supplement reflects approximately 1,000 entries added to the database during the past year, bringing the total to approximately 7,000 entries. More than half of the new entries were published in the last year, and the remainder are earlier publications not previously included in the database. Most of the new entries were published in the academic and professional literature. The remainder are press reports from newspapers of record and scientific journals. The topical listing of the second edition has been followed in the Supplement, with a few changes. The topics of Cystic Fibrosis, Huntington`s Disease, and Sickle Cell Anemia have been combined in a single topic, Disorders. Also, all the entries published in the past year are included in a new topic, Publications: September 1993--September 1994, which provides a comprehensive view of recent reporting and commentary on the science and ELSI of genetics.

  11. Tea, coffee and prostate cancer.

    Science.gov (United States)

    Lee, Andy H; Fraser, Michelle L; Binns, Colin W

    2009-02-01

    Worldwide, prostate cancer has the second highest incidence of all cancers in males with incidence and mortality being much higher in affluent developed countries. Risk and progression of the disease may be linked to both genetic and environmental factors, especially dietary factors. Tea and coffee are two of the most popular beverages in the world and have been investigated for possible effects on health outcomes, including cancer. However, very little dietary advice for their consumption exists. The evidence for a relationship between coffee or tea consumption and prostate cancer is reviewed in this paper. While current evidence indicates that coffee is a safe beverage, its consumption probably has no relationship with prostate cancer. Tea, especially green tea, has shown some potential in the prevention of prostate cancer. While evidence from epidemiologic studies is currently inconclusive, strong evidence has emerged from animal and in vitro studies. We also consider what level of evidence is required to make recommendations for preventive measures to the public. Although evidence on the relationship between coffee, tea and prostate cancer is not complete, we consider it strong enough to recommend tea as a healthier alternative to coffee.

  12. Good news for coffee addicts.

    Science.gov (United States)

    Lee, Thomas H

    2009-06-01

    Whether it's a basic Mr. Coffee or a gadget that sports a snazzy device for grinding beans on demand, the office coffee machine offers a place for serendipitous encounters that can improve the social aspect of work and generate new ideas. What's more, a steaming cup of joe may be as good for your health as it is for the bottom line, says Lee, a professor of medicine at Harvard Medical School and the CEO of Partners Community HealthCare. Fears of coffee's carcinogenic effects now appear to be unfounded, and, in fact, the brew might even protect against some types of cancer. What's more, coffee may guard against Alzheimer's disease and other forms of dementia and somehow soften the blow of a heart attack. Of course, its role as a pick-me-up is well known. So there's no need to take your coffee with a dollop of guilt, especially if you ease up on the sugar, cream, double chocolate, and whipped-cream topping.

  13. ASSESSMENT OF METALS IN ROASTED INDIGENOUS COFFEE ...

    African Journals Online (AJOL)

    1Department of Chemistry, College of Natural Sciences, Addis Ababa University, P.O. Box. 1176, Addis .... cultivation region of Ethiopian coffee by elemental analysis. ... health regulatory limits of the metals in coffee to provide guideline information on the .... Procedures tested for digestion of roasted coffee samples. No.

  14. How Competitive is the Dutch Coffee market?

    NARCIS (Netherlands)

    L.J.H. Bettendorf (Leon); F. Verboven

    1997-01-01

    textabstractWorld coffee bean prices have shown large fluctuations during the past years. Consumer prices for roasted coffee, in contrast, have varied considerably less. This article investigates whether the weak relationship between coffee bean and consumer prices can be explained by a lack of

  15. Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards.

    Science.gov (United States)

    Francisco, Carolina S; Ceresini, Paulo C; Almeida, Rodrigo P P; Coletta-Filho, Helvécio D

    2017-04-01

    Xylella fastidiosa, an economically important plant-pathogenic bacterium, infects both coffee and citrus trees in Brazil. Although X. fastidiosa in citrus is well studied, knowledge about the population structure of this bacterium infecting coffee remains unknown. Here, we studied the population structure of X. fastidiosa infecting coffee trees in São Paulo State, Brazil, in four regions where citrus is also widely cultivated. Genotyping of over 500 isolates from coffee plants using 14 genomic microsatellite markers indicated that populations were largely geographically isolated, as previously found with populations of X. fastidiosa infecting citrus. These results were supported by a clustering analysis, which indicated three major genetic groups among the four sampled regions. Overall, approximately 38% of isolates showed significant membership coefficients not related to their original geographical populations (i.e., migrants), characterizing a significant degree of genotype flow among populations. To determine whether admixture occurred between isolates infecting citrus and coffee plants, one site with citrus and coffee orchards adjacent to each other was selected; over 100 isolates were typed from each host plant. No signal of natural admixture between citrus- and coffee-infecting isolates was found; artificial cross-infection assays with representative isolates also yielded no successful cross infection. A comparison determined that X. fastidiosa populations from coffee have higher genetic diversity and allelic richness compared with citrus. The results showed that coffee and citrus X. fastidiosa populations are effectively isolated from each other and, although coffee populations are spatially structured, migration has an important role in shaping diversity.

  16. Proyecto genoma humano: un arma de doble filo The Human Genome Project: A double edge weapon

    Directory of Open Access Journals (Sweden)

    Elizabeth Hernández Moore

    2001-04-01

    Full Text Available Después de breve reseña histórica que informa sobre los sorprendentes avances de la genética a partir del descubrimiento de la estructura helicoidal del DNA, el artículo centra su atención en el nacimiento de los estudios genómicos en los Estados Unidos de Norteamérica, las causas y condiciones que los motivaron, hasta desembocar en el multinacional Proyecto Genoma Humano. Sin olvidar la estatura científica de tal empresa, se intenta una mirada desde la perspectiva de las relaciones Norte-Sur, remitiéndonos de modo más incisivo a los aspectos éticos más controvertidos del PGH. Argumentamos que en las sociedades del Sur debemos ocuparnos en jerarquizar los principales problemas bioéticos que nos aquejan y que están aún muy distantes de los que se "encargan" al PGH . Referimos que las sociedades del Sur deben insertar en su agenda, proyecciones en Ciencia, Tecnología y Sociedad, entre las que el PGH no califica como una prioridad autóctona, aún cuando no descalificamos en su esencia tales megaproyectos, originados en los centros y circuitos propios de la ciencia del NorteAlter brief historical review that informs on the surprising advances of the genetics starting from the discovery of the spiral structure of the DNA, the article centres its attention in the birth of the genetic studies in the United Status of America, the causes and conditions that motivated them, intil ending in the I multinacional Human Genome Project without forgetting the scientific stature of such Project. It is attempted a llok from the perspective of the North-South relationships, remiting us of the more incisive way to the most controversial ethical aspects of the HPG. We argue that in the societies of the South we shoujd be in charge of organizing hierchically the main bioethical problems that we suffer and they are even very distant of those that are in charge of the HGP. We refer that the societies of the South should insert in their calendar

  17. Heavier smoking increases coffee consumption

    DEFF Research Database (Denmark)

    Bjørngaard, Johan H; Nordestgaard, Ask Tybjærg; Taylor, Amy E

    2017-01-01

    Background: There is evidence for a positive relationship between cigarette and coffee consumption in smokers. Cigarette smoke increases metabolism of caffeine, so this may represent a causal effect of smoking on caffeine intake. Methods: We performed Mendelian randomization analyses in the UK...... Biobank ( N  = 114 029), the Norwegian HUNT study ( N  = 56 664) and the Copenhagen General Population Study (CGPS) ( N  = 78 650). We used the rs16969968 genetic variant as a proxy for smoking heaviness in all studies and rs4410790 and rs2472297 as proxies for coffee consumption in UK Biobank and CGPS....... Analyses were conducted using linear regression and meta-analysed across studies. Results: Each additional cigarette per day consumed by current smokers was associated with higher coffee consumption (0.10 cups per day, 95% CI: 0.03, 0.17). There was weak evidence for an increase in tea consumption per...

  18. Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality

    Energy Technology Data Exchange (ETDEWEB)

    Ramalho, T.O.; Figueira, A.R.; Sotero, A.J. [Universidade Federal de Lavras, Departamento de Fitopatologia, Caixa Postal 3037, CEP 37200-000 Lavras, MG (Brazil); Wang, R. [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States); Geraldino Duarte, P.S. [Universidade Federal de Lavras, Departamento de Fitopatologia, Caixa Postal 3037, CEP 37200-000 Lavras, MG (Brazil); Farman, M. [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States); Goodin, M.M., E-mail: mgoodin@uky.edu [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States)

    2014-09-15

    The emergence of viruses in Coffee (Coffea arabica and Coffea canephora), the most widely traded agricultural commodity in the world, is of critical concern. The RNA1 (6552 nt) of Coffee ringspot virus is organized into five open reading frames (ORFs) capable of encoding the viral nucleocapsid (ORF1p), phosphoprotein (ORF2p), putative cell-to-cell movement protein (ORF3p), matrix protein (ORF4p) and glycoprotein (ORF5p). Each ORF is separated by a conserved intergenic junction. RNA2 (5945 nt), which completes the bipartite genome, encodes a single protein (ORF6p) with homology to RNA-dependent RNA polymerases. Phylogenetic analysis of L protein sequences firmly establishes CoRSV as a member of the recently proposed Dichorhavirus genus. Predictive algorithms, in planta protein expression, and a yeast-based nuclear import assay were used to determine the nucleophillic character of five CoRSV proteins. Finally, the temperature-dependent ability of CoRSV to establish systemic infections in an initially local lesion host was quantified. - Highlights: • We report genome sequence determination for Coffee ringspot virus (CoRSV). • CoRSV should be considered a member of the proposed Dichorhavirus genus. • We report temperature-dependent systemic infection of an initially local lesion host. • We report in planta protein and localization data for five CoRSV proteins. • In silico predictions of the CoRSV proteins were validated using in vivo assays.

  19. Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality

    International Nuclear Information System (INIS)

    Ramalho, T.O.; Figueira, A.R.; Sotero, A.J.; Wang, R.; Geraldino Duarte, P.S.; Farman, M.; Goodin, M.M.

    2014-01-01

    The emergence of viruses in Coffee (Coffea arabica and Coffea canephora), the most widely traded agricultural commodity in the world, is of critical concern. The RNA1 (6552 nt) of Coffee ringspot virus is organized into five open reading frames (ORFs) capable of encoding the viral nucleocapsid (ORF1p), phosphoprotein (ORF2p), putative cell-to-cell movement protein (ORF3p), matrix protein (ORF4p) and glycoprotein (ORF5p). Each ORF is separated by a conserved intergenic junction. RNA2 (5945 nt), which completes the bipartite genome, encodes a single protein (ORF6p) with homology to RNA-dependent RNA polymerases. Phylogenetic analysis of L protein sequences firmly establishes CoRSV as a member of the recently proposed Dichorhavirus genus. Predictive algorithms, in planta protein expression, and a yeast-based nuclear import assay were used to determine the nucleophillic character of five CoRSV proteins. Finally, the temperature-dependent ability of CoRSV to establish systemic infections in an initially local lesion host was quantified. - Highlights: • We report genome sequence determination for Coffee ringspot virus (CoRSV). • CoRSV should be considered a member of the proposed Dichorhavirus genus. • We report temperature-dependent systemic infection of an initially local lesion host. • We report in planta protein and localization data for five CoRSV proteins. • In silico predictions of the CoRSV proteins were validated using in vivo assays

  20. A locally funded Puerto Rican parrot (Amazona vittata genome sequencing project increases avian data and advances young researcher education

    Directory of Open Access Journals (Sweden)

    Oleksyk Taras K

    2012-09-01

    Full Text Available Abstract Background Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp, which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp. This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

  1. Short communication: Genomic selection in a crossbred cattle population using data from the Dairy Genetics East Africa Project.

    Science.gov (United States)

    Brown, A; Ojango, J; Gibson, J; Coffey, M; Okeyo, M; Mrode, R

    2016-09-01

    Due to the absence of accurate pedigree information, it has not been possible to implement genetic evaluations for crossbred cattle in African small-holder systems. Genomic selection techniques that do not rely on pedigree information could, therefore, be a useful alternative. The objective of this study was to examine the feasibility of using genomic selection techniques in a crossbred cattle population using data from Kenya provided by the Dairy Genetics East Africa Project. Genomic estimated breeding values for milk yield were estimated using 2 prediction methods, GBLUP and BayesC, and accuracies were calculated as the correlation between yield deviations and genomic breeding values included in the estimation process, mimicking the situation for young bulls. The accuracy of evaluation ranged from 0.28 to 0.41, depending on the validation population and prediction method used. No significant differences were found in accuracy between the 2 prediction methods. The results suggest that there is potential for implementing genomic selection for young bulls in crossbred small-holder cattle populations, and targeted genotyping and phenotyping should be pursued to facilitate this. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  2. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

    Science.gov (United States)

    Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Kuehn, Michael S; Taylor, Christopher M; Neph, Shane; Koch, Christoph M; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A; Andrews, Robert M; Flicek, Paul; Boyle, Patrick J; Cao, Hua; Carter, Nigel P; Clelland, Gayle K; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C; Dorschner, Michael O; Fiegler, Heike; Giresi, Paul G; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D; Johnson, Brett E; Johnson, Ericka M; Frum, Tristan T; Rosenzweig, Elizabeth R; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C; Navas, Patrick A; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu, Man; Collins, Francis S; Dekker, Job; Lieb, Jason D; Tullius, Thomas D; Crawford, Gregory E; Sunyaev, Shamil; Noble, William S; Dunham, Ian; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L; Baertsch, Robert; Keefe, Damian; Dike, Sujit; Cheng, Jill; Hirsch, Heather A; Sekinger, Edward A; Lagarde, Julien; Abril, Josep F; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C; Thomas, Daryl J; Weirauch, Matthew T; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, XiaoDong; Srinivasan, K G; Sung, Wing-Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G; Brown, James B; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Hubbard, Tim; Myers, Richard M; Rogers, Jane; Stadler, Peter F; Lowe, Todd M; Wei, Chia-Lin; Ruan, Yijun; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E; Fu, Yutao; Green, Eric D; Karaöz, Ulaş; Siepel, Adam; Taylor, James; Liefer, Laura A; Wetterstrand, Kris A; Good, Peter J; Feingold, Elise A; Guyer, Mark S; Cooper, Gregory M; Asimenos, George; Dewey, Colin N; Hou, Minmei; Nikolaev, Sergey; Montoya-Burgos, Juan I; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Huang, Haiyan; Zhang, Nancy R; Holmes, Ian; Mullikin, James C; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W James; Stone, Eric A; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C; Haussler, David; Miller, Webb; Sidow, Arend; Trinklein, Nathan D; Zhang, Zhengdong D; Barrera, Leah; Stuart, Rhona; King, David C; Ameur, Adam; Enroth, Stefan; Bieda, Mark C; Kim, Jonghwan; Bhinge, Akshay A; Jiang, Nan; Liu, Jun; Yao, Fei; Vega, Vinsensius B; Lee, Charlie W H; Ng, Patrick; Shahab, Atif; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J; Inman, David; Singer, Michael A; Richmond, Todd A; Munn, Kyle J; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Fowler, Joanna C; Couttet, Phillippe; Bruce, Alexander W; Dovey, Oliver M; Ellis, Peter D; Langford, Cordelia F; Nix, David A; Euskirchen, Ghia; Hartman, Stephen; Urban, Alexander E; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Kim, Tae Hoon; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K; Rosenfeld, M Geoff; Aldred, Shelley Force; Cooper, Sara J; Halees, Anason; Lin, Jane M; Shulha, Hennady P; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N S; Yu, Yong; Ruan, Yijun; Iyer, Vishwanath R; Green, Roland D; Wadelius, Claes; Farnham, Peggy J; Ren, Bing; Harte, Rachel A; Hinrichs, Angie S; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M; Karolchik, Donna; Armengol, Lluis; Bird, Christine P; de Bakker, Paul I W; Kern, Andrew D; Lopez-Bigas, Nuria; Martin, Joel D; Stranger, Barbara E; Woodroffe, Abigail; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; Hallgrímsdóttir, Ingileif B; Huppert, Julian; Zody, Michael C; Abecasis, Gonçalo R; Estivill, Xavier; Bouffard, Gerard G; Guan, Xiaobin; Hansen, Nancy F; Idol, Jacquelyn R; Maduro, Valerie V B; Maskeri, Baishali; McDowell, Jennifer C; Park, Morgan; Thomas, Pamela J; Young, Alice C; Blakesley, Robert W; Muzny, Donna M; Sodergren, Erica; Wheeler, David A; Worley, Kim C; Jiang, Huaiyang; Weinstock, George M; Gibbs, Richard A; Graves, Tina; Fulton, Robert; Mardis, Elaine R; Wilson, Richard K; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B; Chang, Jean L; Lindblad-Toh, Kerstin; Lander, Eric S; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; de Jong, Pieter J

    2007-06-14

    We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

  3. CoffeeScript application development

    CERN Document Server

    Young, Ian

    2013-01-01

    CoffeeScript Application Development is a practical, hands-on guide with step-by-step instructions. Follow the smooth and easy tutorial approach, covering examples that build in complexity. By the final chapter you'll be wondering why you didn't try CoffeeScript sooner.If you are a JavaScript developer who wants to save time and add power to your code, then this is the book that will help you do it. With minimal fuss you will learn a whole new language which will reduce your application development time from weeks to days.

  4. Biodiesel Production from Spent Coffee Grounds

    Science.gov (United States)

    Blinová, Lenka; Bartošová, Alica; Sirotiak, Maroš

    2017-06-01

    The residue after brewing the spent coffee grounds is an oil-containing waste material having a potential of being used as biodiesel feedstock. Biodiesel production from the waste coffee grounds oil involves collection and transportation of coffee residue, drying, oil extraction, and finally production of biodiesel. Different methods of oil extraction with organic solvents under different conditions show significant differences in the extraction yields. In the manufacturing of biodiesel from coffee oil, the level of reaction completion strongly depends on the quality of the feedstock oil. This paper presents an overview of oil extraction and a method of biodiesel production from spent coffee grounds.

  5. Thermodynamic analysis of a solar coffee maker

    International Nuclear Information System (INIS)

    Sosa-Montemayor, F.; Jaramillo, O.A.; Rio, J.A. del

    2009-01-01

    In this paper we present a novel solar concentrating application, a coffee brewing system using a satellite TV mini-Dish concentrator coupled to a stovetop espresso coffee maker. We present a theoretical model for the thermal behavior of the water in the lower chamber of the coffee maker. We validate the model obtaining good agreement with the experimental results. Our findings indicate that the coffee brewing system works, it takes 30-50 min to complete its task. The model and our practical experience encourage us to improve the concentration device in order to obtain a useful solar coffee maker, using the theoretical model as a safe guide to achieve this.

  6. Thermodynamic analysis of a solar coffee maker

    Energy Technology Data Exchange (ETDEWEB)

    Sosa-Montemayor, F.; Jaramillo, O.A. [Centro de Investigacion en Energia, Universidad Nacional Autonoma de Mexico, Privada Xochicalco S/N, Temixco, Morelos CP 62580 (Mexico); del Rio, J.A. [Centro Morelense de Innovacion y Tranferencia Tecnologica, CCyTEM, Camino Temixco a Emiliano Zapata, Km 0.3, Colonia Emiliano Zapata, Morelos CP 62760 (Mexico)

    2009-09-15

    In this paper we present a novel solar concentrating application, a coffee brewing system using a satellite TV mini-Dish concentrator coupled to a stovetop espresso coffee maker. We present a theoretical model for the thermal behavior of the water in the lower chamber of the coffee maker. We validate the model obtaining good agreement with the experimental results. Our findings indicate that the coffee brewing system works, it takes 30-50 min to complete its task. The model and our practical experience encourage us to improve the concentration device in order to obtain a useful solar coffee maker, using the theoretical model as a safe guide to achieve this. (author)

  7. Understanding the Human Genome Project: Using Stations to Provide a Comprehensive Overview

    Science.gov (United States)

    Soto, Julio G.

    2005-01-01

    A lesson was designed for lower division general education, non-major biology lecture-only course that included the historical and scientific context, some of the skills used to study the human genome, results, conclusions and ethical consideration. Students learn to examine and compare the published Human Genome maps, and employ the strategies…

  8. The MICROBE Project, A Report from the Interagency Working Group on Microbial Genomics

    Science.gov (United States)

    2001-01-01

    functional genomics tools (gene chips, technologies, etc.), comparative genomics, proteomics tools, novel culture techniques, in situ analyses, and...interested in supporting microarray/chip development for gene expression analysis for agricultural microbes, bioinformatics, and proteomics , and the...including one fungus ) in various stages of progress. The closely integrated Natural and Accelerated Bioremediation Research Program in the Office of

  9. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  10. Analysis of acrylamide in coffee and dietary exposure to acrylamide from coffee

    DEFF Research Database (Denmark)

    Granby, Kit; Fagt, Sisse

    2004-01-01

    An analytical method for analysing acrylamide in coffee was validated. The analysis of prepared coffee includes a comprehensive clean-up using multimode solid-phase extraction (SPE) by automatic SPE equipment and detection by liquid chromatography tandem mass spectrometry using electrospray...... in the positive mode. The recoveries of acrylamide in ready-to-drink coffee spiked with 5 and 10 mug l(-1) were 96 +/- 14% and 100 +/- 8%, respectively. Within laboratory reproducibility for the same spiking levels were 14% and 9%, respectively. Coffee samples (n = 25) prepared twice by coffee machines and twice...... by a French Press Cafetiere coffee maker contained 8 +/- 3 mug l(-1) and 9 +/- 3 mug l(-1) acrylamide. Five ready-to-drink instant coffee prepared twice contained 8 +/- 2 mug l(-1). Hence, the results do not show significant differences in the acrylamide contents in ready-to-drink coffee prepared by coffee...

  11. Coffee and spent coffee extracts protect against cell mutagens and inhibit growth of food-borne pathogen microorganisms

    OpenAIRE

    Cid, C. (Concepción); Peña, M.P. (María Paz) de; Arbillaga, L. (Leire); Vitas, A.I. (Ana Isabel); Bravo, J. (Jimena); Monente, C. (Carmen)

    2015-01-01

    Coffee consumption decreases the risk of oxidative stress-related diseases. The by-product obtained after brewing process (spent coffee) also has antioxidant capacity. Spent coffee and coffee brews (filter and espresso) extracts were obtained from Arabica and Robusta coffees, respectively. Spent coffee showed slightly high amounts in chlorogenic acids, but caffeine content was similar to their respective coffee brew. All samples exhibited strong protection activity against indirect acting mut...

  12. Dynamics of the international coffee market and instrumental in price formation

    Directory of Open Access Journals (Sweden)

    Ricardo Candéa Sá Barreto

    2016-12-01

    Full Text Available This study's main general objective of studying the behavior of coffee beans on the international market. Empirical analysis uses econometric tool as a model of simultaneous equations using least squares in a three-stage annual data base extending over the period 1964 / 65-2014 / 15. The results suggest that the factors that affect the production of coffee beans are the actual prices and the planted area. However, demand is affected by the growth of the world economy. The price simulations for the period 2014/15 - 2020/21 indicate that a yearly growth (GDP of 2.1% there is a tendency of small high price to 3.6% moderate rise in the price of coffee until 2018/19 and a stronger growth trend of prices from 2019/20 and a growth of 4.7% a high coffee prices trend in grain on the international market. Thus the tendency of the projections 3 and the key market factors continue to favor the maintenance of current high coffee prices. For the full period 1964/65 to 2014/15 there is a moderate relationship between coffee prices and the stock. It follows that the results obtained with the scenarios developed in this work can be useful to rethink measures to recover income from coffee producing countries

  13. Thorough analysis of unorthodox ABO deletions called by the 1000 Genomes project.

    Science.gov (United States)

    Möller, M; Hellberg, Å; Olsson, M L

    2018-02-01

    ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G. DNA samples from selected 1000G donors and African blood donors were examined by allele-specific PCR and Sanger sequencing to characterize predicted deletions. A 5821-bp deletion encompassing exons 5-7 was called in twenty 1000G individuals, predominantly Africans. This allele was confirmed and its exact deletion point defined by bioinformatic analyses and in vitro experiments. A PCR assay was developed, and screening of African samples revealed three donors heterozygous for this deletion, which was thereby phenotypically established as an O allele. Analysis of upstream genetic markers indicated an ancestral origin from ABO*O.01.02. We estimate this deletion as the 3rd most common mechanism behind O alleles. A 24-bp deletion was called in nine individuals and showed greater diversity regarding ethnic distribution and allelic background. It could neither be confirmed by in silico nor in vitro experiments. A previously uncharacterized ABO deletion among Africans was comprehensively mapped and a genotyping strategy devised. The false prediction of another deletion emphasizes the need for cautious interpretation of NGS data and calls for strict validation routines. © 2017 International Society of Blood Transfusion.

  14. Geotechnologies for the Characterization of Specialty Coffee Environments of Mantiqueira de Minas in Brazil

    Science.gov (United States)

    Alves, H. M. R.; Vieira, T. G. C.; Volpato, M. M. L.; Lacerda, M. P. C.; Borém, F. M.

    2016-06-01

    Land-use/land-cover change (LUCC) is a major cause of environmental transformation. Distant drivers, often associated with emerging markets for specific products, are now being considered one of the main factors of LUCC and are gaining attention in land change science. Consumers show an increasing interest in local and quality food, certified for its origin and its environmental production standards. A kind of agricultural product certification, Geographic Indication, identifies a product as originating from a specific region where a given quality, reputation or characteristic is attributed to its geographical origin. Sustainable land use is potentially an indirect effect of Geographic Indication, as it requires better land management in order to preserve the natural resources associated with the unique characteristics of the certified product. Located in the southern region of the state of Minas Gerais in Brazil is the region of Mantiqueira de Minas, considered one of the most important regions for the production of specialty coffees in Brazil. In 2011, the region's tradition and reputation were recognized with a Geographic Indication, the second given for coffee regions in the country. To explore the full potential of this area for producing coffees with higher quality and meet the growing demand of this new international market, which aggregates value at specialty coffees, it became fundamental to understand the coffee environments of the region, the "terroirs" where these coffees are obtained. Geotechnology can give a significant contribution in filling this gap. This work is part of a research project that made a detailed characterization of the region's coffee agroecosystems. Geotechnologies were employed to map the areas occupied by coffee plantations by using RapidEye satellite images and SPRING and ArcGIS software. All the segments of the environment were characterized and mapped in detail and the relations with coffee quality were evaluated. The results

  15. GEOTECHNOLOGIES FOR THE CHARACTERIZATION OF SPECIALTY COFFEE ENVIRONMENTS OF MANTIQUEIRA DE MINAS IN BRAZIL

    Directory of Open Access Journals (Sweden)

    H. M. R. Alves

    2016-06-01

    Full Text Available Land-use/land-cover change (LUCC is a major cause of environmental transformation. Distant drivers, often associated with emerging markets for specific products, are now being considered one of the main factors of LUCC and are gaining attention in land change science. Consumers show an increasing interest in local and quality food, certified for its origin and its environmental production standards. A kind of agricultural product certification, Geographic Indication, identifies a product as originating from a specific region where a given quality, reputation or characteristic is attributed to its geographical origin. Sustainable land use is potentially an indirect effect of Geographic Indication, as it requires better land management in order to preserve the natural resources associated with the unique characteristics of the certified product. Located in the southern region of the state of Minas Gerais in Brazil is the region of Mantiqueira de Minas, considered one of the most important regions for the production of specialty coffees in Brazil. In 2011, the region’s tradition and reputation were recognized with a Geographic Indication, the second given for coffee regions in the country. To explore the full potential of this area for producing coffees with higher quality and meet the growing demand of this new international market, which aggregates value at specialty coffees, it became fundamental to understand the coffee environments of the region, the “terroirs” where these coffees are obtained. Geotechnology can give a significant contribution in filling this gap. This work is part of a research project that made a detailed characterization of the region’s coffee agroecosystems. Geotechnologies were employed to map the areas occupied by coffee plantations by using RapidEye satellite images and SPRING and ArcGIS software. All the segments of the environment were characterized and mapped in detail and the relations with coffee quality

  16. Evaluation of an ergonomics intervention among Nicaraguan coffee harvesting workers.

    Science.gov (United States)

    Bao, Stephen; Silverstein, Barbara; Stewart, Kate

    2013-01-01

    This study evaluated an ergonomics intervention among Nicaraguan coffee harvesting workers, using electromyography and questionnaire survey techniques. Nicaraguan researchers were involved in the study so that they could gain hands-on experience with ergonomics research and applications, and eventually be the specialists conducting ergonomics interventions in Nicaraguan workplaces. Coffee harvesting activities were studied individually and physical hazards were identified accordingly. The results showed decreased muscle loading on the erector spinae muscle and improved comfort reporting in the back region compared to the commonly used baskets. This fulfils the design objective of a newly developed bag that was used in the intervention to reduce physical workload on the coffee harvesting workers. Workers' opinion survey results showed some issues related to the size of the new bag and the lumbar-shoulder belt mechanism. This information can be used in the modification of the bag in the next design. Key players in the process have been identified. Stimulating ergonomics activities in developing countries is suggested by many experts. This study provided an example from coffee workers in Nicaragua. Commonly used job evaluation procedures and physical load quantification methods were used. Ergonomics researchers and practitioners in developing countries may do similar projects on their own in the future.

  17. Say goodbye to coffee stains

    NARCIS (Netherlands)

    Eral, Burak; van den Ende, Henricus T.M.; Mugele, Friedrich Gunther

    2012-01-01

    Discussing ideas over a mug of coffee or tea is the lifeblood of science, but have you ever thought about the stains that can be inadvertently left behind? H Burak Eral, Dirk van den Ende and Frieder Mugele explain how these stains, which can be a major annoyance in some biology techniques, can be

  18. Coffee Cup Atomic Force Microscopy

    Science.gov (United States)

    Ashkenaz, David E.; Hall, W. Paige; Haynes, Christy L.; Hicks, Erin M.; McFarland, Adam D.; Sherry, Leif J.; Stuart, Douglas A.; Wheeler, Korin E.; Yonzon, Chanda R.; Zhao, Jing; Godwin, Hilary A.; Van Duyne, Richard P.

    2010-01-01

    In this activity, students use a model created from a coffee cup or cardstock cutout to explore the working principle of an atomic force microscope (AFM). Students manipulate a model of an AFM, using it to examine various objects to retrieve topographic data and then graph and interpret results. The students observe that movement of the AFM…

  19. Double Coffee opens in China

    Index Scriptorium Estoniae

    2009-01-01

    Läti suursaadik Ingrida Levrence avas esimese Double Coffee kohviku Hiina pealinnas Pekingi südames. Rahvusvaheline kohvikukett kavatseb laieneda mõne kohviku võrra igal aastal. Seni tegutsetakse Lätis, Eestis, Leedus, Ukrainas ja Valgevenes

  20. Coffee berry disease in Kenya

    NARCIS (Netherlands)

    Vermeulen, H.

    1979-01-01

    Data are presented on research in Kenya in 1964 - 1969 on anatomical, mycological, epidemiological, chemical control and cultural aspects of coffee berry disease, Colletotrichum coffeanum Noack, of Coffea arabica L. The pathogen causes flower and berry

  1. Pest Management Strategies Against the Coffee Berry Borer (Coleoptera: Curculionidae: Scolytinae).

    Science.gov (United States)

    Infante, Francisco

    2018-03-22

    Coffee ( Coffea arabica and C. canephora) is one of the most widely traded agricultural commodities and the main cash crop in ∼80 tropical countries. Among the factors that limit coffee production, the coffee berry borer, Hypothenemus hampei (Ferrari) has been considered the main insect pest, causing losses of over U.S. $500 million dollars annually. Control of this pest has been hindered by two main factors: the cryptic nature of the insect (i.e., protected inside the coffee berry) and the availability of coffee berries in the field allowing the survival of the pest from one generation to the next. Coffee berry borer control has primarily been based on the use of synthetic insecticides. Management strategies have focused on the use of African parasitoids ( Cephalonomia stephanoderis, Prorops nasuta, and Phymastichus coffea), fungal entomopathogens ( Beauveria bassiana), and insect traps. These approaches have had mixed results. Recent work on the basic biology of the insect has provided novel insights that might be useful in developing novel pest management strategies. For example, the discovery of symbiotic bacteria responsible for caffeine breakdown as part of the coffee berry borer microbiome opens new possibilities for pest management via the disruption of these bacteria. Some chemicals with repellent propieties have been identified, and these have a high potential for field implementation. Finally, the publication of the CBB genome has provided insights on the biology of the insect that will help us to understand why it has been so successful at exploiting the coffee plant. Here I discuss the tools we now have against the CBB and likely control strategies that may be useful in the near future.

  2. The Micronutrient Genomics Project: A community-driven knowledge base for micronutrient research

    NARCIS (Netherlands)

    Ommen, B. van; El-Sohemy, A.; Hesketh, J.; Kaput, J.; Fenech, M.; Evelo, C.T.; McArdle, H.J.; Bouwman, J.; Lietz, G.; Mathers, J.C.; Fairweather-Tait, S.; Kranen, H. van; Elliott, R.; Wopereis, S.; Ferguson, L.R.; Méplan, C.; Perozzi, G.; Allen, L.; Rivero, D.

    2010-01-01

    Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes. Optimum micronutrient supply is important for the maintenance of homeostasis in metabolism and, ultimately, for maintaining good health. With advances in systems biology and genomics technologies, it

  3. Controlling our destinies: Historical, philosophical, social and ethical perspectives on the Human Genome Project: Final report, July 1, 1995-June 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Sloan, P.R.

    1996-09-25

    This report briefly describes the efforts by the organizing committee in preparation for the conference entitled Controlling Our Destinies: Historical, Philosophical, Social, and Ethical Perspectives on the Human Genome Project. The conference was held October 5-8, 1995.

  4. Contributing to Tumor Molecular Characterization Projects with a Global Impact | Office of Cancer Genomics

    Science.gov (United States)

    My name is Nicholas Griner and I am the Scientific Program Manager for the Cancer Genome Characterization Initiative (CGCI) in the Office of Cancer Genomics (OCG). Until recently, I spent most of my scientific career working in a cancer research laboratory. In my postdoctoral training, my research focused on identifying novel pathways that contribute to both prostate and breast cancers and studying proteins within these pathways that may be targeted with cancer drugs.

  5. The Impact of Coffee on Health.

    Science.gov (United States)

    Nieber, Karen

    2017-11-01

    Coffee is one of the most popular and widely consumed beverages worldwide due to its stimulating effects on the central nervous system as well as its taste and aroma. Coffee is a complex mixture of more than 800 volatile compounds whereas caffeine and chlorogenic acids are the most common compounds. During the last years, coffee has progressively moved to a less negative position on health due to its better-known pharmacology. Caffeine, e.g., in a cup of coffee, appears to exert most of its effects through an antagonism of the adenosine receptors. Novel approaches in epidemiological studies and experimental researches suggest that coffee consumption may help to prevent several chronic diseases, including type 2 diabetes mellitus and liver disease. Most prospective cohort studies have not found coffee consumption to be associated with a significantly increased cardiovascular disease risk. There is also evidence that decaffeinated coffee may, in some respect, have similar benefits as regular coffee, indicating that besides caffeine other components contribute to the health protecting effects. For adults consuming moderate amounts of coffee (3 - 4 cups/d providing 300 - 400 mg/d of caffeine), there is little evidence of health risks and some evidence of health benefits. This review provides up-to-date information about coffee on health. Topics addressed include the cardiovascular system, liver diseases, and diabetes as well as gastrointestinal disorders. Georg Thieme Verlag KG Stuttgart · New York.

  6. Magnetically modified spent coffee grounds for dyes removal

    Czech Academy of Sciences Publication Activity Database

    Šafařík, Ivo; Horská, Kateřina; Svobodová, Barbora; Šafaříková, Miroslava

    2012-01-01

    Roč. 234, č. 2 (2012), s. 345-350 ISSN 1438-2377 R&D Projects: GA MŠk OC09052; GA MPO 2A-1TP1/094 Institutional research plan: CEZ:AV0Z60870520 Keywords : coffee grounds * magnetic fluid * adsorption * dyes * magnetic solid-phase extraction Subject RIV: GM - Food Processing Impact factor: 1.436, year: 2012

  7. Preliminary design of a coffee harvester

    Directory of Open Access Journals (Sweden)

    Raphael Magalhães Gomes Moreira

    2016-10-01

    Full Text Available Design of an agricultural machine is a highly complex process due to interactions between the operator, machine, and environment. Mountain coffee plantations constitute an economic sector that requires huge investments for the development of agricultural machinery to improve the harvesting and post-harvesting processes and to overcome the scarcity of work forces in the fields. The aim of this study was to develop a preliminary design for a virtual prototype of a coffee fruit harvester. In this study, a project methodology was applied and adapted for the development of the following steps: project planning, informational design, conceptual design, and preliminary design. The construction of a morphological matrix made it possible to obtain a list of different mechanisms with specific functions. The union between these mechanisms resulted in variants, which were weighed to attribute scores for each selected criterion. From each designated proposal, two variants with the best scores were selected and this permitted the preparation of the preliminary design of both variants. The archetype was divided in two parts, namely the hydraulically articulated arms and the harvesting system that consisted of the vibration mechanism and the detachment mechanism. The proposed innovation involves the use of parallel rods, which were fixed in a plane and rectangular metal sheet. In this step, dimensions including a maximum length of 4.7 m, a minimum length of 3.3 m, and a total height of 2.15 m were identified based on the functioning of the harvester in relation to the coupling point of the tractor.

  8. Identification and Analysis of Jasmonate Pathway Genes in Coffea canephora (Robusta Coffee) by In Silico Approach.

    Science.gov (United States)

    Bharathi, Kosaraju; Sreenath, H L

    2017-07-01

    Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica . Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase. There is no report on the genes involved in JA pathway in coffee plants. We made an attempt to identify and analyze the genes coding for these enzymes in C. canephora . First, protein sequences of jasmonate pathway genes from model plant Arabidopsis thaliana were identified in the National Center for Biotechnology Information (NCBI) database. These protein sequences were used to search the web-based database Coffee Genome Hub to identify homologous protein sequences in C. canephora genome using Basic Local Alignment Search Tool (BLAST). Homologous protein sequences for key genes were identified in the C. canephora genome database. Protein sequences of the top matches were in turn used to search in NCBI database using BLAST tool to confirm the identity of the selected proteins and to identify closely related genes in species. The protein sequences from C. canephora database and the top matches in NCBI were aligned, and phylogenetic trees were constructed using MEGA6 software and identified the genetic distance of the respective genes. The study identified the four key genes of JA pathway in C. canephora , confirming the conserved nature of the pathway in coffee. The study expected to be useful to further explore the defense mechanisms of coffee plants. JA is a plant hormone that plays an important role in plant defense against insect pests. Genes coding for the 4 key enzymes involved in the production of JA viz., LOX, AOS, AOC, and OPR are identified in C. canephora (robusta coffee) by

  9. Brazilian Coffee Production as Function of Global Warming.

    Science.gov (United States)

    Avila, A. M. H. D.; Pinto, H. S.; Alfonsi, E. L., Sr.; Alfonsi, W. M. V.; Pereira, V. R.

    2016-12-01

    According to the Brazilian Government the actual area of coffee production in the country is close to 2.25 million hectares. The sector involves 290.000 of farmers with a production of 44 million of 60 Kg bags in 2015. The Arabica Coffee specie is cultivated in the country where the climate condition are characterized by a year mean temperatures between 18°C and 22°C. Temperatures higher than 33°C can cause abortion of flowers during the spring season and reduce the production while lower than 18°C can be affected by frost during winter when the minimum temperature can be lower than 2°C in the shelter. For a better quality of the final product the winter, between July and August, must be dry with rainfall lower than 50 mm/month. The Ministry of Agriculture defines those conditions for the Official Coffee Climatic Risk Zoning. In 2002, a partnership with the British Embassy and 2 Brazilian institutions, i. e. the State University of Campinas - UNICAMP and the Brazilian Agricultural Research Corporation - Embrapa, published the study "Global Warming and the New Geography of Agricultural Production in Brazil" (Pinto and Assad, 2002). This study was based on the PRECIS/Hadley Centre Regional Climate Model future projections. The crop simulations indicated a decrease in the grain production due to temperature rise. Later in 2012, a new study was developed in cooperation with the World Bank to evaluate the future of nine main commodities in Brazil under climate change, including the Arabica coffee. The worst scenario considering any mitigation and adaptation action indicated that the two most affected crops would be the soybean and coffee, with a reduction of 22% and 6.7 % in the yield respectively. Field surveys to evaluate the historical spatial dynamic and migration of Arabica coffee cultivated areas confirmed the results of the previous studies and indicated a recent increase in the search for cooler altitude areas to plant coffee. Also the field observations

  10. The performances of coffee processors and coffee market in the Republic of Serbia

    Directory of Open Access Journals (Sweden)

    Nuševa Daniela

    2017-01-01

    Full Text Available The main aim of this paper is to investigate the performances of coffee processors and coffee market in Serbia based on the market concentration analysis, profitability analysis, and profitability determinants analysis. The research was based on the sample of 40 observations of coffee processing companies divided into two groups: large and small coffee processors. The results indicate that two large coffee processors have dominant market share. Even though the Serbian coffee market is an oligopolistic, profitability analysis indicates that small coffee processors have a significant better profitability ratio than large coffee processors. Furthermore, results show that profitability ratio is positively related to the inventory turnover and negatively related to the market share.

  11. Adaptive Measures for the Factors Affecting Marketing of Coffee ...

    African Journals Online (AJOL)

    Adaptive Measures for the Factors Affecting Marketing of Coffee ( Coffea robusta ... of coffee in the study area was poor pricing and marketing systems; this is as a ... of quality control and relevant information on improved coffee technologies.

  12. Antioxidant effect of Arabian coffee (Coffea arabica L) blended with ...

    African Journals Online (AJOL)

    antioxidants (GSH, vitamins C and E) were significantly elevated (p < 0.05) in mice administered. Arabian coffee ... cancer [9,10]. In addition ... HFD alone. IV. HFD + Arabian coffee + cardamom. V. HFD + Arabian coffee + cardamom + cloves.

  13. Coffee Production in Kigoma Region, Tanzania: Profitability and ...

    African Journals Online (AJOL)

    Farmers processed at CPU gained about TZS 1350/kg as coffee improvement gain. Coffee production ... explored, keeping in mind the theories put forth in the theoretical ... Information used in the gross margin analysis encompass total coffee ...

  14. Influence of coffee/water ratio on the final quality of espresso coffee

    OpenAIRE

    Andueza, S. (Susana); Vila, M.A. (María A.); Peña, M.P. (María Paz) de; Cid, C. (Concepción)

    2007-01-01

    Espresso coffee is a polyphasic beverage in which the physico-chemical and sensory characteristics obviously depend on both the selection of ground roasted coffee and the technical conditions of the percolation process. The aim of this work was to evaluate the influence of the coffee/water ratio on the physico-chemical and sensory quality of espresso coffee. Furthermore, the influence of botanical varieties (Arabica and Robusta) and the type of roast (conventional and torrefacto) on the selec...

  15. Coffee Berry Borer Joins Bark Beetles in Coffee Klatch

    Science.gov (United States)

    Jaramillo, Juliana; Torto, Baldwyn; Mwenda, Dickson; Troeger, Armin; Borgemeister, Christian; Poehling, Hans-Michael; Francke, Wittko

    2013-01-01

    Unanswered key questions in bark beetle-plant interactions concern host finding in species attacking angiosperms in tropical zones and whether management strategies based on chemical signaling used for their conifer-attacking temperate relatives may also be applied in the tropics. We hypothesized that there should be a common link in chemical signaling mediating host location by these Scolytids. Using laboratory behavioral assays and chemical analysis we demonstrate that the yellow-orange exocarp stage of coffee berries, which attracts the coffee berry borer, releases relatively high amounts of volatiles including conophthorin, chalcogran, frontalin and sulcatone that are typically associated with Scolytinae chemical ecology. The green stage of the berry produces a much less complex bouquet containing small amounts of conophthorin but no other compounds known as bark beetle semiochemicals. In behavioral assays, the coffee berry borer was attracted to the spiroacetals conophthorin and chalcogran, but avoided the monoterpenes verbenone and α-pinene, demonstrating that, as in their conifer-attacking relatives in temperate zones, the use of host and non-host volatiles is also critical in host finding by tropical species. We speculate that microorganisms formed a common basis for the establishment of crucial chemical signals comprising inter- and intraspecific communication systems in both temperate- and tropical-occurring bark beetles attacking gymnosperms and angiosperms. PMID:24073204

  16. Assessment of Cellular Mutagenicity of Americano Coffees from Popular Coffee Chains.

    Science.gov (United States)

    Liu, Zhen-Shu; Chen, Po-Wen; Wang, Jung-Yu; Kuo, Tai-Chen

    2017-09-01

    Coffee is a popular beverage worldwide, but coffee beans can be contaminated with carcinogens. The Ames Salmonella mutagenicity test is often used for analysis of carcinogens for mutagenicity. However, previous studies have provided controversial data about the direct mutagenicity of coffee beans based on Ames test results. This study was conducted to determine the mutagenicity of popular Americano coffee based on results from the Ames test. Coffee samples without additives that were served by five international coffee chain restaurants were subjected to the analysis using Salmonella Typhimurium tester strains TA98, TA100, and TA1535. The levels of bacterial revertants in samples from coffee chains were lower than the twofold criterion of the control sets, and no significant dose-response effect was observed with or without rat liver enzyme activation. These data indicate that Americano coffees from the selected coffee chains possessed no direct mutagenic activity with or without enzyme activation. These findings suggest a low mutagenic risk from Americano coffees served by the selected coffee chains and support the use of other methods to confirm the nonmutagenicity of coffee products. These results are consistent with most recent epidemiological reports.

  17. What every dentist should know about coffee.

    Science.gov (United States)

    Seidman, Lara M; Eckenrode, Kelsey N; Bloom, Ira T; Bashirelahi, Nasir

    2016-01-01

    Coffee is one of the most widely consumed beverages throughout the world. Its stimulating nature is responsible for much of its popularity, which paradoxically has resulted in its reputation for negative effects on consumer health. This review will address recent research on the systemic and dental health effects of coffee. Many of its supposed harmful effects have been disproved, while many protective and beneficial roles for coffee are emerging.

  18. Furan in roasted, ground and brewed coffee

    Science.gov (United States)

    Gruczyńska, Eliza; Kowalska, Dorota; Kozłowska, Mariola; Majewska, Ewa; Tarnowska, Katarzyna

    2018-01-01

    Coffee is the most popular hot beverage in the world. The annual coffee production in 2010, 2014 and 2016 was 8.1, 9.0 and 9.3 million tons respectively. There are more than 100 coffee species, but only two of them: Arabica (Coffea arabica) and Robusta (Coffea canephora) have gained commercial importance. During roasting of green coffee beans not only desirable compounds are formed, that exert positive influence on the taste and flavour of coffee, but also small quantities of undesirable ones. Furan (C4H4O) is one of the latter. Furan is a volatile compound (boiling temp. of 31.4 oC) formed during thermal processing of food. The toxicity of furan has been well documented and it is classified as “possible human carcinogen” (Group 2B) by the International Agency for Research on Cancer. Various pathways have been reported for furan formation during food processing. It can be formed from carbohydrates, amino acids by their thermal degradation or thermal re-arrangement and by oxidation of ascorbic acid and polyunsaturated acids and carotenoids. High concentrations of furan have been reported in coffee, baked and roasted food and in food subjected to preserving in cans and jars. Furan levels in brewed coffee are typically near or below 120 μg/L, but it can approach thousands μg/kg in roasted whole beans or ground coffee. The highest concentration of furan in roasted coffee reaches the level of 7000 μg/kg. Taking into account that coffee is the most popular hot drink, it becomes the main contributor to furan exposure from dietary sources for adults. In this article the published scientific papers concerned with the presence of furan in roasted non-brewed and brewed coffee have been reviewed. The formation mechanisms and occurrence of furan in coffee and the harmful influence of furan on the consumer health have been discussed.

  19. Coffee: The magical bean for liver diseases

    OpenAIRE

    Heath, Ryan D; Brahmbhatt, Mihir; Tahan, Asli C; Ibdah, Jamal A; Tahan, Veysel

    2017-01-01

    Coffee has long been recognized as having hepatoprotective properties, however, the extent of any beneficial effect is still being elucidated. Coffee appears to reduce risk of hepatocellular carcinoma, reduce advancement of fibrotic disease in a variety of chronic liver diseases, and perhaps reduce ability of hepatitis C virus to replicate. This review aims to catalog the evidence for coffee as universally beneficial across a spectrum of chronic liver diseases, as well as spotlight opportunit...

  20. HOW COFFEE COMPANIES CAN STAY COMPETITIVE

    OpenAIRE

    RALUCA DANIELA RIZEA; ROXANA SARBU; ELENA CONDREA

    2014-01-01

    The coffee shop industry in the U.S. includes 20,000 stores with combined annual revenue of about $11 billion. Major companies include Starbucks, Dunkin’ Donuts, Caribou, Coffee Bean and Tea Leaf, and Diedrich (Gloria Jean’s). The industry is highly concentrated at the top and fragmented at the bottom: the top 50 companies have over 70 percent of industry sales. Coffee is one of the world’s largest commodities. The top green coffee producing countries are Brazil, Colombia, and Vietnam. Many...

  1. The Little Book on CoffeeScript

    CERN Document Server

    MacCaw, Alex

    2012-01-01

    This little book shows JavaScript developers how to build superb web applications with CoffeeScript, the remarkable little language that's gaining considerable interest. Through example code, this guide demonstrates how CoffeeScript abstracts JavaScript, providing syntactical sugar and preventing many common errors. You'll learn CoffeeScript's syntax and idioms step by step, from basic variables and functions to complex comprehensions and classes. Written by Alex MacCaw, author of JavaScript Web Applications (O'Reilly), with contributions from CoffeeScript creator Jeremy Ashkenas, this book

  2. Coffee: biochemistry and potential impact on health.

    Science.gov (United States)

    Ludwig, Iziar A; Clifford, Michael N; Lean, Michael E J; Ashihara, Hiroshi; Crozier, Alan

    2014-08-01

    This review provides details on the phytochemicals in green coffee beans and the changes that occur during roasting. Key compounds in the coffee beverage, produced from the ground, roasted beans, are volatile constituents responsible for the unique aroma, the alkaloids caffeine and trigonelline, chlorogenic acids, the diterpenes cafestol and kahweol, and melanoidins, which are Maillard reaction products. The fate of these compounds in the body following consumption of coffee is discussed along with evidence of the mechanisms by which they may impact on health. Finally, epidemiological findings linking coffee consumption to potential health benefits including prevention of several chronic and degenerative diseases, such as cancer, cardiovascular disorders, diabetes, and Parkinson's disease, are evaluated.

  3. PAH in tea and coffee

    DEFF Research Database (Denmark)

    Duedahl-Olesen, Lene; Navarantem, Marin; Adamska, Joanna

    For food regulation in the European Union maximum limits on other foods than tea and coffee includes benzo[a]pyrene and the sum of PAH4 (sum of benzo[a]pyrene, chrysene, benz[a]anthracene and benzo[b]fluoranthene). This study includes analysis of the above mentioned PAH in both, tea leaves, coffee...... beans and ready-to-drink preparations. Compared to other food matrices (e.g. fish), the analytical methods were challenged by the hot water extracts. Preparation of tea includes roasting and drying of the tea leaves using combustion gases from burning wood, oil, or coal. These are responsible...... for accumulation of PAH in tea leaves. Different varieties of tea leaves were analyzed and highest concentrations were found in leaves from mate and black tea with maximum concentrations of 32 μg/kg for benzo[a]pyrene and 115 μg/kg for the sum of PAH4. Also, coffee beans are roasted during processing. However...

  4. Whitehead Policy Symposium. The Human Genome Project: Science, law, and social change in the 21st century

    Energy Technology Data Exchange (ETDEWEB)

    Nichols, E.K.

    2000-02-17

    Advances in the biomedical sciences, especially in human genomics, will dramatically influence law, medicine, public health, and many other sectors of our society in the decades ahead. The public already senses the revolutionary nature of genomic knowledge. In the US and Europe, we have seen widespread discussions about genetic discrimination in health insurance; privacy issues raised by the proliferation of DNA data banks; the challenge of interpreting new DNA diagnostic tests; changing definitions of what it means to be healthy; and the science and ethics of cloning animals and human beings. The primary goal of the Whitehead/ASLME Policy Symposium was to provide a bridge between the research community and professionals, who were just beginning to grasp the potential impact of new genetic technologies on their fields. The ''Human Genome Project: Science, Law, and Social Change in the 21st Century'' initially was designed as a forum for 300-500 physicians, lawyers, consumers, ethicists, and scientists to explore the impact of new genetic technologies and prepare for the challenges ahead.

  5. Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

    Directory of Open Access Journals (Sweden)

    Tjaart A P de Beer

    Full Text Available The 1000 Genomes Project data provides a natural background dataset for amino acid germline mutations in humans. Since the direction of mutation is known, the amino acid exchange matrix generated from the observed nucleotide variants is asymmetric and the mutabilities of the different amino acids are very different. These differences predominantly reflect preferences for nucleotide mutations in the DNA (especially the high mutation rate of the CpG dinucleotide, which makes arginine mutability very much higher than other amino acids rather than selection imposed by protein structure constraints, although there is evidence for the latter as well. The variants occur predominantly on the surface of proteins (82%, with a slight preference for sites which are more exposed and less well conserved than random. Mutations to functional residues occur about half as often as expected by chance. The disease-associated amino acid variant distributions in OMIM are radically different from those expected on the basis of the 1000 Genomes dataset. The disease-associated variants preferentially occur in more conserved sites, compared to 1000 Genomes mutations. Many of the amino acid exchange profiles appear to exhibit an anti-correlation, with common exchanges in one dataset being rare in the other. Disease-associated variants exhibit more extreme differences in amino acid size and hydrophobicity. More modelling of the mutational processes at the nucleotide level is needed, but these observations should contribute to an improved prediction of the effects of specific variants in humans.

  6. Smoking, alcohol, and coffee consumption preceding Parkinson's disease: a case-control study.

    Science.gov (United States)

    Benedetti, M D; Bower, J H; Maraganore, D M; McDonnell, S K; Peterson, B J; Ahlskog, J E; Schaid, D J; Rocca, W A

    2000-11-14

    To study the association of PD with preceding smoking, alcohol, and coffee consumption using a case-control design. The authors used the medical records linkage system of the Rochester Epidemiology Project to identify 196 subjects who developed PD in Olmsted County, MN, during the years 1976 to 1995. Each incident case was matched by age (+/-1 year) and sex to a general population control subject. The authors reviewed the complete medical records of cases and control subjects to abstract exposure information. For coffee consumption, the authors found an OR of 0.35 (95% CI = 0.16 to 0.78, p = 0.01), a dose-effect trend (p = 0.003), and a later age at PD onset in cases who drank coffee compared with those who never did (median 72 versus 64 years; p = 0.0002). The inverse association with coffee remained significant after adjustment for education, smoking, and alcohol drinking and was restricted to PD cases with onset at age coffee drinking and PD; however, this association does not imply that coffee has a direct protective effect against PD. Alternative explanations for the association should be considered.

  7. Association of coffee and caffeine intake with the risk of Parkinson disease.

    Science.gov (United States)

    Ross, G W; Abbott, R D; Petrovitch, H; Morens, D M; Grandinetti, A; Tung, K H; Tanner, C M; Masaki, K H; Blanchette, P L; Curb, J D; Popper, J S; White, L R

    The projected expansion in the next several decades of the elderly population at highest risk for Parkinson disease (PD) makes identification of factors that promote or prevent the disease an important goal. To explore the association of coffee and dietary caffeine intake with risk of PD. Data were analyzed from 30 years of follow-up of 8004 Japanese-American men (aged 45-68 years) enrolled in the prospective longitudinal Honolulu Heart Program between 1965 and 1968. Incident PD, by amount of coffee intake (measured at study enrollment and 6-year follow-up) and by total dietary caffeine intake (measured at enrollment). During follow-up, 102 men were identified as having PD. Age-adjusted incidence of PD declined consistently with increased amounts of coffee intake, from 10.4 per 10,000 person-years in men who drank no coffee to 1.9 per 10,000 person-years in men who drank at least 28 oz/d (Pcoffee sources (P=.03 for trend). Consumption of increasing amounts of coffee was also associated with lower risk of PD in men who were never, past, and current smokers at baseline (P=.049, P=.22, and P=.02, respectively, for trend). Other nutrients in coffee, including niacin, were unrelated to PD incidence. The relationship between caffeine and PD was unaltered by intake of milk and sugar. Our findings indicate that higher coffee and caffeine intake is associated with a significantly lower incidence of PD. This effect appears to be independent of smoking. The data suggest that the mechanism is related to caffeine intake and not to other nutrients contained in coffee. JAMA. 2000;283:2674-2679.

  8. The Climate Change and Rwandan Coffee Sector

    Directory of Open Access Journals (Sweden)

    Fidele Hakorimana

    2017-10-01

    Full Text Available This paper provides a detailed overview of the current situation of the coffee sector in the Rwandan economy and identifies the possible challenges that the sector is currently facing. The study has identified the economic and the livelihood indicators for farmers who are engaged in coffee production and also gives the Rwandan coffee sector’ situation and its position in the global coffee market. Also, the research has found out that in Rwanda, nearly 500,000 farmers produce coffee along with other crops, notably beans, savory banana and corn and found out that in 2012, coffee accounted for almost 30 percent of Rwanda’s total export revenue. On the other hand, the study revealed that the sector throughout all the coffee production process, has undergone different challenges especially climate change as it is reported by the Ministry of Agriculture and Animal resources. A low yield was reported in 2007 and climate variability was quoted among the causes. Insufficient rainfall in the last three months of 2006 (the period of coffee flowering proceeding the short dry season in the first two months of 2007 was recorded. The reduced rainfall was also poorly distributed across coffee growing regions in Rwanda. In addition, the research revealed that even though the area under coffee production is increasing, the coffee production is decreasing due to unexpected climate change and variability in current years and also the improper use of chemical fertilizers by coffee farmers is very critical. The study concluded that adding value to the coffee supply chain of Rwanda is adding direct economic benefits and important indirect social benefits to the lives of individuals and to the health of communities in Rwanda. Moreover, more effort should continue to raise the profile of the Rwandan coffee sector suggesting that proper use of chemical fertilizers, solid marketing channels and climate change adaptations measures would be the fair ways of making the

  9. High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

    Science.gov (United States)

    Florez, Juan Carlos; Mofatto, Luciana Souto; do Livramento Freitas-Lopes, Rejane; Ferreira, Sávio Siqueira; Zambolim, Eunize Maciel; Carazzolle, Marcelo Falsarella; Zambolim, Laércio; Caixeta, Eveline Teixeira

    2017-12-01

    We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

  10. HOW COFFEE COMPANIES CAN STAY COMPETITIVE

    Directory of Open Access Journals (Sweden)

    RALUCA DANIELA RIZEA

    2014-04-01

    Full Text Available The coffee shop industry in the U.S. includes 20,000 stores with combined annual revenue of about $11 billion. Major companies include Starbucks, Dunkin’ Donuts, Caribou, Coffee Bean and Tea Leaf, and Diedrich (Gloria Jean’s. The industry is highly concentrated at the top and fragmented at the bottom: the top 50 companies have over 70 percent of industry sales. Coffee is one of the world’s largest commodities. The top green coffee producing countries are Brazil, Colombia, and Vietnam. Many grower countries are small, poor developing nations that depend on coffee to sustain local economies. The U.S. is the world’s largest importer of green coffee beans and the largest consumer of coffee. The main objective of this study is to investigate the competitive strategies that U.S. coffee franchise companies adopt considering customers’ expectations and industry best practices. In order to achieve this objective, a best practice benchmarking analysis was performed taking into account the top U.S. coffee companies This analysis showed that product and service innovation are necessary in order to stay competitive in the market and attract new or to keep existing customers successfully. Many customers focus on the special atmosphere each store has and which is characterized by the location, music, interior design, seating or whether internet access is provided. Particularly for specialty coffee shops it is important not to sell only the beverage but the whole experience. Coffee shops have to establish a unique image that prevents customers from buying products from another shop or use home-brewing systems which are also on the rise in American households. In addressing the increased level of competition, every company’s focus should be on differentiating from the rest of the market in every possible business segment (products, atmosphere, location, image etc..

  11. Consumer Acceptance of a Polyphenolic Coffee Beverage.

    Science.gov (United States)

    Nguyen, Thuy; Kuchera, Meredith; Smoot, Katie; Diako, Charles; Vixie, Beata; Ross, Carolyn F

    2016-10-05

    The objective of this study was to determine if Chardonnay grape seed pomace (GSP), a waste stream of wine production, could be used as a functional ingredient in brewed coffee. Two consumer panels were conducted to assess the acceptance of coffee at coffee replacement (w/w) values of 0% (control), 6.25%, 12.50%, 18.75%, or 25% GSP. The 1st consumer panel (n = 80) assessed the coffee samples served "black." The 2nd panel (n = 67) assessed the coffee samples with adjustment (that is, sweeteners, milk, and cream) options available. Consumer sensory evaluation involved evaluating the 5 treatments individually for acceptance of appearance, aroma, taste/flavor, and overall acceptance using a 9-point hedonic scale. A check-all-that-apply questionnaire surveyed the sensory attributes describing aroma, appearance, and taste/flavor of the samples. Oxygen radical absorbance capacity was used to measure the effects of antioxidant levels in GSP coffee samples. Results showed that GSP could be added at 6.25% replacement without significantly affecting the overall consumer acceptance of coffee compared to the control (0% GSP). Above 6.25% GSP supplementation, the coffee beverage was described as more tan, milky, watery/dilute, and mild, and was generally less accepted by the consumers. GSP also increased the antioxidant capacity of the coffee compared to the control (0% GSP), with no significant differences among replacement values. Therefore, 6.25% GSP replacement is recommended for creating coffee beverages acceptable to consumers. Further in vivo investigation may substantiate the free-radical scavenging capacity of GSP coffee and its potential health benefits. © 2016 Institute of Food Technologists®.

  12. Tea and coffee consumption in relation to DNA methylation in four European cohorts.

    Science.gov (United States)

    Ek, Weronica E; Tobi, Elmar W; Ahsan, Muhammad; Lampa, Erik; Ponzi, Erica; Kyrtopoulos, Soterios A; Georgiadis, Panagiotis; Lumey, L H; Heijmans, Bastiaan T; Botsivali, Maria; Bergdahl, Ingvar A; Karlsson, Torgny; Rask-Andersen, Mathias; Palli, Domenico; Ingelsson, Erik; Hedman, Åsa K; Nilsson, Lena M; Vineis, Paolo; Lind, Lars; Flanagan, James M; Johansson, Åsa

    2017-08-15

    Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea have been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation. To investigate if DNA methylation in blood is associated with coffee and tea consumption, we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096). DNA methylation was measured from whole blood at 421,695 CpG sites distributed throughout the genome and analysed in men and women both separately and together in each cohort. Meta-analyses of the results and additional regional-level analyses were performed. After adjusting for multiple testing, the meta-analysis revealed that two individual CpG-sites, mapping to DNAJC16 and TTC17, were differentially methylated in relation to tea consumption in women. No individual sites were associated with men or with the sex-combined analysis for tea or coffee. The regional analysis revealed that 28 regions were differentially methylated in relation to tea consumption in women. These regions contained genes known to interact with estradiol metabolism and cancer. No significant regions were found in the sex-combined and male-only analysis for either tea or coffee consumption. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Can Coffee Chemical Compounds and Insecticidal Plants Be Harnessed for Control of Major Coffee Pests?

    Science.gov (United States)

    Green, Paul W C; Davis, Aaron P; Cossé, Allard A; Vega, Fernando E

    2015-11-04

    Pests and pathogens threaten coffee production worldwide and are difficult to control using conventional methods, such as insecticides. We review the literature on the chemistry of coffee, concentrating on compounds most commonly reported from Coffea arabica and Coffea canephora. Differences in chemistry can distinguish coffee species and varieties, and plants grown under different biogeographic conditions exhibit different chemotypes. A number of chemical groups, such as alkaloids and caffeoylquinic acids, are known to be insecticidal, but most studies have investigated their effects on coffee quality and flavor. More research is required to bridge this gap in knowledge, so that coffee can be bred to be more resistant to pests. Furthermore, we report on some pesticidal plants that have been used for control of coffee pests. Locally sourced pesticidal plants have been underutilized and offer a sustainable alternative to conventional insecticides and could be used to augment breeding for resilience of coffee plants.

  14. Coffee farming and soil management in Rwanda

    NARCIS (Netherlands)

    Nzeyimana, I.; Hartemink, A.E.; Graaff, de J.

    2013-01-01

    Agriculture is the cornerstone of Rwanda's economy. The authors review how the sector has changed and specifically what soil management practices are now being implemented to enhance coffee production. Coffee covers around 2.3% of total cultivated arable land, and is grown mainly by smallholder

  15. Coffee and cardiovascular risk; an epidemiological study

    NARCIS (Netherlands)

    A.A.A. Bak (Annette)

    1990-01-01

    textabstractThis thesis comprises several studies on the effect of coffee and caffeine on cardiovascular risk in general, and the effect on serum lipids, blood pressure and selected hemostatic variables in particular. The association between coffee use and cardiovascular morbidity and

  16. Saving coffee | IDRC - International Development Research Centre

    International Development Research Centre (IDRC) Digital Library (Canada)

    2017-09-26

    Sep 26, 2017 ... These orange patches, caused by a microscopic fungus that eats away at the ... 70% of coffee trees in Central America and Mexico were affected. ... broca, in Spanish) exclusively eats the fruit of coffee trees, and its life cycle is ...

  17. Coffee Consumption During Pregnancy and Birth Weight

    DEFF Research Database (Denmark)

    Bech, Bodil Hammer; Frydenberg, Morten; Henriksen, Tine Brink

    2015-01-01

    weight and whether it was modified by the mothers' smoking habits. Methods: In the Danish National Birth Cohort, coffee intake and smoking during pregnancy were recorded prospectively in 89,539 pregnancies that ended with live born singletons. Information on birth weight was obtained from the Danish......Background: A previous randomized trial demonstrated an association between coffee intake and birth weight in smokers only. This could be a chance finding or because smoking interferes with caffeine metabolism. This study assessed the association between coffee intake during pregnancy and birth....../cup/day). Compared to non-coffee drinkers, intake of eight or more cups of coffee per day was associated with an adjusted birth weight difference of −65 g [95% confidence interval (CI) −92 to −39] for non-smokers and −79 g [95% CI −124 to −34] for women smoking more than 10 cigarettes per day. Women drinking eight...

  18. Caffeine, coffee, and appetite control: a review.

    Science.gov (United States)

    Schubert, Matthew M; Irwin, Christopher; Seay, Rebekah F; Clarke, Holly E; Allegro, Deanne; Desbrow, Ben

    2017-12-01

    Coffee and caffeine consumption has global popularity. However, evidence for the potential of these dietary constituents to influence energy intake, gut physiology, and appetite perceptions remains unclear. The purpose of this review was to examine the evidence regarding coffee and caffeine's influence on energy intake and appetite control. The literature was examined for studies that assessed the effects of caffeine and coffee on energy intake, gastric emptying, appetite-related hormones, and perceptual measures of appetite. The literature review indicated that coffee administered 3-4.5 h before a meal had minimal influence on food and macronutrient intake, while caffeine ingested 0.5-4 h before a meal may suppress acute energy intake. Evidence regarding the influence of caffeine and coffee on gastric emptying, appetite hormones, and appetite perceptions was equivocal. The influence of covariates such as genetics of caffeine metabolism and bitter taste phenotype remain unknown; longer controlled studies are needed.

  19. Caffeine adsorption of montmorillonite in coffee extracts.

    Science.gov (United States)

    Shiono, Takashi; Yamamoto, Kenichiro; Yotsumoto, Yuko; Yoshida, Aruto

    2017-08-01

    The growth in health-conscious consumers continues to drive the demand for a wide variety of decaffeinated beverages. We previously developed a new technology using montmorillonite (MMT) in selective decaffeination of tea extract. This study evaluated and compared decaffeination of coffee extract using MMT and activated carbon (AC). MMT adsorbed caffeine without significant adsorption of caffeoylquinic acids (CQAs), feruloylquinic acids (FQAs), dicaffeoylquinic acids (di-CQAs), or caffeoylquinic lactones (CQLs). AC adsorbed caffeine, chlorogenic acids (CGAs) and CQLs simultaneously. The results suggested that the adsorption selectivity for caffeine in coffee extract is higher in MMT than AC. The caffeine adsorption isotherms of MMT in coffee extract fitted well to the Langmuir adsorption model. The adsorption properties in coffee extracts from the same species were comparable, regardless of roasting level and locality of growth. Our findings suggest that MMT is a useful adsorbent in the decaffeination of a wide range of coffee extracts.

  20. Coordinating quality practices in Direct Trade coffee

    DEFF Research Database (Denmark)

    Holland, Emil; Kjeldsen, Chris; Kerndrup, Søren

    2016-01-01

    Over the past few decades, many food niches have emerged with a specific focus on quality. In specialty coffee, micro roasters have brought about Direct Trade coffee as a way of organising an alternative around new tastes and qualities through ongoing and ‘direct’ relations to farmers...... and cooperatives. But Direct Trade also involves exporters. We ask, how do exporters and roasters work together in these new coffee relations, and what do they work on? We observe and participate in a situation where Colombian coffee exporters visit Danish roasters. They tour the roasting facilities and taste...... a number of coffees. Often, the term power is used to analyse such value chain interactions, but we argue that the term coordination better opens up these interactions for exploration and analysis. What emerges is a coordination of quality. Through touring and tasting, issues emerge and differences...

  1. Effect of Superheated Steam Roasting on Radical Scavenging Activity and Phenolic Content of Robusta Coffee Beans

    OpenAIRE

    Ooi Ee Shan; Wahidu Zzaman; Tajul A. Yang

    2015-01-01

    Robusta coffee is one of the coffee species grown in Malaysia. However, there is little research conducted on Robusta coffee beans as Arabica coffee is more popular among the consumers. Coffee is a rich source of antioxidants, therefore research on antioxidant properties of Robusta coffee beans is important to explore its market value. Nowadays, most of coffee analysis is on conventional roasted coffee which reduces their antioxidant properties. In this study, Robusta coffee beans (Coffea can...

  2. Innovative Strategies for Control of Coffee Insect Pests in Tanzania ...

    African Journals Online (AJOL)

    Coffee insect pests are one of the major factors which affect coffee production and quality. globally, coffee insect pests are estimated to cause losses of about 13%. However in Africa, yield losses can be much higher, particularly where Arabica and Robusta coffee are grown for a long time. In Tanzania the major insect pests ...

  3. Development of a method for the mineralization of coffee husk ...

    African Journals Online (AJOL)

    Every year, large quantities of husk resulting from the dry method of treatment of robusta coffee are dumped into nature. This generates multiple harmful ecological effects. The downward trend of coffee prices and the rise in the cost of manure has urged coffee farmers to better exploit the by-products of coffee transformation.

  4. Spices Coffee : Innovation Strategy To Increase Quality On Powder Coffee Farmers

    Science.gov (United States)

    Amir, I. T.; Indah, P. N.; Widayanti, S.

    2018-01-01

    The purpose of the study is a) to analyze the condition of internal environment industry spices coffee, b) to analyze the condition of the external environment industry spices coffee, and c) to determine the technological innovation strategy spices coffee in order to improve the competitiveness of the coffee people. Most of the coffee grown in Tutur district is cultivated by smallholder farms, resulting in low quality. The strategy of coffee spice agro-industry aims to increase the added value of the products so that farmers obtain higher coffee prices. Activities include the provision of raw materials, processing, supply of final products, and marketing.The results showed that the internal environmental conditions that have the highest value is the strengthen factors. The highest score of strengthen factors is the availability of coffee, availability of labor and communications group. The highest score of opportunity factors is technological assistance from the government and other government support for the development of people’s coffee industry and high market potential. The development of agrotourism should improve as well as expand the network to seize market. The strategy should be applied in the development of spices coffee industry is to support aggressive growth (Growth-oriented strategy).

  5. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.

    Science.gov (United States)

    Ballenghien, Marion; Faivre, Nicolas; Galtier, Nicolas

    2017-03-29

    Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient F IT , and Tajima's D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.

  6. An information and dialogue conference on the human genome project (HGP) for the minority communities in the state of Louisiana

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-06-01

    Zeta Phi Beta Sorority National Educational Foundation, in cooperation with Xavier University of New Orleans, and the New Orleans District Office of the United States Equal Employment Opportunity Commission, held the Information and Dialogue Conference on the Human Genome Project for the Minority Communities in the State of Louisiana on April 16-17, 1999. The Conference was held on the campus of Xavier University in New Orleans. Community leaders, government officials, minority professional and social organizations leaders, religious leaders, persons from the educational and academic community, and students were invited. Conference objectives included bringing HGP information and a focus in the minority community on the project, in clear and understandable terms, to spread the work in the minority community about the project; to explore the likely positive implications with respect to health care and related matters; to explore possible negative results and strategies to meet them; to discuss the social, legal, and ethical implications; and to facilitate minority input into the HGP as it develops.

  7. Public health genomics and personalized prevention: lessons from the COGS project.

    Science.gov (United States)

    Pashayan, N; Hall, A; Chowdhury, S; Dent, T; Pharoah, P D P; Burton, H

    2013-11-01

    Using the principles of public health genomics, we examined the opportunities and challenges of implementing personalized prevention programmes for cancer at the population level. Our model-based estimates indicate that polygenic risk stratification can potentially improve the effectiveness and cost-effectiveness of screening programmes. However, compared with 'one-size-fits-all' screening programmes, personalized screening adds further layers of complexity to the organization of screening services and raises ethical, legal and social challenges. Before polygenic inheritance is translated into population screening strategy, evidence from empirical research and engagement with and education of the public and the health professionals are needed. © 2013 The Association for the Publication of the Journal of Internal Medicine.

  8. Integrating Public Health and Deliberative Public Bioethics: Lessons from the Human Genome Project Ethical, Legal, and Social Implications Program.

    Science.gov (United States)

    Meagher, Karen M; Lee, Lisa M

    2016-01-01

    Public health policy works best when grounded in firm public health standards of evidence and widely shared social values. In this article, we argue for incorporating a specific method of ethical deliberation--deliberative public bioethics--into public health. We describe how deliberative public bioethics is a method of engagement that can be helpful in public health. Although medical, research, and public health ethics can be considered some of what bioethics addresses, deliberative public bioethics offers both a how and where. Using the Human Genome Project Ethical, Legal, and Social Implications program as an example of effective incorporation of deliberative processes to integrate ethics into public health policy, we examine how deliberative public bioethics can integrate both public health and bioethics perspectives into three areas of public health practice: research, education, and health policy. We then offer recommendations for future collaborations that integrate deliberative methods into public health policy and practice.

  9. Biological Parameters and Molecular Markers of Clone CL Brener - The Reference Organism of the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Bianca Zingales

    1997-11-01

    Full Text Available Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT medium at 28oC is 58±13 hr; (b differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace´s medium; (c trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37oC; (d blood forms are highly infective to mice; (e blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a isoenzymatic profiles are characteristic of zymodeme ZB; (b PCR amplification of a 24Sa ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c schizodeme, randomly amplified polymorphic DNA (RAPD and DNA fingerprinting analyses were performed

  10. Fostering corporate sustainability in the Mexican coffee industry

    Directory of Open Access Journals (Sweden)

    Nora Munguia

    2017-04-01

    Full Text Available Purpose – At the 21st Conference of the Parties to the United Nations Convention on Climate Change (COP 21 in Paris, 195 governments reached an agreement pivotal not only for countries but also for companies. The Paris Agreement makes it impossible to practice business as usual. The transition to a low-carbon coffee industry could be achieved by fostering corporate sustainability. Accordingly, the purpose of this paper is to provide empirical evidence of how to adopt the principles of Paris Agreement by enhancing the corporate sustainability of a Mexican coffee-roaster company using the inventory phase of the life cycle assessment tool. Design/methodology/approach – The data collection process followed the requirements of the International Reference Life Cycle Data System Handbook, developed by the Institute for Environment and Sustainability in the European Commission Joint Research Centre, and data on packaging materials and energy production were drawn from a commercially available database in the LCA software SimaPro. Findings – Compiling data on the energy of the firm’s material flows in a firm revealed opportunities to improve energy efficiency and to reduce greenhouse gas emissions. The results of the inventory analysis can be used to evaluate the specific environmental impacts of the coffee-roasting process at this Mexican coffee company. Data compilation activities for energy flows identified the need to install liquefied petroleum gas measuring devices and individual measuring devices for electricity consumption in different areas of the coffee plant. It is recommended that, while implementing this option, the company also develop an energy management program to achieve energy efficiency. Practical implications – The inventory data in this case study permit comparisons of the current state of the system studied and its possible future states and offer stakeholders relevant information on resource use. Similarly, the project

  11. Comparative effect of coffee robusta and coffee arabica (Qahwa) on memory and attention.

    Science.gov (United States)

    Alharbi, Waheeb D M; Azmat, Aisha; Ahmed, Muhammad

    2018-04-13

    The comparative effects of coffee robusta and coffee arabica (Qahwa) on different attention and memory related assignments were measured in a double-blind study of 300 healthy young adult women who were randomly assigned to one of three different drinks: Group I (coffee robusta sachet dissolved in 100 ml of hot water): Group II (coffee arabica): and group III (100 ml water only). Cognitive function was assessed by standardized tests. Several monitoring cognitive tests and tasks were specifically chosen and performed to investigate the comparative effects of coffee robusta (CR) and coffee arabica (Qahwa; AC) on sleepiness (sleep and clear headed scale), attention (trail A & B, symbol digit, letter cancellation), general cognitive ability (stroop test) and memory (card test). Data was interpreted by analysis of variance (ANOVA). The present study revealed that coffee robusta has beneficial effects on attention, general cognitive ability and memory. Higher though non-significant cognitive scores were associated with coffee robusta consumption. Although, consumption of coffee arabica (Qahwa) has significant effects (P < 0.05) on sleepiness, attention, general cognitive ability and memory and it significantly improve reaction time and correct responses. Since different tasks were related to the sustained attention and working memory processes, results would suggest that coffee arabica (qahwa) could increase the memory and efficiency of the attentional system might be due to the presence of chlorogenic acids (CGA) which are found in less quantity in coffee robusta. However, more studies using larger samples and different tasks are necessary to better understand the effects of coffee robusta and arabica (Qahwa) on attention and memory.

  12. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

    Science.gov (United States)

    Frampton, Dan; Gallo Cassarino, Tiziano; Raffle, Jade; Hubb, Jonathan; Ferns, R. Bridget; Waters, Laura; Tong, C. Y. William; Kozlakidis, Zisis; Hayward, Andrew; Kellam, Paul; Pillay, Deenan; Clark, Duncan; Nastouli, Eleni; Leigh Brown, Andrew J.

    2018-01-01

    Background & methods The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. Results The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. Conclusions

  13. Green coffee decontamination by electron beam irradiation

    International Nuclear Information System (INIS)

    Nemtanu, Monica R.; Brasoveanu, Mirela; Grecu, Maria Nicoleta; Minea, R.

    2005-01-01

    Microbiological load of green coffee is a real problem considering that it is extremely sensitive to contamination. Irradiation is a decontamination method for a lot of foodstuffs, being a feasible, very effective and environment friendly one. Beans and ground green coffee were irradiated with electron beams up to 40 kGy. Microbial load, rheological behavior, electron paramagnetic resonance (EPR) and visible spectroscopy were carried out. The results show that electron beam irradiation of green coffee could decontaminate it without severe changes in its properties

  14. What is more addictive : cannabis or coffee?

    OpenAIRE

    Hili, Alexander

    2016-01-01

    The answer is coffee. Coffee is drunk by around 80% of Americans. The large numbers call for extensive studies on the effect of this drug on the brain. Caffeine is a stimulant. It has a similar molecular structure to adenosine, a chemical linked to us feeling tired. Caffeine binds to adenosine and stops it from working. Coffee does not wake you up but makes your body forget it is tired. Taking that espresso in the morning makes your body increase the number of receptors to caffeine in the bra...

  15. Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.

    Science.gov (United States)

    Biesecker, Leslie G

    2012-04-01

    The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.

  16. Production of Flammulina velutipes on coffee husk and coffee spent-ground

    Directory of Open Access Journals (Sweden)

    Leifa Fan

    2001-01-01

    Full Text Available Solid state cultivation (SSC was carried out to evaluate the feasibility of using coffee husk and spent-ground as substrates for the production of edible mushroom Flammulina under different conditions of moisture and spawn rate. The strain of F. velutipes LPB 01 was adapted for a coffee husk extract medium. Best results were obtained with 25% spawn rate, though there was not much difference when lower spawn rates (10-20% were used. Ideal moisture content for mycelial growth was 60% and 55% for coffee husk and spent-ground, respectively. With coffee husk as substrate, first fructification occurred after 25 days of inoculation and the biological efficiency reached about 56% with two flushes after 40 days. With spent-ground as substrate, first fructification occurred 21 days after inoculation and the biological efficiency reached about 78% in 40 days. There was decrease in the caffeine and tannins contents (10.2 and 20.4%, respectively in coffee husk after 40 days. In coffee spent-ground, the tannin contents decreased by 28% after 40 days. These decrease was attributed to the degradation of caffeine or tannins by the culture because these were not adsorbed in the fungal mycelia. Results showed the feasibility of using coffee husk and coffee spent-ground as substrate without any nutritional supplementation for cultivation of edible fungus in SSC. Spent ground appeared better than coffee husk.

  17. Lack of replication of the GRIN2A-by-coffee interaction in Parkinson disease.

    OpenAIRE

    Ahmed, Ismaïl; Lee, Pei-Chen; Lill, Christina M; Searles Nielsen, Susan; Artaud, Fanny; Gallagher, Lisa G; Loriot, Marie-Anne; Mulot, Claire; Nacfer, Magali; Liu, Tian; Biernacka, Joanna ,; Armasu, Sebastian; Anderson, Kari; Farin, Federico ,; Lassen, Christina Funch

    2014-01-01

    International audience; Overview The etiology of Parkinson disease (PD) involves both genetic susceptibility and environmental exposures. In particular, coffee consumption is inversely associated with PD but the mechanisms underlying this intriguing association are unknown. According to a recent genome-wide gene–environment interaction study, the inverse coffee–PD association was two times stronger among carriers of the T allele of SNP rs4998386 in gene GRIN2A than in homozygotes for the C al...

  18. Do Coffee Farmers Benefit in Food Security from Participating in Coffee Cooperatives? Evidence from Southwest Ethiopia Coffee Cooperatives.

    Science.gov (United States)

    Shumeta, Zekarias; D'Haese, Marijke

    2018-06-01

    Most coffee in Ethiopia is produced by smallholder farmers who face a daily struggle to get sufficient income but also to feed their families. At the same time, many smallholder coffee producers are members of cooperatives. Yet, literature has paid little attention to the effect of cooperatives on combating food insecurity among cash crop producers including coffee farmers. The objective of the study was to investigate how coffee cooperative membership may affect food security among coffee farm households in Southwest Ethiopia. The study used cross-sectional household data on income, expenditure on food, staple food production (maize and teff), and utilization of improved inputs (fertilizer and improved seed) collected from 256 randomly selected farm households (132 cooperative members and 124 nonmembers) and applied an inverse probability weighting (IPW) estimation to assess the impact of cooperative membership on food security. The result revealed that cooperative membership has a positive and significant effect on staple food production (maize and teff) and facilitated technological transformation via increased utilization of fertilizer and improved seeds. Nonetheless, the effect on food expenditure and income could not be confirmed. Findings suggest a trade-off between coffee marketing and input supply functions of the cooperatives, impairing their true food security impact from the pooled income and production effect.

  19. Review: Utilization of Waste From Coffee Production

    Science.gov (United States)

    Blinová, Lenka; Sirotiak, Maroš; Bartošová, Alica; Soldán, Maroš

    2017-06-01

    Coffee is one of the most valuable primary products in the world trade, and also a central and popular part of our culture. However, coffees production generate a lot of coffee wastes and by-products, which, on the one hand, could be used for more applications (sorbent for the removal of heavy metals and dyes from aqueous solutions, production of fuel pellets or briquettes, substrate for biogas, bioethanol or biodiesel production, composting material, production of reusable cups, substrat for mushroom production, source of natural phenolic antioxidants etc.), but, on the other hand, it could be a source of severe contamination posing a serious environmental problem. In this paper, we present an overview of utilising the waste from coffee production.

  20. Coffee Consumption Attenuates Insulin Resistance and Glucose ...

    African Journals Online (AJOL)

    olayemitoyin

    Alzheimer's disease (CBS 2012), dementia (Health news 2012) and ... the effects of coffee on insulin resistance and glucose tolerance as ..... mortality among patients with type 2 diabetes. ... transporter family: Structure, function and tissue-.

  1. High Molecular Weight Melanoidins from Coffee Brew

    NARCIS (Netherlands)

    Bekedam, E.K.; Schols, H.A.; Boekel, van T.; Smit, G.

    2006-01-01

    The composition of high molecular weight (HMw) coffee melanoidin populations, obtained after ethanol precipitation, was studied. The specific extinction coefficient (Kmix) at 280, 325, 405 nm, sugar composition, phenolic group content, nitrogen content, amino acid composition, and non-protein

  2. Coffee consumption and risk of fatal cancers.

    Science.gov (United States)

    Snowdon, D A; Phillips, R L

    1984-01-01

    In 1960, the coffee consumption habits and other lifestyle characteristics of 23,912 white Seventh-day Adventists were assessed by questionnaire. Between 1960 and 1980, deaths due to cancer were identified. There were positive associations between coffee consumption and fatal colon and bladder cancer. The group consuming two or more cups of coffee per day had an estimated relative risk (RR) of 1.7 for fatal colon cancer and 2.0 for fatal bladder cancer, compared to the group that consumed less than one cup per day (RR = 1.0). These positive associations were apparently not confounded by age, sex, cigarette smoking, or meat consumption habits. In this study, there were no significant or suggestive associations between coffee consumption and fatal pancreatic, breast, and ovarian cancer, or a combined group of all other cancer sites. PMID:6742274

  3. Process technology of luwak coffee through bioreactor utilization

    Science.gov (United States)

    Hadipernata, M.; Nugraha, S.

    2018-01-01

    Indonesia has an advantage in producing exotic coffee that is Luwak coffee. Luwak coffee is produced from the fermentation process in digestion of civet. Luwak coffee production is still limited due to the difficulty level in the use of civet animals as the only medium of Luwak coffee making. The research was conducted by developing technology of luwak coffee production through bioreactor utilization and addition the bacteria isolate from gastric of civet. The process conditions in the bioreactor which include temperature, pH, and bacteria isolate of civet are adjusted to the process that occurs in civet digestion, including peristaltic movement on the stomach and small intestine of the civet will be replaced by the use of propellers that rotate on the bioreactor. The result of research showed that proximat analysis data of artificial/bioreactor luwak coffee did not significant different with original luwak coffee. However, the original luwak coffee has higher content of caffeine compared to bioreactor luwak coffee. Based on the cuping test the bioreactor luwak coffee has a value of 84.375, while the original luwak coffee is 84.875. As the result, bioreactor luwak coffee has excellent taste that similiar with original luwak coffee taste.

  4. Climate change impacts on coffee rust disease

    Science.gov (United States)

    Alfonsi, W. M. V.; Koga-Vicente, A.; Pinto, H. S.; Alfonsi, E. L., Sr.; Coltri, P. P.; Zullo, J., Jr.; Patricio, F. R.; Avila, A. M. H. D.; Gonçalves, R. R. D. V.

    2016-12-01

    Changes in climate conditions and in extreme weather events may affect the food security due to impacts in agricultural production. Despite several researches have been assessed the impacts of extremes in yield crops in climate change scenarios, there is the need to consider the effects in pests and diseases which increase losses in the sector. Coffee Arabica is an important commodity in world and plays a key role in Brazilian agricultural exports. Although the coffee crop has a world highlight, its yield is affected by several factors abiotic or biotic. The weather as well pests and diseases directly influence the development and coffee crop yield. These problems may cause serious damage with significant economic impacts. The coffee rust, caused by the fungus Hemileia vastarix,is among the diseases of greatest impact for the crop. The disease emerged in Brazil in the 70s and is widely spread in all producing regions of coffee in Brazil, and in the world. Regions with favorable weather conditions for the pathogen may exhibit losses ranging from 30% to 50% of the total grain production. The evaluation of extreme weather events of coffee rust disease in futures scenarios was carried out using the climatic data from CMIP5 models, data field of coffee rust disease incidence and, incubation period simulation data for Brazilian municipalities. Two Regional Climate Models were selected, Eta-HadGEM2-ES and Eta-MIROC5, and the Representative Concentration Pathways 8.5 w/m2 was adopted. The outcomes pointed out that in these scenarios the period of incubation tends to decrease affecting the coffee rust disease incidence, which tends to increase. Nevertheless, the changing in average trends tends to benefit the reproduction of the pathogen. Once the temperature threshold for the disease reaches the adverse conditions it may be unfavorable for the incidence.

  5. REGIA, An EU Project on Functional Genomics of Transcription Factors from Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Javier Paz-Ares

    2002-01-01

    and metabolic profiling; 5. the systematic analysis of interactions between TFs; and 6. the generation of a bioinformatics infrastructure to access and integrate all this information. We expect that this programme will establish the full biotechnological potential of plant TFs, and provide insights into hierarchies, redundancies, and interdependencies, and their evolution. The project involves the preparation of both a TF gene array for expression analysis and a normalised full length open reading frame (ORF library of TFs in a yeast two hybrid vector; the applications of these resources should extend beyond the scope of this programme.

  6. Prediction of specialty coffee cup quality based on near infrared spectra of green coffee beans.

    Science.gov (United States)

    Tolessa, Kassaye; Rademaker, Michael; De Baets, Bernard; Boeckx, Pascal

    2016-04-01

    The growing global demand for specialty coffee increases the need for improved coffee quality assessment methods. Green bean coffee quality analysis is usually carried out by physical (e.g. black beans, immature beans) and cup quality (e.g. acidity, flavour) evaluation. However, these evaluation methods are subjective, costly, time consuming, require sample preparation and may end up in poor grading systems. This calls for the development of a rapid, low-cost, reliable and reproducible analytical method to evaluate coffee quality attributes and eventually chemical compounds of interest (e.g. chlorogenic acid) in coffee beans. The aim of this study was to develop a model able to predict coffee cup quality based on NIR spectra of green coffee beans. NIR spectra of 86 samples of green Arabica beans of varying quality were analysed. Partial least squares (PLS) regression method was used to develop a model correlating spectral data to cupping score data (cup quality). The selected PLS model had a good predictive power for total specialty cup quality and its individual quality attributes (overall cup preference, acidity, body and aftertaste) showing a high correlation coefficient with r-values of 90, 90,78, 72 and 72, respectively, between measured and predicted cupping scores for 20 out of 86 samples. The corresponding root mean square error of prediction (RMSEP) was 1.04, 0.22, 0.27, 0.24 and 0.27 for total specialty cup quality, overall cup preference, acidity, body and aftertaste, respectively. The results obtained suggest that NIR spectra of green coffee beans are a promising tool for fast and accurate prediction of coffee quality and for classifying green coffee beans into different specialty grades. However, the model should be further tested for coffee samples from different regions in Ethiopia and test if one generic or region-specific model should be developed. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Wake up and smell the coffee. Caffeine, coffee, and the medical consequences.

    Science.gov (United States)

    Chou, T

    1992-11-01

    Caffeine is a methylxanthine whose primary biologic effect is antagonism of the adenosine receptor. Its presence in coffee, tea, soda beverages, chocolate, and many prescription and over-the-counter drugs makes it the most commonly consumed stimulant drug. Initially caffeine increases blood pressure, plasma catecholamine levels, plasma renin activity, serum free fatty acid levels, urine production, and gastric acid secretion. Its long-term effects have been more difficult to substantiate. Most of the caffeine consumed in the United States is in coffee, which contains many other chemicals that may have other biologic actions. The consumption of coffee is a self-reinforcing behavior, and caffeine dependence and addiction are common. Coffee and caffeine intake have been linked to many illnesses, but definitive correlations have been difficult to substantiate. Initial trials showing coffee's association with coronary disease and myocardial infarction have been difficult to reproduce and have many confounding variables. Recent studies showing a larger effect over long follow-up periods and with heavy coffee consumption have again brought the question of the role of coffee in disease states to the fore. Caffeine in average dosages does not seem to increase the risk of arrhythmia. At present there is no convincing evidence that caffeine or coffee consumption increases the risk for any solid tumor. The intake of coffee and caffeine has clearly been decreasing in this country over the past two decades, largely brought about by the increasing health consciousness of Americans. Although there have been many studies that hint that the fears of increased disease with coffee drinking may be warranted, many questions have yet to be answered about the health effects of coffee and caffeine use.

  8. HPLC determination of caffeine in coffee beverage

    Science.gov (United States)

    Fajara, B. E. P.; Susanti, H.

    2017-11-01

    Coffee is the second largest beverage which is consumed by people in the world, besides the water. One of the compounds which contained in coffee is caffeine. Caffeine has the pharmacological effect such as stimulating the central nervous system. The purpose of this study is to determine the level of caffeine in coffee beverages with HPLC method. Three branded coffee beverages which include in 3 of Top Brand Index 2016 Phase 2 were used as samples. Qualitative analysis was performed by Parry method, Dragendorff reagent, and comparing the retention time between sample and caffeine standard. Quantitative analysis was done by HPLC method with methanol-water (95:5v/v) as mobile phase and ODS as stationary phasewith flow rate 1 mL/min and UV 272 nm as the detector. The level of caffeine data was statistically analyzed using Anova at 95% confidence level. The Qualitative analysis showed that the three samples contained caffeine. The average of caffeine level in coffee bottles of X, Y, and Z were 138.048 mg/bottle, 109.699 mg/bottle, and 147.669 mg/bottle, respectively. The caffeine content of the three coffee beverage samples are statistically different (pcoffee beverage samples were not meet the requirements set by the Indonesian Standard Agency of 50 mg/serving.

  9. Bioethanol Quality Improvement of Coffee Fruit Leather

    Directory of Open Access Journals (Sweden)

    Edahwati Luluk

    2016-01-01

    Full Text Available Recently, Indonesia’s dependence on petroleum is to be reduced and even eliminated. To overcome the problem of finding the needed alternative materials that can produce ethanol, in this case as a substitute material or a transport fuel mix, boosting the octane number, and gasoline ethanol (gasohol can be conducted. In the red coffee processing (cooking that will produce 65% and 35% of coffee beans, coffee leather waste is a source of organic material with fairly high cellulose content of 46.82%, 3.01% of pectin and 7.68% of lignin. In this case, its existence is abundant in Indonesia and optimally utilized. During the coffee fruit peeling, the peel waste is only used as a mixture of animal feed or simply left to rot. The purpose of this study was to produce and improve the quality of the fruit skin of bioethanol from coffee cellulose. However, to improve the quality of bioethanol, the production of the lignin content in the skin of the coffee fruit should be eliminated or reduced. Hydrolysis process using organosolve method is expected to improve the quality of bioethanol produced. In particular, the use of enzyme Saccharomyces and Zymmomonas will change the resulting sugar into bioethanol. On one hand, by using batch distillation process for 8 hours with Saccharomyces, bioethanol obtains high purity which is 39.79%; on the other hand, by using the same batch distillation process with Zymmomonas, the bioethanol obtains 38.78%.

  10. Ochratoxin A in Brazilian green coffee

    Directory of Open Access Journals (Sweden)

    LEONI Luís A.B.

    2001-01-01

    Full Text Available Ochratoxin A is a nephrotoxic, teratogenic and imunotoxic compound produced by Aspergillus and Penicillium spp. It is a suspected carcinogen to humans and it is carcinogenic to rats. Recently it has drawn attention because it has been found in coffee and it has been the object of regulation by coffee importing countries. Brazil is the largest coffee producing country and its largest consumer. In order to conduct an initial assessment of the situation of the coffee produced in the country and offered to its population, one hundred and thirty two samples of Brazilian green coffee from 5 producing states (Minas Gerais, Paraná, São Paulo, Espírito Santo and Bahia and destined for the home market, were collected at sales points at the cities of Londrina and Santos, Brazil, and analyzed for ochratoxin A. The toxin was isolated in immunoaffinity columns and quantified by HPLC with florescence detection. The limit of detection was 0.7ng/g and the average RSD for duplicates of the samples was 11%. Twenty seven samples were found contaminated with the toxin and the average concentration for the contaminated samples was 7.1ng/g ochratoxin A. Neither the total number of defects nor the number of specific defects according to the Brazilian coffee classification system (black, partly -- black, sour, stinkers-black, stinkers-green, pod beans showed any relation to the contamination of the samples with ochratoxin A.

  11. Resolution effects in reconstructing ancestral genomes.

    Science.gov (United States)

    Zheng, Chunfang; Jeong, Yuji; Turcotte, Madisyn Gabrielle; Sankoff, David

    2018-05-09

    The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

  12. Balancing Benefits and Risks of Immortal Data: Participants' Views of Open Consent in the Personal Genome Project.

    Science.gov (United States)

    Zarate, Oscar A; Brody, Julia Green; Brown, Phil; Ramirez-Andreotta, Mónica D; Perovich, Laura; Matz, Jacob

    2016-01-01

    An individual's health, genetic, or environmental-exposure data, placed in an online repository, creates a valuable shared resource that can accelerate biomedical research and even open opportunities for crowd-sourcing discoveries by members of the public. But these data become "immortalized" in ways that may create lasting risk as well as benefit. Once shared on the Internet, the data are difficult or impossible to redact, and identities may be revealed by a process called data linkage, in which online data sets are matched to each other. Reidentification (re-ID), the process of associating an individual's name with data that were considered deidentified, poses risks such as insurance or employment discrimination, social stigma, and breach of the promises often made in informed-consent documents. At the same time, re-ID poses risks to researchers and indeed to the future of science, should re-ID end up undermining the trust and participation of potential research participants. The ethical challenges of online data sharing are heightened as so-called big data becomes an increasingly important research tool and driver of new research structures. Big data is shifting research to include large numbers of researchers and institutions as well as large numbers of participants providing diverse types of data, so the participants' consent relationship is no longer with a person or even a research institution. In addition, consent is further transformed because big data analysis often begins with descriptive inquiry and generation of a hypothesis, and the research questions cannot be clearly defined at the outset and may be unforeseeable over the long term. In this article, we consider how expanded data sharing poses new challenges, illustrated by genomics and the transition to new models of consent. We draw on the experiences of participants in an open data platform-the Personal Genome Project-to allow study participants to contribute their voices to inform ethical consent

  13. Poor man’s 1000 genome project: Recent human population expansion confounds the detection of disease alleles in 7,098 complete mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Hie Lim eKim

    2013-02-01

    Full Text Available Rapid growth of the human population has caused the accumulation of rare genetic variants that may play a role in the origin of genetic diseases. However, it is challenging to identify those rare variants responsible for specific diseases without genetic data from an extraordinarily large population sample. Here we focused on the accumulated data from the human mitochondrial (mt genome sequences because this data provided 7,098 whole genomes for analysis. In this dataset we identified 6,110 single nucleotide variants (SNVs and their frequency and determined that the best-fit demographic model for the 7,098 genomes included severe population bottlenecks and exponential expansions of the non-African population. Using this model, we simulated the evolution of mt genomes in order to ascertain the behavior of deleterious mutations. We found that such deleterious mutations barely survived during population expansion. We derived the threshold frequency of a deleterious mutation in separate African, Asian, and European populations and used it to identify pathogenic mutations in our dataset. Although threshold frequency was very low, the proportion of variants showing a lower frequency than that threshold was 82%, 83%, and 91% of the total variants for the African, Asian, and European populations, respectively. Within these variants, only 18 known pathogenic mutations were detected in the 7,098 genomes. This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study.

  14. The Hawaii protocol for scientific monitoring of coffee berry borer: a model for coffee agroecosystems worldwide

    Science.gov (United States)

    Coffee Berry Borer (CBB) is the most devastating insect pest for coffee crops worldwide. We developed a scientific monitoring protocol aimed at capturing and quantifying the dynamics and impact of this invasive insect pest as well as the development of its host plant across a heterogeneous landscape...

  15. Coffee harvest management by manipulation of coffee flowering with plant growth regulators

    Science.gov (United States)

    The breaking of coffee flower bud dormancy is known to be associated with one or more significant rainfall events following an extended period of dryness. In Hawaii, lack of a distinct wet-dry season poses serious problems for coffee growers because flowering is spread over several months. Multiple...

  16. Roasted and Ground Coffee: A Study of Extenders, Substitutes and Alternative Coffee Sources

    Science.gov (United States)

    1984-02-01

    other large food service organizations. The policy of adjusting the amount of R&G coffee used in brewing recipes according to consumer preferences , as...health, such as in the reduction of caffeine levels, as well as’ general consumer preferences for hot beverages with lower levels of coffee- like

  17. Diversity in smallholder farms growing coffee and their use of recommended coffee management practices in Uganda

    NARCIS (Netherlands)

    Bongers, G.; Fleskens, L.; Ven, van de G.W.J.; Mukasa, D.; Giller, K.E.; Asten, van P.

    2015-01-01

    Many smallholder farm systems in Uganda produce coffee as an important cash crop. Yet coffee yields are poor. To increase farmers’ production, a range of agronomic practices have been recommended by national and international agencies. Yet the adoption potential of recommendations differs between

  18. Determination of trace elements in coffee beans and instant coffee of various origins by INAA

    International Nuclear Information System (INIS)

    Zaidi, J.H.; Fatima, I.; Arif, M.; Qureshi, I.H.

    2006-01-01

    Extensive use of coffee, by one-third of world's population, entails the evaluation of trace element contents in it. Instrumental neutron activation analysis (INAA) was successfully employed to determine the concentration of 20 trace elements (essential, toxic and nonessential) in four samples of coffee beans of various origins and two instant coffee brands most commonly consumed in Pakistan. Base-line values of certain toxic and essential elements in coffee are provided. The daily intake of essential and toxic elements through coffee was estimated and compared with the recommended values. The cumulative intake of Mn is four times higher than the recommended value and that of toxic elements is well below the tolerance limits. (author)

  19. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  20. In silico comparative analysis of EST-SSRs in three cotton genomes

    African Journals Online (AJOL)

    reading 6

    2012-08-28

    Aug 28, 2012 ... genic microsatellite markers for genome analyses of coffee and ... Conservation genetics: where are we now? ...... 38 TA7685_29729 Non-green plastid inner envelope membrane protein precursor [Brassica oleracea (Wild ...

  1. Coffee Production in Kavre and Lalitpur Districts, Nepal

    Directory of Open Access Journals (Sweden)

    Yogendra Kumar Karki

    2018-05-01

    Full Text Available Coffee (Coffea spp is an important and emerging cash crop having potential to provide farmers employment and income generation opportunities. This crop is well adapted to the climatic conditions of mid-hills of Nepal. Thus, majority of the farmers are attracted towards cultivation of coffee because of demands in national and international market. Coffee is now becoming integral part of farming system in rural areas. However, information on performance of coffee and farmers response has not been well documented. Therefore, we undertook the present work to analyze demography, ethnicity, household occupation, literacy status, average land holding, coffee cultivation area, livelihood and sources of income of coffee growers, production and productivity, pricing, cropping pattern of the coffee and problesm faced by them in mid hill district of Kavrepalanchowk (hereafter ‘Kavre’ and Lalitpur Districts. All the samples were taken randomly and selected from coffee producing cooperative of Kavre and Lalitpur. Our analysis showed that the male farmer dominant over female on adopting coffee cultivation in both districts with higher value in Kavre. Brahmin and Chetri ethnic communities were in majority over others in adopting the coffee cultivation. Literate farmers were more dominant over illiterates on adopting the coffee cultivation, The mean land holding was less, ranging from 0.15 to 2.30 ha for coffee cultivation, the history of coffee cultivation in Kavre showed that highest number of farmers were engaged in coffee farming from last 16 years. The mean yield of fresh cherry was 1027.20 kg/ha in Kavre, while it was 1849.36 kg/ha in Lalitpur. The study revealed that majority of the coffee plantations were between 6-10 years old. The major problems facing by coffee farmers were diseases spread, lack of irrigation facility and drying of plants. Despite of that the coffee farming was one of the rapidly emerging occupations among the farmers in both

  2. Coffee consumption and risk of renal cell carcinoma.

    Science.gov (United States)

    Antwi, Samuel O; Eckel-Passow, Jeanette E; Diehl, Nancy D; Serie, Daniel J; Custer, Kaitlynn M; Arnold, Michelle L; Wu, Kevin J; Cheville, John C; Thiel, David D; Leibovich, Bradley C; Parker, Alexander S

    2017-08-01

    Studies have suggested an inverse association between coffee consumption and risk of renal cell carcinoma (RCC); however, data regarding decaffeinated coffee are limited. We conducted a case-control study of 669 incident RCC cases and 1,001 frequency-matched controls. Participants completed identical risk factor questionnaires that solicited information about usual coffee consumption habits. The study participants were categorized as non-coffee, caffeinated coffee, decaffeinated coffee, or both caffeinated and decaffeinated coffee drinkers. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression, adjusting for multiple risk factors for RCC. Compared with no coffee consumption, we found an inverse association between caffeinated coffee consumption and RCC risk (OR 0.74; 95% CI 0.57-0.99), whereas we observed a trend toward increased risk of RCC for consumption of decaffeinated coffee (OR 1.47; 95% CI 0.98-2.19). Decaffeinated coffee consumption was associated also with increased risk of the clear cell RCC (ccRCC) subtype, particularly the aggressive form of ccRCC (OR 1.80; 95% CI 1.01-3.22). Consumption of caffeinated coffee is associated with reduced risk of RCC, while decaffeinated coffee consumption is associated with an increase in risk of aggressive ccRCC. Further inquiry is warranted in large prospective studies and should include assessment of dose-response associations.

  3. Construction of coffee transcriptome networks based on gene annotation semantics

    Directory of Open Access Journals (Sweden)

    Castillo Luis F.

    2012-12-01

    Full Text Available Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  4. Coffee and cancer risk: a summary overview.

    Science.gov (United States)

    Alicandro, Gianfranco; Tavani, Alessandra; La Vecchia, Carlo

    2017-09-01

    We reviewed available evidence on coffee drinking and the risk of all cancers and selected cancers updated to May 2016. Coffee consumption is not associated with overall cancer risk. A meta-analysis reported a pooled relative risk (RR) for an increment of 1 cup of coffee/day of 1.00 [95% confidence interval (CI): 0.99-1.01] for all cancers. Coffee drinking is associated with a reduced risk of liver cancer. A meta-analysis of cohort studies found an RR for an increment of consumption of 1 cup/day of 0.85 (95% CI: 0.81-0.90) for liver cancer and a favorable effect on liver enzymes and cirrhosis. Another meta-analysis showed an inverse relation for endometrial cancer risk, with an RR of 0.92 (95% CI: 0.88-0.96) for an increment of 1 cup/day. A possible decreased risk was found in some studies for oral/pharyngeal cancer and for advanced prostate cancer. Although data are mixed, overall, there seems to be some favorable effect of coffee drinking on colorectal cancer in case-control studies, in the absence of a consistent relation in cohort studies. For bladder cancer, the results are not consistent; however, any possible direct association is not dose and duration related, and might depend on a residual confounding effect of smoking. A few studies suggest an increased risk of childhood leukemia after maternal coffee drinking during pregnancy, but data are limited and inconsistent. Although the results of studies are mixed, the overall evidence suggests no association of coffee intake with cancers of the stomach, pancreas, lung, breast, ovary, and prostate overall. Data are limited, with RR close to unity for other neoplasms, including those of the esophagus, small intestine, gallbladder and biliary tract, skin, kidney, brain, thyroid, as well as for soft tissue sarcoma and lymphohematopoietic cancer.

  5. Coffee consumption and periodontal disease in males.

    Science.gov (United States)

    Ng, Nathan; Kaye, Elizabeth Krall; Garcia, Raul I

    2014-08-01

    Coffee is a major dietary source of antioxidants as well as of other anti-inflammatory factors. Given the beneficial role of such factors in periodontal disease, whether coffee intake is associated with periodontal disease in adult males was explored. Existing data collected by a prospective, closed-panel cohort study of aging and oral health in adult males was used. Participants included the 1,152 dentate males in the Veterans Affairs (VA) Dental Longitudinal Study who presented for comprehensive medical and dental examinations from 1968 to 1998. Mean age at baseline was 48 years; males were followed for up to 30 years. Participants are not VA patients; rather, they receive their medical and dental care in the private sector. Periodontal status was assessed by probing depth (PD), bleeding on probing, and radiographic alveolar bone loss (ABL), measured on intraoral periapical radiographs with a modified Schei ruler method. Moderate-to-severe periodontal disease was defined as cumulative numbers of teeth exhibiting PD ≥4 mm or ABL ≥40%. Coffee intake was obtained from participant self-reports using the Cornell Medical Index and food frequency questionnaires. Multivariate repeated-measures generalized linear models estimated mean number of teeth with moderate-to-severe disease at each examination by coffee intake level. It was found that higher coffee consumption was associated with a small but significant reduction in number of teeth with periodontal bone loss. No evidence was found that coffee consumption was harmful to periodontal health. Coffee consumption may be protective against periodontal bone loss in adult males.

  6. The Impact of Market Reform Programmes on Coffee Prices in ...

    African Journals Online (AJOL)

    (ICA) and liberalization of coffee marketing in Tanzania on coffee prices. The motivation for this ... indirect effects of market reforms on the level of prices, their variance ..... This strategy could be achieved through dedicated support to farmers to ...

  7. Assessment of metals in roasted indigenous coffee varieties of ...

    African Journals Online (AJOL)

    Assessment of metals in roasted indigenous coffee varieties of Ethiopia. ... Bulletin of the Chemical Society of Ethiopia ... values and drinking two cups of coffee is safe for an adult person and free from the risks of Cd and Pb toxicity.

  8. Differential returns from globalization to women smallholder coffee ...

    African Journals Online (AJOL)

    Differential returns from globalization to women smallholder coffee and food ... the same area, female coffee producers represented a higher level of integration ... involved in small-scale production, and of a similar age and education level.

  9. The Investigation of the Element Contents in the Turkish Coffees

    OpenAIRE

    Demir, Funda; Selvi, Nigar; Kıpçak, Seyhun; Özdemir, Özgül; Piskin, Mehmet; Moroydor Derun, Emek

    2015-01-01

    The Investigation of the Element Contents in the Turkish CoffeesCoffee is one of the most popular drinks across the world and its enormous commercial and social importance is obvious. Coffee has become the essential consumption matter and one of the rituals of many societies for several years.Turkish people's first confrontation with it dates back to 16th century, in Ottoman era. Since then, because of the differences in terms of preparation and presentation styles, the coffee has been n...

  10. Investigation on the extractability of melanoidins in portioned espresso coffee

    OpenAIRE

    Bartel, C.; Mesías, Marta; Morales, F. J.

    2015-01-01

    © 2014 Elsevier Ltd. Coffee melanoidins have attracted interest as a result of its potential health benefits. This investigation aims to elucidate the extraction behavior of melanoidins and their populations during the preparation of portioned espresso coffee and its relationship with the antioxidant activity of the coffee brew. Filter-paper pods, FAP capsule, and clone capsule containing light roasted coffee have been investigated. An accumulative fractionation approach has applied to model ...

  11. The coffee-time challenge

    CERN Document Server

    CERN Bulletin

    2010-01-01

    The challenge to identify the LEP events displayed on coffee tables in Restaurant 1 (Bulletin 02-03/2010) sparked interest among readers who do not have the opportunity to see them . Table 1, Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12 Table 13, Table 14, Table 15, Table 16       We have therefore decided to open the challenge to these readers by displaying the events on the web. We are also extending the deadline accordingly to 2 March. There are 16 events in total (in two areas), four from each of the four LEP experiments, and they include examples of different particle decays observed at LEP during its 11 years of operation. The list below indicates the decay channels represented. We are offering a prize of the ATLAS pop-up book, Voyage to the Heart of Matter, for the correct identification of all 16 events.  Entries should indicate the table number corresponding to each of the decays listed. There wi...

  12. A coffee-time challenge

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    Can you tell a Z from a WW? The Bulletin is offering a prize for deciphering LEP events on show in Restaurant No. 1.   If you’ve been to the coffee areas in Restaurant 1 you’ve probably noticed the ‘LEP event’ table tops, installed for the symposium and exhibition ‘From the Proton Synchrotron to the Large Hadron Collider - 50 Years of Nobel Memories in High-Energy Physics’. There are 16 events in total (in two areas), four from each of the four LEP experiments, and they include examples of different particle decays observed at LEP during its 11 years of operation. The list below indicates the decay channels represented. We are offering a prize of the ATLAS pop-up book, ‘Voyage to the Heart of Matter’, for the correct identification of all 16 events. Entries should indicate the table number corresponding to each of the decays listed. There will be a draw on 19 January to pick the winner from entries that correctl...

  13. Coffee consumption and risk of colorectal cancer.

    Science.gov (United States)

    Bidel, S; Hu, G; Jousilahti, P; Antikainen, R; Pukkala, E; Hakulinen, T; Tuomilehto, J

    2010-09-01

    The possible association between coffee consumption and risk of colorectal cancer has been extensively studied in the many populations. The aim of this study is to examine this relationship among Finns, who are the heaviest coffee consumers in the world. A total of 60 041 Finnish men and women who were 26-74 years of age and without history of any cancer at baseline were included in the present analyses. Their coffee consumption and other study characteristics were determined at baseline, and they were prospectively followed up for onset of colon and rectal cancer, emigration, death or until 30 June 2006. During a mean follow-up period of 18 years, 538 cases of colorectal cancer (304 cases of colon cancer and 234 cases of rectal cancer) were diagnosed. The multivariate-adjusted hazard ratio of colorectal cancer incidence for > or =10 cups of coffee per day compared with non-drinkers was 0.98 (95% CI, 0.47-2.03) for men (P for trend=0.86), 1.24 (95% CI, 0.49-3.14) for women (p for trend=0.83) and 1.03 (95% CI, 0.58-1.83) for men and women combined (P for trend=0.61). In this study, we found no association between coffee consumption and the risk of colorectal, colon and rectal cancer.

  14. The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

    OpenAIRE

    Willnow, TE; Antignac, C; Brändli, AW; Christensen, EI; Cox, RD; Davidson, D; Davies, JA; Devuyst, O; Eichele, G; Hastie, ND; Verroust, PJ; Schedl, A; Meij, IC

    2005-01-01

    Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a thr...

  15. Roasting Effects on Formation Mechanisms of Coffee Brew Melanoidins

    NARCIS (Netherlands)

    Bekedam, E.K.; Loots, M.J.; Schols, H.A.; Boekel, van M.A.J.S.; Smit, G.

    2008-01-01

    The effect of the roasting degree on coffee brew melanoidin properties and formation mechanisms was studied. Coffee brew fractions differing in molecular weight (Mw) were isolated from green and light-, medium-, and dark-roasted coffee beans. Isolated fractions were characterized for their

  16. Population dynamics and distribution of the coffee berry borer ...

    African Journals Online (AJOL)

    Population dynamics and distribution of coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae) were studied on Coffea arabica L. in southwestern region of Ethiopia. Thirty coffee trees were sampled at weekly intervals from 2000 to 2001. Findings of this study showed that coffee berry borer population ...

  17. Incomplete resistance to coffee leaf rust (Hemileia vastatrix)

    NARCIS (Netherlands)

    Eskes, A.B.

    1983-01-01

    Incomplete resistance to coffee leaf rust ( Hemileia vastatrix ) may be of value in obtaining durable resistance, which is of great importance for the perennial coffee crop. Methods were developed to assess incomplete resistance to coffee leaf rust by using illustrated scales

  18. The structural changes in the Mexican coffee sector

    NARCIS (Netherlands)

    Padron, Benigno Rodriguez; Burger, Kees

    2015-01-01

    This paper analyses the structural changes which have been present since the economic clauses of the International Coffee Agreements have no longer been in effect. It studies the elements that modified the coffee policy over time. It also investigates the main characteristics of the entire coffee

  19. Diversification and Labor Market Effects of the Mexican Coffee Crisis

    NARCIS (Netherlands)

    Rodriguez Padron, B.; Burger, C.P.J.

    2015-01-01

    This paper analyses how coffee-producing households responded to the low coffee prices prevailing around 2003. We provide theory on differential responses in regions dedicated to coffee growing, compared to more diversified or better accessible regions. We show how labor market effects can explain

  20. Correlation between caffeine contents of green coffee beans and ...

    African Journals Online (AJOL)

    A moderate negative correlation (R = 0.5463) was found between the caffeine contents of green coffee beans and the altitudes at which the coffee plants were grown. The caffeine contents of 9 of the green coffee bean samples analyzed by high performance liquid chromatography (HPLC) provided comparable results in the ...

  1. Color stability of restorative materials in response to Arabic coffee, Turkish coffee and Nescafe.

    Science.gov (United States)

    Al-Samadani, Khalid H

    2013-07-01

    To evaluate the effect of Arabic coffee, Turkish coffee and Nescafe on the color stability of four different composite resins after a period of aging time 1, 7 and 30 days. Twenty specimens from each type of tested composite resin material were prepared. Five specimens from each tested material (Z350 XT, Artist, GC and Z250) was evaluated after storage in Arabic coffee, Turkish coffee, Nescafe and distil water (control) at 37°C in a dark container for 1, 7 and 30 days. Color measurement was done using colorimeter based on the CIE L* a* b* color scale. Color differences ΔE*ab, Δb* and Δa* among specimens immersed in distil water and staining coffee beverages were evaluated overtime. Mean values were statistically analyzed with one-way analysis of variance (ANOVA), followed by Tukey test with p Nescafe except Δa*. The highest total color difference ΔE*ab after 30 days was in group A Arabic coffee (ΔE > 1.5 perceivable) and not perceivable in group B Turkish coffee and group C Nescafe. For Δb* all materials discolored toward yellowness after 30 days except Arabic coffee group which shifted from yellowness toward blueness (Δb*> 1.5 perceivable). The effect of staining beverages on the resin composite materials increases with time of aging toward yellowness and not perceivable in all groups except with Arabic coffee which had highest effect after 30 days and the discoloration shifted from yellowness to blueness perceivable.

  2. Analisis Customer Segment, Channels, Dan Customer Relationship Dalam Pembentukan Value Proposition Di Starbucks Coffee (Studi Kasus Pada Starbucks Coffee Indonesia)

    OpenAIRE

    Nurmanisa, Aisy; Wilopo,; Sanawiri, Brillyanes

    2016-01-01

    This research aims to understand and explain; How to Starbucks Coffee create value proposition for their customer? How to Starbucks Coffee segmented the customer, to create the value proposition? How to Starbucks Coffee build and choose the channels to grab the customer and create value proposition? How to Starbucks Coffee build a customer relationship and create value proposition from the process? .This reaserch uses primery data descriptive analysis method with fenomelogy kualitative o...

  3. Spatial distribution of the coffee-leaf-miner (Leucoptera coffeella) in an organic coffee (Coffea arabica L.) field in formation

    OpenAIRE

    Scalon, João Domingos; Universidade Federal de Lavras; Freitas, Gabriela Alves; DEX/UFLA; Avelar, Maria Betania Lopes; DEX/UFLA; Zacarias, Mauricio Sérgio; EPAMIG/EcoCentro

    2011-01-01

    Coffee production has been one of the economy pillars of many tropical countries. Unfortunately, this crop is susceptible to infestation by the coffee-leaf-miner (Leucoptera coffeella (Guérin-Mèneville & Perrottet, 1842)) which causes severe damage to coffee plantations with losses that may reach 80% of the total production. In recent years, researchers have been trying to develop practices for minimizing the use of pesticides in the coffee-leaf-miner control. It is well known that the un...

  4. High participation rate among 25 721 patients with broad age range in a hospital-based research project involving whole-genome sequencing - the Lausanne Institutional Biobank.

    Science.gov (United States)

    Bochud, Murielle; Currat, Christine; Chapatte, Laurence; Roth, Cindy; Mooser, Vincent

    2017-10-24

    We aimed to evaluate the interest of adult inpatients and selected outpatients in engaging in a large, real-life, hospital-based, genomic medicine research project and in receiving clinically actionable incidental findings. Within the framework of the cross-sectional Institutional Biobank of Lausanne, Switzerland, a total of 25721 patients of the CHUV University Hospital were systematically invited to grant researchers access to their biomedical data and to donate blood for future analyses, including whole-genome sequencing. Multivariable logistic regression analysis was used to identify personal factors, including age, gender, religion, ethnicity, citizenship, education level and mode of admission, associated with willingness to participate in this genomic research project and with interest in receiving clinically actionable incidental findings. The overall participation rate was 79% (20343/25721). Participation rate declined progressively with age, averaging 83%, 75%, 67% and 62% in patients aged rate, but not with higher willingness to receive incidental findings within the population who had agreed to participate. A large proportion of adult patients, even among the elderly, are willing to actively participate and receive incidental findings in this systematic hospital-based precision and genomic medicine research program with broad consent.

  5. Coffee intake, cardiovascular disease and allcause mortality

    DEFF Research Database (Denmark)

    Nordestgaard, Ask Tybjærg; Nordestgaard, Børge Grønne

    2016-01-01

    Background: Coffee has been associated with modestly lower risk of cardiovascular disease and all-cause mortality in meta-analyses; however, it is unclear whether these are causal associations. We tested first whether coffee intake is associated with cardiovascular disease and all-cause mortality...... observationally; second, whether genetic variations previously associated with caffeine intake are associated with coffee intake; and third, whether the genetic variations are associated with cardiovascular disease and all-cause mortality. Methods: First, we used multivariable adjusted Cox proportional hazard......- and age adjusted Cox proportional hazard regression models to examine genetic associations with cardiovascular disease and all-cause mortality in 112 509 Danes. Finally, we used sex and age-adjusted logistic regression models to examine genetic associations with ischaemic heart disease including...

  6. Acute effects of decaffeinated coffee and the major coffee components chlorogenic acid and trigonelline on glucose tolerance

    NARCIS (Netherlands)

    van Dijk, A.E.; Olthof, M.R.; Meeuse, J.C.; Seebus, E.; Heine, R.J.; van Dam, R.M.

    2009-01-01

    OBJECTIVE - Coffee consumption has been associated with lower risk of type 2 diabetes. We evaluated the acute effects of decaffeinated coffee and the major coffee components chlorogenic acid and trigonelline on glucose tolerance. RESEARCH DESIGN AND METHODS - We conducted a randomized crossover

  7. Freezing as a treatment to prevent the spread of coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae) in coffee

    Science.gov (United States)

    Coffee berry borer, Hypothenemus hampei (Ferrari) is the most serious insect pest of coffee around the world. While it is already present in most of the world’s major coffee growing regions, it is important to delay further spread and to prevent re-introductions which might include hyperparasites or...

  8. Micro-CT unveils the secret life of the coffee berry borer (Hypothenemus hampei; Coleoptera, Curculionidae: Scolytinae) inside coffee berries

    Science.gov (United States)

    The coffee berry borer (Hypothenemus hampei (Ferrari); Coleoptera: Curculionidae: Scolytinae) is the most important insect pest of coffee worldwide, and due to the cryptic life habit of the insect inside coffee berries, effective pest management strategies have been difficult to develop. In this pap...

  9. Briu: A Coffee Roasting Startup

    OpenAIRE

    Beck, Maximilian

    2015-01-01

    The purpose of this study is to examine the German coffee market and its appropriateness as a new market to enter for the startup Company Briu. The company has been continuously growing since its initial start. The Chilean Coffee startup has since then looked for new markets opportunities in Europe. Their favored market is Germany. The research conducted in this paper is supposed to reveal the market its suitability for the company its expansion. The following key areas are assessed in order ...

  10. BUSINESS DEVELOPMENT STRATEGY FOR SPECIALTY COFFEE

    Directory of Open Access Journals (Sweden)

    Vharessa Aknesia

    2015-01-01

    Full Text Available Specialty coffee is a coffee of premium quality that has been made through various stages of post-harvest processing and strictly controlled to produce distinctive taste of origins. PT Sinar Mayang Lestari is one of the companies that currently produce and develop specialty coffee type, Arabica Java Preanger. The objectives of the study are to examine competitive advantages and develop an alternative strategy that need to be done by PT Sinar Mayang Lestari for their business development. The research methods used are value chain analysis and VRIO framework to explore competitive advantage owned by the company. The result shows the company currently has a temporary competitive advantage of the technological resources and reputation. By using SWOT-AHP technique, the alternative strategies that can be done by company are as follows: 1 increasing the production of natural and honey coffee  type; 2 building coffee center in plantation site for sharing knowledge and innovation media to the farmers; 3 improving the competency of human resource in plantation, post harvest, and promoting area; 4 building management system gradually 5 forwarding integration by building roast and ground coffee business; and 6 maximizing the ability of the land and human resources through research and development.Keywords: competitive advantage, specialty coffee, SWOT-AHP, value chain, VRIOABSTRAKKopi special merupakan kopi dengan kualitas premium yang sudah melalui berbagai tahapan pengolahan pascapanen yang diawasi dengan ketat sehingga menghasilkan cita rasa yang khas sesuai dengan daerah asalnya. PT Sinar Mayang Lestari adalah salah satu perusahaan yang saatini memproduksi dan mengembangkan kopi spesial jenis Arabika Java Preanger. Tujuan dari penelitian ini adalah menganalisis keunggulan bersaing yang dimiliki dan mengembangkan alternative strategi yang perlu dilakukanoleh PT Sinar Mayang Lestari untuk pengembangan usahanya. Penelitian ini menggunakan analisis rantai

  11. Polymicrogyria-associated epilepsy: a multi-center phenotypic study from the Epilepsy Phenome/Genome Project

    Science.gov (United States)

    Shain, Catherine; Ramgopal, Sriram; Fallil, Zianka; Parulkar, Isha; Alongi, Richard; Knowlton, Robert; Poduri, Annapurna

    2013-01-01

    Purpose Polymicrogyria (PMG) is an epileptogenic malformation of cortical development. We describe the clinical epilepsy and imaging features of a large cohort with PMG-related epilepsy. Methods Participants were recruited through the Epilepsy Phenome/Genome Project, a multi-center collaborative effort to collect detailed phenotypic data on individuals with epilepsy. We reviewed phenotypic data from participants with epilepsy and PMG. Key Findings We identified 87 participants, 43 female and 44 male, with PMG and epilepsy. Median age of seizure onset was 3 years (range <1 month-37 years). Most presented with focal epilepsy (87.4%), some in combination with seizures generalized from onset (23.0%). Focal seizures with dyscognitive features were most common (54.3%). Of those presenting with generalized seizure types, infantile spasms were most prevalent (45.2%). The most common topographic pattern was perisylvian PMG (77.0%), of which the majority was bilateral (56.7%). Generalized PMG presented with an earlier age of seizure onset (median age of 8 months) and an increased prevalence of developmental delay prior to seizure onset (57.1%). Of the focal, unilateral and asymmetric bilateral groups where PMG was more involved in one hemisphere, the majority (71.4%) of participants had seizures that lateralized to the same hemisphere as the PMG or the hemisphere with greater involvement. Significance Participants with PMG had both focal and generalized onset of seizures. Our data confirm the involvement of known topographic patterns of PMG and suggest that more extensive distributions of PMG present with an earlier age of seizure onset and increased prevalence of developmental delay prior to seizure onset. PMID:23750890

  12. A Real Options Analysis of Coffee Planting in Vietnam

    OpenAIRE

    Luong, Quoc; Tauer, Loren W.

    2004-01-01

    Vietnam grew from an insignificant to the world’s second largest coffee producer during the 1990s. To understand this growth, this paper examines Vietnamese coffee growers’ investment decisions using real options theory. The study finds that producers, with variable costs of 19 cents/lb and total cost of 29.3 cents/lb, would enter coffee production at a coffee price of 47 cents/lb and exit at a coffee price of 14 cents/lb. Most Vietnamese growers appear to be sufficiently efficient to continu...

  13. [Coffee can be beneficial for patients with liver diseases].

    Science.gov (United States)

    Kjærgaard, Maria; Thiele, Maja; Krag, Aleksander

    2014-10-20

    Coffee is one of the most commonly consumed beverages in the world. Consequently, it is important to consider the impact of coffee on health and disease. A daily intake of at least three cups of coffee is likely to have beneficial health effects, especially in patients at risk of liver diseases. Coffee has been associated with decreased liver inflammation, prevention of cirrhosis, reduced steatosis and lower incidence of hepatocellular carcinoma. It is not yet possible to make clear recommendations, but coffee can likely be included as part of a healthy diet for patients with liver diseases.

  14. Coffee drinking enhances the analgesic effect of cigarette smoking

    DEFF Research Database (Denmark)

    Nastase, Anca; Ioan, Silvia; Braga, Radu I

    2007-01-01

    Nicotine (from cigarette smoke) and caffeine (from coffee) have analgesic effects in humans and experimental animals. We investigated the combined effects of coffee drinking and cigarette smoking on pain experience in a group of moderate nicotine-dependent, coffee drinking, young smokers. Pain...... threshold and pain tolerance were measured during cold pressor test following the habitual nocturnal deprivation of smoking and coffee drinking. Smoking increased pain threshold and pain tolerance in both men and women. Coffee drinking, at a dose that had no independent effect, doubled the increase in pain...

  15. Impact of caffeine and coffee on our health.

    Science.gov (United States)

    Gonzalez de Mejia, Elvira; Ramirez-Mares, Marco Vinicio

    2014-10-01

    Coffee is the most frequently consumed caffeine-containing beverage. The caffeine in coffee is a bioactive compound with stimulatory effects on the central nervous system and a positive effect on long-term memory. Although coffee consumption has been historically linked to adverse health effects, new research indicates that coffee consumption may be beneficial. Here we discuss the impact of coffee and caffeine on health and bring attention to the changing caffeine landscape that includes new caffeine-containing energy drinks and supplements, often targeting children and adolescents. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    UTTERBACK, TERESA RIGGS, FLORENCE VAN AKEN, SUSAN RIZZO, MICHAEL VISWANATHAN, LAKSHMI ROMERO , CALUDIA DEVI ROONEY, TIMOTHY VON ARX, ANNA RUCH, KAREN...Clark*, R. Clark*, C. Corton *, well with the predictions from the optical map. Chromosome 13 is A. Cronin*, R. Davies*, P. Davis*, P. Dear§, F. Dearden

  17. the human genome project

    African Journals Online (AJOL)

    Enrique

    have resulted in the biological diversity, both past and present, on this planet. ... Consortium. He is principal investigator on ... Leeuwenhoek was a necessary prerequisite to the vast array of high-definition .... with evidence left at crime scenes.

  18. New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination.

    Science.gov (United States)

    Jacques, Marie-Agnès; Denancé, Nicolas; Legendre, Bruno; Morel, Emmanuelle; Briand, Martial; Mississipi, Stelly; Durand, Karine; Olivier, Valérie; Portier, Perrine; Poliakoff, Françoise; Crouzillat, Dominique

    2015-12-28

    Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. Variation in caffeine concentration in single coffee beans.

    Science.gov (United States)

    Fox, Glen P; Wu, Alex; Yiran, Liang; Force, Lesleigh

    2013-11-13

    Twenty-eight coffee samples from around the world were tested for caffeine levels to develop near-infrared reflectance spectroscopy (NIRS) calibrations for whole and ground coffee. Twenty-five individual beans from five of those coffees were used to develop a NIRS calibration for caffeine concentration in single beans. An international standard high-performance liquid chromatography method was used to analyze for caffeine content. Coffee is a legal stimulant and possesses a number of heath properties. However, there is variation in the level of caffeine in brewed coffee and other caffeinated beverages. Being able to sort beans on the basis of caffeine concentration will improve quality control in the level of caffeine in those beverages. The range in caffeine concentration was from 0.01 mg/g (decaffeinated coffee) to 19.9 mg/g (Italian coffee). The majority of coffees were around 10.0-12.0 mg/g. The NIRS results showed r(2) values for bulk unground and ground coffees were >0.90 with standard errors coffee beans. One application of this calibration could be sorting beans on caffeine concentration to provide greater quality control for high-end markets. Furthermore, bean sorting may open new markets for novel coffee products.

  20. Recent Advances in the Genetic Transformation of Coffee

    Science.gov (United States)

    Mishra, M. K.; Slater, A.

    2012-01-01

    Coffee is one of the most important plantation crops, grown in about 80 countries across the world. The genus Coffea comprises approximately 100 species of which only two species, that is, Coffea arabica (commonly known as arabica coffee) and Coffea canephora (known as robusta coffee), are commercially cultivated. Genetic improvement of coffee through traditional breeding is slow due to the perennial nature of the plant. Genetic transformation has tremendous potential in developing improved coffee varieties with desired agronomic traits, which are otherwise difficult to achieve through traditional breeding. During the last twenty years, significant progress has been made in coffee biotechnology, particularly in the area of transgenic technology. This paper provides a detailed account of the advances made in the genetic transformation of coffee and their potential applications. PMID:22970380

  1. Water and coffee: a systems approach to improving coffee harvesting work in Nicaragua.

    Science.gov (United States)

    Silverstein, Barbara A; Bao, Stephen S; Russell, Steven; Stewart, Kate

    2012-12-01

    The aim of this study was to reduce the physical load on coffee-harvesting workers while maintaining productivity. Coffee is second to oil in commodity trading. Water is becoming scarce worldwide. The global virtual water footprint for one cup of coffee is 140 liters. Shade-grown coffee is one approach to reducing the water footprint. A participatory ergonomics approach was used during two Nicaraguan shade-grown coffee harvesting seasons to reduce the physical load on harvesters with the use of a newly designed bag instead of a basket strapped around the waist. Productivity in the mountainous, shade-grown coffee farms was maintained while physical load on the worker was improved somewhat.Among basket users, 84.2% reported pain in at least one body area compared with 78.9% of bag users (ns). Nonetheless, 74% of participants liked the bag "much better" than the basket. Workers identified ways the bag could be improved further with the use of local materials.These suggestions included (a) reducing the horizontal distance of the bag to reduce reach and (b) having waterproof material on the bag between the worker and the bag to reduce moisture and damage to the berries.There was no difference in productivity between using the bag and using the small basket. Workers are extending this participatory approach to how to get the harvested coffee cherries down the mountain other than carrying 40-kg bags on their backs. The ultimate goal is to make the coffee-harvesting bag design available to harvesters around the world.

  2. Study of composition of espresso coffee prepared from various roast degrees of Coffea arabica L. coffee beans.

    Science.gov (United States)

    Kučera, Lukáš; Papoušek, Roman; Kurka, Ondřej; Barták, Petr; Bednář, Petr

    2016-05-15

    Espresso coffee samples prepared at various roasting degrees defined according to its basic conventional classification (light, medium, medium-dark and dark roasted) were analyzed by ultra-performance liquid chromatography/tandem mass spectrometry. Obtained raw data were processed using multivariate statistical analysis (Principal Component Analysis, PCA) to evaluate chemical differences between each roasting degrees (untargeted part of study). All four roasting degrees were resolved in appropriate Score plot. Orthogonal Projections to Latent Structures provided signals of significant markers describing the differences among particular roasting degrees. Detailed interpretation of those signals by targeted LC/MS(2) analysis revealed four groups of compounds. The first two groups involve chlorogenic acids and related lactones. The signals of other two sets of markers were ascribed to some specific atractylosides and particular melanoidins. Ratios of contents of selected representatives of each group to the sum of all identified markers were proposed as definite parameters for determination of roasting degree of Brazilian coffee Arabica. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Fourier transform infrared spectroscopy for Kona coffee authentication.

    Science.gov (United States)

    Wang, Jun; Jun, Soojin; Bittenbender, H C; Gautz, Loren; Li, Qing X

    2009-06-01

    Kona coffee, the variety of "Kona typica" grown in the north and south districts of Kona-Island, carries a unique stamp of the region of Big Island of Hawaii, U.S.A. The excellent quality of Kona coffee makes it among the best coffee products in the world. Fourier transform infrared (FTIR) spectroscopy integrated with an attenuated total reflectance (ATR) accessory and multivariate analysis was used for qualitative and quantitative analysis of ground and brewed Kona coffee and blends made with Kona coffee. The calibration set of Kona coffee consisted of 10 different blends of Kona-grown original coffee mixture from 14 different farms in Hawaii and a non-Kona-grown original coffee mixture from 3 different sampling sites in Hawaii. Derivative transformations (1st and 2nd), mathematical enhancements such as mean centering and variance scaling, multivariate regressions by partial least square (PLS), and principal components regression (PCR) were implemented to develop and enhance the calibration model. The calibration model was successfully validated using 9 synthetic blend sets of 100% Kona coffee mixture and its adulterant, 100% non-Kona coffee mixture. There were distinct peak variations of ground and brewed coffee blends in the spectral "fingerprint" region between 800 and 1900 cm(-1). The PLS-2nd derivative calibration model based on brewed Kona coffee with mean centering data processing showed the highest degree of accuracy with the lowest standard error of calibration value of 0.81 and the highest R(2) value of 0.999. The model was further validated by quantitative analysis of commercial Kona coffee blends. Results demonstrate that FTIR can be a rapid alternative to authenticate Kona coffee, which only needs very quick and simple sample preparations.

  4. Occurrence of acrylamide carcinogen in Arabic coffee Qahwa, coffee and tea from Saudi Arabian market

    Science.gov (United States)

    Khan, Mohammad Rizwan; Alothman, Zeid Abdullah; Naushad, Mu; Alomary, Ahmed Khodran; Alfadul, Sulaiman Mohammed; Alsohaimi, Ibrahim Hotan; Algamdi, Mohammad Saad

    2017-02-01

    The present work describes the outcomes of the assessment on acrylamide contents in a number of thermally treated foods (Arabic coffee Qahwa, coffee and tea) obtained from the Saudi Arabian markets. A total of 56 food samples of different brands and origin were studied, the amounts of acrylamide in Arabic coffee Qahwa, coffee and tea were obtained in the range of 10 to 682 μg kg-1. In comparison to coffee (152-682 μg kg-1), the Arabic coffee Qahwa (73-108 μg kg-1) and tea (10-97 μg kg-1) contain lower amounts of acrylamide. Among the analyzed samples, the green tea contained low amounts of acrylamide ranged from 10 to 18 μg kg-1, and thus the green tea could be considered as a healthier hot drink. A great variation of acrylamide formation has been observed in these food products. This divergence may be due to the initial concentration of amino acids especially asparagines and reducing sugars in food products, in addition to roasting temperature and time, pH and water activity. The obtained data can also be used in epidemiological investigation to estimate the acrylamide exposure from nutritional survey.

  5. Development of Noninvasive Classification Methods for Different Roasting Degrees of Coffee Beans Using Hyperspectral Imaging

    Science.gov (United States)

    Chu, Bingquan; Yu, Keqiang; Zhao, Yanru

    2018-01-01

    This study aimed to develop an approach for quickly and noninvasively differentiating the roasting degrees of coffee beans using hyperspectral imaging (HSI). The qualitative properties of seven roasting degrees of coffee beans (unroasted, light, moderately light, light medium, medium, moderately dark, and dark) were assayed, including moisture, crude fat, trigonelline, chlorogenic acid, and caffeine contents. These properties were influenced greatly by the respective roasting degree. Their hyperspectral images (874–1734 nm) were collected using a hyperspectral reflectance imaging system. The spectra of the regions of interest were manually extracted from the HSI images. Then, principal components analysis was employed to compress the spectral data and select the optimal wavelengths based on loading weight analysis. Meanwhile, the random frog (RF) methodology and the successive projections algorithm were also adopted to pick effective wavelengths from the spectral data. Finally, least squares support vector machine (LS-SVM) was utilized to establish discriminative models using spectral reflectance and corresponding labeled classes for each degree of roast sample. The results showed that the LS-SVM model, established by the RF selecting method, with eight wavelengths performed very well, achieving an overall classification accuracy of 90.30%. In conclusion, HSI was illustrated as a potential technique for noninvasively classifying the roasting degrees of coffee beans and might have an important application for the development of nondestructive, real-time, and portable sensors to monitor the roasting process of coffee beans. PMID:29671781

  6. Development of Noninvasive Classification Methods for Different Roasting Degrees of Coffee Beans Using Hyperspectral Imaging.

    Science.gov (United States)

    Chu, Bingquan; Yu, Keqiang; Zhao, Yanru; He, Yong

    2018-04-19

    This study aimed to develop an approach for quickly and noninvasively differentiating the roasting degrees of coffee beans using hyperspectral imaging (HSI). The qualitative properties of seven roasting degrees of coffee beans (unroasted, light, moderately light, light medium, medium, moderately dark, and dark) were assayed, including moisture, crude fat, trigonelline, chlorogenic acid, and caffeine contents. These properties were influenced greatly by the respective roasting degree. Their hyperspectral images (874⁻1734 nm) were collected using a hyperspectral reflectance imaging system. The spectra of the regions of interest were manually extracted from the HSI images. Then, principal components analysis was employed to compress the spectral data and select the optimal wavelengths based on loading weight analysis. Meanwhile, the random frog (RF) methodology and the successive projections algorithm were also adopted to pick effective wavelengths from the spectral data. Finally, least squares support vector machine (LS-SVM) was utilized to establish discriminative models using spectral reflectance and corresponding labeled classes for each degree of roast sample. The results showed that the LS-SVM model, established by the RF selecting method, with eight wavelengths performed very well, achieving an overall classification accuracy of 90.30%. In conclusion, HSI was illustrated as a potential technique for noninvasively classifying the roasting degrees of coffee beans and might have an important application for the development of nondestructive, real-time, and portable sensors to monitor the roasting process of coffee beans.

  7. Development of Noninvasive Classification Methods for Different Roasting Degrees of Coffee Beans Using Hyperspectral Imaging

    Directory of Open Access Journals (Sweden)

    Bingquan Chu

    2018-04-01

    Full Text Available This study aimed to develop an approach for quickly and noninvasively differentiating the roasting degrees of coffee beans using hyperspectral imaging (HSI. The qualitative properties of seven roasting degrees of coffee beans (unroasted, light, moderately light, light medium, medium, moderately dark, and dark were assayed, including moisture, crude fat, trigonelline, chlorogenic acid, and caffeine contents. These properties were influenced greatly by the respective roasting degree. Their hyperspectral images (874–1734 nm were collected using a hyperspectral reflectance imaging system. The spectra of the regions of interest were manually extracted from the HSI images. Then, principal components analysis was employed to compress the spectral data and select the optimal wavelengths based on loading weight analysis. Meanwhile, the random frog (RF methodology and the successive projections algorithm were also adopted to pick effective wavelengths from the spectral data. Finally, least squares support vector machine (LS-SVM was utilized to establish discriminative models using spectral reflectance and corresponding labeled classes for each degree of roast sample. The results showed that the LS-SVM model, established by the RF selecting method, with eight wavelengths performed very well, achieving an overall classification accuracy of 90.30%. In conclusion, HSI was illustrated as a potential technique for noninvasively classifying the roasting degrees of coffee beans and might have an important application for the development of nondestructive, real-time, and portable sensors to monitor the roasting process of coffee beans.

  8. Setting the Stage for California Coffee Farming

    Science.gov (United States)

    Traditional coffee farming has occurred worldwide at equatorial latitudes below 25° under very specific growing conditions with acidic soils, warm temperatures and high humidity. Environmental conditions have been found to have large impacts on the quality and taste of the berry, which in turn affec...

  9. The Coffee-Milk Mixture Problem Revisited

    Science.gov (United States)

    Marion, Charles F.

    2015-01-01

    This analysis of a problem that is frequently posed at professional development workshops, in print, and on the Web--the coffee-milk mixture riddle--illustrates the timeless advice of George Pólya's masterpiece on problem solving in mathematics, "How to Solve It." In his book, Pólya recommends that problems previously solved and put…

  10. Self Reported Symptoms Associated with Coffee Consumption ...

    African Journals Online (AJOL)

    Nekky Umera

    caffeine ingestion often leads to inhibition of logical, connected thought, and ... consumption produced a pattern of physiological and psychological reactions ... professionals in Nigeria after several years of research at .... experienced by daily users of coffee and occasional users. .... Brain Research and Review 17: 139 –.

  11. Design Guidelines for Coffee Vending Machines

    OpenAIRE

    Schneidermeier, Tim; Burghardt, Manuel; Wolff, Christian

    2013-01-01

    Walk-up-and-use-systems such as vending and self-service machines request special attention concerning an easy to use and self-explanatory user interface. In this paper we present a set of design guidelines for coffee vending machines based on the results of an expert-based usability evaluation of thirteen different models.

  12. Fungal biomass production from coffee pulp juice

    Energy Technology Data Exchange (ETDEWEB)

    De Leon, R.; Calzada, F.; Herrera, R.; Rolz, C.

    1980-01-01

    Coffee pulp or skin represents about 40% of the weight of the fresh coffee fruit. It is currently a waste and its improper handling creates serious pollution problems for coffee producing countries. Mechanical pressing of the pulp will produce two fractions: coffee pulp juice (CPJ) and pressed pulp. Aspergillus oryzae, Trichoderma harzianum, Penicillium crustosum and Gliocladium deliquescens grew well in supplemented CPJ. At shake flask level the optimum initial C/N ratio was found to be in the range of 8 to 14. At this scale, biomass values of up to 50 g/l were obtained in 24 hours. Biomass production and total sugar consumption were not significantly different to all fungal species tested at the bench-scale level, even when the initial C/N ratio was varied. Best nitrogen consumption values were obtained when the initial C/N ratio was 12. Maximum specific growth rates occurred between 4-12 hours for all fungal species tested. (Refs. 8).

  13. Caffeine Content of Tea and Coffee

    African Journals Online (AJOL)

    1974-03-13

    Mar 13, 1974 ... The xanthines (caffeine, theophylline, and theobromine) occur in plants widely distributed throughout the world. Best known for the preparation of beverages are coffee beans which contain caffeine, tea leaves which contain caffeine and theophylline, and cocoa seeds which contain caffeine and ...

  14. ASSESSMENT OF METALS IN ROASTED INDIGENOUS COFFEE ...

    African Journals Online (AJOL)

    *Corresponding author. E-mail: bscv2006@yahoo.com. This work is licensed under the Creative Commons Attribution 4.0 International License. ASSESSMENT OF METALS IN ROASTED INDIGENOUS COFFEE VARIETIES OF. ETHIOPIA. Abera Gure1,2, Bhagwan Singh Chandravanshi1* and Taddese Wondimu Godeto1, ...

  15. Difference Spectroscopy in the Analysis of the Effects of Coffee Cherry Processing Variables on the Flavor of Brewed Coffee

    International Nuclear Information System (INIS)

    Lyman, D.J.; Benck, R.M.; Merle, S.F.

    2011-01-01

    Infrared difference spectroscopy was used to study how changes in the processing of Arabica coffee cherries into green beans affected the flavor of coffee brewed from roasted green beans. Paired samples of green beans, in which the drying step or fermentation/washing step in their processing was altered, were roasted and brewed in a standard manner and their ATR-FT-IR spectra obtained. Difference spectra of the 1800 to 1680 cm-1 carbonyl region of water-subtracted spectra of paired samples of these brewed coffees provided data which indicated differences in brewed coffee flavor due to changes in fermentation/washing steps and drying steps involved in the processing of coffee cherries. The role of acid, ketone, aldehyde, ester, lactone, and vinyl ester carbonyl components on the flavor of brewed coffee is proposed that is consistent with the flavors as perceived by the coffee tasters.

  16. Difference Spectroscopy in the Analysis of the Effects of Coffee Cherry Processing Variables on the Flavor of Brewed Coffee

    Directory of Open Access Journals (Sweden)

    Donald J. Lyman

    2011-01-01

    Full Text Available Infrared difference spectroscopy was used to study how changes in the processing of Arabica coffee cherries into green beans affected the flavor of coffee brewed from roasted green beans. Paired samples of green beans, in which the drying step or fermentation/washing step in their processing was altered, were roasted and brewed in a standard manner and their ATR-FT-IR spectra obtained. Difference spectra of the 1800 to 1680 cm−1 carbonyl region of water-subtracted spectra of paired samples of these brewed coffees provided data which indicated differences in brewed coffee flavor due to changes in fermentation/washing steps and drying steps involved in the processing of coffee cherries. The role of acid, ketone, aldehyde, ester, lactone, and vinyl ester carbonyl components on the flavor of brewed coffee is proposed that is consistent with the flavors as perceived by the coffee tasters.

  17. Furan Levels and Sensory Profiles of Commercial Coffee Products Under Various Handling Conditions.

    Science.gov (United States)

    Han, Jeesoo; Kim, Mina K; Lee, Kwang-Geun

    2017-11-01

    In this study, the levels of furan in coffee with consideration towards common coffee consumption was investigated. The concentration of furan in brewed coffee was the highest among the coffee types studied, with an average of 110.73 ng/mL, followed by canned coffee (28.08 ng/mL) and instant coffee (8.55 ng/mL). In instant and brewed coffee, the furan levels decreased by up to an average of 20% and 22%, after 5 min of pouring in a cup without a lid. The degree of reduction was greater when coffee was served without a lid, regardless of coffee type (P coffee, the level of furan decreased by an average of 14% after storage at 60 °C without a lid, and the degree of furan reduction in coffee was greater in coffee served warm (60 °C) than in coffee served cold (4 °C). A time-dependent intensities of sensory attributes in commercial coffees with various handling condition were different (P coffee kept in a cup with lid closed, holds the aroma of coffee longer than coffee in a cup without a lid. Consumption of coffee has increased rapidly in Korea over the past few years. Consequently, the probability of exposure to chemical hazards presence in coffee products increases. Furan is a heterocyclic compound, formed mainly from Maillard reaction, therefore present in coffee products. This work demonstrated the strategy to reduce the levels of furan in coffee products at individual consumer level, by investigating the levels of furan served in common handling scenarios of coffee in Korea: canned coffee, instant coffee, and brewed coffee. Findings of this study can practically guide industry, government, and consumer agencies to reduce the risk exposure to furan during coffee consumptions. © 2017 Institute of Food Technologists®.

  18. Evaluation of a treatment system type septic tank - filter anaerobic of upward flow for the residual waters of the ecological benefit of the coffee

    International Nuclear Information System (INIS)

    Sanchez C, Jose Alejandro

    1997-01-01

    Colombia is the first country in the production of soft coffee in the world. The benefit for humid way it makes that this quality of coffee is obtained; however, the high consumption of water in the process and the later discharge to the superficial or underground sources, they have generated an environmental problem of great magnitude. Also, the sources of water that they have been contaminated with the discharges of the liquid waste that come from benefit of coffee they present, among other, serious inconveniences to be used as supplying sources of drinkable water. In time of crop, the coffee areas and their superficial sources of water usually register high indexes of contamination like consequence of the discharges of residual waters that come from the benefit of the coffee. In the Departments of Quindio, Valle, Caldas, Antioquia, etc., they have been come executing investigations of the residuals treatment that are derived of the pulp removal of the coffee (via humid), for anaerobic methods with satisfactory results. This project had the collaboration of the Departmental Committee of Coffee of Antioquia and the Environmental Engineering of the Antioquia University and it is formulated toward the evaluation of a Anaerobic filter of Ascendant flow, FAFA, preceded of a septic tank (biological sedimentation), as a treatment system of the coffee residual waters, with a waste native of a ecological benefit area. The obtained results were satisfactory although the generated waste is very intermittent and in times that are not of coffee crop it doesn't take place; what hinders more the application of biological systems for its treatment

  19. Kibale forest wild coffee: challenges to market-based conservation in Africa.

    Science.gov (United States)

    Lilieholm, Robert J; Weatherly, W Paul

    2010-08-01

    Declining rural security and pressures to reduce public-sector expenditures in the late 1990s spurred efforts to develop alternative funding models for Uganda's Kibale National Park (KNP). The Wild Coffee Project, established in 1999 with support from the U.S. Agency for International Development, the World Bank, and the Ford Foundation, sought to develop a market for wild coffee that had been harvested traditionally from areas within today's KNP. The Kibale Forest Foundation, a U.S.-based nonprofit organization, was created to legalize harvests, obtain third-party wild and organic certification, and coordinate management between KNP, the coffee industry, and local communities. Although the project was successful in legalizing, harvesting, and processing the world's first certified wild and organic coffee, efforts to gain entry into the international marketplace failed. Chief among the lessons learned from this project is that for many wild-grown products, the value of "the story"--in both human and conservation terms--is likely to far exceed actual product values. This value differential should be captured through high-value niche markets to avoid low commodity pricing and subsequent pressures to improve financial returns through over harvesting. In addition, local producers should hold significant assets in whatever brands are developed, creating a shared-equity approach that serves social responsibility goals, fosters project sustainability, and ensures a steady stream of positive stories for use in marketing to build brand value. Shared equity--in this case ownership interest in the intellectual property embodied in the brand--provides a second incentive beyond transactional profits that can only be realized if resource conservation is maintained.

  20. Calibration of Ocean Forcing with satellite Flux Estimates (COFFEE)

    Science.gov (United States)

    Barron, Charlie; Jan, Dastugue; Jackie, May; Rowley, Clark; Smith, Scott; Spence, Peter; Gremes-Cordero, Silvia

    2016-04-01

    Predicting the evolution of ocean temperature in regional ocean models depends on estimates of surface heat fluxes and upper-ocean processes over the forecast period. Within the COFFEE project (Calibration of Ocean Forcing with satellite Flux Estimates, real-time satellite observations are used to estimate shortwave, longwave, sensible, and latent air-sea heat flux corrections to a background estimate from the prior day's regional or global model forecast. These satellite-corrected fluxes are used to prepare a corrected ocean hindcast and to estimate flux error covariances to project the heat flux corrections for a 3-5 day forecast. In this way, satellite remote sensing is applied to not only inform the initial ocean state but also to mitigate errors in surface heat flux and model representations affecting the distribution of heat in the upper ocean. While traditional assimilation of sea surface temperature (SST) observations re-centers ocean models at the start of each forecast cycle, COFFEE endeavors to appropriately partition and reduce among various surface heat flux and ocean dynamics sources. A suite of experiments in the southern California Current demonstrates a range of COFFEE capabilities, showing the impact on forecast error relative to a baseline three-dimensional variational (3DVAR) assimilation using operational global or regional atmospheric forcing. Experiment cases combine different levels of flux calibration with assimilation alternatives. The cases use the original fluxes, apply full satellite corrections during the forecast period, or extend hindcast corrections into the forecast period. Assimilation is either baseline 3DVAR or standard strong-constraint 4DVAR, with work proceeding to add a 4DVAR expanded to include a weak constraint treatment of the surface flux errors. Covariance of flux errors is estimated from the recent time series of forecast and calibrated flux terms. While the California Current examples are shown, the approach is

  1. FDM 3D printed coffee glove embedded with flexible electronic

    KAUST Repository

    Bahri, Meznan

    2017-10-31

    With the advances in 3D printing technology, Flexible Electronics can now be exploited to form the so-called “Embedded Electronics”. This paper describes experiences learned from a research project which ran during summer 2016 at KAUST, in collaboration with the Electrical and Computer Engineering Department at Effat University, and aimed at creating a heating coffee glove product operating on double alkaline batteries using Kapton© as a flexible substrate for the circuit. The circuit and its batteries are encapsulated in a 3D printed glove, designed using SolidWorks©. The proposed methodology and techniques applied during this work could be further used in implementing other technologies, such as thermoelectric coolers head patches, smart garments, and flexible smartphones. Limitation and recommendation of the present methodology are also discussed.

  2. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  3. Coffee drinking and mortality in 10 European countries : A multinational cohort study

    NARCIS (Netherlands)

    Gunter, Marc J.; Murphy, Neil; Cross, Amanda J.; Dossus, Laure; Dartois, Laureen; Fagherazzi, Guy; Kaaks, Rudolf; Kühn, Tilman; Boeing, Heiner; Aleksandrova, Krasimira; Tjønneland, Anne; Olsen, Anja; Overvad, Kim; Larsen, Sofus Christian; Cornejo, Maria Luisa Redondo; Agudo, Antonio; Pérez, María José Sánchez; Altzibar, Jone M.; Navarro, Carmen; Ardanaz, Eva; Khaw, Kay Tee; Butterworth, Adam; Bradbury, Kathryn E.; Trichopoulou, Antonia; Lagiou, Pagona; Trichopoulos, Dimitrios; Palli, Domenico; Grioni, Sara; Vineis, Paolo; Panico, Salvatore; Tumino, Rosario; Bueno-De-Mesquita, Bas; Siersema, Peter; Leenders, Max; Beulens, Joline W.J.; Uiterwaal, Cuno U.; Wallström, Peter; Nilsson, Lena Maria; Landberg, Rikard; Weiderpass, Elisabete; Skeie, Guri; Braaten, Tonje; Brennan, Paul; Licaj, Idlir; Muller, David C.; Sinha, Rashmi; Wareham, Nick; Riboli, Elio

    2017-01-01

    Background: The relationship between coffee consumption and mortality in diverse European populations with variable coffee preparation methods is unclear. Objective: To examine whether coffee consumption is associated with all-cause and cause-specific mortality. Design: Prospective cohort study.

  4. Physical and sensory quality of Java Arabica green coffee beans

    Science.gov (United States)

    Sunarharum, W. B.; Yuwono, S. S.; Pangestu, N. B. S. W.; Nadhiroh, H.

    2018-03-01

    Demand on high quality coffee for consumption is continually increasing not only in the consuming countries (importers) but also in the producing countries (exporters). Coffee quality could be affected by several factors from farm to cup including the post-harvest processing methods. This research aimed to investigate the influence of different post-harvest processing methods on physical and sensory quality of Java Arabica green coffee beans. The two factors being evaluated were three different post-harvest processing methods to produce green coffee beans (natural/dry, semi-washed and fully-washed processing) under sun drying. Physical quality evaluation was based on The Indonesian National Standard (SNI 01-2907-2008) while sensory quality was evaluated by five expert judges. The result shows that less defects observed in wet processed coffee as compared to the dry processing. The mechanical drying was also proven to yield a higher quality green coffee beans and minimise losses.

  5. Characterization of Organic and Conventional Coffee Using Neutron Activation Analysis

    International Nuclear Information System (INIS)

    E. A. De Nadai Fernandes; P. Bode; F. S. Tagliaferro

    2000-01-01

    Countries importing organic coffee are facing the difficulty of assessing the quality of the product to distinguish original organic coffee from other coffees, thereby eliminating possible fraud. Many analytical methods are matrix sensitive and require matrix-matching reference materials for validation, which are currently nonexistent. This work aims to establish the trace element characterization of organic and conventional Brazilian coffees and to establish correlations with the related soil and the type of fertilizer and agrochemicals applied. It was observed that the variability in element concentrations between the various types of coffee is not so large, which emphasizes the need for analytical methods of high accuracy, reproducibility, and a well-known uncertainty. Moreover, the analyses indicate that sometimes the coffee packages may contain some soil remnants

  6. The New World of Human Genetics: A dialogue between Practitioners & the General Public on Ethical, Legal & Social Implications of the Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Schofield, Amy

    2014-12-08

    The history and reasons for launching the Human Genome project and the current uses of genetic human material; Identifying and discussing the major issues stemming directly from genetic research and therapy-including genetic discrimination, medical/ person privacy, allocation of government resources and individual finances, and the effect on the way in which we perceive the value of human life; Discussing the sometimes hidden ethical, social and legislative implications of genetic research and therapy such as informed consent, screening and preservation of genetic materials, efficacy of medical procedures, the role of the government, and equal access to medical coverage.

  7. Determination of the Element Contents in Turkish Coffee and Effect of Sugar Addition

    OpenAIRE

    M. M. Fercan; A. S. Kipcak; O. Dere Ozdemir; M. B. Piskin; E. Moroydor Derun

    2016-01-01

    Coffee is a widely consumed beverage with many components such as caffeine, flavonoids, phenolic compounds, and minerals. Coffee consumption continues to increase due to its physiological effects, its pleasant taste, and aroma. Robusta and Arabica are two basic types of coffee beans. The coffee bean used for Turkish coffee is Arabica. There are many elements in the structure of coffee and have various effect on human health such as Sodium (Na), Boron (B), Magnesium (Mg) and Iron (Fe). In this...

  8. What is the Difference in Profit per Acre between Organic and Conventional Coffee?

    OpenAIRE

    Jensen, Jennifer; Dicks, Michael R.

    2012-01-01

    The research addresses the economic problem of deforestation. A contributing factor to deforestation is coffee production. Coffee is an indigenous plant that is naturally occurring in the native tropical forests. However, conventional coffee is grown on cleared forest soil. In the native forest there is the potential for additional fruits (bananas, mangoes, avocados) and wood products while in the conventional coffee production system the only product is coffee. Conventional coffee production...

  9. THE LATIN AMERICAN ORGANIC COFFEE INDUSTRY: U.S. MARKET INROADS

    OpenAIRE

    Rodriguez, Danilo; Epperson, James E.

    2001-01-01

    Certified organic coffee is a minuscule but important portion of coffee production and trade and is the fastest growing sector in sales revenue. Organic coffee has its roots in sustainable crop production and economic development policy. Latin America has become the center of the organic coffee movement, representing a change from the old market structure of the coffee trade. The U.S. organic coffee market has experienced extraordinary growth in the past five years because of an increase in c...

  10. TRACKING THE PROCESSES OF MELANODIN FORMATION IN COFFEE

    OpenAIRE

    Snezhana Ivanova

    2017-01-01

    Melanoidins are high molecular brown colored substances and products of sugar-amine reaction of Maillard. They are formed during roasting a green coffee beans under different thermal regimes of heat treatment. In the technological production of different types coffee beverages, the coffee powder is subjected to after-heat treatment. In these additional operations again become active processes of melanoidin formation and their changing their structures. This is changes of the Melanoidins have ...

  11. Polycyclic aromatic hydrocarbons in some grounded coffee brands.

    Science.gov (United States)

    Grover, Inderpreet Singh; Sharma, Rashmi; Singh, Satnam; Pal, Bonamali

    2013-08-01

    Potentially toxic 16 priority polycyclic aromatic hydrocarbons (PAHs) were determined in four brands of grounded coffee. Four to 13 PAHs were detected. Concentrations of total PAHs in different brands of coffee samples were in the range of 831.7-1,589.7 μg/kg. Benzo[a]pyrene (2A: probable human carcinogen) was found in Nescafe Premium whereas naphthalene (2B: possible human carcinogen) was found in all the samples of coffee.

  12. Suppression of coffee ring: (Particle) size matters

    Science.gov (United States)

    Bansal, Lalit; Seth, Pranjal; Murugappan, Bhubesh; Basu, Saptarshi

    2018-05-01

    Coffee ring patterns in drying sessile droplets are undesirable in various practical applications. Here, we experimentally demonstrate that on hydrophobic substrates, the coffee ring can be suppressed just by increasing the particle diameter. Particles with larger size flocculate within the evaporation timescale, leading to a significant gravimetric settling (for Pe > 1) triggering a uniform deposit. Interestingly, the transition to a uniform deposit is found to be independent of the internal flow field and substrate properties. Flocculation of particles also alters the particle packing at the nanoscale resulting in order to disorder transitions. In this letter, we exhibit a physical exposition on how particle size affects morphodynamics of the droplet drying at macro-nano length scales.

  13. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  14. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  15. Chronic coffee consumption and respiratory disease: A systematic review.

    Science.gov (United States)

    Alfaro, Tiago M; Monteiro, Rita A; Cunha, Rodrigo A; Cordeiro, Carlos Robalo

    2018-03-01

    The widespread consumption of coffee means that any biological effects from its use can lead to significant public health consequences. Chronic pulmonary diseases are extremely prevalent and responsible for one of every six deaths on a global level. Major medical databases for studies reporting on the effects of coffee or caffeine consumption on a wide range of non-malignant respiratory outcomes, including incidence, prevalence, evolution or severity of respiratory disease in adults were searched. Studies on lung function and respiratory mortality were also considered. Fifteen studies, including seven cohort, six cross-sectional, one case control and one randomized control trial were found. Coffee consumption was generally associated with a reduction in prevalence of asthma. The association of coffee with natural honey was an effective treatment for persistent post-infectious cough. One case-control study found higher risk of chronic obstructive pulmonary disease (COPD) with coffee consumption. No association was found with the evolution of COPD or sarcoidosis. Coffee was associated with a reduction in respiratory mortality, and one study found improved lung function in coffee consumers. Smoking was a significant confounder in most studies. Coffee consumption was associated with some positive effects on the respiratory system. There was however limited available evidence, mostly from cross sectional and retrospective studies. The only prospective cohort studies were those reporting on respiratory mortality. These results suggest that coffee consumption may be a part of a healthy lifestyle leading to reduced respiratory morbidity. © 2017 John Wiley & Sons Ltd.

  16. Coffee Consumption and the Incidence of Colorectal Cancer in Women

    International Nuclear Information System (INIS)

    Groessl, E. J.; Allison, M. A.; Ho, S. B.; Groessl, E. J.; Allison, M. A.; Ho, S. B.; Larson, J. C.; Snetslaar, L. G.; Lane, D. S.; Tharp, K. M.; Stefanick, M. L.

    2016-01-01

    Higher coffee consumption has been associated with decreased incidence of colorectal cancer. Our objective was to examine the relationship of coffee intake to colorectal cancer incidence in a large observational cohort of postmenopausal US women. Methods. Data were collected for the Women’s Health Initiative Observational Study providing a follow-up period of 12.9 years. The mean age of our sample ( N = 83,778 women) was 63.5 years. Daily coffee intake was grouped into 3 categories: None, moderate (>0-<4 cups), and high (4+ cups). Proportional hazards modeling was used to evaluate the relationship between coffee intake and colorectal cancer. Results. There were 1,282 (1.53%) new cases of colorectal cancer during follow-up. Compared to nondrinkers, moderate and high coffee drinkers had an increased incidence of colorectal cancer in multivariate analysis (HR 1.15, 1.02-1.29; HR 1.14, 0.93-1.38). Moderate drip brew coffee intake (HR 1.20, 1.05-1.36) and high non drip brew coffee intake (HR 1.43, 1.01-2.02) were associated with increased odds. Conclusion. Our results suggesting increased incidence of colorectal cancer associated with higher coffee consumption contradict recent meta-analyses but agree with a number of other studies showing that coffee increases risk or has no effect. Brew method results are novel and warrant further research.

  17. Natural radiation source fabricated from commercially available instant coffee

    International Nuclear Information System (INIS)

    Kawano, Takao; Ando, Yoshiaki; Izumi, Yuuichi

    2015-01-01

    Commercially available instant coffee, Nescafe Excella, contained the radionuclide 40 K. From the instant coffee, sixteen coffee-block radiation sources were successfully fabricated with sufficiently low production dependences. The coffee-block radiation sources were examined their suitability for a radiation protection course. Although a part of radiation counts(cpm) obtained with 1 minute measurement were largely deviated, those determined by 5 minute measurements and five times of 1 minute measurement were less deviated, enabling better comprehension of the three cardinal principles of radiation protection. (author)

  18. How coffee affects metabolic syndrome and its components.

    Science.gov (United States)

    Baspinar, B; Eskici, G; Ozcelik, A O

    2017-06-21

    Metabolic syndrome, with its increasing prevalence, is becoming a major public health problem throughout the world. Many risk factors including nutrition play a role in the emergence of metabolic syndrome. Of the most-consumed beverages in the world, coffee contains more than 1000 components such as caffeine, chlorogenic acid, diterpenes and trigonelline. It has been proven in many studies that coffee consumption has a positive effect on chronic diseases. In this review, starting from the beneficial effects of coffee on health, the relationship between coffee consumption and metabolic syndrome and its components has been investigated. There are few studies investigating the relationship between coffee and metabolic syndrome, and the existing ones put forward different findings. The factors leading to the differences are thought to stem from coffee variety, the physiological effects of coffee elements, and the nutritional ingredients (such as milk and sugar) added to coffee. It is reported that consumption of coffee in adults up to three cups a day reduces the risk of Type-2 diabetes and metabolic syndrome.

  19. Coffee and health: a review of recent human research.

    Science.gov (United States)

    Higdon, Jane V; Frei, Balz

    2006-01-01

    Coffee is a complex mixture of chemicals that provides significant amounts of chlorogenic acid and caffeine. Unfiltered coffee is a significant source of cafestol and kahweol, which are diterpenes that have been implicated in the cholesterol-raising effects of coffee. The results of epidemiological research suggest that coffee consumption may help prevent several chronic diseases, including type 2 diabetes mellitus, Parkinson's disease and liver disease (cirrhosis and hepatocellular carcinoma). Most prospective cohort studies have not found coffee consumption to be associated with significantly increased cardiovascular disease risk. However, coffee consumption is associated with increases in several cardiovascular disease risk factors, including blood pressure and plasma homocysteine. At present, there is little evidence that coffee consumption increases the risk of cancer. For adults consuming moderate amounts of coffee (3-4 cups/d providing 300-400 mg/d of caffeine), there is little evidence of health risks and some evidence of health benefits. However, some groups, including people with hypertension, children, adolescents, and the elderly, may be more vulnerable to the adverse effects of caffeine. In addition, currently available evidence suggests that it may be prudent for pregnant women to limit coffee consumption to 3 cups/d providing no more than 300 mg/d of caffeine to exclude any increased probability of spontaneous abortion or impaired fetal growth.

  20. Coffee Bean Grade Determination Based on Image Parameter

    Directory of Open Access Journals (Sweden)

    F. Ferdiansjah

    2011-12-01

    Full Text Available Quality standard for coffee as an agriculture commodity in Indonesia uses defect system which is regulated in Standar Nasional Indonesia (SNI for coffee bean, No: 01-2907-1999. In the Defect System standard, coffee bean is classified into six grades, from grade I to grade VI depending on the number of defect found in the coffee bean. Accuracy of this method heavily depends on the experience and the expertise of the human operators. The objective of the research is to develop a system to determine the coffee bean grading based on SNI No: 01-2907-1999. A visual sensor, a webcam connected to a computer, was used for image acquisition of coffee bean image samples, which were placed under uniform illumination of 414.5+2.9 lux. The computer performs feature extraction from parameters of coffee bean image samples in the term of texture (energy, entropy, contrast, homogeneity and color (R mean, G mean, and B mean and determines the grade of coffee bean based on the image parameters by implementing neural network algorithm. The accuracy of system testing for the coffee beans of grade I, II, III, IVA, IVB, V, and VI have the value of 100, 80, 60, 40, 100, 40, and 100%, respectively.

  1. Physico chemical evaluation of coffee husk, wastes of enset (Enset ...

    African Journals Online (AJOL)

    Physico chemical evaluation of coffee husk, wastes of enset (Enset ventricosum), vegetable and khat (Catha edulis) through vermicomposting employing an epigeic earthworm Dendrobaena veneta (Rosa, 1886)

  2. Coffee Consumption and the Risk of Obesity in Korean Women.

    Science.gov (United States)

    Lee, Jeonghee; Kim, Hye Young; Kim, Jeongseon

    2017-12-08

    Instant coffee mixes that contain sugar and non-dairy creamer account for 80-90% of the total coffee market in Korea. The objective of this study was to investigate the relationship between coffee consumption and obesity in Korean women. We included 5995 women who participated in a health screening examination at the Korean National Cancer Center between 2007 and 2016. Daily coffee consumption and the use of sugar and creamer in coffee was evaluated using a 106-item food frequency questionnaire. Obesity was assessed by body mass index (BMI), and abdominal obesity was assessed by waist circumference (WC). A multiple logistic regression model was used to calculate the odds ratio (OR) of obesity according to coffee consumption. After multivariate adjustment, high coffee consumption was positively associated with obesity as measured by BMI (≥3 cups vs. no drinks, OR = 2.52; 95% confidence interval (CI) = 1.91-3.34; p for the trend coffee consumption and obesity prevalence was not altered by menopause. The amount of coffee with additives consumed per day by Korean women was positively correlated with the prevalence of obesity, but causation cannot be determined due to the cross-sectional nature of the study design. The mechanism underlying the observed relationship is yet to be elucidated.

  3. A Bumper Crop of Fair Trade Coffee Books

    Directory of Open Access Journals (Sweden)

    John M. Talbot

    2015-08-01

    Full Text Available The history of the world coffee market is a story of cycles of boom and bust. The most recent bust, one of the most severe in history, began in 1998 and started to ease in 2005. This period of severe crisis across the coffee producing countries in the developing world stimulated a growing interest in fair trade coffee as a means of helping the small farmers who were being devastated by historically low prices. As public interest and consumption grew, social scientists, as is their wont, set out to study the phenomenon. The result is the current bumper crop of books analyzing fair trade coffee.

  4. Thermogenic Effect from Nutritionally Enriched Coffee Consumption

    Directory of Open Access Journals (Sweden)

    Jennings Peter F

    2006-06-01

    Full Text Available Abstract Background The purpose of this study was to examine the effect of nutritionally enriched JavaFit™ (JF coffee (450 mg of caffeine, 1200 mg of garcinia cambogia, 360 mg of citrus aurantium extract, and 225 mcg of chromium polynicotinate on resting oxygen uptake (VO2, respiratory exchange ratio (RER, heart rate (HR, and blood pressure (BP in healthy and physically active individuals. Method Ten subjects (8 male, 2 female; 20.9 ± 1.7 y; 178.1 ± 10.4 cm; 71.8 ± 12.1 kg underwent two testing sessions administered in a randomized and double-blind fashion. During each session, subjects reported to the Human Performance Laboratory after at least 3-h post-absorptive state and were provided either 354 ml (1.5 cups of freshly brewed JF or commercially available caffeinated coffee (P. Subjects then rested in a semi-recumbent position for three hours. VO2 and HR were determined every 5 min during the first 30 min and every 10 min during the next 150 min. BP was determined every 15 min during the first 30 min and every 30 min thereafter. Area under the curve (AUC analysis was computed for VO2, whereas a session-average was calculated for RER, HR and BP. Results Initial analysis revealed no significant differences. However, seven of the ten subjects were considered responders to JF (had a higher AUC for VO2during JF than P. Statistical analysis showed the difference between JF and P (12% to be significantly different in these responders. In addition, the average systolic BP was higher (p Conclusion It appears that consuming a nutritionally-enriched coffee beverage may increase resting energy expenditure in individuals that are sensitive to the caffeine and herbal coffee supplement. In addition, this supplement also appears to affect cardiovascular dynamics by augmenting systolic arterial blood pressure.

  5. Ecosystem Service of Shade Trees on Nutrient Cycling and Productivity of Coffee Agro-ecosystems

    Directory of Open Access Journals (Sweden)

    Rusdi Evizal

    2009-05-01

    Full Text Available Shade trees are significant in certification scheme of sustainable coffee production. They play an importance role on ecosystem functioning. This research is aimed to study ecosystem service of shade trees in some coffee agro-ecosystems particularly on nutrient cycling and land productivity. Four agro-ecosys tems of Robusta coffee (Coffea canephora, namely sun coffee (without shade trees, coffee shaded by Michelia champaca, coffee shaded by Gliricidia sepium, and coffee shaded by Erythrina indica are evaluated during 2007—2008. Smallholder coffee plantation in Sumberjaya Subdistrict, West Lampung, which managed under local standard were employed using Randomized Complete Block Design with 3 replications. The result showed that litter fall dynamic from shade trees and from coffee trees was influenced by rainfall. Shade trees decreased weed biomass while increased litter fall production. In dry season, shade trees decreased litter fall from coffee shaded by M. champaca. G. sepium and E. indica shaded coffee showed higher yield than sun coffee and M. champaca shaded coffee. Except for M. champaca shaded coffee, yield had positive correlation (r = 0.99 with litter fall production and had negative correlation (r = —0.82 with weed biomass production. Biomass production (litter fall + weed of sun coffee and shaded coffee was not significantly different. Litter fall of shade trees had significance on nutrient cycle mainly to balance the lost of nitrogen in coffee bean harvesting.Key Words: Coffea canephora, Michelia champaca, Gliricidia sepium, Erythrina indica, litter production, nutrient cycle, coffee yield.

  6. How Brazil Transferred Billions to Foreign Coffee Importers: The International Coffee Agreement, Rent Seeking and Export Tax Rebates

    OpenAIRE

    Jarvis, Lovell S.

    2003-01-01

    Rent seeking is well known, but empirical evidence of its effects is relatively rare. This paper analyzes how the domestic and international rent seeking caused Brazil to provide coffee export tax rebates that transferred foreign exchange to coffee importers. Although Brazil was the world's largest exporter, it began to pay export tax rebates to selected coffee importers in 1965 and, by 1988, had paid rebates totaling $8 billion. Brazil explained these rebates as a mechanism to price disc...

  7. THE RISE AND DECLINE OF RENT-SEEKING ACTIVITY IN THE BRAZILIAN COFFEE SECTOR: LESSONS FROM THE IMPOSITION AND REMOVAL OF COFFEE EXPORT QUOTAS

    OpenAIRE

    Jarvis, Lovell S.

    2004-01-01

    Brazil, the world's largest coffee exporter, encouraged efforts in the 1960s to form the International Coffee Agreement (ICA), which restricted total coffee exports via country export quotas. The quotas led to significant domestic quota rents in producing countries. This paper analyzes the effects of rent seeking in Brazil. The Brazilian Institute of Coffee (IBC), which was responsible for coffee policy, was the focus of rent seeking. The paper models the policy instruments used by the IB...

  8. Challenges to the Transdisciplinarity of Climate Services: A Coffee Farming Case from Jamaica's Blue Mountains

    Science.gov (United States)

    Guido, Z.

    2017-12-01

    Climate information is heralded as helping to build adaptive capacity, improve resource management, and contribute to more effective risk management. However, decision makers often find it challenging to use climate information for reasons attributed to a disconnect between technical experts who produce the information and end users. Consequently, many climate service projects are now applying an end-to-end approach that links information users and producers in the design, development, and delivery of services. This collaboration confronts obstacles that can undermine the objectives of the project. Despite this, few studies in the burgeoning field of climate services have assessed the challenges. To address this gap, I provide a reflective account and analysis of the collaborative challenges experienced in an ongoing, complex four-year project developing climate services for small-scale coffee producers in Jamaica. The project has involved diverse activities, including social data collection, research and development of information tools, periodic engagement with coffee sector representatives, and community-based trainings. Contributions to the project were made routinely by 18 individuals who represent 9 institutions located in three countries. These individuals work for academic and governmental organizations and bring expertise in anthropology, plant pathology, and climatology, among others. In spanning diverse disciplines, large geographic distances, and different cultures, the project team has navigated challenges in communication, problem framing, organizational agendas, disciplinary integration, and project management. I contextualize these experiences within research on transdisciplinary and team science, and share some perspectives on strategies to lessen their impact.

  9. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Taxation and Mexican Coffee. The Porfiriato's Strategies for Promoting Coffee Production and Sale (1870-1910

    Directory of Open Access Journals (Sweden)

    Mabel M. Rodríguez Centeno

    2004-07-01

    Full Text Available The author analyzes how Mexican liberal policies for economic development combined with international markets in the late-Nineteenth century.  It focuses on the case of coffee because it clearly  shows  that  the  grower's main incentive  were  the high prices of this product in international markets. The analysis centers on the specific cases of Michoacan, Jalisco, Colima, Oaxaca, Chiapas  and Veracruz,  emphasizing  the central  role of federal and state government  support for expanding coffee production, through fiscal incentives and the development of transportation means.

  11. Use of Coffee Pulp and Minerals for Natural Soil Ameliorant

    Directory of Open Access Journals (Sweden)

    Pujiyanto Pujiyanto

    2007-05-01

    Full Text Available In coffee plantation, solid waste of coffee pulp is usually collected as heap nearby processing facilities for several months prior being used as compost. The practice is leading to the formation of odor and liquid which contaminate the environment. Experiments to evaluate the effect of natural soil ameliorant derived from coffee pulp and minerals were conducted at The Indonesian Coffee and Cocoa Research Institute in Jember, East Java. The experiments were intended to optimize the use of coffee pulp to support farming sustainability and minimize negative impacts of solid waste disposal originated from coffee cherry processing. Prior to applications, coffee pulp was hulled to organic paste. The paste was then mixed with 10% minerals (b/b. Composition of the minerals was 50% zeolite and 50% rock phosphate powder. The ameliorant was characterized for their physical and chemical properties. Agronomic tests were conducted on coffee and cocoa seedling. The experiments were arranged according to Randomized Completely Design with 2 factors, consisted of natural ameliorant and inorganic fertilizer respectively. Natural ameliorant derived from coffee pulp was applied at 6 levels: 0, 30, 60, 90, 120 and 150 g dry ameliorant/seedling of 3 kg soil, equivalent to 0, 1, 2, 3, 4 and 5% (b/b of ameliorant respectively. Inorganic fertilizer was applied at 2 levels: 0 and 2 g fertilizer/application of N-P-K compound fertilizer of 15-15-15 respectively. The inorganic fertilizer was applied 4 times during nursery of coffee and cocoa. The result of the experiment indicated that coffee pulp may be used as natural soil ameliorant. Composition of ameliorant of 90% coffee pulp and 10% of minerals has good physical and chemical characteristics for soil amelioration. The composition has high water holding capacity; cations exchange capacity, organic carbon and phosphorus contents which are favorable to increase soil capacity to support plant growth. Application of

  12. Effects of coffee management on deforestation rates and forest integrity.

    Science.gov (United States)

    Hylander, Kristoffer; Nemomissa, Sileshi; Delrue, Josefien; Enkosa, Woldeyohannes

    2013-10-01

    Knowledge about how forest margins are utilized can be crucial for a general understanding of changes in forest cover, forest structure, and biodiversity across landscapes. We studied forest-agriculture transitions in southwestern Ethiopia and hypothesized that the presence of coffee (Coffea arabica)decreases deforestation rates because of coffee's importance to local economies and its widespread occurrence in forests and forest margins. Using satellite images and elevation data, we compared changes in forest cover over 37 years (1973-2010) across elevations in 2 forest-agriculture mosaic landscapes (1100 km(2) around Bonga and 3000 km(2) in Goma-Gera). In the field in the Bonga area, we determined coffee cover and forest structure in 40 forest margins that differed in time since deforestation. Both the absolute and relative deforestation rates were lower at coffee-growing elevations compared with at higher elevations (-10/20% vs. -40/50% comparing relative rates at 1800 m asl and 2300-2500 m asl, respectively). Within the coffee-growing elevation, the proportion of sites with high coffee cover (>20%) was significantly higher in stable margins (42% of sites that had been in the same location for the entire period) than in recently changed margins (0% of sites where expansion of annual crops had changed the margin). Disturbance level and forest structure did not differ between sites with 30% or 3% coffee. However, a growing body of literature on gradients of coffee management in Ethiopia reports coffee's negative effects on abundances of forest-specialist species. Even if the presence of coffee slows down the conversion of forest to annual-crop agriculture, there is a risk that an intensification of coffee management will still threaten forest biodiversity, including the genetic diversity of wild coffee. Conservation policy for Ethiopian forests thus needs to develop strategies that acknowledge that forests without coffee production may have higher deforestation

  13. Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience

    Science.gov (United States)

    Fossey, Robyn; Kochan, David; Winkler, Erin; Pacyna, Joel E.; Olson, Janet; Thibodeau, Stephen; Connolly, John J.; Harr, Margaret; Behr, Meckenzie A.; Prows, Cynthia A.; Cobb, Beth; Myers, Melanie F.; Leslie, Nancy D.; Namjou-Khales, Bahram; Milo Rasouly, Hila; Wynn, Julia; Fedotov, Alexander; Chung, Wendy K.; Gharavi, Ali; Williams, Janet L.; Pais, Lynn; Holm, Ingrid; Aufox, Sharon; Smith, Maureen E.; Scrol, Aaron; Leppig, Kathleen; Jarvik, Gail P.; Wiesner, Georgia L.; Li, Rongling; Stroud, Mary; Smoller, Jordan W.; Sharp, Richard R.; Kullo, Iftikhar J.

    2018-01-01

    We examined the Institutional Review Board (IRB) process at 9 academic institutions in the electronic Medical Records and Genomics (eMERGE) Network, for proposed electronic health record-based genomic medicine studies, to identify common questions and concerns. Sequencing of 109 disease related genes and genotyping of 14 actionable variants is being performed in ~28,100 participants from the 9 sites. Pathogenic/likely pathogenic variants in actionable genes are being returned to study participants. We examined each site’s research protocols, informed-consent materials, and interactions with IRB staff. Research staff at each site completed questionnaires regarding their IRB interactions. The time to prepare protocols for IRB submission, number of revisions and time to approval ranged from 10–261 days, 0–11, and 11–90 days, respectively. IRB recommendations related to the readability of informed consent materials, specifying the full range of potential risks, providing options for receiving limited results or withdrawal, sharing of information with family members, and establishing the mechanisms to answer participant questions. IRBs reviewing studies that involve the return of results from genomic sequencing have a diverse array of concerns, and anticipating these concerns can help investigators to more effectively engage IRBs. PMID:29301385

  14. Projectables

    DEFF Research Database (Denmark)

    Rasmussen, Troels A.; Merritt, Timothy R.

    2017-01-01

    CNC cutting machines have become essential tools for designers and architects enabling rapid prototyping, model-building and production of high quality components. Designers often cut from new materials, discarding the irregularly shaped remains. We introduce ProjecTables, a visual augmented...... reality system for interactive packing of model parts onto sheet materials. ProjecTables enables designers to (re)use scrap materials for CNC cutting that would have been previously thrown away, at the same time supporting aesthetic choices related to wood grain, avoiding surface blemishes, and other...... relevant material properties. We conducted evaluations of ProjecTables with design students from Aarhus School of Architecture, demonstrating that participants could quickly and easily place and orient model parts reducing material waste. Contextual interviews and ideation sessions led to a deeper...

  15. An integrated framework for assessing vulnerability to climate change and developing adaptation strategies for coffee growing families in Mesoamerica.

    Directory of Open Access Journals (Sweden)

    María Baca

    Full Text Available The Mesoamerican region is considered to be one of the areas in the world most vulnerable to climate change. We developed a framework for quantifying the vulnerability of the livelihoods of coffee growers in Mesoamerica at regional and local levels and identify adaptation strategies. Following the Intergovernmental Panel on Climate Change (IPCC concepts, vulnerability was defined as the combination of exposure, sensitivity and adaptive capacity. To quantify exposure, changes in the climatic suitability for coffee and other crops were predicted through niche modelling based on historical climate data and locations of coffee growing areas from Mexico, Guatemala, El Salvador and Nicaragua. Future climate projections were generated from 19 Global Circulation Models. Focus groups were used to identify nine indicators of sensitivity and eleven indicators of adaptive capacity, which were evaluated through semi-structured interviews with 558 coffee producers. Exposure, sensitivity and adaptive capacity were then condensed into an index of vulnerability, and adaptation strategies were identified in participatory workshops. Models predict that all target countries will experience a decrease in climatic suitability for growing Arabica coffee, with highest suitability loss for El Salvador and lowest loss for Mexico. High vulnerability resulted from loss in climatic suitability for coffee production and high sensitivity through variability of yields and out-migration of the work force. This was combined with low adaptation capacity as evidenced by poor post harvest infrastructure and in some cases poor access to credit and low levels of social organization. Nevertheless, the specific contributors to vulnerability varied strongly among countries, municipalities and families making general trends difficult to identify. Flexible strategies for adaption are therefore needed. Families need the support of government and institutions specialized in impacts of

  16. A Preliminary Study on Rainfall Interception Loss and Water Yield Analysis on Arabica Coffee Plants in Central Aceh Regency, Indonesia

    Directory of Open Access Journals (Sweden)

    Reza Benara

    2012-12-01

    Full Text Available Rainfall interception loss from plants or trees can reduce a net rainfall as source of water yield. The amount of rainfall interception loss depends on kinds of plants and hydro-meteorological characteristics. Therefore, it is important to study rainfall interception loss such as from Arabica Coffee plantation which is as main agricultural commodity for Central Aceh Regency. In this study, rainfall interception loss from Arabica Coffee plants was studied in Kebet Village of Central Aceh Regency, Indonesia from January 20 to March 9, 2011. Arabica coffee plants used in this study was 15 years old, height of 1.5 m and canopy of 4.567 m2. Rainfall interception loss was determined based on water balance approach of daily rainfall, throughfall, and stemflow data. Empirical regression equation between rainfall interception loss and rainfall were adopted as a model to estimate rainfall interception loss from Arabica Coffee plantation, which the coefficient of correlation, r is 0.98. In water yield analysis, this formula was applied and founded that Arabica Coffee plants intercept 76% of annual rainfall or it leaved over annual net rainfall 24% of annual rainfall. Using this net rainfall, water yield produced from Paya Bener River which is the catchment area covered by Arabica Coffee plantation was analyzed in a planning of water supply project for water needs domestic of 3 sub-districts in Central Aceh Regency. Based on increasing population until year of 2025, the results showed that the water yield will be not enough from year of 2015. However, if the catchment area is covered by forest, the water yield is still enough until year of 2025

  17. A proposal to correct external effects in the coffee market: a tax on regular coffee and tea to subsidise the fair trade coffee

    OpenAIRE

    Galarraga, Ibon; Markandya, Anil

    2006-01-01

    This paper justifies the need to introduce a tax on regular coffee drinkers in the UK to subsidise the fair trade/organic coffee production. This policy will allow to take full account of the negative external effect of regular coffee production while internalising the positive effect of fair trade initiatives. Designing such a policy is possible and the benefits of it can be calculated. This paper shows how. Propuesta para corregir las externalidades en el mercado de café: un impuesto sobre ...

  18. Coffee consumption and coronary calcification - The Rotterdam Coronary Calcification Study

    NARCIS (Netherlands)

    van Woudenbergh, Geertruida J.; Vliegenthart, Rozemarijn; van Rooij, Frank J. A.; Hofman, Albert; Oudkerk, Matthijs; Witteman, Jacqueline C. M.; Geleijnse, Johanna M.

    Background-The role of coffee in the cardiovascular system is not yet clear. We examined the relation of coffee intake with coronary calcification in a population-based cohort. Methods and Results-The study involved 1570 older men and women without coronary heart disease who participated in the

  19. Coffee consumption and coronary calcification: The Rotterdam coronary calcification study

    NARCIS (Netherlands)

    G.J. van Woudenbergh (Geertruida); R. Vliegenthart (Rozemarijn); F.J.A. van Rooij (Frank); A. Hofman (Albert); M. Oudkerk (Matthijs); J.C.M. Witteman (Jacqueline); J.M. Geleijnse (Marianne)

    2008-01-01

    textabstractBACKGROUND - The role of coffee in the cardiovascular system is not yet clear. We examined the relation of coffee intake with coronary calcification in a population-based cohort. METHODS AND RESULTS - The study involved 1570 older men and women without coronary heart disease who

  20. Coffee Consumption and Coronary Calcification: The Rotterdam Coronary Calcification Study

    NARCIS (Netherlands)

    Woudenbergh, van G.J.; Vliegenthart, R.; Rooij, van F.J.A.; Hofman, A.; Oudkerk, M.; Witteman, J.C.M.; Geleijnse, J.M.

    2008-01-01

    Background¿ The role of coffee in the cardiovascular system is not yet clear. We examined the relation of coffee intake with coronary calcification in a population-based cohort. Methods and Results¿ The study involved 1570 older men and women without coronary heart disease who participated in the

  1. El Nino phenomenon, effects on the tree of coffee

    International Nuclear Information System (INIS)

    Jaramillo Robledo, Alvaro; Baldion Rincon, Jose Vicente; Guzman Martinez, Orlando

    1998-01-01

    El Nino phenomenon is manifested in the coffee by a deficiency of water in the plant, that which affects its normal development in its fruits; the author describes other alterations that affect the plants of coffee due to El Nino phenomenon

  2. Metabolomics as a research tool for coffee and cocoa

    NARCIS (Netherlands)

    Hall, R.D.

    2014-01-01

    Coffee and cocoa quality is of evergrowing importance and bemg able to determine the key quality aspects of different batches of coffee or cocoa and their products Is central to match1ng industrial processes with mcreas1ng consumer demand for specific quality attnbutes. But what do we actually mean

  3. Activity of some isoenzymatic systems in stored coffee grains

    Directory of Open Access Journals (Sweden)

    Reni Saath

    2014-02-01

    Full Text Available Considering the worldwide consumption of coffee, it is natural that throughout the history many people have dedicated the research to markers that contribute somehow on gauging its quality. This research aimed to evaluate the biochemical performance of arabica coffee during storage. Coffee in beans (natural and in parchment (pulped dried in concrete terrace and in dryer with heated air were packed in jute bags and stored in not controlled environmental conditions. Enzymatic activities of superoxide dismutase, catalase, peroxidase, polyphenoloxidase, esterase and lipoxygenase in coffee grains were evaluated at zero, three, six, nine and twelve months by means of electrophoresis. Independently of the drying method, the activity of isoenzymatic complexes highlighted deteriorative processes in stored grains of coffee. The treatments 60/40º C and 60º C used to reduce the water content imposed a greater stress condition, accelerated metabolism of natural coffee in the storage with decreased activity of defense mechanisms due to latent damage in these grains. Natural coffees are more sensible to high drying temperatures and its quality reduces faster than pulped coffee in the storage.

  4. Viscosity and Electrical Conductivity of Concentrated Solutions of Soluble Coffee

    Czech Academy of Sciences Publication Activity Database

    Sobolík, Václav; Žitný, R.; Tovčigrečko, Valentin; Delgado, M.; Allaf, K.

    2002-01-01

    Roč. 51, č. 2 (2002), s. 93-98 ISSN 0260-8774 Institutional research plan: CEZ:AV0Z4072921; CEZ:MSM 212200008 Keywords : coffee extract * soluble coffee * viscosity Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.085, year: 2002

  5. Practices of Third Wave Coffee : A Burundian Producer's Perspective

    NARCIS (Netherlands)

    Rosenberg, Lauren; Swilling, Mark; Vermeulen, Walter J.V.

    2018-01-01

    The relationship between coffee quality and sustainability is typically analysed using symbolic quality attributes, not material quality. This article provides a bottom-up perspective of Burundi's current competitive advantage in the global coffee market: material quality. The research agenda was

  6. Boosting climate resilience for Colombian coffee growers | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-09-29

    Sep 29, 2016 ... This will help farmers stabilize their livelihoods and be more competitive in the face of climate change, while securing the supply and quality of their coffee. Cenicafé researchers will also receive assistance from staff at the Tim Hortons Coffee Partnership, a farmer-support program established in 2005 to ...

  7. Coffee and gastrointestinal function: facts and fiction. A review

    NARCIS (Netherlands)

    Boekema, P. J.; Samsom, M.; van Berge Henegouwen, G. P.; Smout, A. J.

    1999-01-01

    BACKGROUND: Effects of coffee on the gastrointestinal system have been suggested by patients and the lay press, while doctors tend to discourage its consumption in some diseases. METHODS: The literature on the effects of coffee and caffeine on the gastrointestinal system is reviewed with emphasis on

  8. Let’s have a cup of coffee!

    DEFF Research Database (Denmark)

    Strøbæk, Pernille Solveig

    2013-01-01

    Coffee breaks are the main target in this investigation as the paper draws upon a qualitative focus group among Danish public family law caseworkers employed in a newly merged workplacesite. Coffee breaks were identified as the utmost important factor for the social and personal survival well-bei...

  9. A Poetry Coffee House: Creating a Cool Community of Writers

    Science.gov (United States)

    Ferguson, Kristen

    2017-01-01

    This article explores the sharing of writing through a coffee house--style poetry reading. Although this article focuses on a workshop and share activity used in a preservice teacher language arts and literacy course, it contains tips and ideas for implementing poetry coffee houses with elementary and secondary school students and preservice and…

  10. A better brew: Toward a sustainable coffee industry | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2011-01-31

    Jan 31, 2011 ... At the consumer end of the supply chain, coffee devotees pay a ... as roasters — that dominate the global coffee market have benefited from current ... (ICAs) have put in place supply management techniques, such as quotas, ...

  11. Quality and value chain analyses of Ethiopian coffee | Beshah ...

    African Journals Online (AJOL)

    The objective of this paper is to analyze the quality and value chain of Ethiopian coffee in a way to identify opportunities that maximize the benefits from the sector. First the Ethiopian coffee sector is overviewed and then analyzed qualitatively and quantitatively starting from the crop up to the cup based on data collected from ...

  12. A review of coffee wilt disease, Gibberella xylarioides (Fusarium ...

    African Journals Online (AJOL)

    Coffee is vital to the economy of East and Central Africa, providing a major source of foreign exchange earnings and as a cash crop, supporting the livelihood of millions of people who are involved in cultivation, processing, marketing, and export. Coffee is attacked by various disease-causing organisms such as fungi, ...

  13. Crop protection strategies for major diseases of cocoa, coffee and ...

    African Journals Online (AJOL)

    In Nigeria, crop protection measures that are cheap, simple, cost-effective and sustainable are desirable to combat Phytophthora pod rot (black pod) and cocoa swollen shoot virus diseases of cocoa, coffee leaf rust and coffee berry diseases, inflorescence blight disease of cashew in order to make farming profitable and ...

  14. Quantification and antibacterial activity of flavonoids in coffee samples

    African Journals Online (AJOL)

    Background: Flavonoids are the phenolic substances widely found in fruits, vegetables, grains, bark, roots, stems, flowers, tea and coffee. Methodology: In the current study quantity of flavonoids and antibacterial activities were determined in different coffee samples namely Nescafe classic, Nescafe gold, Nescafe martina, ...

  15. Uganda Coffee Supply Response and Export Demand: An ...

    African Journals Online (AJOL)

    Econometric methods were used to estimate the supply and demand functions for Uganda's coffee using time series data for the period 1971-91. Eight major importing countries for Uganda's coffee: U.S., U.K., Japan, France, Italy, Spain, Germany, and the Netherlands were considered in export demand analysis.

  16. Recent advances in coffee berry disease (CBD) control in Uganda

    African Journals Online (AJOL)

    Waller & Bridge) attacks arabic a coffee in most African arabica coffee growing countries. The disease was first recorded in Uganda in 1959 and surveys on the disease indicated that up to 50% crop losses were being incurred. Most of the ...

  17. Institutions in the Mexican coffee sector : changes and responses

    NARCIS (Netherlands)

    Rodriguez Padron, B.

    2012-01-01

    Keywords: Cooperation, contract arrangements, traders´ performance, market uncertainty, diversification, coffee, Mexico.

    The main aim of this thesis is to investigate the institutional environment prevailing in the Mexican coffee sector and its effect on the producers, traders and

  18. Selection of Arabica coffee types resistant to coffee berry disease in Ethiopia

    NARCIS (Netherlands)

    Graaff, van der N.A.

    1981-01-01

    Descriptive part. A review is given of: the importance of Coffea arabica to Ethiopia; coffee research; habitus, origin and cultivation of C. arabica ; theoretical aspects of resistance and its implications for the system C.

  19. Whitefly (Bemisia tabaci genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous cDNA libraries

    Directory of Open Access Journals (Sweden)

    Czosnek Henryk

    2006-04-01

    of eggs. Conclusion This is the first functional genomics project involving a hemipteran (Homopteran insect from the subtropics/tropics. The B. tabaci sequence database now provides an important tool to initiate identification of whitefly genes involved in development, behaviour, and B. tabaci-mediated begomovirus transmission.

  20. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  1. National Human Genome Research Institute

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  2. TRACKING THE PROCESSES OF MELANODIN FORMATION IN COFFEE

    Directory of Open Access Journals (Sweden)

    Snezhana Ivanova

    2017-06-01

    Full Text Available Melanoidins are high molecular brown colored substances and products of sugar-amine reaction of Maillard. They are formed during roasting a green coffee beans under different thermal regimes of heat treatment. In the technological production of different types coffee beverages, the coffee powder is subjected to after-heat treatment. In these additional operations again become active processes of melanoidin formation and their changing their structures. This is changes of the Melanoidins have different effects on human health. It is therefore important to know their chemical structures and changes. Previous studies have shown that polysaccharides, proteins and chlorogenic acids are included in the formation of these melanoidins. However, the precise structures of coffee melanoidins and mechanisms involved in the formation are not yet clarified. This article systematize available information and provides an overview of research obtained so far on the structure of coffee melanoidins and mechanisms of their formation and potential health effects.

  3. Physiological measurements of coffee young plants coexisting with sourgrass

    Directory of Open Access Journals (Sweden)

    Pedro Luis da Costa Aguiar Alves

    2012-03-01

    Full Text Available Coffee is an important crop planted in Brazil and commonly infested by sourgrass plants. Crescent densities of sourgrass growing with coffee young plants were maintained up to weed full flowering when physiological measurements were performed in the crop to evaluate photosynthetic coffee plant responses to increasing of weed competition. Experiments were arranged in a completely randomized design with seven replicates. The concentration of CO2 within the leaf, the leaf transpiration, the stomatal conductance, the CO2 assimilation rate, and the ratio Fv/Fm of coffee plants were not affected by increasing of sourgrass density. On the other hand, relative content of total chlorophyll was reduced by 13.9% in the density of 8 sourgrass plants. Gas exchange and fluorescence of chlorophyll of young coffee plants were not dependent on increasing of the intensity of competition while an opposite response occurred for chlorophyll content.

  4. The role of dissolved cations in coffee extraction.

    Science.gov (United States)

    Hendon, Christopher H; Colonna-Dashwood, Lesley; Colonna-Dashwood, Maxwell

    2014-05-28

    The flavorsome compounds in coffee beans exist in the form of aprotic charge neutral species, as well as a collection of acids and conjugate salts. The dissolution and extraction of these organic molecules is a process dependent on the dissolved mineral content of the water. It is known that different rates and compositions of coffee extraction are achieved through the control of the water "impurities", Na(+), Mg(2+), and Ca(2+), which coordinate to nucleophilic motifs in coffee. Using density functional theory, we quantify the thermodynamic binding energies of five familiar coffee-contained acids, caffeine, and a representative flavor component, eugenol. From this, we provide insight into the mechanism and ideal mineral composition of water for extraction of flavorsome compounds in coffee.

  5. Isotopes as Tracers of the Hawaiian Coffee-Producing Regions

    Science.gov (United States)

    2011-01-01

    Green coffee bean isotopes have been used to trace the effects of different climatic and geological characteristics associated with the Hawaii islands. Isotope ratio mass spectrometry (IRMS) and inductively coupled plasma mass spectrometry ((MC)-ICP-SFMS and ICP-QMS) were applied to determine the isotopic composition of carbon (δ13C), nitrogen (δ15N), sulfur (δ34S), and oxygen (δ18O), the isotope abundance of strontium (87Sr/86Sr), and the concentrations of 30 different elements in 47 green coffees. The coffees were produced in five Hawaii regions: Hawaii, Kauai, Maui, Molokai, and Oahu. Results indicate that coffee plant seed isotopes reflect interactions between the coffee plant and the local environment. Accordingly, the obtained analytical fingerprinting could be used to discriminate between the different Hawaii regions studied. PMID:21838232

  6. Sound of a cup with and without instant coffee

    Science.gov (United States)

    Morrison, Andrew; Rossing, Thomas D.

    2002-05-01

    An empty coffee cup, like an ancient Chinese two-tone bell, emits two distinctly different tones, depending upon where it is tapped. When it is filled with hot water, and some instant coffee is added, however, a whole new set of sounds is heard when the cup is tapped. The pitch rises an octave or more as the foam clears due to the dramatic change in the speed of sound in the bubble-filled liquid. A similar, but smaller, effect was noted in beer by Bragg [The World of Sound (1968)] and in hot chocolate by Crawford [Am. J. Phys. (1982)]. We describe the modes of vibration in a coffee cup and the sound emitted by a coffee cup as filled with instant coffee as the bubble density changes.

  7. VALUACIÓN BIOÉTICA DEL PROYECTO "GENOMA HUMANO" AVALIAÇÃO BIOÉTICA DO PROJETO "GENOME HUMANO" BIOETHICAL VALIDATION OF THE "HUMAN GENOME PROJECT"

    Directory of Open Access Journals (Sweden)

    Leonides Santos y Vargas

    2002-01-01

    Full Text Available Este texto propone una serie de reflexiones que se desprenden de los recientes progresos acaecidos en las investigaciones sobre el Proyecto del Genoma Humano, los cuales conducen al fortalecimiento acelerado de conocimientos y tecnologías biomédicas. Las nuevas afirmaciones sobre la naturaleza biológica de la especie humana, legitimadas por estos nuevos progresos, posibilitan reexaminar explicaciones mitológicas y metafísicas acumuladas desde hace milenios, en el contexto de una nueva antropología filosófica. Los progresos en las intervenciones de la ciencia médica sobre la salud y la calidad de la vida humana permiten evaluar nuevamente la legitimidad de una serie de nuevas posibilidades biomédicas. Es así como este texto aborda también, de manera particular, la temática de la clonación y de sus distintos aspectos económicos y políticosEste texto propõe reflexões sobre os recentes progressos apresentados pelas investigações decorrentes do Projeto Genoma Humano que conduzem a sólidos conhecimentos em tecnologias biomedicas. As novas informações sobre a natureza da espécie humana obtidas por esses avanços permitem reexaminar explicações mitológicas e metafísicas acumuladas por milênios através da ótica da antropologia filosófica. Os progressos nas intervenções da ciência sobre a saúde e qualidade de vida humana permitem avaliar a legitimidade de uma série de proposições biomédicas. Nesse sentido, o presente texto apresenta reflexões sobre o tema da clonagem e seus diferentes aspectos econômicos e políticosThis text proposes a number of reflections that issue fron the recent advancements that have taken place in investigations on the Human Genoma Project, which lead to the accelerated reinforcement of biomedical knowledge and technologies. The new statements upon human species’ biological nature, legitimated by these new progress, allow us to reexamine the mythological and metaphysical explanations

  8. Coffee Consumption and the Risk of Colorectal Cancer.

    Science.gov (United States)

    Schmit, Stephanie L; Rennert, Hedy S; Rennert, Gad; Gruber, Stephen B

    2016-04-01

    Coffee contains several bioactive compounds relevant to colon physiology. Although coffee intake is a proposed protective factor for colorectal cancer, current evidence remains inconclusive. We investigated the association between coffee consumption and risk of colorectal cancer in 5,145 cases and 4,097 controls from the Molecular Epidemiology of Colorectal Cancer (MECC) study, a population-based case-control study in northern Israel. We also examined this association by type of coffee, by cancer site (colon and rectum), and by ethnic subgroup (Ashkenazi Jews, Sephardi Jews, and Arabs). Coffee data were collected by interview using a validated, semi-quantitative food frequency questionnaire. Coffee consumption was associated with 26% lower odds of developing colorectal cancer [OR (drinkers vs. non-drinkers), 0.74; 95% confidence interval (CI), 0.64-0.86; P consumption alone (OR, 0.82; 95% CI, 0.68-0.99; P = 0.04) and for boiled coffee (OR, 0.82; 95% CI, 0.71-0.94; P = 0.004). Increasing consumption of coffee was associated with lower odds of developing colorectal cancer. Compared with 2.5 servings/day (OR, 0.46; 95% CI, 0.39-0.54; P colorectal cancer (Ptrend cancers. Coffee consumption may be inversely associated with risk of colorectal cancer in a dose-response manner. Global coffee consumption patterns suggest potential health benefits of the beverage for reducing the risk of colorectal cancer. Cancer Epidemiol Biomarkers Prev; 25(4); 634-9. ©2016 AACR. ©2016 American Association for Cancer Research.

  9. Effects of tea and coffee on cardiovascular disease risk.

    Science.gov (United States)

    Bøhn, Siv K; Ward, Natalie C; Hodgson, Jonathan M; Croft, Kevin D

    2012-06-01

    Tea and coffee have been associated with risk of cardiovascular disease (CVD), both positively and negatively. Epidemiological data suggest that black and green tea may reduce the risk of both coronary heart disease and stroke by between 10 and 20%. Experimental and clinical trial data generally indicate either neutral or beneficial effects on risk factors and pathways linked to the development of CVD. Controversy still exists regarding the effects of coffee, where there have been concerns regarding associations with hypercholesterolaemia, hypertension and myocardial infarction. However, long term moderate intake of coffee is not associated with detrimental effects in healthy individuals and may even protect against the risk of developing type 2 diabetes. The detrimental effects of coffee may be associated with the acute pressor effects, most likely due to caffeine at high daily intakes, and lipids from boiled coffee can contribute to raised serum cholesterol. Genetic polymorphisms in enzymes involved in uptake, metabolism and excretion of tea and coffee compounds are also associated with differential biological effects. Potential mechanisms by which tea and coffee phytochemicals can exert effects for CVD protection include the regulation of vascular tone through effects on endothelial function, improved glucose metabolism, increased reverse cholesterol transport and inhibition of foam cell formation, inhibition of oxidative stress, immunomodulation and effects on platelet function (adhesion and activation, aggregation and clotting). The phytochemical compounds in tea and coffee and their metabolites are suggested to influence protective endogenous pathways by modulation of gene-expression. It is not known exactly which compounds are responsible for the suggestive protective effects of tea and coffee. Although many biologically active compounds have been identified with known biological effects, tea and coffee contain many unidentified compounds with potential

  10. Predation by Flat Bark Beetles (Coleoptera: Silvanidae and Laemophloeidae) on Coffee Berry Borer (Coleoptera: Curculionidae) in Hawaii coffee

    Science.gov (United States)

    Coffee berry borer(CBB), Hypothenemus hampei, is a serious pest of coffee worldwide and a new invasive pest in Hawaii. Adult flat bark beetles, mainly Leptophloeus sp.(75%) and Cathartus quadricollis(21%) (Coleoptera: Laemophloeidae and Silvanidae, respectively), were found feeding in CBB-infested c...

  11. [Spectroscopic methods applied to component determination and species identification for coffee].

    Science.gov (United States)

    Chen, Hua-zhou; Xu, Li-li; Qin, Qiang

    2014-06-01

    Spectroscopic analysis was applied to the determination of the nutrient quality of ground, instant and chicory coffees. By using inductively coupled plasma atomic emission spectrometry (ICP-ES), nine mineral elements were determined in solid coffee samples. Caffeine was determined by ultraviolet (UV) spectrometry and organic matter was investigated by Fourier transform infrared (FTIR) spectroscopy. Oxidation-reduction titration was utilized for measuring the oxalate. The differences between ground coffee and instant coffee was identified on the basis of the contents of caffeine, oxalate and mineral elements. Experimental evidence showed that, caffeine in instant coffee was 2-3 times higher than in ground coffee. Oxalate in instant coffee was significantly higher in ground coffee. Mineral elements of Mg, P and Zn in ground coffee is lower than in instant coffee, while Cu is several times higher. The mineral content in chicory coffee is overall lower than the instant coffee. In addition, we determined the content of Ti for different types of coffees, and simultaneously detected the elements of Cu, Ti and Zn in chicory coffee. As a fast detection technique, FTIR spectroscopy has the potential of detecting the differences between ground coffee and instant coffee, and is able to verify the presence of caffeine and oxalate.

  12. The cholesterol-raising factor from boiled coffee does not pass a paper filter.

    NARCIS (Netherlands)

    Dusseldorp, van M.; Katan, M.B.; Vliet, van T.; Demacker, P.N.M.; Stalenhoef, A.F.H.

    1991-01-01

    Previous studies have indicated that consumption of boiled coffee raises total and low density lipoprotein (LDL) cholesterol, whereas drip-filtered coffee does not. We have tested the effect on serum lipids of consumed coffee that was first boiled and then filtered through commercial paper coffee

  13. Boron levels in soils cropped to coffee and their relationships to ...

    African Journals Online (AJOL)

    Studies on boron levels in soils cropped to coffee were carried out in Ghana due to widespread reports on boron deficiency in soils of some coffee producing countries. Leaves and soils were sampled from Cocobod coffee plantations at Bogoso, Suhuma, Manso-Mim, Bunso and Bepong, which represent the main coffee ...

  14. The dynamic of the “Coffee Quality Paraná” contest in the production of specialty coffees

    Directory of Open Access Journals (Sweden)

    Lorian Voigt-Gair

    2013-12-01

    Full Text Available In Paraná, the concentration of efforts of various organizations have collaborated to improve the image of coffee. This work aims to study the coffee samples, through the sensory attributes scored in the “Test Cup” Contest of “Coffee Quality Paraná” from 2004 to 2009 and to prove the qualification of rural extension technicians and producers in order to obtain a differentiated with high quality product, linked to the methodology of marketing strategy. The study was conducted with 570 samples from 55 municipalities and analyzed in state steps of this contest. It was concluded that the methodology used in the Contest “Coffee Quality Paraná” encourages constant improvement and disseminates technical and scientific innovations in various links in the productive chain, having as the final result the increasing of the amount of coffee produced in Paraná with excellent quality drink.

  15. Fiscal 1998 achievement report. Industrial technology research and development project. (Strategic human cDNA genome application technology development); 1998 nendo senryakuteki hito cDNA genome oyo gijutsu kaihatsu seika hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    A human genome related project named above was started, and studies were conducted for base sequence determination and function analysis for approximately 10,000 kinds of full-length or long-chain human cDNA clones owned by research organizations in this country. The Institute of Medical Science of University of Tokyo and Helix Research Institute dealt with a full-length human cDNA library constructed by oligo-capping, and determined the base sequences of all specimens in the library. The Kazusa DNA Research Institute determined partial sequences for long-chain clones which are not shorter than 4-5kbp, and determined entire sequences for some bases. The obtained base sequence data were subjected to homology analysis, the base sequences were converted into amino acid sequences, and functions of proteins were predicted. In the analysis of gene functions, ATAC-PCR (adaptor tagged competitive-polymerase chain reaction) was applied to the clones covered by this project, and a database was prepared by use of the results of analyses of frequency-related information. For the preparation of a comprehensive gene expression profile, technologies for cDNA microarray construction were established. (NEDO)

  16. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset.

    Science.gov (United States)

    Ignatieva, Elena V; Levitsky, Victor G; Yudin, Nikolay S; Moshkin, Mikhail P; Kolchanov, Nikolay A

    2014-01-01

    The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors), which are activated by olfactory stimuli (ligands). Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter [a region of DNA about 100-1000 base pairs long located upstream of the transcription start site (TSS)]. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.). In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  17. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset

    Directory of Open Access Journals (Sweden)

    Elena V. Ignatieva

    2014-03-01

    Full Text Available The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors, which are activated by olfactory stimuli (ligands. Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter (a region of DNA about 100–1000 base pairs long located upstream of the transcription start site. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.. In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  18. Social implications of the Human Genome Project: Policy roundtable series and journals. Final progress report, March 15, 2001 - March 15, 2002

    Energy Technology Data Exchange (ETDEWEB)

    Seiguer, Erica

    2002-12-30

    This report reflects the activities of the Harvard Health Caucus at Harvard Medical School that were supported, in part, by the Department of Energy. The following policy roundtables and panels were held: Spring 2001 Policy Roundtable Series: The social implications of the Human Genome Project; Spring 2002 Policy Roundtable Series: Managing globalization to improve health; 13 February 2002 Keynote Address: The globalization of health; 25 February 2002 Healthier or Wealthier: Which comes first in the new global era?; 28 February 2002 The crisis of neglected diseases: Creating R&D incentives for diseases of developing countries; 7 March 2002 Health care education in the developing world: Bridging global and local health care practices; 20 March 2002 Building a legal framework for global health: How can the US and UN work to reduce global disparities?; 25 April 2002 The role of mass media and tobacco control efforts. Caucus organizational information is also included.

  19. Coffee as a risk factor for cardiovascular diseases. A literature study

    OpenAIRE

    Rijal, Prashamsa

    2016-01-01

    Coffee is the most widely drunk beverage around the world, especially within Scandinavia.However, there have been conflicting evidence on the consumption of coffee as a risk factor for cardiovascular diseases. The importance to explore the full effects of coffee related health problems, including brewing methods, is mainly due to the high consumption rate of coffee around the world. In the context of public health, knowing how a popular beverage such as coffee effects the cardiovascular risks...

  20. Environmental-economic benefits and trade-offs on sustainably certified coffee farms

    OpenAIRE

    Haggar, Jeremy; Soto, Gabriela; Casanoves, Fernando; de Melo Virginio, Elias

    2017-01-01

    Coffee with diverse shade trees is recognized as conserving greater biodiversity than more intensive production methods. Sustainable certification has been proposed as an incentive to conserve shade grown coffee. With 40% of global coffee production certified as sustainable, evidence is needed to demonstrate whether certification supports the environmental benefits of shade coffee. Environmen-tal and economic data were taken from 278 coffee farms in Nicaragua divided between non-certified and...

  1. DNA pyrosequencing evidence for large diversity differences between natural and managed coffee mycorrhizal fungal communities

    OpenAIRE

    De Beenhouwer , Matthias; Muleta , Diriba; Peeters , Bram; Van Geel , Maarten; Lievens , Bart; Honnay , Olivier

    2015-01-01

    International audience; Arabica coffee is a major agricultural commodity worldwide, representing 60 % of the world’s coffee production. Arabica coffee is cultivated in more than 36 countries and is a key cash crop for many developing countries. Despite the coffee’s huge economic importance, there is very limited knowledge on the association of arbuscular mycorrhizal fungi with coffee roots. Therefore, we assessed the mycorrhizal diversity and community composition in Arabica coffee (Coffea ar...

  2. Properties of dune sand concrete containing coffee waste

    Directory of Open Access Journals (Sweden)

    Mohamed Guendouz

    2018-01-01

    Full Text Available In the last years, an increase of coffee beverages consumption has been observed all over the world; and its consumption increases the waste coffee grounds which will become an environmental problems. Recycling of this waste to produce new materials like sand concrete appears as one of the best solutions for reduces the problem of pollution. This work aims to study the possibility of recycling waste coffee grounds (Spent Coffee Grounds (SCG as a fine aggregate by replacing the sand in the manufacturing of dune sand concrete. For this; sand concrete mixes were prepared with substitution of sand with the spent coffee grounds waste at different percentage (0%, 5%, 10%, 15% and 20% by volume of the sand in order to study the influence of this wastes on physical (Workability, bulk density and porosity, mechanical (compressive and flexural strength and Thermal (Thermal conductivity and thermal diffusivity properties of dune sand concrete. The results showed that the use of spent coffee grounds waste as partial replacement of natural sand contributes to reduce workability, bulk density and mechanical strength of sand concrete mixes with an increase on its porosity. However, the thermal characteristics are improved and especially for a level of 15% and 20% of substitution. So, it is possible to obtain an insulating material which can be used in the various types of structural components. This study ensures that reusing of waste coffee grounds in dune sand concrete gives a positive approach to reduce the cost of materials and solve some environmental problems.

  3. Habitual coffee consumption enhances attention and vigilance in hemodialysis patients.

    Science.gov (United States)

    Nikić, Petar M; Andrić, Branislav R; Stojimirović, Biljana B; Trbojevic-Stanković, Jasna; Bukumirić, Zoran

    2014-01-01

    Coffee drinking is the main source of caffeine intake among adult population in the western world. It has been reported that low to moderate caffeine intake has beneficial effect on alertness and cognitive functions in healthy subjects. The aim of this study is to evaluate the impact of habitual coffee consumption on cognitive function in hemodialysis patients. In a cross-sectional study, 86 patients from a single-dialysis centre underwent assessment by the Montreal Cognitive Assessment tool and evaluation for symptoms of fatigue, mood, and sleep disorders by well-validated questionnaires. The habitual coffee use and the average daily caffeine intake were estimated by participants' response to a dietary questionnaire. Sixty-seven subjects (78%) consumed black coffee daily, mostly in low to moderate dose. Cognitive impairment was found in three-quarters of tested patients. Normal mental performance was more often in habitual coffee users (25% versus 16%). Regular coffee drinkers achieved higher mean scores on all tested cognitive domains, but a significant positive correlation was found only for items that measure attention and concentration (P = 0.024). Moderate caffeine intake by habitual coffee consumption could have beneficial impact on cognitive function in hemodialysis patients due to selective enhancement of attention and vigilance.

  4. Coffee and Depression: A Short Review of Literature.

    Science.gov (United States)

    Tenore, Gian Carlo; Daglia, Maria; Orlando, Valentina; D'Urso, Emanuela; Saadat, Seyed Hassan; Novellino, Ettore; Nabavi, Seyed Fazel; Nabavi, Seyed Mohammad

    2015-01-01

    Coffee is among the most widespread and healthiest beverages in the world. It is known to be a highly rich source of biologically active natural metabolites which possess therapeutic effects (i.e. caffeine) and functional properties (i.e. chlorogenic acids). Therefore, coffee can be considered a drink which has different positive effects on human health such as cardioprotective, neuroprotective, hepatoprotective, nephroprotective, etc. However, heavy coffee consumption may be related to some unpleasant symptoms, mainly anxiety, headache, increased blood pressure, nausea, and restlessness. During the past two decades, several studies have indicated that there is a close correlation between consumption of coffee and incidence of depression. In addition, phytochemical studies showed that caffeine is the main responsible constituent for antidepressant effects of coffee through multiple molecular mechanisms. The aim of the present paper was to collect the latest literature data (from 1984 to 2014) on the positive and negative impacts of coffee consumption on the major depressive disorders and to clarify the role of bioactive constituents of coffee in the related different clinical trials. To the best of our knowledge, this the first review on this topic.

  5. Coffee and tea: perks for health and longevity?

    Science.gov (United States)

    Bhatti, Salman K; O'Keefe, James H; Lavie, Carl J

    2013-11-01

    Tea and coffee, after water, are the most commonly consumed beverages in the world and are the top sources of caffeine and antioxidant polyphenols in the American diet. The purpose of this review is to assess the health effects of chronic tea and/or coffee consumption. Tea consumption, especially green tea, is associated with significantly reduced risks for stroke, diabetes and depression, and improved levels of glucose, cholesterol, abdominal obesity and blood pressure. Habitual coffee consumption in large epidemiological studies is associated with reduced mortality, both for all-cause and cardiovascular deaths. In addition, coffee intake is associated with risks of heart failure, stroke, diabetes mellitus and some cancers in an inverse dose-dependent fashion. Surprisingly, coffee is associated with neutral to reduced risks for both atrial and ventricular arrhythmias. However, caffeine at high doses can increase anxiety, insomnia, calcium loss and possibly the risk of fractures. Coffee and tea can generally be recommended as health-promoting additions to an adult diet. Adequate dietary calcium intake may be particularly important for tea and coffee drinkers.

  6. Habitual Coffee Consumption Enhances Attention and Vigilance in Hemodialysis Patients

    Directory of Open Access Journals (Sweden)

    Petar M. Nikić

    2014-01-01

    Full Text Available Objective. Coffee drinking is the main source of caffeine intake among adult population in the western world. It has been reported that low to moderate caffeine intake has beneficial effect on alertness and cognitive functions in healthy subjects. The aim of this study is to evaluate the impact of habitual coffee consumption on cognitive function in hemodialysis patients. Methods. In a cross-sectional study, 86 patients from a single-dialysis centre underwent assessment by the Montreal Cognitive Assessment tool and evaluation for symptoms of fatigue, mood, and sleep disorders by well-validated questionnaires. The habitual coffee use and the average daily caffeine intake were estimated by participants’ response to a dietary questionnaire. Results. Sixty-seven subjects (78% consumed black coffee daily, mostly in low to moderate dose. Cognitive impairment was found in three-quarters of tested patients. Normal mental performance was more often in habitual coffee users (25% versus 16%. Regular coffee drinkers achieved higher mean scores on all tested cognitive domains, but a significant positive correlation was found only for items that measure attention and concentration (P=0.024. Conclusions. Moderate caffeine intake by habitual coffee consumption could have beneficial impact on cognitive function in hemodialysis patients due to selective enhancement of attention and vigilance.

  7. The inclusion of coffee in commercial layer diets

    Directory of Open Access Journals (Sweden)

    LR Mendes

    2013-06-01

    Full Text Available This experiment aimed at evaluating the effect of the dietary inclusion of caffeinated and decaffeinated coffee on the performance and internal and external egg quality of commercial layers. One hundred and twenty 25-week-old Hy-line Brown layers, with 1575 ± 91 average body weight, were distributed according to a completely randomized experimental design with three treatments (control, 1.2% caffeinated coffee, or 1.2% decaffeinated coffee of five replicates of eight birds each. The inclusion of 1.2% caffeinated coffee was calculated to supply 6mg caffeine per kg body weight, which is considered a moderate dose. The applied treatments did not influence (p>0.05 feed intake, egg production, egg weight, egg mass, feed conversion ratio, Haugh units, yolk color or albumen and yolk percentages. The eggs of hens fed 1.2% caffeinated coffee presented lower (p<0.05 eggshell thickness and egg specific density. The eggs of layers fed 1.2% caffeinated coffee tended (p=0.0637 to present lower eggshell percentage. It was concluded that feeding caffeinated coffee to commercial layers does not affect their performance or internal egg quality; however, eggshell quality is impaired.

  8. Soil phosphorus dynamics and availability and irrigated coffee yield

    Directory of Open Access Journals (Sweden)

    Thiago Henrique Pereira Reis

    2011-04-01

    Full Text Available Research data have demonstrated that the P demand of coffee (Coffea arabica L. is similar to that of short-cycle crops. In this context, the objective of this study was to evaluate the influence of annual P fertilization on the soil P status by the quantification of labile, moderately labile, low-labile, and total P fractions, associating them to coffee yield. The experiment was installed in a typical dystrophic Red Latosol (Oxisol cultivated with irrigated coffee annually fertilized with triple superphosphate at rates of 0, 50, 100, 200, and 400 kg ha-1 P2O5. Phosphorus fractions were determined in two soil layers: 0-10 and 10-20 cm. The P leaf contents and coffee yield in 2008 were also evaluated. The irrigated coffee responded to phosphate fertilization in the production phase with gains of up to 138 % in coffee yield by the application of 400 kg ha-1 P2O5. Coffee leaf P contents increased with P applications and stabilized around 1.98 g kg-1, at rates of 270 kg ha-1 P2O5 and higher. Soil P application caused, in general, an increase in bioavailable P fractions, which constitute the main soil P reservoir.

  9. A comprehensive review on utilization of wastewater from coffee processing.

    Science.gov (United States)

    Rattan, Supriya; Parande, A K; Nagaraju, V D; Ghiwari, Girish K

    2015-05-01

    The coffee processing industry is one of the major agro-based industries contributing significantly in international and national growth. Coffee fruits are processed by two methods, wet and dry process. In wet processing, coffee fruits generate enormous quantities of high strength wastewater requiring systematic treatment prior to disposal. Different method approach is used to treat the wastewater. Many researchers have attempted to assess the efficiency of batch aeration as posttreatment of coffee processing wastewater from an upflow anaerobic hybrid reactor (UAHR)-continuous and intermittent aeration system. However, wet coffee processing requires a high degree of processing know-how and produces large amounts of effluents which have the potential to damage the environment. Characteristics of wastewater from coffee processing has a biological oxygen demand (BOD) of up to 20,000 mg/l and a chemical oxygen demand (COD) of up to 50,000 mg/l as well as the acidity of pH below 4. In this review paper, various methods are discussed to treat coffee processing wastewaters; the constitution of wastewater is presented and the technical solutions for wastewater treatment are discussed.

  10. Bird communities in sun and shade coffee farms in Kenya

    Directory of Open Access Journals (Sweden)

    C. Smith

    2015-07-01

    Full Text Available Agricultural expansion to meet rising crop demand is one of the greatest threats to terrestrial biodiversity. Coffee, one of the most valuable trade items in tropical countries, can provide both economic livelihood and wildlife habitat. Previous work, conducted primarily on Neotropical coffee farms, indicates that birds are generally more abundant and diverse in farms with a canopy of shade trees, though regional variation exists. To date, few studies have examined birds on coffee farms in Africa, which contains 20% of the world’s coffee acreage. We studied differences in the bird communities between sun and shade monoculture coffee in central Kenya, and we examined effects of vegetation on bird abundance and diversity. Sun coffee had higher species richness and abundances of all major guilds (omnivores, insectivores, and granivores, and showed low community similarity to shade. Unlike findings from the Neotropics, canopy cover appeared to have a negative influence on all guilds, while understory volume of weeds increased bird abundance and species richness with a similar magnitude as canopy cover. These differences highlight the need for further studies in the general East Africa region with a wider variety of shade coffee systems.

  11. Espresso coffees, caffeine and chlorogenic acid intake: potential health implications.

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    Crozier, Thomas W M; Stalmach, Angelique; Lean, Michael E J; Crozier, Alan

    2012-01-01

    HPLC analysis of 20 commercial espresso coffees revealed 6-fold differences in caffeine levels, a 17-fold range of caffeoylquinic acid contents, and 4-fold differences in the caffeoylquinic acid : caffeine ratio. These variations reflect differences in batch-to-batch bean composition, possible blending of arabica with robusta beans, as well as roasting and grinding procedures, but the predominant factor is likely to be the amount of beans used in the coffee-making/barista processes. The most caffeine in a single espresso was 322 mg and a further three contained >200 mg, exceeding the 200 mg day(-1) upper limit recommended during pregnancy by the UK Food Standards Agency. This snap-shot of high-street expresso coffees suggests the published assumption that a cup of strong coffee contains 50 mg caffeine may be misleading. Consumers at risk of toxicity, including pregnant women, children and those with liver disease, may unknowingly ingest excessive caffeine from a single cup of espresso coffee. As many coffee houses prepare larger volume coffees, such as Latte and Cappuccino, by dilution of a single or double shot of expresso, further study on these products is warranted. New data are needed to provide informative labelling, with attention to bean variety, preparation, and barista methods.

  12. Coffee consumption modulates inflammatory processes in an individual fashion.

    Science.gov (United States)

    Muqaku, Besnik; Tahir, Ammar; Klepeisz, Philip; Bileck, Andrea; Kreutz, Dominique; Mayer, Rupert L; Meier, Samuel M; Gerner, Marlene; Schmetterer, Klaus; Gerner, Christopher

    2016-12-01

    Anti-inflammatory effects of coffee consumption have been reported to be caused by caffeine and adenosine receptor signaling. However, contradictory effects have been observed. Many kinds of chronic diseases are linked to inflammation; therefore a profound understanding of potential effects of coffee consumption is desirable. We performed ex vivo experiments with eight individuals investigating peripheral blood mononuclear cells isolated from venous blood before and after coffee consumption, as well as in vitro experiments applying caffeine on isolated cells. After in vitro inflammatory stimulation of the cells, released cytokines, chemokines, and eicosanoids were determined and quantified using targeted mass spectrometric methods. Remarkably, the release of inflammation mediators IL6, IL8, GROA, CXCL2, CXCL5 as well as PGA2, PGD2, prostaglandin E2 (PGE2), LTC4, LTE4, and 15S-HETE was significantly affected after coffee consumption. While in several individuals coffee consumption or caffeine treatment caused significant downregulation of most inflammation mediators, in other healthy individuals exactly the opposite effects were observed. Ruling out age, sex, coffee consumption habits, the metabolic kinetics of caffeine in blood and the individual amount of regulatory T cells or CD39 expression as predictive parameters, we demonstrated here that coffee consumption may have significant pro- or anti-inflammatory effects in an individual fashion. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Molecular Bases Underlying the Hepatoprotective Effects of Coffee

    Directory of Open Access Journals (Sweden)

    Federico Salomone

    2017-01-01

    Full Text Available Coffee is the most consumed beverage worldwide. Epidemiological studies with prospective cohorts showed that coffee intake is associated with reduced cardiovascular and all-cause mortality independently of caffeine content. Cohort and case-control studies reported an inverse association between coffee consumption and the degree of liver fibrosis as well as the development of liver cancer. Furthermore, the beneficial effects of coffee have been recently confirmed by large meta-analyses. In the last two decades, various in vitro and in vivo studies evaluated the molecular determinants for the hepatoprotective effects of coffee. In the present article, we aimed to critically review experimental evidence regarding the active components and the molecular bases underlying the beneficial role of coffee against chronic liver diseases. Almost all studies highlighted the beneficial effects of this beverage against liver fibrosis with the most solid results indicating a pivot role for both caffeine and chlorogenic acids. In particular, in experimental models of fibrosis, caffeine was shown to inhibit hepatic stellate cell activation by blocking adenosine receptors, and emerging evidence indicated that caffeine may also favorably impact angiogenesis and hepatic hemodynamics. On the other side, chlorogenic acids, potent phenolic antioxidants, suppress liver fibrogenesis and carcinogenesis by reducing oxidative stress and counteract steatogenesis through the modulation of glucose and lipid homeostasis in the liver. Overall, these molecular insights may have translational significance and suggest that coffee components need clinical evaluation.

  14. Characterization of Pectinase from Bacillus subtilis Strain Btk 27 and Its Potential Application in Removal of Mucilage from Coffee Beans

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    Oliyad Jeilu Oumer

    2017-01-01

    Full Text Available The demand for enzymes in the global market is projected to rise at a fast pace in recent years. There has been a great increase in industrial applications of pectinase owing to their significant biotechnological uses. For applying enzymes at industrial scale primary it is important to know the features of the enzyme. Thus, this study was undertaken with aims of characterizing the pectinase enzyme from Bacillus subtilis strain Btk27 and proving its potential application in demucilisation of coffee. In this study, the maximum pectinase activity was achieved at pH 7.5 and 50°C. Also, the enzyme activity was found stimulated with Mg2+ and Ca2+ metal ions. Moreover, it was stable on EDTA, Trixton-100, Tween 80, and Tween 20. Since Bacillus subtilis strain Btk27 was stable in most surfactants and inhibitors it could be applicable in various industries whenever pectin degradation is needed. The enzyme Km and Vmax values were identified as 1.879 mg/ml and 149.6 U, respectively. The potential application of the enzyme for coffee processing was studied, and it is found that complete removal of mucilage from coffee beans within 24 hours of treatment indicates the potential application in coffee processing.

  15. Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation.

    Science.gov (United States)

    Wood, Andrew R; Perry, John R B; Tanaka, Toshiko; Hernandez, Dena G; Zheng, Hou-Feng; Melzer, David; Gibbs, J Raphael; Nalls, Michael A; Weedon, Michael N; Spector, Tim D; Richards, J Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B; Frayling, Timothy M

    2013-01-01

    Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10(-12)). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.

  16. Coffee and autoimmunity: More than a mere hot beverage!

    Science.gov (United States)

    Sharif, Kassem; Watad, Abdulla; Bragazzi, Nicola Luigi; Adawi, Mohammad; Amital, Howard; Shoenfeld, Yehuda

    2017-07-01

    Coffee is one of the world's most consumed beverage. In the last decades, coffee consumption has attracted a huge body of research due to its impact on health. Recent scientific evidences showed that coffee intake could be associated with decreased mortality from cardiovascular and neurological diseases, diabetes type II, as well as from endometrial and liver cancer, among others. In this review, on the basis of available data in the literature, we aimed to investigate the association between coffee intake and its influence on the immune system and the insurgence of the most relevant autoimmune diseases. While some studies reported conflicting results, general trends have been identified. Coffee consumption seems to increase the risk of developing rheumatoid arthritis (RA) and type 1 diabetes mellitus (T1DM). By contrast, coffee consumption may exert a protective role against multiple sclerosis, primary sclerosing cholangitis, and ulcerative colitis. Concerning other autoimmune diseases such as systemic lupus erythematosus, psoriasis, primary biliary cholangitis and Crohn's disease, no significant association was found. In other studies, coffee consumption was shown to influence disease course and management options. Coffee intake led to a decrease in insulin sensitivity in T1DM, in methotrexate efficacy in RA, and in levothyroxine absorption in Hashimoto's disease. Further, coffee consumption was associated with cross reactivity with gliadin antibodies in celiac patients. Data on certain autoimmune diseases like systemic sclerosis, Sjögren's syndrome, and Behçet's disease, among others, are lacking in the existent literature. As such, further research is warranted. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Association between coffee consumption and serum lipid profile.

    Science.gov (United States)

    Karabudak, Efsun; Türközü, Duygu; Köksal, Eda

    2015-05-01

    The aim of the present study was to investigate the association between coffee consumption and serum lipid levels in a study population of 122 Turkish subjects (mean age, 41.4±12.69 years), including 48 males and 74 females. A questionnaire was compiled to determine baseline characteristics, and food and coffee consumption. Subjects were divided into three groups, which included non-drinkers, Turkish coffee and instant coffee drinkers, and anthropometric measurements were acquired, including weight, height and body mass index. Serum lipid levels were analyzed, including the total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and very low-density lipoprotein cholesterol (VLDL-C) levels. Of the population studied, 76.2% had consumed at least one cup of coffee per week over the previous year. Daily consumption values were 62.3±40.60 ml (0.7±0.50 cup) for Turkish coffee and 116.3±121.96 ml (0.7±0.81 cup) for instant coffee. No statistically significant differences were observed in the serum levels of TC, TG, LDL-C, HDL-C or VLDL-C among the three groups. In addition, no statistically significant differences were observed in the serum lipid levels when comparing individuals who consumed coffee with sugar/cream or who smoked and those who did not (P>0.05). Therefore, the present observations indicated no significant association between the consumption of Turkish or instant coffee and serum lipid levels.

  18. Weather and Climate Indicators for Coffee Rust Disease

    Science.gov (United States)

    Georgiou, S.; Imbach, P. A.; Avelino, J.; Anzueto, F.; del Carmen Calderón, G.

    2014-12-01

    Coffee rust is a disease that has significant impacts on the livelihoods of those who are dependent on the Central American coffee sector. Our investigation has focussed on the weather and climate indicators that favoured the high incidence of coffee rust disease in Central America in 2012 by assessing daily temperature and precipitation data available from 81 weather stations in the INSIVUMEH and ANACAFE networks located in Guatemala. The temperature data were interpolated to determine the corresponding daily data at 1250 farms located across Guatemala, between 400 and 1800 m elevation. Additionally, CHIRPS five day (pentad) data has been used to assess the anomalies between the 2012 and the climatological average precipitation data at farm locations. The weather conditions in 2012 displayed considerable variations from the climatological data. In general the minimum daily temperatures were higher than the corresponding climatology while the maximum temperatures were lower. As a result, the daily diurnal temperature range was generally lower than the corresponding climatological range, leading to an increased number of days where the temperatures fell within the optimal range for either influencing the susceptibility of the coffee plants to coffee rust development during the dry season, or for the development of lesions on the coffee leaves during the wet season. The coffee rust latency period was probably shortened as a result, and farms at high altitudes were impacted due to these increases in minimum temperature. Factors taken into consideration in developing indicators for coffee rust development include: the diurnal temperature range, altitude, the environmental lapse rate and the phenology. We will present the results of our study and discuss the potential for each of the derived weather and climatological indicators to be used within risk assessments and to eventually be considered for use within an early warning system for coffee rust disease.

  19. Reinforcing effects of caffeine in coffee and capsules.

    Science.gov (United States)

    Griffiths, R R; Bigelow, G E; Liebson, I A

    1989-09-01

    In a residential research ward the reinforcing and subjective effects of caffeine were studied under double-blind conditions in volunteer subjects with histories of heavy coffee drinking. In Experiment 1, 6 subjects had 13 opportunities each day to self-administer either a caffeine (100 mg) or a placebo capsule for periods of 14 to 61 days. All subjects developed a clear preference for caffeine, with intake of caffeine becoming relatively stable after preference had been attained. Preference for caffeine was demonstrated whether or not preference testing was preceded by a period of 10 to 37 days of caffeine abstinence, suggesting that a recent history of heavy caffeine intake (tolerance/dependence) was not a necessary condition for caffeine to function as a reinforcer. In Experiment 2, 6 subjects had 10 opportunities each day to self-administer a cup of coffee or (on different days) a capsule, dependent upon completing a work requirement that progressively increased and then decreased over days. Each day, one of four conditions was studied: caffeinated coffee (100 mg/cup), decaffeinated coffee, caffeine capsules (100 mg/capsule), or placebo capsules. Caffeinated coffee maintained the most self-administration, significantly higher than decaffeinated coffee and placebo capsules but not different from caffeine capsules. Both decaffeinated coffee and caffeine capsules were significantly higher than placebo capsules but not different from each other. In both experiments, subject ratings of "linking" of coffee or capsules covaried with the self-administration measures. These experiments provide the clearest demonstrations to date of the reinforcing effects of caffeine in capsules and in coffee.

  20. HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects.

    Science.gov (United States)

    Saunders, Rebecca E; Instrell, Rachael; Rispoli, Rossella; Jiang, Ming; Howell, Michael

    2013-01-01

    High-throughput screening (HTS) uses technologies such as RNA interference to generate loss-of-function phenotypes on a genomic scale. As these technologies become more popular, many research institutes have established core facilities of expertise to deal with the challenges of large-scale HTS experiments. As the efforts of core facility screening projects come to fruition, focus has shifted towards managing the results of these experiments and making them available in a useful format that can be further mined for phenotypic discovery. The HTS-DB database provides a public view of data from screening projects undertaken by the HTS core facility at the CRUK London Research Institute. All projects and screens are described with comprehensive assay protocols, and datasets are provided with complete descriptions of analysis techniques. This format allows users to browse and search data from large-scale studies in an informative and intuitive way. It also provides a repository for additional measurements obtained from screens that were not the focus of the project, such as cell viability, and groups these data so that it can provide a gene-centric summary across several different cell lines and conditions. All datasets from our screens that can be made available can be viewed interactively and mined for further hit lists. We believe that in this format, the database provides researchers with rapid access to results of large-scale experiments that might facilitate their understanding of genes/compounds identified in their own research. DATABASE URL: http://hts.cancerresearchuk.org/db/public.