WorldWideScience

Sample records for schistosome genome project

  1. Exploring the function of protein kinases in schistosomes: perspectives from the laboratory and from comparative genomics

    Directory of Open Access Journals (Sweden)

    Anthony John Walker

    2014-07-01

    Full Text Available Eukaryotic protein kinases are well conserved through evolution. The genome of Schistosoma mansoni, which causes intestinal schistosomiasis, encodes over 250 putative protein kinases with all of the main eukaryotic groups represented. However, unraveling functional roles for these kinases is a considerable endeavour, particularly as protein kinases regulate multiple and sometimes overlapping cell and tissue functions in organisms. In this article, elucidating protein kinase signal transduction and function in schistosomes is considered from the perspective of the state-of-the-art methodologies used and comparative organismal biology, with a focus on current advances and future directions. Using the free-living nematode Caenorhabditis elegans as a comparator we predict roles for various schistosome protein kinases in processes vital for host invasion and successful parasitism such as sensory behaviour, growth and development. It is anticipated that the characterization of schistosome protein kinases in the context of parasite function will catalyze cutting edge research into host-parasite interactions and will reveal new targets for developing drug interventions against human schistosomiasis.

  2. 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.

  3. The Materials Genome Project

    Science.gov (United States)

    Aourag, H.

    2008-09-01

    In the past, the search for new and improved materials was characterized mostly by the use of empirical, trial- and-error methods. This picture of materials science has been changing as the knowledge and understanding of fundamental processes governing a material's properties and performance (namely, composition, structure, history, and environment) have increased. In a number of cases, it is now possible to predict a material's properties before it has even been manufactured thus greatly reducing the time spent on testing and development. The objective of modern materials science is to tailor a material (starting with its chemical composition, constituent phases, and microstructure) in order to obtain a desired set of properties suitable for a given application. In the short term, the traditional "empirical" methods for developing new materials will be complemented to a greater degree by theoretical predictions. In some areas, computer simulation is already used by industry to weed out costly or improbable synthesis routes. Can novel materials with optimized properties be designed by computers? Advances in modelling methods at the atomic level coupled with rapid increases in computer capabilities over the last decade have led scientists to answer this question with a resounding "yes'. The ability to design new materials from quantum mechanical principles with computers is currently one of the fastest growing and most exciting areas of theoretical research in the world. The methods allow scientists to evaluate and prescreen new materials "in silico" (in vitro), rather than through time consuming experimentation. The Materials Genome Project is to pursue the theory of large scale modeling as well as powerful methods to construct new materials, with optimized properties. Indeed, it is the intimate synergy between our ability to predict accurately from quantum theory how atoms can be assembled to form new materials and our capacity to synthesize novel materials atom

  4. Proteomic analysis of human skin treated with larval schistosome peptidases reveals distinct invasion strategies among species of blood flukes.

    Directory of Open Access Journals (Sweden)

    Jessica Ingram

    2011-09-01

    Full Text Available Skin invasion is the initial step in infection of the human host by schistosome blood flukes. Schistosome larvae have the remarkable ability to overcome the physical and biochemical barriers present in skin in the absence of any mechanical trauma. While a serine peptidase with activity against insoluble elastin appears to be essential for this process in one species of schistosomes, Schistosoma mansoni, it is unknown whether other schistosome species use the same peptidase to facilitate entry into their hosts.Recent genome sequencing projects, together with a number of biochemical studies, identified alternative peptidases that Schistosoma japonicum or Trichobilharzia regenti could use to facilitate migration through skin. In this study, we used comparative proteomic analysis of human skin treated with purified cercarial elastase, the known invasive peptidase of S. mansoni, or S. mansoni cathespin B2, a close homolog of the putative invasive peptidase of S. japonicum, to identify substrates of either peptidase. Select skin proteins were then confirmed as substrates by in vitro digestion assays.This study demonstrates that an S. mansoni ortholog of the candidate invasive peptidase of S. japonicum and T. regenti, cathepsin B2, is capable of efficiently cleaving many of the same host skin substrates as the invasive serine peptidase of S. mansoni, cercarial elastase. At the same time, identification of unique substrates and the broader species specificity of cathepsin B2 suggest that the cercarial elastase gene family amplified as an adaptation of schistosomes to human hosts.

  5. Deciphering the glycogenome of schistosomes

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    Megan Lee Mickum

    2014-08-01

    Full Text Available Schistosoma mansoni and other Schistosoma sp. are multicellular parasitic helminths (worms that infect humans and mammals worldwide. Infection by these parasites, which results in developmental maturation and sexual differentiation over a period of five to six weeks, induces antibodies to glycan antigens expressed in surface and secreted glycoproteins and glycolipids. There is growing interest in defining these unusual parasite-synthesized glycan antigens and using them to understand immune responses, their roles in immunomodulation, and in using glycan antigens as potential vaccine targets. A key problem in this area, however, has been the lack of information about the enzymes involved in elaborating the complex repertoire of glycans represented by the schistosome glycome. Recent availability of the nuclear genome sequences for Schistosoma sp. has created the opportunity to define the glycogenome, which represents the specific genes and cognate enzymes that generate the glycome. Here we describe the current state of information in regard to the schistosome glycogenome and glycome and highlight the important classes of glycans and glycogenes that may be important in their generation.

  6. TRP channels in schistosomes

    Directory of Open Access Journals (Sweden)

    Swarna Bais

    2016-12-01

    Full Text Available Praziquantel (PZQ is effectively the only drug currently available for treatment and control of schistosomiasis, a disease affecting hundreds of millions of people worldwide. Many anthelmintics, likely including PZQ, target ion channels, membrane protein complexes essential for normal functioning of the neuromusculature and other tissues. Despite this fact, only a few classes of parasitic helminth ion channels have been assessed for their pharmacological properties or for their roles in parasite physiology. One such overlooked group of ion channels is the transient receptor potential (TRP channel superfamily. TRP channels share a common core structure, but are widely diverse in their activation mechanisms and ion selectivity. They are critical to transducing sensory signals, responding to a wide range of external stimuli. They are also involved in other functions, such as regulating intracellular calcium and organellar ion homeostasis and trafficking. Here, we review current literature on parasitic helminth TRP channels, focusing on those in schistosomes. We discuss the likely roles of these channels in sensory and locomotor activity, including the possible significance of a class of TRP channels (TRPV that is absent in schistosomes. We also focus on evidence indicating that at least one schistosome TRP channel (SmTRPA has atypical, TRPV1-like pharmacological sensitivities that could potentially be exploited for future therapeutic targeting.

  7. 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.

  8. Schistosome feeding and regurgitation.

    Directory of Open Access Journals (Sweden)

    Patrick J Skelly

    2014-08-01

    Full Text Available Schistosomes are parasitic flatworms that infect >200 million people worldwide, causing the chronic, debilitating disease schistosomiasis. Unusual among parasitic helminths, the long-lived adult worms, continuously bathed in blood, take up nutrients directly across the body surface and also by ingestion of blood into the gut. Recent proteomic analyses of the body surface revealed the presence of hydrolytic enzymes, solute, and ion transporters, thus emphasising its metabolic credentials. Furthermore, definition of the molecular mechanisms for the uptake of selected metabolites (glucose, certain amino acids, and water establishes it as a vital site of nutrient acquisition. Nevertheless, the amount of blood ingested into the gut per day is considerable: for males ∼100 nl; for the more actively feeding females ∼900 nl, >4 times body volume. Ingested erythrocytes are lysed as they pass through the specialized esophagus, while leucocytes become tethered and disabled there. Proteomics and transcriptomics have revealed, in addition to gut proteases, an amino acid transporter in gut tissue and other hydrolases, ion, and lipid transporters in the lumen, implicating the gut as the site for acquisition of essential lipids and inorganic ions. The surface is the principal entry route for glucose, whereas the gut dominates amino acid acquisition, especially in females. Heme, a potentially toxic hemoglobin degradation product, accumulates in the gut and, since schistosomes lack an anus, must be expelled by the poorly understood process of regurgitation. Here we place the new observations on the proteome of body surface and gut, and the entry of different nutrient classes into schistosomes, into the context of older studies on worm composition and metabolism. We suggest that the balance between surface and gut in nutrition is determined by the constraints of solute diffusion imposed by differences in male and female worm morphology. Our conclusions have

  9. Parasite genome analysis. Progress in the Leishmania genome project.

    Science.gov (United States)

    Blackwell, J M

    1997-01-01

    Genome projects have been established for 7 major groups of human parasitic infections: malaria, leishmaniasis, African trypanosomiasis, American trypanosomiasis, toxoplasmosis, schistosomiasis and filariasis. All except malaria and toxoplasmosis have come under the umbrella of the World Health Organization's Strategic Committee on Parasite Genome Analysis. The focus of this meeting of the Society was to review progress made in the Leishmania and African trypanosome genome projects. This paper introduces the genome projects and reviews briefly progress in pulsed-field gel karyotype mapping and gene identification via expressed sequence tag sequencing for the leishmaniasis genome project. The overall aim of the genome projects is to harness the latest developments in molecular genetic technology and sequence analysis for the rapid-generation of new data which may, in turn, revolutionize our approaches to the study of the biology of these organisms.

  10. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

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    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

  11. Tick genomics: the Ixodes genome project and beyond.

    Science.gov (United States)

    Pagel Van Zee, J; Geraci, N S; Guerrero, F D; Wikel, S K; Stuart, J J; Nene, V M; Hill, C A

    2007-10-01

    Ticks and mites (subphylum Chelicerata; subclass Acari) include important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a blood-feeding tick vector of human disease and a member of the subphylum Chelicerata. Genome projects for other species of Acari are forthcoming and their genome sequences will likely feature significantly in the future of tick research. Parasitologists interested in advancing the field of tick genomics research will be faced with specific challenges. The development of genetic tools and resources, and the size and repetitive nature of tick genomes are important considerations. Innovative approaches may be required to sequence, assemble, annotate and analyse tick genomes. Overcoming these challenges will enable scientists to investigate the genes and genome organisation of this important group of arthropods and may ultimately lead to new solutions for control of ticks and tick-borne diseases.

  12. BIOCHEMICAL ASPECTS OF SCHISTOSOME BEHAVIOUR ...

    African Journals Online (AJOL)

    BIOCHEMICAL ASPECTS OF SCHISTOSOME BEHAVIOUR. P.J.FRIPP. Bilharzia. Research Unit, South African Institute for Medical Research, Johannesburg. ABSTRACT. The haematophagous blood trematodes that comprise the genus SchistolJlOmIl live in a stable environment with an adequate food supply and an ...

  13. 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...

  14. All about the Human Genome Project (HGP)

    Science.gov (United States)

    ... New Five-Year Plan for the United States Human Genome Project Originally published in 1993 in Science . Ethical, Legal and Social Implications (ELSI) Research Program The continuing research program ...

  15. Schistosomal glomerular disease (a review

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    Zilton A. Andrade

    1984-12-01

    Full Text Available In this review paper schistosomal glomerulopathy is defined as an immune-complex disease. The disease appears in 12-15 per cent of the individuals with hepatosplenic schistosomiasis. Portal hypertension with collateral circulation helps the by pass of the hepatic clearance process and the parasite antigens can bind to antibodies in the circulation and be trapped in the renal glomerulus. Chronic membranousproliferative glomerulonephritis is the most commom lesion present and the nephrotic syndrome is the usual form of clinical presentation. The disease can be experimentally produced, and schistosomal antigens and antibodies, as well as complement, can be demonstrated in the glomerular lesions. Specific treatment of schistosomiasis does not seem to alter the clinical course of schistosomal nephropathy.A glomerulopatia esquistossomotica e um exemplo de doenca causada por complexos imunes. Ela se manifesta em 12 a 15% dos portadores de forma hepato-eplenica da esquistossomose. A hipertensao porta, com circulacao colateral, facilita a ultrapassagem do filtro hepatico e os antigenos esquistossomoticos podem se acoplar aos anticorpos na circulacao e vir a se depositar nos glomerulos. O tipo histologico mais frequente e a glomerulonefrite cronica membrano-proliferativa, geralmente com sindrome nefrotica. A doenca e passivel de reproducao experimental e os antigenos esquistossomoticos, os anticorpos e fracoes do complemento podem ser demonstrados nas lesoes glomerulares. O tratamento especifico da esquistossomose nao mostrou ate o momento a capacidade de alterar o curso da nefropatia.

  16. Phylogenetic Placement of a Schistosome from an Unusual Marine Snail Host, the False Limpet (Siphonaria lessoni) and Gulls (Larus dominicanus) from Argentina with a Brief Review of Marine Schistosomes from Snails.

    Science.gov (United States)

    Brant, Sara V; Loker, Eric S; Casalins, Laura; Flores, Veronica

    2017-02-01

    In the blood fluke family Schistosomatidae, marine snails are well known as intermediate hosts. Eight families of marine snails have thus far been reported to host schistosomes across the world, most of which have been implicated in human cercarial dermatitis (HCD) outbreaks. As part of our larger effort to define the species diversity and biology of schistosomes in Argentina, in particular their role in causing HCD, we searched in the marine pulmonate snail (Siphonaria lessoni) for a schistosome species described previously from S. lessoni from southern Argentina. Additionally, gulls (Larus dominicanus) collected from a different project locality (inland) were examined, because they are known to spend time in the intertidal regions. Schistosome sporocysts were found in S. lessoni, and a small worm fragment was retrieved from a gull. Molecular phylogenies for 28S, ITS1-5.8S-ITS2, and cox1 genes revealed that the specimens from the gull and S. lessoni grouped closely together, suggesting they are conspecifics. Also, ITS1-5.8S-ITS2 sequences suggested one of the schistosomes from S. lessoni and a schistosome from a South African penguin were also conspecifics. Further study is needed to verify if these specimens comprise a distinct marine clade within the larger avian schistosome clade that is comprised mostly of species using freshwater snail hosts. Thus far, it appears this group of marine schistosomes may be more likely found in the southern hemisphere. It is unclear if the observed distribution pattern of schistosomes in Siphonaria is a result of sampling bias and/or indicative of a specific bird-snail-schistosome association. It is clear they are sharply differentiated from the basal marine clade of avian schistosomes that includes Austrobilharzia.

  17. Acute Perforated Schistosomal Appendicitis: A Case Report ...

    African Journals Online (AJOL)

    Appendicitis is occasionally the first clinical manifestation of schistosomal infestation which may require treatment. A rare case of perforated schistosomal appendicitis in a 12 –year old Nigerian boy diagnosed on the basis of histological evaluation of the appendectomy specimen is reported to highlight the clinical ...

  18. [Human genomic project and human genomic haplotype map project: opportunitiy, challenge and strategy in stomatology].

    Science.gov (United States)

    Wu, Rui-qing; Zeng, Xin; Wang, Zhi

    2010-08-01

    The human genomic project and the international HapMap project were designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases, thus lead to molecular diagnosis and personnel therapy. The article briefly reviewed the creation, target and achievement of those two projects. Furthermore, the authors have given four suggestions in facing to the opportunities and challenges brought by the two projects, including cultivation improvement of elites, cross binding of multi-subjects, strengthening construction of research base and initiation of natural key scientific project.

  19. Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells

    Science.gov (United States)

    Duvoisin, Raphaël; Ayuk, Mary A.; Rinaldi, Gabriel; Suttiprapa, Sutas; Mann, Victoria H.; Lee, Clarence M.; Harris, Nicola; Brindley, Paul J.

    2011-01-01

    Blood flukes or schistosomes are the causative agents of human schistosomiasis, one of the major neglected tropical diseases. Draft genome sequences have been reported for schistosomes, but functional genomics tools are needed to investigate the role and essentiality of the newly reported genes. Vector based RNA interference can contribute to functional genomics analysis for schistosomes. Using mRNA encoding reporter firefly luciferase as a model target, we compared the performance of a schistosome and a human promoter from the U6 gene in driving shRNA in human fibrosarcoma cells and in cultured schistosomes. Further, both a retroviral (Murine leukemia virus [MLV]) and plasmid (piggyBac, pXL-Bac II) vector were utilized. The schistosome U6 gene promoter was 270 bp in length, the human U6 gene promoter was 264 bp; they shared 41% identity. Following transduction of both HT1080 fibrosarcoma cells and schistosomules of Schistosoma mansoni with pseudotyped MLV virions, stronger knockdown of luciferase activity was seen with the virions encoding the human U6 promoter driven shRNA than the schistosome U6 promoter. A similar trend was seen after transfection of HT1080 cells and schistosomules with the pXL-Bac-II constructs – stronger knockdown of luciferase activity was seen with constructs encoding the human compared to schistosome U6 promoter. The findings indicate that a human U6 gene promoter drives stronger shRNA activity than its schistosome orthologue, not only in a human cancer cell line but also in larval schistosomes. This RNA polymerase III promoter represents a potentially valuable component for vector based RNA interference studies in schistosomes and related platyhelminth parasites. PMID:21953124

  20. 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.

  1. 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.

  2. Indian Schistosomes: A Need for Further Investigations

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    M. C. Agrawal

    2011-01-01

    Full Text Available India is uniquely positioned with regard to schistosomes and schistosomiasis—discovering seven new mammalian species with the existence of three more schistosome species: Orientobilharzia turkestanicum, O. harinasutai, and Schistosoma haematobium(?. An endemic focus of urinary schistosomiasis was reported from Gimvi village of Ratnagiri, Maharashtra with infrequent occurrence of schistosome eggs in human stools. Cercarial dermatitis has been reported to be more abundant in rural population using ponds, tanks, and so forth, for their domestic purposes. Few dermatitis cases were tested positive by CHR. Schistosome antigen was also detected in urine of five cases suggesting existence of active schistosomiasis in India. Nevertheless, human kind does not appear to be the usual host for Indian schistosomes in contrast to S. haematobium, S. mansoni, or S. japonicum. Various reasons for this phenomenon are discussed including evolution of Indian schistosomes, immune mechanisms, and environmental conditions. These and other aspects such as seasonal effect on the prevalence, snail infectivity, heterologous mating, existence of hybrids, and number of schistosomes in heterologous infections need further investigations with application of molecular techniques. Joint efforts by the national as well as international scientific community would be much more rewarding for better understanding of the parasite and the infection.

  3. 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.

  4. 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.

  5. Genome project: An experiment in sharing

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, L.

    1990-05-25

    The Human Genome Project is in many respects a gigantic experiment in data sharing. Around the world, investigators are working on pieces of the same puzzle. And whether the project succeeds will depend in large measure on these investigators making available their data and materials - cell lines, probes, and clones - to their colleagues and competitors. While sharing may be the norm in, say, immunology or bacterial genetics, human genetics has always been intensely competitive. So should the National Institutes of Health and the Department of Energy, which both fund the genome project, promulgate rules to govern access to data and sharing of materials A DOE committee has drafted some guidelines, which have yet to be formally endorsed. They stipulate that data and materials must be publicly available 6 months after they are generated or characterized. But at NIH, James Watson, who heads the genome project, is shying away from setting rules. He points to the new collaborative plans to map chromosome 21 as evidence that the community will develop its own ways of sharing data. Because of its known role in Down syndrome and its suspected role in Alzheimer's disease, chromosome 21 has generated a vast amount of interest. Lots of groups are already hard at work constructing maps of the chromosome - first developing a series of landmarks spaced along the chromosome, and then a collection of ordered DNA fragments. But the maps all these groups generate will be essentially useless unless they pool their data and adopt a common language.

  6. 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.

  7. 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.

  8. Free will and the Genome Project.

    Science.gov (United States)

    Greenspan, P S

    1993-01-01

    ...I want to argue that the Human Genome Project itself poses no special problem for human freedom, understood in relation to the philosophical issue of free will versus determinism. It seems to pose a problem only if one muddles the interpretation of the issue or of the project that is supposed to bear on it. There is a need for conceptual clarification to point this out, perhaps, but I see no need for "research" in the sense that implies original investigation. However, I also want to probe a bit deeper to identify a distinct set of philosophical worries about freedom that seem to have been misplaced onto the standard issue, the issue of freedom versus determinism, in this discussion and elsewhere. After arguing that the genome project has no real bearing on free will versus determinism, I shall attempt to identify the threat it poses to freedom partly by detaching it from this standard version of the free will question. I shall argue that the worrisome forms of genetic influence that the project might uncover do not really presuppose determinism. But what they do presuppose -- some form of internal or psychological constraint on behavior -- suggests an alternative version of the free will question as the source of popular fears about scientific explanation of human behavior. What is under threat on this version of the question is the Aristotelian notion of character formation and self-control.

  9. Exuberant innovation: The Human Genome Project

    CERN Document Server

    Gisler, Monika; Woodard, Ryan

    2010-01-01

    We present a detailed synthesis of the development of the Human Genome Project (HGP) from 1986 to 2003 in order to test the "social bubble" hypothesis that strong social interactions between enthusiastic supporters of the HGP weaved a network of reinforcing feedbacks that led to a widespread endorsement and extraordinary commitment by those involved in the project, beyond what would be rationalized by a standard cost-benefit analysis in the presence of extraordinary uncertainties and risks. The vigorous competition and race between the initially public project and several private initiatives is argued to support the social bubble hypothesis. We also present quantitative analyses of the concomitant financial bubble concentrated on the biotech sector. Confirmation of this hypothesis is offered by the present consensus that it will take decades to exploit the fruits of the HGP, via a slow and arduous process aiming at disentangling the extraordinary complexity of the human complex body. The HGP has ushered other...

  10. Purinergic signaling in schistosomal infection

    Directory of Open Access Journals (Sweden)

    Claudia Lucia Martins Silva

    2016-10-01

    Full Text Available Human schistosomiasis is a chronic inflammatory disease caused by blood fluke worms belonging to the genus Schistosoma. Health metrics indicate that the disease is related to an elevated number of years lost-to-disability and years lost-to-life. Schistosomiasis is an intravascular disease that is related to a Th1 and Th2 immune response polarization, and the degree of polarization affects the outcome of the disease. The purinergic system is composed of adenosine and nucleotides acting as key messenger molecules. Moreover, nucleotide-transforming enzymes and cell-surface purinergic receptors are obligatory partners of this purinergic signaling. In mammalian cells, purinergic signaling modulates innate immune responses and inflammation among other functions; conversely purinergic signaling may also be modulated by inflammatory mediators. Moreover, schistosomes also express some enzymes of the purinergic system, and it is possible that worms modulate host purinergic signaling. Current data obtained in murine models of schistosomiasis support the notion that the host purinergic system is altered by the disease. The dysfunction of adenosine receptors, metabotropic P2Y and ionotropic P2X7 receptors, and NTPDases likely contributes to disease morbidity. Keywords: Purinergic receptor, NTPDases, Schistosomiasis, Macrophages, Endothelial cell, Inflammation

  11. Schistosome serine protease inhibitors: parasite defense or homeostasis?

    Directory of Open Access Journals (Sweden)

    Landys A. Lopez Quezada

    2011-06-01

    Full Text Available Serpins are a structurally conserved family of macromolecular inhibitors found in numerous biological systems. The completion and annotation of the genomes of Schistosoma mansoni and Schistosoma japonicum has enabled the identification by phylogenetic analysis of two major serpin clades. S. mansoni shows a greater multiplicity of serpin genes, perhaps reflecting adaptation to infection of a human host. Putative targets of schistosome serpins can be predicted from the sequence of the reactive center loop (RCL. Schistosome serpins may play important roles in both post-translational regulation of schistosome-derived proteases, as well as parasite defense mechanisms against the action of host proteases.Serpinas são uma família de inibidores macromoleculares estruturalmente conservados encontrados em inúmeros sistemas biológicos. O término e a anotação dos genomas de Schistosoma mansoni e de Schistosoma japonicum permitiram a identificação por análise filogenética de dois principais clados de serpinas. S. mansoni mostra uma multiplicidade maior de genes de serpinas, talvez refletindo uma adaptação à infecção de um hospedeiro humano. Alvos putativos das serpinas de esquistossomos podem ser preditos a partir da sequência do "loop" do centro reativo. Serpinas de esquistossomos podem ter importantes papeis tanto na regulação pós-traducional de proteases derivadas do esquistossoma, quanto nos mecanismos de defesa contra a ação de proteases do hospedeiro.

  12. Schistosomes and snails: a molecular encounter

    Directory of Open Access Journals (Sweden)

    Matty eKnight

    2014-07-01

    Full Text Available Biomphalaria glabrata snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis in the Western hemisphere. For the past two decades, tremendous advances have been made in research aimed at elucidating the molecular basis of the snail/parasite interaction. The growing concern that there is no vaccine to prevent schistosomiasis and only one effective drug in existence provides the impetus to develop new control strategies based on eliminating schistosomes at the snail-stage of the life cycle. To elucidate why a given snail is not always compatible to each and every schistosome it encounters, B. glabrata that are either resistant or susceptible to a given strain of S. mansoni have been employed to track molecular mechanisms governing the snail/schistosome relationship. With such snails, genetic markers for resistance and susceptibility were identified. Additionally, differential gene expression studies have led to the identification of genes that underlie these phenotypes. Lately, the role of schistosomes in mediating non-random relocation of gene loci has been identified for the first time, making B. glabrata a model organism where chromatin regulation by changes in nuclear architechture, known as spatial epigenetics, orchestrated by a major human parasite can now be investigated. This review will highlight the progress that has been made in using molecular approaches to describe snail/schistosome compatibility issues. Uncovering the signaling networks triggered by schistosomes that provide the impulse to turn genes on and off in the snail host, thereby controlling the outcome of infection, could also yield new insights into anti-parasite mechanism(s that operate in the human host as well.

  13. Genomics :GTL project quarterly report April 2005.

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-11-01

    This SAND report provides the technical progress through April 2005 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science GenomicsGTL 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 microamy 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

  14. Developmental expression and antigenicity of schistosome glycans

    NARCIS (Netherlands)

    Smit, C.H.

    2016-01-01

    Schistosomiasis is a tropical disease affecting over 230 million people worldwide. Although effective drug treatment is available, reinfections are common, and development of immunity is slow. Most antibodies raised during schistosome infection are directed against glycans, some of which are thought

  15. Schistosomal infestation: under investigation with attendant surgical ...

    African Journals Online (AJOL)

    Schistosomal infestation: under investigation with attendant surgical complications. Barnabas M Mandong, Abio JK Madaki. Abstract. No Abstract. Nigerian Medical Practitioner Vol. 48(5-6) 2005: 117-119. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT.

  16. The rice genome project in Japan

    OpenAIRE

    Sasaki, Takuji

    1998-01-01

    Since 1991, the Rice Genome Research Program in Japan has carried out rice genomics, such as large-scale cDNA analysis, construction of a fine-scale restriction fragment length polymorphism map, and physical mapping of the rice genome with yeast artificial chromosome clones. These studies have made a great impact on research into grass genomes and made rice a model plant for other cereal crop research. Starting in 1998, the Rice Genome Research Program will step in...

  17. Evaluation of schistosome promoter expression for transgenesis and genetic analysis.

    Directory of Open Access Journals (Sweden)

    Shuang Liang

    Full Text Available Schistosome worms of the genus Schistosoma are the causative agents of schistosomiasis, a devastating parasitic disease affecting more than 240 million people worldwide. Schistosomes have complex life cycles, and have been challenging to manipulate genetically due to the dearth of molecular tools. Although the use of gene overexpression, gene knockouts or knockdowns are straight-forward genetic tools applied in many model systems, gene misexpression and genetic manipulation of schistosome genes in vivo has been exceptionally challenging, and plasmid based transfection inducing gene expression is limited. We recently reported the use of polyethyleneimine (PEI as a simple and effective method for schistosome transfection and gene expression. Here, we use PEI-mediated schistosome plasmid transgenesis to define and compare gene expression profiles from endogenous and nonendogenous promoters in the schistosomula stage of schistosomes that are potentially useful to misexpress (underexpress or overexpress gene product levels. In addition, we overexpress schistosome genes in vivo using a strong promoter and show plasmid-based misregulation of genes in schistosomes, producing a clear and distinct phenotype--death. These data focus on the schistosomula stage, but they foreshadow strong potential for genetic characterization of schistosome molecular pathways, and potential for use in overexpression screens and drug resistance studies in schistosomes using plasmid-based gene expression.

  18. International network of cancer genome projects.

    OpenAIRE

    Aretz, Axel; Bernabé, Rosa R.; Calvo, Fabien; Eerola, Iiro; Hemsley, Fiona M.; Jennings, Jennifer L; Kerr, David; Klatt, Peter; Kolar, Patrik; Lane, David P; Laplace, Frank; Nettekoven, Gerd; Remacle, Jacques; Watanabe, Koichi; Matthew M. F. Yuen

    2010-01-01

    The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeut...

  19. International network of cancer genome projects

    NARCIS (Netherlands)

    Hudson, Thomas J.; Anderson, Warwick; Aretz, Axel; Barker, Anna D.; Bell, Cindy; Bernabé, Rosa R.; Bhan, M. K.; Calvo, Fabien; Eerola, Iiro; Gerhard, Daniela S.; Guttmacher, Alan; Guyer, Mark; Hemsley, Fiona M.; Jennings, Jennifer L.; Kerr, David; Klatt, Peter; Kolar, Patrik; Kusuda, Jun; Lane, David P.; Laplace, Frank; Lu, Youyong; Nettekoven, Gerd; Ozenberger, Brad; Peterson, Jane; Rao, T. S.; Remacle, Jacques; Schafer, Alan J.; Shibata, Tatsuhiro; Stratton, Michael R.; Vockley, Joseph G.; Watanabe, Koichi; Yang, Huanming; Yuen, Matthew M. F.; Knoppers, Bartha M.; Bobrow, Martin; Cambon-Thomsen, Anne; Dressler, Lynn G.; Dyke, Stephanie O. M.; Joly, Yann; Kato, Kazuto; Kennedy, Karen L.; Nicolás, Pilar; Parker, Michael J.; Rial-Sebbag, Emmanuelle; Romeo-Casabona, Carlos M.; Shaw, Kenna M.; Wallace, Susan; Wiesner, Georgia L.; Zeps, Nikolajs; Lichter, Peter; Biankin, Andrew V.; Chabannon, Christian; Chin, Lynda; Clément, Bruno; de Alava, Enrique; Degos, Françoise; Ferguson, Martin L.; Geary, Peter; Hayes, D. Neil; Johns, Amber L.; Kasprzyk, Arek; Nakagawa, Hidewaki; Penny, Robert; Piris, Miguel A.; Sarin, Rajiv; Scarpa, Aldo; van de Vijver, Marc; Futreal, P. Andrew; Aburatani, Hiroyuki; Bayés, Mónica; Bowtell, David D. L.; Campbell, Peter J.; Estivill, Xavier; Grimmond, Sean M.; Gut, Ivo; Hirst, Martin; López-Otín, Carlos; Majumder, Partha; Marra, Marco; McPherson, John D.; Ning, Zemin; Puente, Xose S.; Ruan, Yijun; Stunnenberg, Hendrik G.; Swerdlow, Harold; Velculescu, Victor E.; Wilson, Richard K.; Xue, Hong H.; Yang, Liu; Spellman, Paul T.; Bader, Gary D.; Boutros, Paul C.; Flicek, Paul; Getz, Gad; Guigó, Roderic; Guo, Guangwu; Haussler, David; Heath, Simon; Hubbard, Tim J.; Jiang, Tao; Jones, Steven M.; Li, Qibin; López-Bigas, Nuria; Luo, Ruibang; Muthuswamy, Lakshmi; Ouellette, B. F. Francis; Pearson, John V.; Quesada, Victor; Raphael, Benjamin J.; Sander, Chris; Speed, Terence P.; Stein, Lincoln D.; Stuart, Joshua M.; Teague, Jon W.; Totoki, Yasushi; Tsunoda, Tatsuhiko; Valencia, Alfonso; Wheeler, David A.; Wu, Honglong; Zhao, Shancen; Zhou, Guangyu; Lathrop, Mark; Thomas, Gilles; Yoshida, Teruhiko; Axton, Myles; Gunter, Chris; Miller, Linda J.; Zhang, Junjun; Haider, Syed A.; Wang, Jianxin; Yung, Christina K.; Cross, Anthony; Liang, Yong; Gnaneshan, Saravanamuttu; Guberman, Jonathan; Hsu, Jack; Chalmers, Don R. C.; Hasel, Karl W.; Kaan, Terry S. H.; Lowrance, William W.; Masui, Tohru; Rodriguez, Laura Lyman; Vergely, Catherine; Cloonan, Nicole; Defazio, Anna; Eshleman, James R.; Etemadmoghadam, Dariush; Gardiner, Brooke A.; Kench, James G.; Sutherland, Robert L.; Tempero, Margaret A.; Waddell, Nicola J.; Wilson, Peter J.; Gallinger, Steve; Tsao, Ming-Sound; Shaw, Patricia A.; Petersen, Gloria M.; Mukhopadhyay, Debabrata; DePinho, Ronald A.; Thayer, Sarah; Shazand, Kamran; Beck, Timothy; Sam, Michelle; Timms, Lee; Ballin, Vanessa; Ji, Jiafu; Zhang, Xiuqing; Chen, Feng; Hu, Xueda; Yang, Qi; Tian, Geng; Zhang, Lianhai; Xing, Xiaofang; Li, Xianghong; Zhu, Zhenggang; Yu, Yingyan; Yu, Jun; Tost, Jörg; Brennan, Paul; Holcatova, Ivana; Zaridze, David; Brazma, Alvis; Egevad, Lars; Prokhortchouk, Egor; Banks, Rosamonde Elizabeth; Uhlén, Mathias; Viksna, Juris; Ponten, Fredrik; Skryabin, Konstantin; Birney, Ewan; Borg, Ake; Børresen-Dale, Anne-Lise; Caldas, Carlos; Foekens, John A.; Martin, Sancha; Reis-Filho, Jorge S.; Richardson, Andrea L.; Sotiriou, Christos; van't Veer, Laura; Birnbaum, Daniel; Blanche, Hélène; Boucher, Pascal; Boyault, Sandrine; Masson-Jacquemier, Jocelyne D.; Pauporté, Iris; Pivot, Xavier; Vincent-Salomon, Anne; Tabone, Eric; Theillet, Charles; Treilleux, Isabelle; Bioulac-Sage, Paulette; Decaens, Thomas; Franco, Dominique; Gut, Marta; Samuel, Didier; Zucman-Rossi, Jessica; Eils, Roland; Brors, Benedikt; Korbel, Jan O.; Korshunov, Andrey; Landgraf, Pablo; Lehrach, Hans; Pfister, Stefan; Radlwimmer, Bernhard; Reifenberger, Guido; Taylor, Michael D.; von Kalle, Christof; Majumder, Partha P.; Pederzoli, Paolo; Lawlor, Rita T.; Delledonne, Massimo; Bardelli, Alberto; Gress, Thomas; Klimstra, David; Zamboni, Giuseppe; Nakamura, Yusuke; Miyano, Satoru; Fujimoto, Akihiro; Campo, Elias; de Sanjosé, Silvia; Montserrat, Emili; González-Díaz, Marcos; Jares, Pedro; Himmelbaue, Heinz; Bea, Silvia; Aparicio, Samuel; Easton, Douglas F.; Collins, Francis S.; Compton, Carolyn C.; Lander, Eric S.; Burke, Wylie; Green, Anthony R.; Hamilton, Stanley R.; Kallioniemi, Olli P.; Ley, Timothy J.; Liu, Edison T.; Wainwright, Brandon J.

    2010-01-01

    The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the

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

    Science.gov (United States)

    ... turn Javascript on. Feature: Genetics 101 Understanding the Human Genome Project — A Fact Sheet Past Issues / Summer 2013 ... body. This concerted, public effort was the Human Genome Project. The Human Genome Project's goal was to provide researchers with ...

  1. Human Schistosome Infection and Allergic Sensitisation

    Directory of Open Access Journals (Sweden)

    Nadine Rujeni

    2012-01-01

    Full Text Available Several field studies have reported an inverse relationship between the prevalence of helminth infections and that of allergic sensitisation/atopy. Recent studies show that immune responses induced by helminth parasites are, to an extent, comparable to allergic sensitisation. However, helminth products induce regulatory responses capable of inhibiting not only antiparasite immune responses, but also allergic sensitisation. The relative effects of this immunomodulation on the development of protective schistosome-specific responses in humans has yet to be demonstrated at population level, and the clinical significance of immunomodulation of allergic disease is still controversial. Nonetheless, similarities in immune responses against helminths and allergens pose interesting mechanistic and evolutionary questions. This paper examines the epidemiology, biology and immunology of allergic sensitisation/atopy, and schistosome infection in human populations.

  2. 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.

  3. Cancer Genome Anatomy Project (CGAP) | Office of Cancer Genomics

    Science.gov (United States)

    CGAP generated a wide range of genomics data on cancerous cells that are accessible through easy-to-use online tools. Researchers, educators, and students can find "in silico" answers to biological questions through the CGAP website. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov to learn how to navigate the website.

  4. 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.

  5. 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.

  6. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project.

    Science.gov (United States)

    Kyrpides, Nikos C; Woyke, Tanja; Eisen, Jonathan A; Garrity, George; Lilburn, Timothy G; Beck, Brian J; Whitman, William B; Hugenholtz, Phil; Klenk, Hans-Peter

    2014-06-15

    The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both of the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.

  7. 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.

  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. 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 ...

  10. Neurotransmitter transporters in schistosomes: structure, function and prospects for drug discovery.

    Science.gov (United States)

    Ribeiro, Paula; Patocka, Nicholas

    2013-12-01

    Neurotransmitter transporters (NTTs) play a fundamental role in the control of neurotransmitter signaling and homeostasis. Sodium symporters of the plasma membrane mediate the cellular uptake of neurotransmitter from the synaptic cleft, whereas proton-driven vesicular transporters sequester the neurotransmitter into synaptic vesicles for subsequent release. Together these transporters control how much transmitter is released and how long it remains in the synaptic cleft, thereby regulating the intensity and duration of signaling. NTTs have been the subject of much research in mammals and there is growing interest in their activities among invertebrates as well. In this review we will focus our attention on NTTs of the parasitic flatworm Schistosoma mansoni. Bloodflukes of the genus Schistosoma are the causative agents of human schistosomiasis, a devastating disease that afflicts over 200 million people worldwide. Schistosomes have a well-developed nervous system and a rich diversity of neurotransmitters, including many of the small-molecule ("classical") neurotransmitters that normally employ NTTs in their mechanism of signaling. Recent advances in schistosome genomics have unveiled numerous NTTs in this parasite, some of which have now been cloned and characterized in vitro. Moreover new genetic and pharmacological evidence suggests that NTTs are required for proper control of neuromuscular signaling and movement of the worm. Among these carriers are proteins that have been successfully targeted for drug discovery in other organisms, in particular sodium symporters for biogenic amine neurotransmitters such as serotonin and dopamine. Our goal in this chapter is to review the current status of research on schistosome NTTs, with emphasis on biogenic amine sodium symporters, and to evaluate their potential for anti-schistosomal drug targeting. Through this discussion we hope to draw attention to this important superfamily of parasite proteins and to identify new

  11. 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.

    2015-01-01

    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 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. PMID:26272997

  12. 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.

  13. Relevance of the Human Genome Project to inherited metabolic disease.

    Science.gov (United States)

    Burn, J

    1994-01-01

    The Human Genome Project is an international effort to identify the complete structure of the human genome. HUGO, the Human Genome Organization, facilitates international cooperation and exchange of information while the Genome Data Base will act as the on-line information retrieval and storage system for the huge amount of information being accumulated. The clinical register MIM (Mendelian Inheritance in Man) established by Victor McKusick is now an on-line resource that will allow biochemists working with inborn errors of metabolism to access the rapidly expanding body of knowledge. Biochemical and molecular genetics are complementary and should draw together to find solutions to the academic and clinical problems posed by inborn errors of metabolism.

  14. 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.

  15. 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

  16. 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…

  17. 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 ...

  18. 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.

  19. 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

  20. Project 1: Microbial Genomes: A Genomic Approach to Understanding the Evolution of Virulence. Project 2: From Genomes to Life: Drosophilia Development in Space and Time

    Energy Technology Data Exchange (ETDEWEB)

    Robert DeSalle

    2004-09-10

    This project seeks to use the genomes of two close relatives, A. actinomycetemcomitans and H. aphrophilus, to understand the evolutionary changes that take place in a genome to make it more or less virulent. Our primary specific aim of this project was to sequence, annotate, and analyze the genomes of Actinobacillus actinomycetemcomitans (CU1000, serotype f) and Haemophilus aphrophilus. With these genome sequences we have then compared the whole genome sequences to each other and to the current Aa (HK1651 www.genome.ou.edu) genome project sequence along with other fully sequenced Pasteurellaceae to determine inter and intra species differences that may account for the differences and similarities in disease. We also propose to create and curate a comprehensive database where sequence information and analysis for the Pasteurellaceae (family that includes the genera Actinobacillus and Haemophilus) are readily accessible. And finally we have proposed to develop phylogenetic techniques that can be used to efficiently and accurately examine the evolution of genomes. Below we report on progress we have made on these major specific aims. Progress on the specific aims is reported below under two major headings--experimental approaches and bioinformatics and systematic biology approaches.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Interference with the host haemostatic system by schistosomes.

    Directory of Open Access Journals (Sweden)

    Mirjam M Mebius

    Full Text Available Schistosomes, parasitic flatworms that cause the tropical disease schistosomiasis, are still a threat. They are responsible for 200 million infections worldwide and an estimated 280,000 deaths annually in sub-Saharan Africa alone. The adult parasites reside as pairs in the mesenteric or perivesicular veins of their human host, where they can survive for up to 30 years. The parasite is a potential activator of blood coagulation according to Virchow's triad, because it is expected to alter blood flow and endothelial function, leading to hypercoagulability. In contrast, hepatosplenic schistosomiasis patients are in a hypocoagulable and hyperfibrinolytic state, indicating that schistosomes interfere with the haemostatic system of their host. In this review, the interactions of schistosomes with primary haemostasis, secondary haemostasis, fibrinolysis, and the vascular tone will be discussed to provide insight into the reduction in coagulation observed in schistosomiasis patients. Interference with the haemostatic system by pathogens is a common mechanism and has been described for other parasitic worms, bacteria, and fungi as a mechanism to support survival and spread or enhance virulence. Insight into the mechanisms used by schistosomes to interfere with the haemostatic system will provide important insight into the maintenance of the parasitic life cycle within the host. This knowledge may reveal new potential anti-schistosome drug and vaccine targets. In addition, some of the survival mechanisms employed by schistosomes might be used by other pathogens, and therefore, these mechanisms that interfere with host haemostasis might be a broad target for drug development against blood-dwelling pathogens. Also, schistosome antithrombotic or thrombolytic molecules could form potential new drugs in the treatment of haemostatic disorders.

  6. 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

    2017-01-01

    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. PMID:27638885

  7. Receptor tyrosine kinases and schistosome reproduction: new targets for chemotherapy

    Directory of Open Access Journals (Sweden)

    Marion eMorel

    2014-07-01

    Full Text Available Schistosome parasites still represent a serious public health concern and a major economic problem in developing countries. Pathology of schistosomiasis is mainly due to massive egg production by these parasites and to inflammatory responses raised against the eggs which are trapped in host tissues. Tyrosine kinases (TKs are key molecules that control cell differentiation and proliferation and they already represent important targets in cancer therapy. During the recent years, it has been shown that receptor tyrosine kinases (RTK signaling was active in reproductive organs and that it could regulate sexual maturation of schistosomes and egg production. This opens interesting perspectives for the control of transmission and pathogenesis of schistosomiasis based on new therapies targeting schistosome RTKs. This review relates the numerous data showing the major roles of kinase signaling in schistosome reproduction. It describes the conserved and particular features of schistosome RTKs, their implication in gametogenesis and reproduction processes and summarizes recent works indicating that RTKs and their signaling partners are interesting chemotherapeutical targets in new programs of control.

  8. Recent advances in Schistosoma genomics.

    Science.gov (United States)

    Mourão, M M; Grunau, C; LoVerde, P T; Jones, M K; Oliveira, G

    2012-01-01

    Schistosome research has entered the genomic era with the publications reporting the Schistosoma mansoni and Schistosoma japonicum genomes. Schistosome genomics is motivated by the need for new control tools. However, much can also be learned about the biology of Schistosoma, which is a tractable experimental model. In this article, we review the recent achievements in the field of schistosome research and discuss future perspectives on genomics and how it can be integrated in a usable format, on the genetic mapping and how it has improved the genome assembly and provided new research approaches, on how epigenetics provides interesting insights into the biology of the species and on new functional genomics tools that will contribute to the understanding of the function of genes, many of which are parasite- or taxon specific. © 2011 Blackwell Publishing Ltd.

  9. 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

  10. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

    Energy Technology Data Exchange (ETDEWEB)

    Fenner, Marsha W; Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

    2007-12-31

    The Genomes On Line Database (GOLD) is a comprehensive resource of information for genome and metagenome projects world-wide. GOLD provides access to complete and ongoing projects and their associated metadata through pre-computed lists and a search page. The database currently incorporates information for more than 2900 sequencing projects, of which 639 have been completed and the data deposited in the public databases. GOLD is constantly expanding to provide metadata information related to the project and the organism and is compliant with the Minimum Information about a Genome Sequence (MIGS) specifications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Liolios, Konstantinos; Chen, Amy; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Phil; Markowitz, Victor; Kyrpides, Nikos C.

    2009-09-01

    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.

  12. DOE project on genome mapping and sequencing. Progress report, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Evans, G.A.

    1992-12-31

    These efforts on the human genome project were initiated in September, 1990, to contribute towards completion of the human genome project physical mapping effort. In the original application, the authors proposed a novel strategy for constructing a physical map of human chromosome 11, based upon techniques derived in this group and by others. The original goals were to (1) produce a set of cosmid reference clones mapped to specific sites by high resolution fluorescence in situ hybridization, (2) produce a set of associated STS sequences and PCR primers for each site, (3) isolate YAC clones corresponding to each STS and, (4) construct YAC contigs such that > 90% of the chromosome would be covered by contigs of 2 mb or greater. Since that time, and with the advent of new technology and reagents, the strategy has been modified slightly but still retains the same goals as originally proposed. The authors have added a project to produce chromosome 11-specific cDNAs and determine the map location and DNA sequence of a selected portion of them.

  13. The p53 gene expression and its developmental regulation in schistosomes

    Directory of Open Access Journals (Sweden)

    Manami Tanaka

    1992-01-01

    Full Text Available We have studied the gene expression, especially of the oncoproteins, and its regulation in schistosomes. Schistosomes have a complex life cycle with defined dimorphic lifestyle. The parasite are so far unique in biology in expressing oncogene products in their adult stage. In order to characterize the expression and developmental regulation, a lambda gt 11 cDNA library and lambda EMBL4 genomic DNA library of each growth stage of Schistosoma mansoni and S. japonicum was constructed, and was screened with various monoclonal antibodies against ongogene products. One positive plaque reacted to anti-p53 antibody (Ab-2, Oncogene Science, Inc. was further analyzed. This fusion protein was about 120 KDa in molecular weights, and expressed as 1.4 Kb RNA in the adult stage. P53 gene is well-known as the negative regulator of the cell cicle, and the mutations in the gene are turning out to be the most common genetic alterations in human cancers. The comparison of the gene structure among species and stages were being conducted. Chromosome structures, C-band formation, and the results of in situ hybridization using the phage probe would be discussed.

  14. Genomes to life project : quarterly report October 2003.

    Energy Technology Data Exchange (ETDEWEB)

    Heffelfinger, Grant S.

    2004-01-01

    This SAND report provides the technical progress through October 2003 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 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

  15. schistosomal appendicitis in a sliding hernia (case report)

    African Journals Online (AJOL)

    uncommonly found in the appendix (2). We report a sliding right inguinal hernia that contained an appendix with histological evidence of intense Schistosoma haematobium ovideposition. The case is presented to highlight the importance of early anti- schistosomal treatment. CASE REPORT. J. A., a 47-year-old male farmer, ...

  16. Molecular diversity of avian schistosomes in Danish freshwater snails

    DEFF Research Database (Denmark)

    Christiansen, Anne Ø.; Olsen, Annette; Buchmann, Kurt

    2016-01-01

    to identify the parasites at species level. In order to do that, 499 pulmonate freshwater snails (Radix sp., Lymnaea stagnalis, Stagnicola sp. and Planorbarius corneus) were sampled from 12 lakes, ponds, and marshes in the greater Copenhagen area. Avian schistosome cercariae were identified by microscopy...

  17. schistosomal appendicitis in a sliding hernia (case report)

    African Journals Online (AJOL)

    We report a rare case of a forty-seven year old Nigeria male with schistosomal appendicitis in a sliding hernia. The clinical and pathological features of the case are discussed, followed by a review of the literature. It is concluded that a high index of suspicion is necessary to diagnose unusual presentations of ...

  18. Interference with the Host Haemostatic System by Schistosomes

    NARCIS (Netherlands)

    R.E. Mebius (Reina); P.J.J. van Genderen (Perry); J. Urbanus (Jos); A.G.M. Tielens (Aloysius); P.G. de Groot; J.J. van Hellemond (Jaap)

    2013-01-01

    textabstractSchistosomes, parasitic flatworms that cause the tropical disease schistosomiasis, are still a threat. They are responsible for 200 million infections worldwide and an estimated 280,000 deaths annually in sub-Saharan Africa alone. The adult parasites reside as pairs in the mesenteric or

  19. Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery

    Science.gov (United States)

    Swain, Martin T.; Larkin, Denis M.; Caffrey, Conor R.; Davies, Stephen J.; Loukas, Alex; Skelly, Patrick J.; Hoffmann, Karl F.

    2011-01-01

    Schistosoma genomes provide a comprehensive resource for identifying the molecular processes that shape parasite evolution and for discovering novel chemotherapeutic or immunoprophylactic targets. Here, we demonstrate how intra- and intergenus comparative genomics can be used to drive these investigations forward, illustrate the advantages and limitations of these approaches and review how post genomic technologies offer complementary strategies for genome characterisation. While sequencing and functional characterisation of other schistosome/platyhelminth genomes continues to expedite anthelmintic discovery, we contend that future priorities should equally focus on improving assembly quality, and chromosomal assignment, of existing schistosome/platyhelminth genomes. PMID:22024648

  20. 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.

  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. Genomes to Life Project Quarterly Report April 2005.

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-02-01

    This SAND report provides the technical progress through April 2005 of the Sandia-led project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling," funded by the DOE Office of Science Genomics:GTL 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 a set of

  3. 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

  4. 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.

  5. Hyperdiverse gene cluster in snail host conveys resistance to human schistosome parasites.

    Directory of Open Access Journals (Sweden)

    Jacob A Tennessen

    2015-03-01

    Full Text Available Schistosomiasis, a neglected global pandemic, may be curtailed by blocking transmission of the parasite via its intermediate hosts, aquatic snails. Elucidating the genetic basis of snail-schistosome interaction is a key to this strategy. Here we map a natural parasite-resistance polymorphism from a Caribbean population of the snail Biomphalaria glabrata. In independent experimental evolution lines, RAD genotyping shows that the same genomic region responds to selection for resistance to the parasite Schistosoma mansoni. A dominant allele in this region conveys an 8-fold decrease in the odds of infection. Fine-mapping and RNA-Seq characterization reveal a 25% haplotypes across the GRC, a significantly non-neutral pattern, suggests that balancing selection maintains diversity at the GRC. Thus, the GRC resembles immune gene complexes seen in other taxa and is likely involved in parasite recognition. The GRC is a potential target for controlling transmission of schistosomiasis, including via genetic manipulation of snails.

  6. 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.

  7. 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.

  8. Transplacental transfer of schistosomal circulating anodic antigens in cows

    OpenAIRE

    Gabriël, Sarah; De Bont, J; Phiri, IK; Masuku, M; Riveau, G; Schacht, AM; DEELDER, AM; Van Dam, GJ; Vercruysse, Jozef

    2002-01-01

    The present work investigated the transplacental passage of circulating anodic schistosome antigens (CAA) and the production of foetal antibodies in response to antigenic stimulation in Schistosoma mattheei infected cows. Three groups were available: six calves born to non-infected cows received colostrum from a pool from non-infected cows (group 1), six calves born to non-infected cows (group 2) and six calves born to infected cows (group 3) received colostrum from a pool from infected cows....

  9. Molecular Detection of Schistosome Infections with a Disposable Microfluidic Cassette.

    Directory of Open Access Journals (Sweden)

    Jinzhao Song

    2015-12-01

    Full Text Available Parasitic helminths such as schistosomes, as well as filarial and soil-transmitted nematodes, are estimated to infect at least a billion people worldwide, with devastating impacts on human health and economic development. Diagnosis and monitoring of infection dynamics and efficacy of treatment depend almost entirely on methods that are inaccurate, labor-intensive, and unreliable. These shortcomings are amplified and take on added significance in mass drug administration programs, where measures of effectiveness depend on accurate monitoring of treatment success (or failure, changes in disease transmission rates, and emergence of possible drug resistance. Here, we adapt isothermal molecular assays such as loop-mediated isothermal amplification (LAMP to a simple, hand-held, custom-made field-ready microfluidic device that allows sensitive and specific detection of schistosome cell-free nucleic acids in serum and plasma (separated with a point-of-care plasma separator from Schistosoma mansoni-infected mice. Cell-free S. mansoni DNA was detected with our device without prior extraction from blood. Our chip exhibits high sensitivity (~2 x 10(-17 g/μL, with a positive signal for S. mansoni DNA detectable as early as one week post infection, several weeks before parasite egg production commences. These results indicate that incorporation of isothermal amplification strategies with our chips could represent a strategy for rapid, simple, low-cost diagnosis of both pre-patent and chronic schistosome infections as well as potential monitoring of treatment efficacy.

  10. Molecular diversity of avian schistosomes in Danish freshwater snails.

    Science.gov (United States)

    Christiansen, Anne Ø; Olsen, Annette; Buchmann, Kurt; Kania, Per W; Nejsum, Peter; Vennervald, Birgitte J

    2016-03-01

    Avian schistosomes are widespread parasites of snails and waterfowl and may cause cercarial dermatitis (swimmer's itch) in humans, a disease that is frequently reported in European countries. These parasites are known to occur in Denmark, but here, we applied a new approach using molecular tools to identify the parasites at species level. In order to do that, 499 pulmonate freshwater snails (Radix sp., Lymnaea stagnalis, Stagnicola sp. and Planorbarius corneus) were sampled from 12 lakes, ponds, and marshes in the greater Copenhagen area. Avian schistosome cercariae were identified by microscopy and subjected to molecular investigation by sequencing and phylogenetic analysis of the 5.8S and ITS2 ribosomal DNA for species identification. Additionally, snail hosts belonging to the genus Radix were identified by sequencing and phylogenetic analysis of partial ITS2 ribosomal DNA. Three out of 499 snails shed different species of Trichobilharzia cercariae: Trichobilharzia szidati was isolated from L. stagnalis, Trichobilharzia franki from Radix auricularia and Trichobilharzia regenti from Radix peregra. In the light of the public health risk represented by bird schistosomes, these findings are of concern and, particularly, the presence of the potentially neuro-pathogenic species, T. regenti, in Danish freshwaters calls for attention.

  11. The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004

    National Research Council Canada - National Science Library

    Wiechers, Ilse R; Perin, Noah C; Cook-Deegan, Robert

    2013-01-01

    .... This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through...

  12. 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 ...

  13. Comparative genomic data of the Avian Phylogenomics Project

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Bo; Li, Cai

    2014-01-01

    , which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts...

  14. Immunologic activity of schistosomal and bacterial TLR2 ligands in Gabonese children

    NARCIS (Netherlands)

    Retra, K.; Riet, E. van; Adegnika, A.A.; Everts, B.; Geest, S. van; Kremsner, P.G.; Hellemond, J.J. van; Kleij, D. van der; Tielens, A.G.M.; Yazdanbakhsh, M.

    2008-01-01

    Schistosomes carry lipid moieties that interact with the immune system. To understand the consequence of interactions in terms of polarizing the cytokine profiles, the effect of two Toll-like receptor-2 (TLR2) activating schistosomal lipid fractions was studied on whole blood from Gabonese children

  15. Sleep-related breathing disorders in patients with schistosomal cor-pulmonale

    Directory of Open Access Journals (Sweden)

    Yehia Khalil

    2012-07-01

    Conclusion: SRBD are highly prevalent in patients with schistosomal pulmonary hypertension (PH. Also, the SA severity was correlated with more advanced PH and more severe cardiovascular impairment. Therefore in the evaluation of patients with schistosomal PH, polysomnography or an ambulatory cardiorespiratory sleep study seems justified to identify potentially treatable SRBD that may additionally challenge the already compromised cardiovascular system in these patients.

  16. Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation

    NARCIS (Netherlands)

    Artigas, Maria Soler; Wain, Louise V.; Miller, Suzanne; Kheirallah, Abdul Kader; Huffman, Jennifer E.; Ntalla, Ioanna; Shrine, Nick; Obeidat, Ma'en; Trochet, Holly; McArdle, Wendy L.; Alves, Alexessander Couto; Hui, Jennie; Zhao, Jing Hua; Joshi, Peter K.; Teumer, Alexander; Albrecht, Eva; Imboden, Medea; Rawal, Rajesh; Lopez, Lorna M.; Marten, Jonathan; Enroth, Stefan; Surakka, Ida; Polasek, Ozren; Lyytikainen, Leo-Pekka; Granell, Raquel; Hysi, Pirro G.; Flexeder, Claudia; Mahajan, Anubha; Beilby, John; Bosse, Yohan; Brandsma, Corry-Anke; Campbell, Harry; Gieger, Christian; Glaeser, Sven; Gonzalez, Juan R.; Grallert, Harald; Hammond, Chris J.; Harris, Sarah E.; Hartikainen, Anna-Liisa; Heliovaara, Markku; Henderson, John; Hocking, Lynne; Horikoshi, Momoko; Hutri-Kahonen, Nina; Ingelsson, Erik; Johansson, Asa; Kemp, John P.; Kolcic, Ivana; Kumar, Ashish; Lind, Lars; Melen, Erik; Musk, Arthur W.; Navarro, Pau; Nickle, David C.; Padmanabhan, Sandosh; Raitakari, Olli T.; Ried, Janina S.; Ripatti, Samuli; Schulz, Holger; Scott, Robert A.; Sin, Don D.; Starr, John M.; Vinuela, Ana; Voelzke, Henry; Wild, Sarah H.; Wright, Alan F.; Zemunik, Tatijana; Jarvis, Deborah L.; Spector, Tim D.; Evans, David M.; Lehtimaki, Terho; Vitart, Veronique; Kahonen, Mika; Gyllensten, Ulf; Rudan, Igor; Deary, Ian J.; Karrasch, Stefan; Probst-Hensch, Nicole M.; Heinrich, Joachim; Stubbe, Beate; Wilson, James F.; Wareham, Nicholas J.; James, Alan L.; Morris, Andrew P.; Jarvelin, Marjo-Riitta; Hayward, Caroline; Sayers, Ian; Strachan, David P.; Hall, Ian P.; Tobin, Martin D.; Deloukas, Panos; Hansell, Anna L.; Hubbard, Richard; Jackson, Victoria E.; Marchini, Jonathan; Pavord, Ian; Thomson, Neil C.; Zeggini, Eleftheria

    2015-01-01

    Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed

  17. Schistosome infections induce significant changes in the host biliary proteome.

    Science.gov (United States)

    de la Torre-Escudero, Eduardo; Pérez-Sánchez, Ricardo; Manzano-Román, Raúl; Oleaga, Ana

    2015-01-30

    Schistosomiasis is a disease caused by blood trematodes affecting man and animals that represents an important human health and veterinary problem. Main damages caused by this infection are a consequence of the host inflammatory reaction against the parasite eggs trapped inside the liver. Despite that the hepatic pathology of schistosomiasis is very well known, there are no specific studies dealing with the schistosome infection effects on the biliary function. The purpose of this work was to analyse the changes induced by Schistosoma bovis infection in the biliary proteome. For this, whole gallbladders from S. bovis-infected and non-infected mice were dissected, homogenized and fractionated by differential centrifugation. The resulting protein fractions were resolved by SDS-PAGE, the gels were sliced, and the gel pieces analysed by LC-MS/MS. Altogether, we identified 1937 proteins, which were classified according to their "protein class" and "molecular function", and then subjected to an "Enrichment analysis". The differences found in gallbladder proteomes between S. bovis-infected and non-infected mice are analysed. We show that chronic schistosome infections cause significant changes in the biliary proteome that may produce physiological alterations and affect the therapeutic actions of drugs when administered to human patients and animals with schistosomiasis. To identify the changes induced by the schistosome infection in bile protein composition, and therefore in bile function, we compared the proteome of the gallbladders collected from non-infected healthy mice and from mice infected with S. bovis during 4months. For this, gallbladders from both groups of mice were homogenized and these homogenates were fractionated by serial centrifugation and acrylamide gel electrophoresis. The proteins were in gel digested and analysed by LC-MS/MS for identification. The present work reports the first data on the proteome of the mouse gallbladder and provides a

  18. 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.

  19. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects

    OpenAIRE

    Liu, Binghang; Shi, Yujian; Yuan, Jianying; Hu, Xuesong; Zhang, Hao; Nan LI.; Li, Zhenyu; Chen, Yanxiang; Mu, Desheng; Fan, Wei

    2013-01-01

    Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the accurate genome size and repeat content. Furthermore, many genomes are highly repetitive or heterozygous, posing problems to current assemblers utilizing short reads. Therefore, it is necessary to develop efficient assembly-independent me...

  20. The Human Genome Project: A paradigm for information management in the life sciences

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, M.L. (E.I. du Pont de Nemours Co., Inc., Wilmington, DE (USA)); Soell, D. (Yale Univ., New Haven, CT (USA))

    1991-01-01

    The major product of the Human Genome Project will be a series of linked data sets containing the genetic and physical location of all genes on each chromosome, plus the complete nucleotide sequence of the genome for humans and several model organisms. Here we summarize the current status of attempts to collect, analyze, and distribute this information in an electronically accessible form. Although formidable problems remain to be solved in the acquisition and adequate representation of the genetic, physical, and biological data, this project is a model for the rapid dissemination of genome and related information in biology and medicine.

  1. A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data.

    Science.gov (United States)

    Buchanan, Carrie C; Torstenson, Eric S; Bush, William S; Ritchie, Marylyn D

    2012-01-01

    Since publication of the human genome in 2003, geneticists have been interested in risk variant associations to resolve the etiology of traits and complex diseases. The International HapMap Consortium undertook an effort to catalog all common variation across the genome (variants with a minor allele frequency (MAF) of at least 5% in one or more ethnic groups). HapMap along with advances in genotyping technology led to genome-wide association studies which have identified common variants associated with many traits and diseases. In 2008 the 1000 Genomes Project aimed to sequence 2500 individuals and identify rare variants and 99% of variants with a MAF of Project includes all the variants in HapMap, we examined the overlap between single nucleotide polymorphisms (SNPs) genotyped in the two resources using merged phase II/III HapMap data and low coverage pilot data from 1000 Genomes. Comparison of the two data sets showed that approximately 72% of HapMap SNPs were also found in 1000 Genomes Project pilot data. After filtering out HapMap variants with a MAF of HapMap SNPs were found in 1000 Genomes data. Not all variants cataloged in HapMap are also cataloged in 1000 Genomes. This could affect decisions about which resource to use for SNP queries, rare variant validation, or imputation. Both the HapMap and 1000 Genomes Project databases are useful resources for human genetics, but it is important to understand the assumptions made and filtering strategies employed by these projects.

  2. Chronic Schistosome Infection Leads to Modulation of Granuloma Formation and Systemic Immune Suppression

    Directory of Open Access Journals (Sweden)

    Steven K. Lundy

    2013-02-01

    Full Text Available Schistosome worms have been infecting humans for millennia, but it is only in the last half century that we have begun to understand the complexities of this inter-relationship. As our sophistication about the inner workings of every aspect of the immune system has increased, it has also become obvious that schistosome infections have broad ranging effects on nearly all of the innate and adaptive immune response mechanisms. Selective pressures on both the worms and their hosts, has no doubt led to co-evolution of protective mechanisms, particularly those that favor granuloma formation around schistosome eggs and immune suppression during chronic infection. The immune modulatory effects that chronic schistosome infection and egg deposition elicit have been intensely studied, not only because of their major implications to public health issues, but also due to the emerging evidence that schistosome infection may protect humans from severe allergies and autoimmunity. Mouse models of schistosome infection have been extremely valuable for studying immune modulation and regulation, and in the discovery of novel aspects of immunity. A progression of immune reactions occurs during granuloma formation ranging from innate inflammation, to activation of each branch of adaptive immune response, and culminating in systemic immune suppression and granuloma fibrosis. Although molecular factors from schistosome eggs have been identified as mediators of immune modulation and suppressive functions of T and B cells, much work is still needed to define the mechanisms of the immune alteration and determine whether therapies for asthma or autoimmunity could be developed from these pathways.

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

    Indian Academy of Sciences (India)

    2015-12-11

    Dec 11, 2015 ... according to statistics from the National Human Genome. Research Institute's GWAS catalogue (Hindorff et al. 2009). Despite GWAS being widely applied to identify common genetic variants associated with risk across more than 200 diseases and human phenotypic traits, the SNP array-based.

  4. Hyperplasia of elastic tissue in hepatic schistosomal fibrosis

    Directory of Open Access Journals (Sweden)

    Zilton A. Andrade

    1991-12-01

    Full Text Available Elastic tissue hyperplasia, revealed by means of histological, immunocytochemical and ultrastructural methods, appeared as a prominent change in surgical liver biopsies taken from 61 patients with schistosomal periportal and septal fibrosis. Such hyperplasia was absent in ecperimental murine schistosomiasis, including mice with "pipe-stem" fibrosis. Displaced connective tissue cells in periportal areas, such as smooth muscle cells, more frequently observed in human material, could be the site of excessive elastin synthesis, and could explain the differences observed in human and experimental materials. Elastic tissue, sometimes represented by its microfibrillar components, also appeared to be more condensed in areas of matrix (collagen degradation, suggesting a participation of this tissue in the remodelling of the extracellular matrix. By its rectratile properties elastic tissue hyperplasia in hepatic schistosomiasis can cause vascular narrowing and thus play a role in the pathogenesis of portal hypeertension.

  5. The Impact of the Human Genome Project on Complex Disease

    Directory of Open Access Journals (Sweden)

    Jessica N. Cooke Bailey

    2014-07-01

    Full Text Available In the decade that has passed since the initial release of the Human Genome, numerous advancements in science and technology within and beyond genetics and genomics have been encouraged and enhanced by the availability of this vast and remarkable data resource. Progress in understanding three common, complex diseases: age-related macular degeneration (AMD, Alzheimer’s disease (AD, and multiple sclerosis (MS, are three exemplars of the incredible impact on the elucidation of the genetic architecture of disease. The approaches used in these diseases have been successfully applied to numerous other complex diseases. For example, the heritability of AMD was confirmed upon the release of the first genome-wide association study (GWAS along with confirmatory reports that supported the findings of that state-of-the art method, thus setting the foundation for future GWAS in other heritable diseases. Following this seminal discovery and applying it to other diseases including AD and MS, the genetic knowledge of AD expanded far beyond the well-known APOE locus and now includes more than 20 loci. MS genetics saw a similar increase beyond the HLA loci and now has more than 100 known risk loci. Ongoing and future efforts will seek to define the remaining heritability of these diseases; the next decade could very well hold the key to attaining this goal.

  6. 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.

  7. Bidirectional introgressive hybridization between a cattle and human schistosome species.

    Directory of Open Access Journals (Sweden)

    Tine Huyse

    2009-09-01

    Full Text Available Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions, caused by parasitic flatworms of the genus Schistosoma (subclass Digenea. Following major water development schemes in the 1980s, schistosomiasis has become an important parasitic disease of children living in the Senegal River Basin (SRB. During molecular parasitological surveys, nuclear and mitochondrial markers revealed unexpected natural interactions between a bovine and human Schistosoma species: S. bovis and S. haematobium, respectively. Hybrid schistosomes recovered from the urine and faeces of children and the intermediate snail hosts of both parental species, Bulinus truncatus and B. globosus, presented a nuclear ITS rRNA sequence identical to S. haematobium, while the partial mitochondrial cox1 sequence was identified as S. bovis. Molecular data suggest that the hybrids are not 1st generation and are a result of parental and/or hybrid backcrosses, indicating a stable hybrid zone. Larval stages with the reverse genetic profile were also found and are suggested to be F1 progeny. The data provide indisputable evidence for the occurrence of bidirectional introgressive hybridization between a bovine and a human Schistosoma species. Hybrid species have been found infecting B. truncatus, a snail species that is now very abundant throughout the SRB. The recent increase in urinary schistosomiasis in the villages along the SRB could therefore be a direct effect of the increased transmission through B. truncatus. Hybridization between schistosomes under laboratory conditions has been shown to result in heterosis (higher fecundity, faster maturation time, wider intermediate host spectrum, having important implications on disease prevalence, pathology and treatment. If this new hybrid exhibits the same hybrid vigour, it could develop into an emerging pathogen, necessitating further control strategies in zones where both parental species

  8. Bidirectional introgressive hybridization between a cattle and human schistosome species.

    Science.gov (United States)

    Huyse, Tine; Webster, Bonnie L; Geldof, Sarah; Stothard, J Russell; Diaw, Oumar T; Polman, Katja; Rollinson, David

    2009-09-01

    Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions, caused by parasitic flatworms of the genus Schistosoma (subclass Digenea). Following major water development schemes in the 1980s, schistosomiasis has become an important parasitic disease of children living in the Senegal River Basin (SRB). During molecular parasitological surveys, nuclear and mitochondrial markers revealed unexpected natural interactions between a bovine and human Schistosoma species: S. bovis and S. haematobium, respectively. Hybrid schistosomes recovered from the urine and faeces of children and the intermediate snail hosts of both parental species, Bulinus truncatus and B. globosus, presented a nuclear ITS rRNA sequence identical to S. haematobium, while the partial mitochondrial cox1 sequence was identified as S. bovis. Molecular data suggest that the hybrids are not 1st generation and are a result of parental and/or hybrid backcrosses, indicating a stable hybrid zone. Larval stages with the reverse genetic profile were also found and are suggested to be F1 progeny. The data provide indisputable evidence for the occurrence of bidirectional introgressive hybridization between a bovine and a human Schistosoma species. Hybrid species have been found infecting B. truncatus, a snail species that is now very abundant throughout the SRB. The recent increase in urinary schistosomiasis in the villages along the SRB could therefore be a direct effect of the increased transmission through B. truncatus. Hybridization between schistosomes under laboratory conditions has been shown to result in heterosis (higher fecundity, faster maturation time, wider intermediate host spectrum), having important implications on disease prevalence, pathology and treatment. If this new hybrid exhibits the same hybrid vigour, it could develop into an emerging pathogen, necessitating further control strategies in zones where both parental species overlap.

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

    Science.gov (United States)

    Gao, Xiaoyi; Haritunians, Talin; Marjoram, Paul; McKean-Cowdin, Roberta; Torres, Mina; Taylor, Kent D; Rotter, Jerome I; Gauderman, William J; Varma, Rohit

    2012-01-01

    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.

  10. 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.

  11. Insights into Morphology and Disease from the Dog Genome Project

    Science.gov (United States)

    Schoenebeck, Jeffrey J.; Ostrander, Elaine A.

    2017-01-01

    Although most modern dog breeds are less than 200 years old, the symbiosis between man and dog is ancient. Since prehistoric times, repeated selection events have transformed the wolf into man’s guardians, laborers, athletes, and companions. The rapid transformation from pack predator to loyal companion is a feat that is arguably unique among domesticated animals. How this transformation came to pass remained a biological mystery until recently: Within the past decade, the deployment of genomic approaches to study population structure, detect signatures of selection, and identify genetic variants that underlie canine phenotypes is ushering into focus novel biological mechanisms that make dogs remarkable. Ironically, the very practices responsible for breed formation also spurned morbidity; today, many diseases are correlated with breed identity. In this review, we discuss man’s best friend in the context of a genetic model to understand paradigms of heritable phenotypes, both desirable and disadvantageous. PMID:25062362

  12. 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…

  13. 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

  14. 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…

  15. Introgressive hybridization of Schistosoma haematobium group species in Senegal: species barrier break down between ruminant and human schistosomes

    National Research Council Canada - National Science Library

    Webster, Bonnie L; Diaw, Oumar T; Seye, Mohmoudane M; Webster, Joanne P; Rollinson, David

    2013-01-01

    .... Schistosomes undergo a sexual reproductive stage within their mammalian host enabling interactions between different species, which may result in hybridization if the species involved are phylogenetically close...

  16. The susceptibility of adult schistosomes to immune attrition

    Directory of Open Access Journals (Sweden)

    A. M. Agnew

    1992-01-01

    Full Text Available Mouse infection models are described that demonstrate reduction of egg production in Schistosoma haematobium infections and both worm loss and reduced fecundity in S. bovis infections. Neither phenomenum could be shown in S. mansoni infected mice. The immunological basis for these anti-adult responses was inferred by comparison with infections in T-cell deprived mice and by the serum transfer of the ability to reduce a S. bovis worm burden into immunocompromised hosts. Vaccination with irradiation attenuated parasites was also shown to have consequences for the adults of a challenge infections of S. haematobium and S. bovis specifically. Prior vaccination resulted in an abrogation of the anti-fecundity and adult worm elimination that occurred in non-vaccinated similary infected mice. hese models are being used to define the targets and mechanisms involved in anti-adult attrition. A serological assay, quantitation of a circulating antigen (CAA has been assessed for its ability to measure worm burdens of different species of schistosome in mice. This assay will be used to question whether anti-adult immunity contributes to the pattern of infection with S. mansoni and S. haematobium in man.

  17. IMPROVEMENT OF SCHISTOSOMAL PORTAL HYPERTENSIVE COLOPATHY AFTER SURGICAL TREATMENT

    Directory of Open Access Journals (Sweden)

    Maria Angelina Carvalho MIRANDA

    2013-04-01

    Full Text Available Context Data on vascular alterations in patients with hepatosplenic schistosomiasis and portal hypertensive colopathy and changes in these after surgery to decrease portal hypertension are limited. Objective The purpose of this study was to analyse the alterations of portal hypertensive colopathy previously and 6-12 months after splenectomy and gastric devascularization. Methods Twelve patients with hepatosplenic schistosomiasis who also had upper gastrointestinal bleeding were studied prospectively. Their endoscopic findings before and 6-12 months after the surgery were analysed. In addition, mucosal biopsies from ascending colon, sigmoid colon and rectum at these time points were subjected to histological and histomorphometric assessment. It was used a control group due to lack of normal pattern of the histomorphometric measures of vessels in individuals without portal hypertension. The critical level of significance adopted in all tests was of a maximum probability error of 5%. Results Surgery did not lead to significant improvement in histological and endoscopic findings. However, on histomorphometry, there was a significant decrease in the area, diameter and thickness of the vessels in mucosa at all colonic sites. Conclusion Surgery for decompression of schistosomal portal hypertension has a beneficial effect on the associated colopathy, being best indicated in patients with gastrointestinal bleeding and esophageal varices.

  18. Some further observations on schistosome transmission in the Eastern Transvaal*

    Science.gov (United States)

    Pitchford, R. J.; Visser, P. S.

    1965-01-01

    By immersing groups of rodents into several types of natural waters at Malelane, Eastern Transvaal, and subsequently recovering schistosomes from them, the authors have shown that there is seasonal transmission, which is more marked with Schistosoma mansoni than with S. mattheei. Laboratory confirmation of this periodicity was obtained by infecting groups of snails with the appropriate parasite and studying the pattern of sporocyst development and cercarial shedding under outdoor conditions. It was also found that, apart from seasonal periodicity, the amount of transmission is dependent on the density of human population, the proximity of the definitive host to the immersion site, the degree to which the water is protected from pollution and the distance downstream from the polluting source. Negligible numbers of S. haematobium adults were recovered; possible reasons for this are discussed. The authors consider that an annual transmission cycle may be more common in bilharziasis than is generally supposed—although not exclusively or necessarily for the reasons given in this paper—and suggest that such a cycle be taken into consideration in the planning of control schemes. PMID:14292065

  19. 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.

  20. The Human Genome Project in the United States: a perspective on the commercial, ethical, legislative and health care issues.

    Science.gov (United States)

    Mackler, Bruce F; Barach, Micha

    1991-01-01

    The Human Genome Project represents a government supported effort to map and sequence the human genome. Governmental support for the Project should include increased emphasis on grants and contracts to industry. This is particularly true for small highly innovative biotechnology companies that can rapidly integrate and use technology as a base for product development. Private industry must be integrated as a partner into the Project, as it will be in Japan and Europe. There is a consensus in industry that the Genome Project is, at this stage at least, a science research project funded by government and not, at present, a commercial project. It is not seriously expected to have any substantial widespread commercial impact in the near future. The ultimate commercial benefits of the Human Genome Project, in terms of definable health care products, may not be realized until well into the next century. Yet, there are a few companies for which the Genome Project affords immediate commercial opportunities in certain niche areas. The Genome Project can be expected to have a significant impact upon medical knowledge and treatment. Though the Genome Project is just beginning, much of the type of medical knowledge expected to be gained from the Project is already present and even being exploited, albeit on a small scale. The application of genetic understanding to practical applications raises ethical, medical and legal issues central to the Genome Project. Unfortunately, emotion and sensationalism sometimes dominate and prevent a constructive discussion of ethical and social issues pertaining to genetics. To answer public concerns about human gene transfer experiments, the medical and biotechnology communities must constructively discuss the medical realities, the benefits to human health and the adequacy of the current governmental oversights. These presentations must be understandable by the lay public and must address their fears. Failure to assuage public fears and

  1. New Frontiers in Schistosoma Genomics and Transcriptomics

    Science.gov (United States)

    Nahum, Laila A.; Mourão, Marina M.; Oliveira, Guilherme

    2012-01-01

    Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium, S. japonicum, and S. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of six Schistosoma species have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization of Schistosoma genomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies. PMID:23227308

  2. 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/.

  3. [Optimization of time of artificial population schistosome infected Oncomelania hupensis snails].

    Science.gov (United States)

    Xiong, Chun-Rong; Yao, Yun-Yi; Yang, Kun

    2013-12-01

    To explore the optimizational time of artificial population schistosome infected Oncomelania hupensis snails. Under laboratory conditions, the snails were infected with the miracidia of Schistosoma japonicum for 2 h, 3 h and 4 h respectively, and the death rates and the infection rates of the snails, and the quantities of cercariae of each group were observed 60-120 d after the infection, and all the data observed were analyzed to get the optimizational time of artificial population schistosome infected snails. Of the 3 h group, the snail infection rate was the highest and the mortality was the lowest among the 3 groups (P0.05). Under laboratory conditions, the optimizational time is 3 h in artificial population schistosome infected O. hupensis snails.

  4. Morphological Specifications of the Bird Schistosome Cercariae and Surface Carbohydrates as Receptors for Lectins

    Directory of Open Access Journals (Sweden)

    I Moebedi

    2007-04-01

    Full Text Available Background: To determine the morphological specifications of the bird schistosomes cercaria from Lymnaea gedrosiana and to detect the surface carbohydrates as receptors for host lectins in the host-parasite relationship systems such as avian schistosomiasis and human cercarial dermatitis. Methods: One hundred ninety two snails collected from Dezful areas in Khuzestan Province, in the south west of Iran, during 2005-2006 were examined for cercariae using shedding and crushing methods. In addition, surface carbohydrates on the cercariae were detected by lentil (Lens culinaris lectins. Results: From the total number of Lymnaea gedrosiana, which examined for bird schistosomes cercaria, 9(4% snails were found to be infected with furcocercus cercaria of the bird schistosomes (probably Gigantobilharzia sp.. Mannose monosaccharide CH2OH (CHOH4CHO as surface carbohydrate was also detected on the cercariae. Conclusion: Mannose carbohydrate on these cercariae may be used as receptor by lectins.

  5. 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.

  6. A sea urchin genome project: Sequence scan, virtual map, and additional resources

    Science.gov (United States)

    Cameron, R. Andrew; Mahairas, Gregory; Rast, Jonathan P.; Martinez, Pedro; Biondi, Ted R.; Swartzell, Steven; Wallace, James C.; Poustka, Albert J.; Livingston, Brian T.; Wray, Gregory A.; Ettensohn, Charles A.; Lehrach, Hans; Britten, Roy J.; Davidson, Eric H.; Hood, Leroy

    2000-01-01

    Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 125 kb). The BAC-end sequence tag connectors (STCs) occur an average of 10 kb apart, and, together with restriction digest patterns recorded for the same BAC clones, they provide immediate access to contigs of several hundred kilobases surrounding any gene of interest. The STCs survey >5% of the genome and provide the estimate that this genome contains ≈27,350 protein-coding genes. The frequency distribution and canonical sequences of all middle and highly repetitive sequence families in the genome were obtained from the STCs as well. The 500-kb Hox gene complex of this species is being sequenced in its entirety. In addition, arrayed cDNA libraries of >105 clones each were constructed from every major stage of embryogenesis, several individual cell types, and adult tissues and are available to the community. The accumulated STC data and an expanding expressed sequence tag database (at present including >12,000 sequences) have been reported to GenBank and are accessible on public web sites. PMID:10920195

  7. Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes

    Directory of Open Access Journals (Sweden)

    Raphael D. Isokpehi

    2014-01-01

    Full Text Available The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III-responsive transcriptional repressor (ArsR, anion-transporting ATPase (ArsA, arsenical pump membrane protein (ArsB, arsenate reductase (ArsC, arsenical resistance operon transacting repressor (ArsD, water/glycerol transport protein (aquaporins, and universal stress protein (USP. These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus , and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD and cytochrome c biosynthesis (DsbD_2. Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c , produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

  8. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.

    Science.gov (United States)

    Isokpehi, Raphael D; Udensi, Udensi K; Simmons, Shaneka S; Hollman, Antoinesha L; Cain, Antia E; Olofinsae, Samson A; Hassan, Oluwabukola A; Kashim, Zainab A; Enejoh, Ojochenemi A; Fasesan, Deborah E; Nashiru, Oyekanmi

    2014-01-01

    The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

  9. Expression profile of the Schistosoma japonicum degradome reveals differential protease expression patterns and potential anti-schistosomal intervention targets.

    Science.gov (United States)

    Liu, Shuai; Cai, Pengfei; Piao, Xianyu; Hou, Nan; Zhou, Xiaosu; Wu, Chuang; Wang, Heng; Chen, Qijun

    2014-10-01

    Blood fluke proteases play pivotal roles in the processes of invasion, nutrition acquisition, immune evasion, and other host-parasite interactions. Hundreds of genes encoding putative proteases have been identified in the recently published schistosome genomes. However, the expression profiles of these proteases in Schistosoma species have not yet been systematically analyzed. We retrieved and culled the redundant protease sequences of Schistosoma japonicum, Schistosoma mansoni, Echinococcus multilocularis, and Clonorchis sinensis from public databases utilizing bioinformatic approaches. The degradomes of the four parasitic organisms and Homo sapiens were then comparatively analyzed. A total of 262 S. japonicum protease sequences were obtained and the expression profiles generated using whole-genome microarray. Four main clusters of protease genes with different expression patterns were identified: proteases up-regulated in hepatic schistosomula and adult worms, egg-specific or predominantly expressed proteases, cercaria-specific or predominantly expressed proteases, and constantly expressed proteases. A subset of protease genes with different expression patterns were further validated using real-time quantitative PCR. The present study represents the most comprehensive analysis of a degradome in Schistosoma species to date. These results provide a firm foundation for future research on the specific function(s) of individual proteases and may help to refine anti-proteolytic strategies in blood flukes.

  10. 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.

  11. Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project

    National Research Council Canada - National Science Library

    Nannya, Yasuhito; Taura, Kenjiro; Kurokawa, Mineo; Chiba, Shigeru; Ogawa, Seishi

    2007-01-01

    .... We investigated the extent to which this trade-off limits the genome-wide power with this approach by simulating a large number of case-control panels based on the empirical data from the HapMap Project...

  12. 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

  13. Transplacental transfer of schistosomal circulating anodic antigens in cows.

    Science.gov (United States)

    Gabriël, S; De Bont, J; Phiri, I K; Masuku, M; Riveau, G; Schacht, A M; Deelder, A M; Van Dam, G J; Vercruysse, J

    2002-01-01

    The present work investigated the transplacental passage of circulating anodic schistosome antigens (CAA) and the production of foetal antibodies in response to antigenic stimulation in Schistosoma mattheei infected cows. Three groups were available: six calves born to non-infected cows received colostrum from a pool from non-infected cows (group 1), six calves born to non-infected cows (group 2) and six calves born to infected cows (group 3) received colostrum from a pool from infected cows. Schistosoma-specific IgG1 antibody and CAA levels were measured in the colostrum pools, the sera collected from the cows, and the sera collected from the calves at birth, after intake of colostrum and at day 30. The specific IgG1 antibody levels were significantly higher in the sera from cows of group 3. In four cows of group 3 high CAA levels were detected. The specific IgG1 antibody levels were 0.646 and 0.176 OD for the infected and non-infected colostrum pool, respectively, and the CAA levels were 5667 and 2557 pg CAA/mL, respectively. At birth high levels of specific IgG1 antibody and CAA were detected in 4 calves of group 3; levels in the other two calves were negligible. After intake of colostrum, specific IgG1 antibody levels of group 1 increased slightly at day 1 to become again insignificant at day 30. In group 2 specific IgG1 antibody levels increased significantly between days 0 and 1, to decrease, although not significantly, at day 30. Finally, in group 3 the delta OD values increased at day 1 and remained high until day 30. After intake of colostrum the CAA level increased very slightly for groups 1 and 2 to become again undetectable at day 30. In group 3 a nonsignificant decrease in CAA levels was observed at day 1 followed by a further significant decrease to reach low levels at day 30. The suggested intrauterine antigenic stimulation may be important not only for generating immune responses to natural early infections, but also for enhancing the immunogenicity

  14. Schistosome syntenin partially protects vaccinated mice against Schistosoma mansoni infection.

    Directory of Open Access Journals (Sweden)

    Barbara C Figueiredo

    2014-08-01

    Full Text Available Schistosomiasis is a neglected tropical disease caused by several species of trematode of the genus Schistosoma. The disease affects more than 200 million people in the world and causes up to 280,000 deaths per year, besides having high morbidity due to chronic illness that damages internal organs. Current schistosomiasis control strategies are mainly based on chemotherapy, but many researchers believe that the best long-term strategy to control disease is a combination of drug treatment and immunization with an anti-schistosome vaccine. Among the most promising molecules as vaccine candidates are the proteins present in the tegument and digestive tract of the parasite.In this study, we describe for the first time Schistosoma mansoni syntenin (SmSynt and we evaluate its potential as a recombinant vaccine. We demonstrate by real-time PCR that syntenin is mainly expressed in intravascular life stages (schistosomula and adult worms of the parasite life cycle and, by confocal microscopy, we localize it in digestive epithelia in adult worms and schistosomula. Administration of siRNAs targeting SmSynt leads to the knock-down of syntenin gene and protein levels, but this has no demonstrable impact on parasite morphology or viability, suggesting that high SmSynt gene expression is not essential for the parasites in vitro. Mice immunization with rSmSynt, formulated with Freund's adjuvant, induces a Th1-type response, as suggested by the production of IFN-γ and TNF-α by rSmSynt-stimulated cultured splenocytes. The protective effect conferred by vaccination with rSmSynt was demonstrated by 30-37% reduction of worm burden, 38-43% reduction in the number, and 35-37% reduction in the area, of liver granulomas.Our report is the first characterization of syntenin in Schistosoma mansoni and our data suggest that this protein is a potential candidate for the development of a multi-antigen vaccine to control schistosomiasis.

  15. The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004

    Science.gov (United States)

    2013-01-01

    Background Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. Methods A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. Results A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. Conclusions These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004. PMID:24050173

  16. In vitro efflux of lactic acid by schistosomes cultured in varying ...

    African Journals Online (AJOL)

    While residing in the mammalian bloodstream, adult schistosomes consume large quantities of glucose and metabolize it to lactic acid. The accumulating load of this end product in the parasite tissue lowers the cellular pH, hence the need for a system to flux it out to avoid compromising metabolic processes. In the present ...

  17. Copro-PCR based detection of bovine schistosome infection in India.

    Science.gov (United States)

    Lakshmanan, B; Devada, K; Joseph, S; Aravindakshan, T V; Sabu, L

    2016-01-01

    Schistosomosis and amphistomosis are the two economically important and widely prevalent snail-borne trematode infections in grazing cattle of southern India. Acute infections are symptomatically similar and difficult to detect by routine microscopy for eggs. The present study was directed towards the development of a copro-polymerase chain reaction (copro-PCR) for detection of bovine schistosome species, using custom-designed primers targeting 18S and 28S ribosomal RNA as well as mitochondrial DNA. The study demonstrated the enhanced diagnostic specificity of mitochondrial DNA markers over ribosomal RNA genes as genus-specific probes to detect schistosomes. We developed a sensitive PCR assay using primers designed from mitochondrial DNA sequences targeting the partial rrnl (16S rRNA), tCys (transfer RNA for cysteine) and partial rrnS (12S rRNA) genes of Schistosoma spindale to specifically detect schistosome infection from faecal samples of naturally infected bovines. The salient findings of the work also throw light on to the high similarity of the ribosomal RNA gene sequences of schistosomes with those of Gastrothylax crumenifer and Fischoederius elongatus, the most prevalent pouched amphistomes of the region. Further investigation has to be directed towards unravelling the complete gene sequences of 18S and 28S ribosomal RNA as well as mitochondrial DNA sequences of amphistome isolates from India.

  18. Effect of praziquantel treatment during pregnancy on cytokine responses to schistosome antigens

    DEFF Research Database (Denmark)

    Tweyongyere, Robert; Mawa, Patrice A.; Ngom-Wegi, Sophy

    2008-01-01

    . Cytokine responses to S. mansoni worm and egg antigens were measured in whole blood culture before and 6 weeks after each treatment. RESULTS: Schistosome-specific cytokine responses were suppressed during pregnancy. Praziquantel treatment during pregnancy caused significant boosts in interferon-gamma (IFN...

  19. Untying the Gordian knot of creation: metaphors for the Human Genome Project in Greek newspapers.

    Science.gov (United States)

    Gogorosi, Eleni

    2005-12-01

    This article studies the metaphorical expressions used by newspapers to present the near completion of the Human Genome Project (HGP) to the Greek public in the year 2000. The analysis, based on cognitive metaphor theory, deals with the most frequent or captivating metaphors used to refer to the human genome, which give rise to both conventional and novel expressions. The majority of creative metaphorical expressions participate in the discourse of hope and promise propagated by the Greek media in an attempt to present the HGP and its outcome in a favorable light. Instances of the competing discourse of fear and danger are much rarer but can also be found in creative metaphorical expressions. Metaphors pertaining to the Greek culture or to ancient Greek mythology tend to carry a special rhetorical force. However, it will be shown that the Greek press strategically used most of the metaphors that circulated globally at the time, not only culture specific ones.

  20. Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation

    Science.gov (United States)

    Artigas, María Soler; Wain, Louise V.; Miller, Suzanne; Kheirallah, Abdul Kader; Huffman, Jennifer E.; Ntalla, Ioanna; Shrine, Nick; Obeidat, Ma'en; Trochet, Holly; McArdle, Wendy L.; Alves, Alexessander Couto; Hui, Jennie; Zhao, Jing Hua; Joshi, Peter K.; Teumer, Alexander; Albrecht, Eva; Imboden, Medea; Rawal, Rajesh; Lopez, Lorna M.; Marten, Jonathan; Enroth, Stefan; Surakka, Ida; Polasek, Ozren; Lyytikäinen, Leo-Pekka; Granell, Raquel; Hysi, Pirro G.; Flexeder, Claudia; Mahajan, Anubha; Beilby, John; Bossé, Yohan; Brandsma, Corry-Anke; Campbell, Harry; Gieger, Christian; Gläser, Sven; González, Juan R.; Grallert, Harald; Hammond, Chris J.; Harris, Sarah E.; Hartikainen, Anna-Liisa; Heliövaara, Markku; Henderson, John; Hocking, Lynne; Horikoshi, Momoko; Hutri-Kähönen, Nina; Ingelsson, Erik; Johansson, Åsa; Kemp, John P.; Kolcic, Ivana; Kumar, Ashish; Lind, Lars; Melén, Erik; Musk, Arthur W.; Navarro, Pau; Nickle, David C.; Padmanabhan, Sandosh; Raitakari, Olli T.; Ried, Janina S.; Ripatti, Samuli; Schulz, Holger; Scott, Robert A.; Sin, Don D.; Starr, John M.; Deloukas, Panos; Hansell, Anna L.; Hubbard, Richard; Jackson, Victoria E.; Marchini, Jonathan; Pavord, Ian; Thomson, Neil C.; Zeggini, Eleftheria; Viñuela, Ana; Völzke, Henry; Wild, Sarah H.; Wright, Alan F.; Zemunik, Tatijana; Jarvis, Deborah L.; Spector, Tim D.; Evans, David M.; Lehtimäki, Terho; Vitart, Veronique; Kähönen, Mika; Gyllensten, Ulf; Rudan, Igor; Deary, Ian J.; Karrasch, Stefan; Probst-Hensch, Nicole M.; Heinrich, Joachim; Stubbe, Beate; Wilson, James F.; Wareham, Nicholas J.; James, Alan L.; Morris, Andrew P.; Jarvelin, Marjo-Riitta; Hayward, Caroline; Sayers, Ian; Strachan, David P.; Hall, Ian P.; Tobin, Martin D.

    2015-01-01

    Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54,550 Europeans. We identify 14 novel loci (P<5 × 10−8) in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBX3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, and two novel signals at known loci NPNT and GPR126, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered. PMID:26635082

  1. 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.

  2. 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. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  3. 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

  4. 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).

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

    Directory of Open Access Journals (Sweden)

    Jia Wang

    Full Text Available 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/.

  6. 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

  7. Interplay between CKS2, N-cadherin, and PD-ECGF in Non-Schistosomal and Schistosomal-Associated Bladder Cancer: A Prospective Comparative Study in the Egyptian Population

    Directory of Open Access Journals (Sweden)

    Sanaa Shawky

    2017-01-01

    Full Text Available Background: The current study investigated the possible role of the cell cycle regulator, cyclin-dependent kinases regulatory subunit-2; the angiogenic factor, plateletderived endothelial cell growth factor; and the cell adhesive molecule, neural cadherin, as prognostic factors in schistosomal and non-schistosomal-associated urothelial carcinomas. We also investigated the possible correlation between cyclin-dependent kinases regulatory subunit-2, platelet-derived endothelial cell growth factor, neural cadherin, tumor grade, and stage. Methods: The study included 40 patients with primary bladder cancer (25 nonschistosomal- associated and 15 schistosomal-associated who had no prior anticancer treatment. Tumor specimens were collected at the time of the transurethral resection. The vivid portions of the resected tumors were subjected to routine pathological examinations to determine stage, grade, and schistosomal infestation. Control bladder tissues (5 cases were obtained by cystoscopic biopsies from patients who underwent transurethral resection of the prostate. Platelet-derived endothelial cell growth factor and neural cadherin protein expressions were evaluated by immunohistochemical staining. RNA was extracted, reverse transcribed, and amplified by PCR using cyclindependent kinases regulatory subunit-2 specific primers. Relative expression was detected by a comparison of the expression in normal and tumor samples relative to GAPDH (housekeeping gene expression. Results:We detected a positive correlation between neural cadherin and plateletderived endothelial cell growth factor proteins in schistosomal-associated and non-schistosomal-associated bladder cancer. Significant overexpression of relative cyclin-dependent kinases regulatory subunit-2 gene, neural cadherin, and plateletderived endothelial cell growth factor proteins were detected in invasive stages and higher grades of bladder cancer. Differential expressions of neural cadherin and

  8. 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

  9. Introgressive Hybridization of Schistosoma haematobium Group Species in Senegal: Species Barrier Break Down between Ruminant and Human Schistosomes

    OpenAIRE

    WEBSTER, B. L.; Diaw, O. T.; Seye, M M; Webster, J. P.; Rollinson, D

    2013-01-01

    BACKGROUND: Schistosomes are dioecious parasitic flatworms, which live in the vasculature of their mammalian definitive hosts. They are the causative agent of schistosomiasis, a disease of considerable medical and veterinary importance in tropical and subtropical regions. Schistosomes undergo a sexual reproductive stage within their mammalian host enabling interactions between different species, which may result in hybridization if the species involved are phylogenetically close. In Senegal, ...

  10. Host immunity, nutrition and coinfection alter longitudinal infection patterns of schistosomes in a free ranging African buffalo population

    Science.gov (United States)

    Jolles, Anna E.; Ezenwa, Vanessa O.; Smith, Mireya; Steinauer, Michelle L.

    2017-01-01

    Schistosomes are trematode parasites of global importance, causing infections in millions of people, livestock, and wildlife. Most studies on schistosomiasis, involve human subjects; as such, there is a paucity of longitudinal studies investigating parasite dynamics in the absence of intervention. As a consequence, despite decades of research on schistosomiasis, our understanding of its ecology in natural host populations is centered around how environmental exposure and acquired immunity influence acquisition of parasites, while very little is known about the influence of host physiology, coinfection and clearance in the absence of drug treatment. We used a 4-year study in free-ranging African buffalo to investigate natural schistosome dynamics. We asked (i) what are the spatial and temporal patterns of schistosome infections; (ii) how do parasite burdens vary over time within individual hosts; and (iii) what host factors (immunological, physiological, co-infection) and environmental factors (season, location) explain patterns of schistosome acquisition and loss in buffalo? Schistosome infections were common among buffalo. Microgeographic structure explained some variation in parasite burdens among hosts, indicating transmission hotspots. Overall, parasite burdens ratcheted up over time; however, gains in schistosome abundance in the dry season were partially offset by losses in the wet season, with some hosts demonstrating complete clearance of infection. Variation among buffalo in schistosome loss was associated with immunologic and nutritional factors, as well as co-infection by the gastrointestinal helminth Cooperia fuelleborni. Our results demonstrate that schistosome infections are surprisingly dynamic in a free-living mammalian host population, and point to a role for host factors in driving variation in parasite clearance, but not parasite acquisition which is driven by seasonal changes and spatial habitat utilization. Our study illustrates the power of

  11. Host immunity, nutrition and coinfection alter longitudinal infection patterns of schistosomes in a free ranging African buffalo population.

    Directory of Open Access Journals (Sweden)

    Brianna R Beechler

    2017-12-01

    Full Text Available Schistosomes are trematode parasites of global importance, causing infections in millions of people, livestock, and wildlife. Most studies on schistosomiasis, involve human subjects; as such, there is a paucity of longitudinal studies investigating parasite dynamics in the absence of intervention. As a consequence, despite decades of research on schistosomiasis, our understanding of its ecology in natural host populations is centered around how environmental exposure and acquired immunity influence acquisition of parasites, while very little is known about the influence of host physiology, coinfection and clearance in the absence of drug treatment. We used a 4-year study in free-ranging African buffalo to investigate natural schistosome dynamics. We asked (i what are the spatial and temporal patterns of schistosome infections; (ii how do parasite burdens vary over time within individual hosts; and (iii what host factors (immunological, physiological, co-infection and environmental factors (season, location explain patterns of schistosome acquisition and loss in buffalo? Schistosome infections were common among buffalo. Microgeographic structure explained some variation in parasite burdens among hosts, indicating transmission hotspots. Overall, parasite burdens ratcheted up over time; however, gains in schistosome abundance in the dry season were partially offset by losses in the wet season, with some hosts demonstrating complete clearance of infection. Variation among buffalo in schistosome loss was associated with immunologic and nutritional factors, as well as co-infection by the gastrointestinal helminth Cooperia fuelleborni. Our results demonstrate that schistosome infections are surprisingly dynamic in a free-living mammalian host population, and point to a role for host factors in driving variation in parasite clearance, but not parasite acquisition which is driven by seasonal changes and spatial habitat utilization. Our study illustrates

  12. Effects of schistosomal mansoni infection on Calomys callosus coelom-associated lymphomyeloid tissue (milky spots).

    Science.gov (United States)

    Lenzi, J A; Pelajo-Machado, M; Mota, E M; Oliveira, D N; Panasco, M S; Andrade, Z A; Lenzi, H L

    1998-01-01

    Calomys callosus Rengger, 1830 (Rodentia: Cricetidae) is a mouse-like South American wild rodent, which is permissive to Schistosoma mansoni infection. In this paper we studied the effect of schistosomal infection in C. callosus mesenteric and omental milky spots (MS), subsidiary foci of coelom-associated lymphomyeloid tissue (CALT), during the acute, transitional (acute to chronic), and chronic phases of the infection. MS were morphologically analyzed by histological methods, using brightfield and confocal laser scanning microscopies. The MS of infected animals were mainly of lymphomyelocytic (42 to 90 days) and lymphoplasmacytic (160 days of infection) types and showed frequent presence of lymphoid follicles with germinal centers, plasmacytogenesis and plasmacytosis, mastocytosis, megakaryopoiesis, erythropoiesis and less pronounced eosinopoiesis. These results indicate that MS are a preferential site of germinal-center-dependent and independent plasmacytogenesis, and a bone marrow-like organ, committed with various cellular lineages. The consequence of C. callosus MS reactivity for schistosomal infection is still unknown and is under investigation.

  13. 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.

  14. Understanding our Genetic Inheritance: The U.S. Human Genome Project, The First Five Years FY 1991--1995

    Science.gov (United States)

    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.

  15. 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.

  16. 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.

  17. Effects of Schistosomal mansoni infection on Calomys callosus coelom-associated lymphomyeloid tissue (milky spots)

    OpenAIRE

    Lenzi Jane A; Pelajo-Machado Marcelo; Mota Ester M; Oliveira Denise N; Panasco Mônica S; Andrade Zilton A; Lenzi Henrique L.

    1998-01-01

    Calomys callosus Rengger, 1830 (Rodentia: Cricetidae) is a mouse-like South American wild rodent, which is permissive to Schistosoma mansoni infection. In this paper we studied the effect of schistosomal infection in C. callosus mesenteric and omental milky spots (MS), subsidiary foci of coelom-associated lymphomyeloid tissue (CALT), during the acute, transitional (acute to chronic), and chronic phases of the infection. MS were morphologically analyzed by histological methods, using brigthfie...

  18. DIFFERENTIATION OF SCHISTOSOMA HAEMATOBIUM FROM RELATED SCHISTOSOMES BY PCR AMPLIFYING AN INTER-REPEAT SEQUENCE

    OpenAIRE

    Abbasi, Ibrahim; King, Charles H.; Sturrock,Robert F.; Kariuki, Curtis; Muchiri, Eric; HAMBURGER, JOSEPH

    2007-01-01

    Schistosoma haematobium infects nearly 150 million people, primarily in Africa, and is transmitted by select species of local bulinid snails. These snails can host other related trematode species as well, so that effective detection and monitoring of snails infected with S. haematobium requires a successful differentiation between S. haematobium and any closely related schistosome species. To enable differential detection of S. haematobium DNA by simple polymerase chain reaction (PCR), we des...

  19. Accelerated evolution of schistosome genes coding for proteins located at the host-parasite interface.

    Science.gov (United States)

    Philippsen, Gisele S; Wilson, R Alan; DeMarco, Ricardo

    2015-01-06

    Study of proteins located at the host-parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack. Micro-exon gene (MEG) protein products and venom allergen-like (VAL) proteins have been shown to be present in schistosome secretions or associated with glands, which led to the hypothesis that they are important components in the molecular interaction of the parasite with the host. Phylogenetic and structural analysis of genes and their transcripts in these two classes shows that recent species-specific expansion of gene number for these families occurred separately in three different species of schistosomes. Enrichment of transposable elements in MEG and VAL genes in Schistosoma mansoni provides a credible mechanism for preferential expansion of gene numbers for these families. Analysis of the ratio between synonymous and nonsynonymous substitution rates (dN/dS) in the comparison between schistosome orthologs for the two classes of genes reveals significantly higher values when compared with a set of a control genes coding for secreted proteins, and for proteins previously localized in the tegument. Additional analyses of paralog genes indicate that exposure of the protein to the definitive host immune system is a determining factor leading to the higher than usual dN/dS values in those genes. The observation that two genes encoding S. mansoni vaccine candidate proteins, known to be exposed at the parasite surface, also display similar evolutionary dynamics suggests a broad response of the parasite to evolutionary pressure imposed by the definitive host immune system. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. 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

  1. The developing schistosome worms elicit distinct immune responses in different tissue regions.

    Science.gov (United States)

    McWilliam, Hamish E G; Driguez, Patrick; Piedrafita, David; Maupin, Kevin A; Haab, Brian B; McManus, Donald P; Meeusen, Els N T

    2013-08-01

    Schistosome parasites follow a complex migration path through various tissues, changing their antigenic profile as they develop. A thorough understanding of the antibody response in each tissue region could help unravel the complex immunology of these developing parasites and aid vaccine design. Here we used a novel strategy for analysing the local antibody responses induced by Schistosoma japonicum infection at each site of infection. Cells from rat lymph nodes draining the sites of larval migration (the skin and lungs), the liver-lymph nodes where adults reside and the spleens were cultured to allow the in vivo-induced antibody-secreting cells to release antibody into the media. The amount and isotype of antibodies secreted in the supernatants differed significantly in the different lymph nodes and spleen, corresponding with the migration path of the schistosome worms. In addition, there were significant differences in binding specificity, as determined by surface labelling, western blots and by screening a glycan array. Through capturing the local antibody response, this study has revealed dramatic differences in the quality and specificity of the immune response at different tissue sites, and highlighted the existence of stage-specific protein and carbohydrate antigens. This will provide a valuable tool for the isolation of novel vaccine targets against the larval stages of schistosomes.

  2. Differentiation of Schistosoma haematobium from related schistosomes by PCR amplifying an inter-repeat sequence.

    Science.gov (United States)

    Abbasi, Ibrahim; King, Charles H; Sturrock, Robert F; Kariuki, Curtis; Muchiri, Eric; Hamburger, Joseph

    2007-05-01

    Schistosoma haematobium infects nearly 150 million people, primarily in Africa, and is transmitted by select species of local bulinid snails. These snails can host other related trematode species as well, so that effective detection and monitoring of snails infected with S. haematobium requires a successful differentiation between S. haematobium and any closely related schistosome species. To enable differential detection of S. haematobium DNA by simple polymerase chain reaction (PCR), we designed and tested primer pairs from numerous newly identified Schistosoma DNA repeat sequences. However, all pairs tested were found unsuitable for this purpose. Differentiation of S. haematobium from S. bovis, S. mattheei, S. curassoni, and S. intercalatum (but not from S. margrebowiei) was ultimately accomplished by PCR using one primer from a newly identified repeat, Sh110, and a second primer from a known schistosomal splice-leader sequence. For evaluation of residual S. haematobium transmission after control interventions, this differentiation tool will enable accurate monitoring of infected snails in areas where S. haematobium is sympatric with the most prevalent other schistosome species.

  3. Studies on transmission and schistosome interactions in Senegal, Mali and Zambia.

    Science.gov (United States)

    Vercruysse, J; Southgate, V R; Rollinson, D; De Clercq, D; Sacko, M; De Bont, J; Mungomba, L M

    1994-01-01

    The transmission and interaction of schistosomes in the Senegal River Basin in Mali and Zambia are reviewed and some preliminary field data are presented. In the Senegal River Basin four species of schistosomes are prevalent: Schistosoma mansoni, S. haematobium, S. bovis and S. curassoni as well as the following potential intermediate hosts: Biomphalaria pfeifferi, Bulinus globosus, B. umbilicatus, B. truncatus, B. senegalensis and B. forskalii. The role of each of these species in the transmission of schistosomes in man and domestic stock is discussed. Recent ecological changes caused by the construction of dams at Diama and Mananatali on the Senegal River, such as reduction in salinity, more stable water flow, creation of irrigation canals and development and extension of rice culture, have contributed towards the occurrence of new outbreaks of both intestinal and urinary schistosomiasis in the Senegal River Basin. In Mali, the four main areas of high prevalence of S. haematobium are Office du Niger (irrigation areas), Bandiagara (small dams), Selingué (dam areas) and Baguineda (irrigation areas). Apart from the Office du Niger, S. mansoni infections are rare. Surveys were carried out in the Dogon Country (Bandiagara District) in an attempt to confirm the recent independent reports of the presence of S. intercalatum. Data based on egg morphology and Ziehl Neelsen staining of egg shells suggested the possible occurrence of S. haematobium x S. intercalatum hybrids. Potential factors affecting the focal endemicity of S. haematobium in Mali are discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Natural infection with schistosomes of the Schistosoma haematobium group in a dog in Zambia.

    Science.gov (United States)

    Chiti, L; De Bont, J; Fransen, J; Kane, R A; Mwase, M; Southgate, V R; Vercruysse, J

    2000-01-01

    Post-mortem examination of an adult male Jack Russell dog from Zambia revealed that it was heavily infected with schistosomes. The dog had been admitted, with a history of retching, 4 days before its death. At necropsy, the liver was found to be enlarged, with multiple pin-point yellowish-white foci scattered diffusely throughout the organ. Multiple pin-point recent and old haemorrhages were seen on the mucosal surface of the gastrointestinal tract, particularly in the stomach and proximal duodenum. Large numbers of schistosome worm pairs and eggs were found in all mesenteric, gastric and hepatic veins. Histological examination of the intestines, mesenteric lymph nodes, liver, spleen, pancreas, stomach and lungs revealed numerous strongly fibrotic, encapsulated, epithelioid-giant cell granulomata containing dead, degenerating and viable eggs. A few examples of the Splendore-Hoeppli phenomenon were also detected. The eggs collected at necropsy had a terminal spine and an average length and breadth of 187.6+/-14.1 microm and 57. 3+/-4.1 microm, respectively. DNA analysis of female worms indicated that the schistosomes were either Schistosoma haematobium or a hybrid of Schistosoma mattheei and S. haematobium. Copyright 2000 Harcourt Publishers Ltd.

  5. Comparison of Schistosoma mansoni soluble cercarial antigens and soluble egg antigens for serodiagnosing schistosome infections.

    Science.gov (United States)

    Smith, Huw; Doenhoff, Mike; Aitken, Cara; Bailey, Wendi; Ji, Minjun; Dawson, Emily; Gilis, Henk; Spence, Grant; Alexander, Claire; van Gool, Tom

    2012-01-01

    A Schistosoma mansoni cercarial antigen preparation (cercarial transformation fluid--SmCTF) was evaluated for detection of anti-schistosome antibodies in human sera in 4 collaborating laboratories. The performance of SmCTF was compared with that of S. mansoni egg antigens (SmSEA) in an indirect enzyme-immunoassay (ELISA) antigen assay, the latter being used routinely in 3 of the 4 participating laboratories to diagnose S. mansoni and S. haematobium infections. In the fourth laboratory the performance of SmCTF was compared with that of S. japonicum egg antigens (SjSEA) in ELISA for detection of anti-S. japonicum antibodies. In all 4 laboratories the results given by SmCTF in ELISA were very similar to those given by the antigen preparation routinely used in the respective laboratory to detect anti-schistosome antibodies in human infection sera. In so far as the ELISA results from SmCTF are thus so little different from those given by schistosome egg antigens and also cheaper to produce, the former is a potentially useful new diagnostic aid for schistosomiasis.

  6. Comparison of Schistosoma mansoni soluble cercarial antigens and soluble egg antigens for serodiagnosing schistosome infections.

    Directory of Open Access Journals (Sweden)

    Huw Smith

    Full Text Available A Schistosoma mansoni cercarial antigen preparation (cercarial transformation fluid--SmCTF was evaluated for detection of anti-schistosome antibodies in human sera in 4 collaborating laboratories. The performance of SmCTF was compared with that of S. mansoni egg antigens (SmSEA in an indirect enzyme-immunoassay (ELISA antigen assay, the latter being used routinely in 3 of the 4 participating laboratories to diagnose S. mansoni and S. haematobium infections. In the fourth laboratory the performance of SmCTF was compared with that of S. japonicum egg antigens (SjSEA in ELISA for detection of anti-S. japonicum antibodies. In all 4 laboratories the results given by SmCTF in ELISA were very similar to those given by the antigen preparation routinely used in the respective laboratory to detect anti-schistosome antibodies in human infection sera. In so far as the ELISA results from SmCTF are thus so little different from those given by schistosome egg antigens and also cheaper to produce, the former is a potentially useful new diagnostic aid for schistosomiasis.

  7. Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset.

    Science.gov (United States)

    Sengupta, Dhriti; Choudhury, Ananyo; Basu, Analabha; Ramsay, Michèle

    2016-12-31

    Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto-Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. 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

  9. Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans

    Science.gov (United States)

    Pardo-Seco, Jacobo; Amigo, Jorge; Martinón-Torres, Federico

    2015-01-01

    Background 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). Results 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. Conclusions 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. PMID:25786119

  10. Strategies for exome and genome sequence data analysis in disease-gene discovery projects.

    Science.gov (United States)

    Robinson, Peter N; Krawitz, P; Mundlos, S

    2011-08-01

    In whole-exome sequencing (WES), target capture methods are used to enrich the sequences of the coding regions of genes from fragmented total genomic DNA, followed by massively parallel, 'next-generation' sequencing of the captured fragments. Since its introduction in 2009, WES has been successfully used in several disease-gene discovery projects, but the analysis of whole-exome sequence data can be challenging. In this overview, we present a summary of the main computational strategies that have been applied to identify novel disease genes in whole-exome data, including intersect filters, the search for de novo mutations, and the application of linkage mapping or inference of identity-by-descent (IBD) in family studies. © 2011 John Wiley & Sons A/S.

  11. Differentiating Schistosoma haematobium from Schistosoma magrebowiei and other closely related schistosomes by polymerase chain reaction amplification of a species specific mitochondrial gene.

    Science.gov (United States)

    Akinwale, Olaoluwa P; Hock, Tang T; Chia-Kwung, Fan; Zheng, Qi; Haimo, Shen; Ezeh, Charles; Gyang, Pam V

    2014-01-01

    Schistosoma haematobium infection afflicts about 150 million people in 53 countries in Africa and the Middle East. In many endemic areas, S. haematobium is sympatric with Schistosoma bovis, Schistosoma mattheei, Schistosoma curassoni, Schistosoma intercalatum and Schistosoma magrebowiei, its closely related species. In addition, they also develop in the same intermediate snail hosts. Since these schistosome species often infect snails inhabiting the same bodies of water, examining cercariae or infected snails for estimating transmission of S. haematobium is always confounded by the need to differentially identify S. haematobium from these other species. Recently, differentiating S. haematobium by polymerase chain reaction (PCR) from S. bovis, S. mattheei, S. curassoni and S. intercalatum, but not from S. magrebowiei was reported. However, to be able to evaluate residual S. haematobium transmission after control interventions in areas where S. haematobium may be sympatric with S. magrebowiei, a differential tool for accurate monitoring of infected snails is needed. Thus in this study, we developed a new PCR assay using a pair of primers, ShND-1/ShND-2, to amplify a target sequence of 1117 bp (GenBank accession number KF834975) from S. haematobium mitochondrion complete genome (GenBank accession number DQ157222). Sensitivity of the assay was determined by PCR amplification of different concentrations of S. haematobium gDNA serially diluted from 10ng to 0.1pg. For assay specificity, different concentrations of gDNA from S. haematobium and the other schistosome species, 20 positive urine samples and five controls as well as 20 infected snails were subjected to PCR amplification, while some of the PCR products were sequenced. The assay detected up to 1pg of S. haematobium gDNA, while a differential identification of S. haematobium DNA content from other closely related species was achieved when applied to urine and naturally infected snails. When a protein-protein blast

  12. Polypyridylruthenium(II complexes exert anti-schistosome activity and inhibit parasite acetylcholinesterases.

    Directory of Open Access Journals (Sweden)

    Madhu K Sundaraneedi

    2017-12-01

    Full Text Available Schistosomiasis affects over 200 million people and there are concerns whether the current chemotherapeutic control strategy (periodic mass drug administration with praziquantel (PZQ-the only licenced anti-schistosome compound is sustainable, necessitating the development of new drugs.We investigated the anti-schistosome efficacy of polypyridylruthenium(II complexes and showed they were active against all intra-mammalian stages of S. mansoni. Two compounds, Rubb12-tri and Rubb7-tnl, which were among the most potent in their ability to kill schistosomula and adult worms and inhibit egg hatching in vitro, were assessed for their efficacy in a mouse model of schistosomiasis using 5 consecutive daily i.v. doses of 2 mg/kg (Rubb12-tri and 10 mg/kg (Rubb7-tnl. Mice treated with Rubb12-tri showed an average 42% reduction (P = 0.009, over two independent trials, in adult worm burden. Liver egg burdens were not significantly decreased in either drug-treated group but ova from both of these groups showed significant decreases in hatching ability (Rubb12-tri-68%, Rubb7-tnl-56% and were significantly morphologically altered (Rubb12-tri-62% abnormal, Rubb7-tnl-35% abnormal. We hypothesize that the drugs exerted their activity, at least partially, through inhibition of both neuronal and tegumental acetylcholinesterases (AChEs, as worms treated in vitro showed significant decreases in activity of these enzymes. Further, treated parasites exhibited a significantly decreased ability to uptake glucose, significantly depleted glycogen stores and withered tubercules (a site of glycogen storage, implying drug-mediated interference in this nutrient acquisition pathway.Our data provide compelling evidence that ruthenium complexes are effective against all intra-mammalian stages of schistosomes, including schistosomula (refractory to PZQ and eggs (agents of disease transmissibility. Further, the results of this study suggest that schistosome AChE is a target of

  13. Genomic methods and microbiological technologies for profiling novel and extreme environments for the extreme microbiome project (XMP)

    OpenAIRE

    Tighe, S; Afshinnekoo, E; Rock, TM; McGrath, K; Alexander, N; McIntyre, A; Ahsanuddins, S; Bezdan, D; Green, SJ; Joye, S; Johnson, SS; Baldwin, DA; Bivens, N; Ajami, N; Carmical, JR

    2017-01-01

    © 2017, Association of Biomolecular Resource Facilities. All rights reserved. The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characteri...

  14. Performance of genotype imputations using data from the 1000 Genomes Project.

    Science.gov (United States)

    Sung, Yun Ju; Wang, Lihua; Rankinen, Tuomo; Bouchard, Claude; Rao, D C

    2012-01-01

    Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq Project is still underway, we expect that later versions will provide even better imputation performance. Copyright © 2011 S. Karger AG, Basel.

  15. Citrus Greening-HLB Genome Resources Group: A bioinformatics resource for diverse projects related to the biology and diagnosis of citrus greening/HLB

    OpenAIRE

    Saha, Surya; Lindeberg, Magdalen

    2013-01-01

    The CG-HLB Genome Resources Group serves as a bioinformatics resource for diverse projects related to the biology and diagnosis of citrus greening/HLB. Current projects include the identification of bacterial endosymbionts in the Diaphorina citri (Asian citrus psyllid) metagenome. Mapping sequence reads to reference genomes shows evidence for Wolbachia and an enterobacterial endosymbiont related to Salmonella in the metagenome. A draft genome sequence has been produced for the Wolbachia endos...

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

    Science.gov (United States)

    Teeling, Emma; Vernes, Sonja; Davalos, Liliana M; Ray, David A; Gilbert, M Thomas P; Myers, Eugene; Bat K Consortium

    2017-11-20

    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 (>132 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. Expected final online publication date for the Annual Review of Animal Biosciences Volume 6 is February 15, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  17. Natural Products as Leads in Schistosome Drug Discovery

    Directory of Open Access Journals (Sweden)

    Bruno J. Neves

    2015-01-01

    Full Text Available Schistosomiasis is a neglected parasitic tropical disease that claims around 200,000 human lives every year. Praziquantel (PZQ, the only drug recommended by the World Health Organization for the treatment and control of human schistosomiasis, is now facing the threat of drug resistance, indicating the urgent need for new effective compounds to treat this disease. Therefore, globally, there is renewed interest in natural products (NPs as a starting point for drug discovery and development for schistosomiasis. Recent advances in genomics, proteomics, bioinformatics, and cheminformatics have brought about unprecedented opportunities for the rapid and more cost-effective discovery of new bioactive compounds against neglected tropical diseases. This review highlights the main contributions that NP drug discovery and development have made in the treatment of schistosomiasis and it discusses how integration with virtual screening (VS strategies may contribute to accelerating the development of new schistosomidal leads, especially through the identification of unexplored, biologically active chemical scaffolds and structural optimization of NPs with previously established activity.

  18. 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.

  19. 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 ...

  20. Effect of praziquantel treatment of Schistosoma mansoni during pregnancy on immune responses to schistosome antigens among the offspring

    DEFF Research Database (Denmark)

    Tweyongyere, Robert; Mawa, Patrice A.; Kihembo, Macklyn

    2011-01-01

    Offspring of women with schistosomiasis may exhibit immune responsiveness to schistosomes due to in utero sensitisation or trans-placental transfer of antibodies. Praziquantel treatment during pregnancy boosts maternal immune responses to schistosome antigens and reduces worm burden. Effects of p...

  1. 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

  2. In vivo imaging of schistosomes to assess disease burden using positron emission tomography (PET).

    Science.gov (United States)

    Salem, Nicolas; Balkman, Jason D; Wang, Jing; Wilson, David L; Lee, Zhenghong; King, Christopher L; Basilion, James P

    2010-09-21

    Schistosomes are chronic intravascular helminth parasites of humans causing a heavy burden of disease worldwide. Diagnosis of schistosomiasis currently requires the detection of schistosome eggs in the feces and urine of infected individuals. This method unreliably measures disease burden due to poor sensitivity and wide variances in egg shedding. In vivo imaging of schistosome parasites could potentially better assess disease burden, improve management of schistosomiasis, facilitate vaccine development, and enhance study of the parasite's biology. Schistosoma mansoni (S. mansoni) have a high metabolic demand for glucose. In this work we investigated whether the parasite burden in mice could be assessed by positron emission tomography (PET) imaging with 2-deoxy-2[(18)F]fluoro-D-glucose (FDG). Live adult S. mansoni worms FDG uptake in vitro increased with the number of worms. Athymic nude mice infected with S. mansoni 5-6 weeks earlier were used in the imaging studies. Fluorescence molecular tomography (FMT) imaging with Prosense 680 was first performed. Accumulation of the imaging probe in the lower abdomen correlated with the number of worms in mice with low infection burden. The total FDG uptake in the common portal vein and/or regions of elevated FDG uptake in the liver linearly correlated to the number of worms recovered from infected animals (R(2) =0.58, Pworm burden in mice with more than 50 worms (R(2) = 0.85, Pworms in a mouse with a high infection burden were in the portal vein, but not in a mouse with a low infection burden. FDG uptake in recovered worms measured by well counting closely correlated with worm number (R(2) = 0.85, Pworm burden in schistosomiasis-infected animals. Future investigations aiming at minimizing non-specific FDG uptake and to improve the recovery of signal from worms located in the lower abdomen will include the development of more specific radiotracers.

  3. Schistosome infection is negatively associated with mite atopy, but not wheeze and asthma in Ghanaian schoolchildren.

    Science.gov (United States)

    Obeng, B B; Amoah, A S; Larbi, I A; de Souza, D K; Uh, H-W; Fernández-Rivas, M; van Ree, R; Rodrigues, L C; Boakye, D A; Yazdanbakhsh, M; Hartgers, F C

    2014-07-01

    Epidemiological evidence suggests that helminth infection and rural living are inversely associated with allergic disorders. The aim of the study was to investigate the effect of helminth infections and urban versus rural residence on allergy in schoolchildren from Ghana. In a cross-sectional study of 1385 children from urban-high socio-economic status (SES), urban-low SES and rural schools, associations between body mass index (BMI), allergen-specific IgE (sIgE), parasitic infections and allergy outcomes were analysed. Allergy outcomes were skin prick test (SPT) reactivity, reported current wheeze and asthma. Helminth infections were found predominantly among rural subjects, and the most common were hookworm (9.9%) and Schistosoma spp (9.5%). Being overweight was highest among urban-high SES (14.6%) compared to urban-low SES (5.5%) and rural children (8.6%). The prevalence of SPT reactivity to any allergen was 18.3%, and this was highest among rural children (21.4%) followed by urban-high SES (20.2%) and urban-low SES (10.5%) children. Overall, SPT reactivity to mite (12%) was most common. Wheeze and asthma were reported by 7.9% and 8.3%, respectively. In multivariate analyses, factors associated with mite SPT were BMI (aOR 2.43, 95% CI 1.28-4.60, P = 0.007), schistosome infection (aOR 0.15, 95% CI 0.05-0.41) and mite sIgE (aOR 7.40, 95% CI 5.62-9.73, P asthma. Infection with schistosomes appeared to protect against mite SPT reactivity. This needs to be confirmed in future studies, preferably in a longitudinal design where schistosome infections are treated and allergic reactions reassessed. © 2014 John Wiley & Sons Ltd.

  4. Studies on animal schistosomes in Peninsular Malaysia: record of naturally infected animals and additional hosts of Schistosoma spindale.

    Science.gov (United States)

    Inder Singh, K; Krishnasamy, M; Ambu, S; Rasul, R; Chong, N L

    1997-06-01

    Surveillance studies on cercarial dermatitis were carried out in paddy growing areas in Peninsular Malaysia. It was observed that dermatitis in paddy planters occurred in paddy fields which were cultivated using animals such as bafflos or fields where domestic animals were allowed to graze during the off planting season as these animals harbored the parasite. The causative agent of cercarial dermatitis was Schistosoma spindale. A total of 215 small mammals trapped from Alor Setar and 126 trapped from Labu were examined for the schistosome. In Alor Setar Bandicota indica, Rattus argentiventer and Rattus rattus diardii were the only wild mammals found to be infected with the parasite, while in the Labu areas only Rattus tiomanicus jalorensis was positive for the schistosome. The occurrence of S. spindale in R. argentiventer and R.r. diardii in Alor Setar and in R.t. jalorensis in Labu constitute new host and geographic distribution records of the schistosome.

  5. Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project.

    Science.gov (United States)

    Nannya, Yasuhito; Taura, Kenjiro; Kurokawa, Mineo; Chiba, Shigeru; Ogawa, Seishi

    2007-10-15

    With recent advances in high-throughput single nucleotide polymorphism (SNP) typing technologies, genome-wide association studies have become a realistic approach to identify the causative genes that are responsible for common diseases of complex genetic traits. In this strategy, a trade-off between the increased genome coverage and a chance of finding SNPs incidentally showing a large statistics becomes serious due to extreme multiple-hypothesis testing. We investigated the extent to which this trade-off limits the genome-wide power with this approach by simulating a large number of case-control panels based on the empirical data from the HapMap Project. In our simulations, statistical costs of multiple hypothesis testing were evaluated by empirically calculating distributions of the maximum value of the chi(2) statistics for a series of marker sets having increasing numbers of SNPs, which were used to determine a genome-wide threshold in the following power simulations. With a practical study size, the cost of multiple testing largely offsets the potential benefits from increased genome coverage given modest genetic effects and/or low frequencies of causal alleles. In most realistic scenarios, increasing genome coverage becomes less influential on the power, while sample size is the predominant determinant of the feasibility of genome-wide association tests. Increasing genome coverage without corresponding increase in sample size will only consume resources without little gain in power. For common causal alleles with relatively large effect sizes [genotype relative risk > or =1.7], we can expect satisfactory power with currently available large-scale genotyping platforms using realistic sample size ( approximately 1000 per arm).

  6. 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.

  7. Familial aggregation of focal seizure semiology in the Epilepsy Phenome/Genome Project.

    Science.gov (United States)

    Tobochnik, Steven; Fahlstrom, Robyn; Shain, Catherine; Winawer, Melodie R

    2017-07-04

    To improve phenotype definition in genetic studies of epilepsy, we assessed the familial aggregation of focal seizure types and of specific seizure symptoms within the focal epilepsies in families from the Epilepsy Phenome/Genome Project. We studied 302 individuals with nonacquired focal epilepsy from 149 families. Familial aggregation was assessed by logistic regression analysis of relatives' traits (dependent variable) by probands' traits (independent variable), estimating the odds ratio for each symptom in a relative given presence vs absence of the symptom in the proband. In families containing multiple individuals with nonacquired focal epilepsy, we found significant evidence for familial aggregation of ictal motor, autonomic, psychic, and aphasic symptoms. Within these categories, ictal whole body posturing, diaphoresis, dyspnea, fear/anxiety, and déjà vu/jamais vu showed significant familial aggregation. Focal seizure type aggregated as well, including complex partial, simple partial, and secondarily generalized tonic-clonic seizures. Our results provide insight into genotype-phenotype correlation in the nonacquired focal epilepsies and a framework for identifying subgroups of patients likely to share susceptibility genes. © 2017 American Academy of Neurology.

  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. Genome research elucidating environmental adaptation: Dark-fly project as a case study.

    Science.gov (United States)

    Fuse, Naoyuki

    2017-08-01

    Organisms have the capacity to adapt to diverse environments, and environmental adaptation is a substantial driving force of evolution. Recent progress of genome science has addressed the genetic mechanisms underlying environmental adaptation. Whole genome sequencing has identified adaptive genes selected under particular environments. Genome editing technology enables us to directly test the role(s) of a gene in environmental adaptation. Genome science has also shed light on a unique organism, Dark-fly, which has been reared long-term in the dark. We determined the whole genome sequence of Dark-fly and reenacted environmental selections of the Dark-fly genome to identify the genes related to dark-adaptation. Here I will give an overview of current progress in genome science and summarize our study using Dark-fly, as a case study for environmental adaptation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. [Polymorphism of the cox1 gene in bird schistosome cercaria isolates (Trematoda, Schistosomatidae) from ponds of Moscow and Moscow oblast].

    Science.gov (United States)

    Lopatkin, A A; Khrisanfova, G G; Voronin, M V; Zazornova, O P; Beér, S A; Semenova, S K

    2010-07-01

    Polymorphism of a 8 10-bp mitochondrial cox1 gene region was studied in 16 cercaria isolates of bird schistosomes (family Schistosomatidae), which were collected in water bodies of Moscow and Moscow oblast and represented three species: Trichobilharzia szidati, T. franki, and T. regenti. A substantial predominance of AT (65.4%) was characteristic of the cox1 sequences in all three species. Rare single nucleotide substitutions determined low (0.2-0.9%) intraspecific nucleotide and amino acid sequence diversity. Haplotype diversity h was high (80-100%) in all three species, suggesting a unique character for almost all cox1 sequences in the sample. Phylogenetic trees based on the nucleotide and amino acid sequence variations were constructed to study the relationships of the three schistosome species. A high support was observed for the main branching node that reflects differentiation of the monophyletic group Trichobilharzia and species of the genera Bilharziella (B. polonica), Dendritobilharzia (D. pulverulenta), and Gigantobilharzia (G. huronensis). Based on the nucleotide substitutions and amino acid polymorphisms, two groups of isolates, which infect Lymnaea stagnalis (T. szidati) and snails of the group Radix (T. franki and T. regenti) respectively, were isolated in the genus Trichobilharzia. The time of divergence between the two schistosome groups infecting snails of the genera Radix and Lymnaea was calculated from the cox1 nucleotide substitution rate, which is known for Asian and Indian blood flukes from the genus Schistosoma and is 2-3% per million years on average. Divergence of the three bird schistosome species under study and divergence of the Asian species of mammalian schistosome were almost concurrent, dating back to 2.5-3.8 Myr ago. Factors responsible for the lack of intraspecific subdivision with respect to the cox1 gene in bird schistosomes and the lack of separation between two species (T. franki and T. regenti) are discussed.

  11. Pattern of cercarial emergence of Schistosoma curassoni from Niger and comparison with three sympatric species of schistosomes.

    Science.gov (United States)

    Mouchet, F; Théron, A; Brémond, P; Sellin, E; Sellin, B

    1992-02-01

    The emergence pattern of Schistosoma curassoni cercariae from Bulinus umbilicatus, whose adult worms parasitize bovine, caprine, and ovine ungulates in Niger, is of a circadian type with a mean emission time at 0855 hr +/- 1 hr 6 min, characteristic of the schistosome species parasitizing domestic or wild cattle. The comparison of this cercarial emergence pattern with those of the other 3 sympatric species of schistosomes (Schistosoma haematobium, Schistosoma bovis, and Schistosoma mansoni) shows a significant difference between the chronobiology of the cercariae infective for human and those infective for bovine hosts. This difference may improve epidemiological surveys based on snail prevalences by allowing the distinction between bulinids infected with human and bovine parasites.

  12. 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

  13. Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space.

    Science.gov (United States)

    Carter, Phil; Lee, David; Orengo, Christine

    2008-01-01

    Structural genomics aims to solve the three-dimensional structures of proteins at a rapid rate and in a cost-effective manner, with the hope of significantly impacting on the life sciences, biotechnology, and drug discovery in the long-term. Structural genomics initiatives started in Japan in 1997 with the advent of the Protein Folds Project. Since then many new initiatives have begun worldwide, with diverse aims motivating the selection of proteins for structure determination. In this chapter, we consider the biological goals of high-throughput structural biology, while focusing on the Protein Structure Initiative in the United States. This is the most productive of the structural genomics initiatives, having solved 3,363 new structures between September 2000 and October 2008.

  14. Polymerase chain reaction assay based on a highly repeated sequence of Schistosoma haematobium: a potential tool for monitoring schistosome-infested water.

    Science.gov (United States)

    Hamburger, J; He-Na; Abbasi, I; Ramzy, R M; Jourdane, J; Ruppel, A

    2001-12-01

    We have cloned from Schistosoma haematobium genome a repeated sequence, the DraI repeated sequence, which consists of tandemly arranged 121-bp-long units and which is highly abundant (approximately 15% of the S. haematobium genome). By these features, the DraI repeat is similar to the Sm1-7 sequence of Schistosoma mansoni previously described by us. However, their nucleotide sequences are profoundly different. Polymerase chain reaction (PCR) primers were designed on the basis of the DraI sequence information and were used in a PCR assay by which as little as 10 fg of schistosomal DNA as well as individual cercariae were detected. The DraI repeat cross-hybridized with DNA from Schistosoma bovis, Schistosoma magrebowiei, Schistosoma mattheei, Schistosoma curassoni, and Schistosoma intercalatum, but not with DNA from S. mansoni nor from Trichobilharzia ocellata and Echinostoma sp. A potential value of this PCR assay is suggested for monitoring free-living cercariae and infected snails only in bodies free of cross-hybridizing species.

  15. Effects of Schistosomal mansoni infection on Calomys callosus coelom-associated lymphomyeloid tissue (milky spots

    Directory of Open Access Journals (Sweden)

    Jane A Lenzi

    1998-01-01

    Full Text Available Calomys callosus Rengger, 1830 (Rodentia: Cricetidae is a mouse-like South American wild rodent, which is permissive to Schistosoma mansoni infection. In this paper we studied the effect of schistosomal infection in C. callosus mesenteric and omental milky spots (MS, subsidiary foci of coelom-associated lymphomyeloid tissue (CALT, during the acute, transitional (acute to chronic, and chronic phases of the infection. MS were morphologically analyzed by histological methods, using brigthfield and confocal laser scanning microscopies. The MS of infected animals were mainly of lymphomyelocytic (42 to 90 days and lymphoplasmacytic (160 days of infection types and showed frequent presence of lymphoid follicles with germinal centers, plasmacytogenesis and plasmacytosis, mastocytosis, megakaryopoiesis, erythropoiesis and less pronounced eosinopoiesis. These results indicate that MS are a preferential site of germinal-center-dependent and independent plasmacytogenesis, and a bone marrow-like organ, committed with various cellular lineages. The consequence of C. callosus MS reactivity for schistosomal infection is still unknown and is under investigation.

  16. Immunological Consequences of Antihelminthic Treatment in Preschool Children Exposed to Urogenital Schistosome Infection

    Directory of Open Access Journals (Sweden)

    Nadine Rujeni

    2013-01-01

    Full Text Available Urogenital schistosomiasis, due to Schistosoma haematobium, is endemic in sub-Saharan Africa. Control is by targeted treatment with praziquantel but preschool age children are excluded from control programs. Immunological studies on the effect of treatment at this young age are scarce. In light of studies in older individuals showing that praziquantel alters antischistosome immune responses and responses to bystander antigens, this study aims to investigate how these responses would be affected by treatment at this young age. Antibody responses directed against schistosome antigens, Plasmodium falciparum crude and recombinant antigens, and the allergen house dust mite were measured in children aged 3 to 5 years before and 6 weeks after treatment. The change in serological recognition of schistosome proteins was also investigated. Treatment augmented antischistosome IgM and IgE responses. The increase in IgE responses directed against adult worm antigens was accompanied by enhanced antigen recognition by sera from the children. Antibody responses directed against Plasmodium antigens were not significantly affected by praziquantel treatment nor were levels of allergen specific responses. Overall, praziquantel treatment enhanced, quantitatively and qualitatively, the antiworm responses associated with protective immunity but did not alter Plasmodium-specific responses or allergen-specific responses which mediate pathology in allergic disease.

  17. Schistosome infection intensity is inversely related to auto-reactive antibody levels.

    Directory of Open Access Journals (Sweden)

    Francisca Mutapi

    Full Text Available In animal experimental models, parasitic helminth infections can protect the host from auto-immune diseases. We conducted a population-scale human study investigating the relationship between helminth parasitism and auto-reactive antibodies and the subsequent effect of anti-helminthic treatment on this relationship. Levels of antinuclear antibodies (ANA and plasma IL-10 were measured by enzyme linked immunosorbent assay in 613 Zimbabweans (aged 2-86 years naturally exposed to the blood fluke Schistosoma haematobium. ANA levels were related to schistosome infection intensity and systemic IL-10 levels. All participants were offered treatment with the anti-helminthic drug praziquantel and 102 treated schoolchildren (5-16 years were followed up 6 months post-antihelminthic treatment. ANA levels were inversely associated with current infection intensity but were independent of host age, sex and HIV status. Furthermore, after allowing for the confounding effects of schistosome infection intensity, ANA levels were inversely associated with systemic levels of IL-10. ANA levels increased significantly 6 months after anti-helminthic treatment. Our study shows that ANA levels are attenuated in helminth-infected humans and that anti-helminthic treatment of helminth-infected people can significantly increase ANA levels. The implications of these findings are relevant for understanding both the aetiology of immune disorders mediated by auto-reactive antibodies and in predicting the long-term consequences of large-scale schistosomiasis control programs.

  18. A molecular genetic study of the variations in metabolic function during schistosome development

    Directory of Open Access Journals (Sweden)

    Patrick J. Skelly

    1995-04-01

    Full Text Available During their complex life cycle schistosomes alternate between the use of stored glycogen and reliance on host glucose to provide for their energy needs. In addition, there is dramatic variation between the relative contribution of aerobic versus anaerobic glucose metabolism during development. We have cloned a set of representative cDNAs that encode proteins involved in glucose uptake, glycolysis, Kreb's cycle and oxidative phosphorylation. The different cDNAs were used as probes to examine the expression of glucose metabolism genes during the schistosome life cycle. Steady state mRNA levels from whole cercariae, isolated cercarial tails, schistosomula and adult worms were analysed on Northern blots and dot blots which were quantified using storage phosphor technology. These studies reveal: (1 Transcripts encoding glycogen metabolic enzymes are expressed to much higher levels in cercarial tails than whole cercariae or schistosomula while the opposite pattern is found for glucose transporters and hexokinase transcripts; (2 Schistosomula contain low levels of transcripts encoding respiratory enzymes but regain the capacity for aerobic glucose metabolism as they mature to adulthood; (3 Male and female adults contain similar levels of the different transcripts involved in glucose metabolism.

  19. Mobile Diagnostics Based on Motion? A Close Look at Motility Patterns in the Schistosome Life Cycle

    Directory of Open Access Journals (Sweden)

    Ewert Linder

    2016-06-01

    Full Text Available Imaging at high resolution and subsequent image analysis with modified mobile phones have the potential to solve problems related to microscopy-based diagnostics of parasitic infections in many endemic regions. Diagnostics using the computing power of “smartphones” is not restricted by limited expertise or limitations set by visual perception of a microscopist. Thus diagnostics currently almost exclusively dependent on recognition of morphological features of pathogenic organisms could be based on additional properties, such as motility characteristics recognizable by computer vision. Of special interest are infectious larval stages and “micro swimmers” of e.g., the schistosome life cycle, which infect the intermediate and definitive hosts, respectively. The ciliated miracidium, emerges from the excreted egg upon its contact with water. This means that for diagnostics, recognition of a swimming miracidium is equivalent to recognition of an egg. The motility pattern of miracidia could be defined by computer vision and used as a diagnostic criterion. To develop motility pattern-based diagnostics of schistosomiasis using simple imaging devices, we analyzed Paramecium as a model for the schistosome miracidium. As a model for invasive nematodes, such as strongyloids and filaria, we examined a different type of motility in the apathogenic nematode Turbatrix, the “vinegar eel.” The results of motion time and frequency analysis suggest that target motility may be expressed as specific spectrograms serving as “diagnostic fingerprints.”

  20. Detecting hybridization in African schistosome species: does egg morphology complement molecular species identification?

    Science.gov (United States)

    Boon, Nele A M; Fannes, Wouter; Rombouts, Sara; Polman, Katja; Volckaert, Filip A M; Huyse, Tine

    2017-06-01

    Hybrid parasites may have an increased transmission potential and higher virulence compared to their parental species. Consequently, hybrid detection is critical for disease control. Previous crossing experiments showed that hybrid schistosome eggs have distinct morphotypes. We therefore compared the performance of egg morphology with molecular markers with regard to detecting hybridization in schistosomes. We studied the morphology of 303 terminal-spined eggs, originating from 19 individuals inhabiting a hybrid zone with natural crosses between the human parasite Schistosoma haematobium and the livestock parasite Schistosoma bovis in Senegal. The egg sizes showed a high variability and ranged between 92·4 and 176·4 µm in length and between 35·7 and 93·0 µm in width. No distinct morphotypes were found and all eggs resembled, to varying extent, the typical S. haematobium egg type. However, molecular analyses on the same eggs clearly showed the presence of two distinct partial mitochondrial cox1 profiles, namely S. bovis and S. haematobium, and only a single nuclear ITS rDNA profile (S. haematobium). Therefore, in these particular crosses, egg morphology appears not a good indicator of hybrid ancestry. We conclude by discussing strengths and limitations of molecular methods to detect hybrids in the context of high-throughput screening of field samples.

  1. 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.

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

    Science.gov (United States)

    Covell, David G

    2015-01-01

    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.

  3. Whole Genome Selection Project Involving 2,000 Industry AI Sires

    Science.gov (United States)

    Whole genome selection (WGS) uses markers spanning the genome to predict genetic merit for economically important traits. WGS may increase the rate of genetic progress through improved accuracy and reduced generation interval especially for traits that cannot be measured on breeding animals. In cont...

  4. Distribution of freshwater snails in the river Niger basin in Mali with special reference to the intermediate hosts of schistosomes

    DEFF Research Database (Denmark)

    Madsen, Henry; Coulibaly, Godefroy; Furu, Peter

    1987-01-01

    Snail surveys were carried out in various parts of Mali. All areas surveyed are part of the Niger basin being either affluents or irrigation schemes fed by this river. The snail species present varied greatly between areas. The following potential hosts of schistosomes were recorded: Biomphalaria...

  5. Schistosomes of small mammals from the Lake Victoria Basin, Kenya: new species, familiar species, and implications for schistosomiasis control.

    Science.gov (United States)

    Hanelt, B; Mwangi, I N; Kinuthia, J M; Maina, G M; Agola, L E; Mutuku, M W; Steinauer, M L; Agwanda, B R; Kigo, L; Mungai, B N; Loker, E S; Mkoji, G M

    2010-06-01

    Recent schistosomiasis control efforts in sub-Saharan Africa have focused nearly exclusively on treatment of humans with praziquantel. However, the extent to which wild mammals act as reservoirs for Schistosoma mansoni and therefore as sources of renewed transmission following control efforts is poorly understood. With the objective to study the role of small mammals as reservoir hosts, 480 animals belonging to 9 rodent and 1 insectivore species were examined for infection with schistosomes in Kisumu, in the Lake Victoria Basin, Kenya. Animals were collected from 2 sites: near the lakeshore and from Nyabera Marsh draining into the lake. A total of 6.0% of the animals captured, including 5 murid rodent species and 1 species of shrew (Crocidura olivieri) were infected with schistosomes. Four schistosome species were recovered and identified using cox1 DNA barcoding: S. mansoni, S. bovis, S. rodhaini and S. kisumuensis, the latter of which was recently described from Nyabera Marsh. Schistosoma mansoni and S. rodhaini were found infecting the same host individual (Lophuromys flavopunctatus), suggesting that this host species could be responsible for the production of hybrid schistosomes found in the area. Although the prevalence of S. mansoni infection in these reservoir populations was low (1.5%), given their potentially vast population size, their impact on transmission needs further study. Reservoir hosts could perpetuate snail infections and favour renewed transmission to humans once control programmes have ceased.

  6. Polyethyleneimine mediated DNA transfection in schistosome parasites and regulation of the WNT signaling pathway by a dominant-negative SmMef2.

    Directory of Open Access Journals (Sweden)

    Shuang Liang

    Full Text Available Schistosomiasis is a serious global problem and the second most devastating parasitic disease following malaria. Parasitic worms of the genus Schistosoma are the causative agents of schistosomiasis and infect more than 240 million people worldwide. The paucity of molecular tools to manipulate schistosome gene expression has made an understanding of genetic pathways in these parasites difficult, increasing the challenge of identifying new potential drugs for treatment. Here, we describe the use of a formulation of polyethyleneimine (PEI as an alternative to electroporation for the efficacious transfection of genetic material into schistosome parasites. We show efficient expression of genes from a heterologous CMV promoter and from the schistosome Sm23 promoter. Using the schistosome myocyte enhancer factor 2 (SmMef2, a transcriptional activator critical for myogenesis and other developmental pathways, we describe the development of a dominant-negative form of the schistosome Mef2. Using this mutant, we provide evidence that SmMef2 may regulate genes in the WNT pathway. We also show that SmMef2 regulates its own expression levels. These data demonstrate the use of PEI to facilitate effective transfection of nucleic acids into schistosomes, aiding in the study of schistosome gene expression and regulation, and development of genetic tools for the characterization of molecular pathways in these parasites.

  7. 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.

  8. HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni.

    Directory of Open Access Journals (Sweden)

    Sutas Suttiprapa

    2016-10-01

    Full Text Available Schistosomiasis is the most important helminthic disease of humanity in terms of morbidity and mortality. Facile manipulation of schistosomes using lentiviruses would enable advances in functional genomics in these and related neglected tropical diseases pathogens including tapeworms, and including their non-dividing cells. Such approaches have hitherto been unavailable. Blood stream forms of the human blood fluke, Schistosoma mansoni, the causative agent of the hepatointestinal schistosomiasis, were infected with the human HIV-1 isolate NL4-3 pseudotyped with vesicular stomatitis virus glycoprotein. The appearance of strong stop and positive strand cDNAs indicated that virions fused to schistosome cells, the nucleocapsid internalized and the RNA genome reverse transcribed. Anchored PCR analysis, sequencing HIV-1-specific anchored Illumina libraries and Whole Genome Sequencing (WGS of schistosomes confirmed chromosomal integration; >8,000 integrations were mapped, distributed throughout the eight pairs of chromosomes including the sex chromosomes. The rate of integrations in the genome exceeded five per 1,000 kb and HIV-1 integrated into protein-encoding loci and elsewhere with integration bias dissimilar to that of human T cells. We estimated ~ 2,100 integrations per schistosomulum based on WGS, i.e. about two or three events per cell, comparable to integration rates in human cells. Accomplishment in schistosomes of post-entry processes essential for HIV-1replication, including integrase-catalyzed integration, was remarkable given the phylogenetic distance between schistosomes and primates, the natural hosts of the genus Lentivirus. These enigmatic findings revealed that HIV-1 was active within cells of S. mansoni, and provided the first demonstration that HIV-1 can integrate into the genome of an invertebrate.

  9. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data.

    Science.gov (United States)

    Brandt, Débora Y C; Aguiar, Vitor R C; Bitarello, Bárbara D; Nunes, Kelly; Goudet, Jérôme; Meyer, Diogo

    2015-03-17

    Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity. Copyright © 2015 Brandt et al.

  10. Application of DNA-based diagnostics in detection of schistosomal DNA in early infection and after drug treatment

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    Ji Minjun

    2011-08-01

    Full Text Available Abstract Background Research is now focused on identification of sensitive and specific diagnostic tests for early identification of schistosomal infection and evaluation of chemotherapy in field situations in China. Results This study compared loop-mediated isothermal amplification (LAMP with conventional PCR as DNA-based diagnostic techniques for the early detection of schistosomal DNA and the evaluation of chemotherapy. The results showed that both PCR and LAMP assays targeting a 301 base pair (bp sequence of the highly repetitive retrotransposon, SjR2, amplified DNA from schistosomes but were unable to distinguish between schistosome species. LAMP and conventional PCR were shown to amplify the target sequence of the SjR2-pCR2.1 recombinant plasmid template with limits of detection of 10-4 ng and 10-2 ng, respectively, thus demonstrating the superior sensitivity of the LAMP method. Schistosoma japonicum DNA was detected in all serum samples obtained from the three experimental groups at 1 week post-infection by LAMP assay, while the rate of detection by conventional PCR ranged from 50% to 66%. The potential application of PCR and LAMP assays for the evaluation of artesunate and praziquantel chemotherapy was investigated. PCR was shown to be less sensitive for detection of schistosomal DNA in drug-treated rabbit sera than the LAMP method. Conclusions The data presented here indicate that LAMP is suitable for the detection of early infection in the groups primarily infected with Schistosoma japonicum, such as migrants, travellers, military personnel and the younger age groups. However, it is less suitable for evaluation of the efficacy of chemotherapy in the early stages because of its high sensitivity.

  11. Recent studies on the reproductive biology of the schistosomes and their relevance to speciation in the Digenea.

    Science.gov (United States)

    Southgate, V R; Jourdane, J; Tchuenté, L A

    1998-08-01

    The members of the family Schistosomatidae, dioecious Digenea, are discussed with regard to their distribution, intermediate and definitive host-parasite relationships. The biological species concept is considered together with the difficulties of its application to Schistosoma spp. and the Digenea. The correlation between pairing of adult schistosomes, physical and sexual development and the maintenance of reproductive potential is emphasised. Development of the female reproductive system does not depend upon species-specific pairing. In some combinations, e.g., Schistosoma haematobium/Schistosoma intercalatum and Schistosoma bovis/Schistosoma curassoni, a specific mate choice system apparently does not exist, whereas it does in other combinations, e.g., Schistosoma mansoni/Schistosoma intercalatum. In mixed infections change of mate may occur and when the opportunity arises heterospecific pairs of worms will change partners to conspecific pairs. Interspecific pairing in adult schistosomes will lead to either hybridisation or parthenogenesis. Yet the majority of schistosomes that inhabit the same definitive host maintain their genetic identity: specific mate recognition, site selection within the host and heterologous immunity have been suggested as isolating mechanisms. Experimental intraspecific crosses have enabled evaluation of the degree to which some populations separated and became reproductively isolated through pre-mating isolating mechanisms, indicative of incipient speciation, e.g., the Lower Guinea and Zaire strains of S. intercalatum. The occurrence and significance of parthenogenesis in schistosomes and other species of Digenea are discussed. The consequences of interspecific mating interactions in schistosomes with regard to parasite epidemiology, interspecific competition and genetic heterogeneity are debated. Geographical isolation and host specificity represent important pre-zygotic isolating mechanisms. It is suggested that site selection within

  12. In vivo imaging of schistosomes to assess disease burden using positron emission tomography (PET.

    Directory of Open Access Journals (Sweden)

    Nicolas Salem

    2010-09-01

    Full Text Available Schistosomes are chronic intravascular helminth parasites of humans causing a heavy burden of disease worldwide. Diagnosis of schistosomiasis currently requires the detection of schistosome eggs in the feces and urine of infected individuals. This method unreliably measures disease burden due to poor sensitivity and wide variances in egg shedding. In vivo imaging of schistosome parasites could potentially better assess disease burden, improve management of schistosomiasis, facilitate vaccine development, and enhance study of the parasite's biology. Schistosoma mansoni (S. mansoni have a high metabolic demand for glucose. In this work we investigated whether the parasite burden in mice could be assessed by positron emission tomography (PET imaging with 2-deoxy-2[(18F]fluoro-D-glucose (FDG.Live adult S. mansoni worms FDG uptake in vitro increased with the number of worms. Athymic nude mice infected with S. mansoni 5-6 weeks earlier were used in the imaging studies. Fluorescence molecular tomography (FMT imaging with Prosense 680 was first performed. Accumulation of the imaging probe in the lower abdomen correlated with the number of worms in mice with low infection burden. The total FDG uptake in the common portal vein and/or regions of elevated FDG uptake in the liver linearly correlated to the number of worms recovered from infected animals (R(2 =0.58, P<0.001, n = 40. FDG uptake showed a stronger correlation with the worm burden in mice with more than 50 worms (R(2 = 0.85, P<0.001, n = 17. Cryomicrotome imaging confirmed that most of the worms in a mouse with a high infection burden were in the portal vein, but not in a mouse with a low infection burden. FDG uptake in recovered worms measured by well counting closely correlated with worm number (R(2 = 0.85, P<0.001, n = 21. Infected mice showed a 32% average decrease in total FDG uptake after three days of praziquantel treatment (P = 0.12. The total FDG uptake in untreated mice increased

  13. Hsp70 May Be a Molecular Regulator of Schistosome Host Invasion.

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    Kenji Ishida

    2016-09-01

    Full Text Available Schistosomiasis is a debilitating disease that affects over 240 million people worldwide and is considered the most important neglected tropical disease following malaria. Free-swimming freshwater cercariae, one of the six morphologically distinct schistosome life stages, infect humans by directly penetrating through the skin. Cercariae identify and seek the host by sensing chemicals released from human skin. When they reach the host, they burrow into the skin with the help of proteases and other contents released from their acetabular glands and transform into schistosomula, the subsequent larval worm stage upon skin infection. Relative to host invasion, studies have primarily focused on the nature of the acetabular gland secretions, immune response of the host upon exposure to cercariae, and cercaria-schistosomulum transformation methods. However, the molecular signaling pathways involved from host-seeking through the decision to penetrate skin are not well understood. We recently observed that heat shock factor 1 (Hsf1 is localized to the acetabular glands of infectious schistosome cercariae, prompting us to investigate a potential role for heat shock proteins (HSPs in cercarial invasion. In this study, we report that cercarial invasion behavior, similar to the behavior of cercariae exposed to human skin lipid, is regulated through an Hsp70-dependent process, which we show by using chemical agents that target Hsp70. The observation that biologically active protein activity modulators can elicit a direct and clear behavioral change in parasitic schistosome larvae is itself interesting and has not been previously observed. This finding suggests a novel role for Hsp70 to act as a switch in the cercaria-schistosomulum transformation, and it allows us to begin elucidating the pathways associated with cercarial host invasion. In addition, because the Hsp70 protein and its structure/function is highly conserved, the model that Hsp70 acts as a

  14. 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

  15. 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.

  16. [Spatial regression analysis of relationship between schistosome infection rate of Oncomelania hupensis snails and climate factors].

    Science.gov (United States)

    Chen, Yan-yan; Iu, Jian-bing; Xiao, Ying; Zhou, Xiao-rong; Jiang, Yong; Dai, Ling-feng; Cai, Shun-xiang

    2015-04-01

    To explore the relationship between the schistosome infection rate of O. hupensis snails and the climate factors in endemic areas of schistosomiasis, so as to provide the evidence for improving the snail control. The snail and climate data of 18 counties in Hubei Province in 2009 were collected to obtain the infection rate of O. hupensis snails and to fit the spatial regression models. The multiple linear regression model showed that the residuals were autocorrelated (Moran's I = 0.182 8, P snails was positively correlated with the annual average temperature (P 0.05). The spatial regression models could be well applied in the analysis of the relationship between the O. hupensis snails and climate factors. The annual average temperature is the primary climate factor influencing the infection of O. hupensis snails.

  17. Extensive spinal cord involvement in magnetic resonance imaging evaluation on schistosomal myelitis

    Directory of Open Access Journals (Sweden)

    Claudio Henrique Fernandes Vidal

    2012-03-01

    Full Text Available The diagnosis of schistosomal myelitis (SM is frequently presumptive because no findings from any complementary examination are pathognomonic for this disease. The present report describes some abnormalities seen on magnetic resonance imaging (MRI evaluation of a series of SM patients and discusses their etiopathogenesis. Methods: This study evaluated SM patients at the time of their diagnosis. These patients routinely underwent MRI on all segments of the spinal cord. Results: Thirteen patients were evaluated. The MRI was abnormal in 12 (92.3% of them. In 11 patients (84.61%, the damage reached two or more spinal segments. Conclusions: MRI was an important diagnostic aid in this sample, because of the high rate of abnormalities detected. The tissue damage observed on MRI was extensive in the majority of the patients.

  18. Host determinants of reinfection with schistosomes in humans: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Evaristus Chibunna Mbanefo

    2014-09-01

    Full Text Available Schistosomiasis is still a major public health burden in the tropics and subtropics. Although there is an effective chemotherapy (Praziquantel for this disease, reinfection occurs rapidly after mass drug administration (MDA. Because the entire population do not get reinfected at the same rate, it is possible that host factors may play a dominant role in determining resistance or susceptibility to reinfection with schistosomes. Here, we systematically reviewed and meta-analyzed studies that reported associations between reinfection with the principal human-infecting species (S. mansoni, S. japonicum and S. haematobium and host socio-demographic, epidemiological, immunological and genetic factors.PubMed, Scopus, Google Scholar, Cochrane Review Library and African Journals Online public databases were searched in October 2013 to retrieve studies assessing association of host factors with reinfection with schistosomes. Meta-analysis was performed to generate pooled odds ratios and standardized mean differences as overall effect estimates for dichotomous and continuous variables, respectively. Quality assessment of included studies, heterogeneity between studies and publication bias were also assessed. Out of the initial 2739 records, 109 studies were included in the analyses, of which only 32 studies with 37 data sets were eligible for quantitative data synthesis. Among several host factors identified, strong positive association was found with age and pre-treatment intensity, and only slightly for gender. These factors are major determinants of exposure and disease transmission. Significant positive association was found with anti-SWA IgG4 level, and a negative overall effect for association with IgE levels. This reconfirmed the concept that IgE/IgG4 balance is a major determinant of protective immunity against schistosomiasis. Other identified determinants were reported by a small number of studies to enable interpretation.Our data contribute to

  19. Schistosomes with wings: how host phylogeny and ecology shape the global distribution of Trichobilharzia querquedulae (Schistosomatidae).

    Science.gov (United States)

    Ebbs, Erika T; Loker, Eric S; Davis, Norm E; Flores, Veronica; Veleizan, Aylen; Brant, Sara V

    2016-09-01

    Migratory waterfowl play an important role in the maintenance and spread of zoonotic diseases worldwide. An example is cercarial dermatitis, caused when larval stages of schistosomes that normally develop in birds penetrate human skin. Members of the genus Trichobilharzia (Schistosomatidae), transmitted mainly by ducks, are considered to be major etiological agents of cercarial dermatitis globally. To better understand the diversity and distribution of Trichobilharzia spp., we surveyed ducks from the United States, eastern Canada, Argentina, South Africa and New Zealand. To aid in species identification of the Trichobilharzia worms recovered, regions of the Cox1, ND4 and ITS1 were sequenced. Furthermore, we provide molecular phylogenetic evidence for the cosmopolitan distribution and trans-hemispheric gene flow for one species, Trichobilharzia querquedulae, previously thought to be restricted to North America. These new samples from endemic non-migratory duck species indicate that T. querquedulae transmission occurs within each of the regions we sampled and that it is specific to the blue-winged+silver teal duck clade. Prevalence within this host group is >95% across the known range of T. querquedulae, indicating that transmission is common. Genetic divergence is evenly distributed among continents, and no phylogenetic structure associated with geography was observed. The results provide strong support for the global distribution and transmission of T. querquedulae and represent, to our knowledge, the first report of a cosmopolitan schistosome confirmed by genetic data. These data are the first known to support trans-hemispheric genetic exchange in a species responsible for causing cercarial dermatitis, indicating that the epidemiology of this group of poorly known zoonotic parasites is more complex than previously expected. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  20. Identification of the Boudicca and Sinbad retrotransposons in the genome of the human blood fluke Schistosoma haematobium

    Directory of Open Access Journals (Sweden)

    Claudia S Copeland

    2006-08-01

    Full Text Available Schistosomes have a comparatively large genome, estimated for Schistosoma mansoni to be about 270 megabase pairs (haploid genome. Recent findings have shown that mobile genetic elements constitute significant proportions of the genomes of S. mansoni and S. japonicum. Much less information is available on the genome of the third major human schistosome, S. haematobium. In order to investigate the possible evolutionary origins of the S. mansoni long terminal repeat retrotransposons Boudicca and Sinbad, several genomes were searched by Southern blot for the presence of these retrotransposons. These included three species of schistosomes, S. mansoni, S. japonicum, and S. haematobium, and three related platyhelminth genomes, the liver flukes Fasciola hepatica and Fascioloides magna and the planarian, Dugesia dorotocephala. In addition, Homo sapiens and three snail host genomes, Biomphalaria glabrata, Oncomelania hupensis, and Bulinus truncatus, were examined for possible indications of a horizontal origin for these retrotransposons. Southern hybridization analysis indicated that both Boudicca and Sinbad were present in the genome of S. haematobium. Furthermore, low stringency Southern hybridization analyses suggested that a Boudicca-like retrotransposon was present in the genome of B. truncatus, the snail host of S. haematobium.

  1. Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples.

    Science.gov (United States)

    Mandage, Rajendra; Telford, Marco; Rodríguez, Juan Antonio; Farré, Xavier; Layouni, Hafid; Marigorta, Urko M; Cundiff, Caitlin; Heredia-Genestar, Jose Maria; Navarro, Arcadi; Santpere, Gabriel

    2017-01-01

    Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologies.

  2. 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.

  3. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database.

    Science.gov (United States)

    Walsh, Calum J; Guinane, Caitriona M; Hill, Colin; Ross, R Paul; O'Toole, Paul W; Cotter, Paul D

    2015-09-16

    The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project's reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. We identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides. Multiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production.

  4. Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project.

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Choi, Su Ryun; Van Nguyen, Dan; Hossain, Md Jamil; Yang, Hyeon Kook; Lim, Yong Pyo

    2010-11-01

    We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.

  5. Expression of schistosomal cathepsin l1 in Escherichia coli and evaluation of its protective capacity in an animal challenge

    Directory of Open Access Journals (Sweden)

    PA Miyasato

    2009-01-01

    Full Text Available Schistosomes utilize proteinases to accomplish several activities such as tissue penetration, tissue digestion and evasion of host immune responses. Cathepsin L is a cysteine proteinase of the papain superfamily detected in their gut lumen which indicates that this enzyme contributes to the proteolysis of ingested hemoglobin. Due to the roles played in the schistosome biology, proteolytic enzymes are considered potential targets for developing and guiding antischistosomal therapies. In the present work, the cathepsin L1 cDNA coding of Schistosoma mansoni was cloned into the pAE vector that provides high-level expression of heterologous proteins in Escherichia coli. The recombinant protein was expressed as inclusion bodies, purified under denaturing conditions through nickel-charged chromatography and used for experimental animal vaccination. ELISA was performed with the pooled sera. Although this protein was shown to be immunogenic, mice immunized with three doses of recombinant protein plus aluminum hydroxide as adjuvant were not protected against S. mansoni infection.

  6. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

    Science.gov (United States)

    Tighe, Scott; Afshinnekoo, Ebrahim; Rock, Tara M; McGrath, Ken; Alexander, Noah; McIntyre, Alexa; Ahsanuddin, Sofia; Bezdan, Daniela; Green, Stefan J; Joye, Samantha; Stewart Johnson, Sarah; Baldwin, Don A; Bivens, Nathan; Ajami, Nadim; Carmical, Joseph R; Herriott, Ian Charold; Colwell, Rita; Donia, Mohamed; Foox, Jonathan; Greenfield, Nick; Hunter, Tim; Hoffman, Jessica; Hyman, Joshua; Jorgensen, Ellen; Krawczyk, Diana; Lee, Jodie; Levy, Shawn; Garcia-Reyero, Natàlia; Settles, Matthew; Thomas, Kelley; Gómez, Felipe; Schriml, Lynn; Kyrpides, Nikos; Zaikova, Elena; Penterman, Jon; Mason, Christopher E

    2017-04-01

    The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

  7. Schistosome-induced portacaval haemodynamic changes in Rattus rattus are associated with translocation of adult worms to the lungs

    OpenAIRE

    Imbert-Establet, D.; Mone, H.; Coulson, P.S.; Wilson, R A

    1998-01-01

    The presence of naturally portacaval shunts has been investigated in the vasculature of normal and Schistosoma mansoni-infected Rattus rattus. Using the technique of injecting Polystyrene microspheres in the superior mesenteric vein, we demonstrated that the presence of adult schistosomes in the lungs of R. rattus was not due to an innate anomaly of the rat vasculature but resulted from the formation of portacaval shunts during infection. In rats harbouring a bisexual infection, microspheres ...

  8. Isolation and preservation of schistosome eggs and larvae in RNAlater® facilitates genetic profiling of individuals

    Directory of Open Access Journals (Sweden)

    Webster Bonnie L

    2009-10-01

    Full Text Available Abstract Although field-sampling procedures to capture gDNA from individual schistosome larval stages directly from their natural hosts exist, they do pose some technical and logistical challenges hampering certain epidemiological studies. The aim of this study was to develop, refine and evaluate an alternative methodology, which enables better preservation of large numbers of individual schistosome larval stages and eggs collected in low resource endemic areas, to provide PCR-quality DNA for multi-locus genetic analysis. The techniques reported here present simple and effective short-term field and long-term laboratory preservation and storage systems for individually sampled schistosome eggs and larval stages using a commercially available aqueous stabilisation reagent, RNAlater® eliminating the need for more cumbersome resources such as refrigerators, heaters and centrifuge equipment for immediate specimen processing. Adaptations to a general gDNA extraction method are described, that enables the acquisition of a gDNA extract (~50 μl, facilitating multiple molecular analyses of each sampled schistosome. The methodology provided PCR-quality mitochondrial and nuclear DNA from laboratory cercariae, miracidia and eggs that had been stored at up to 37°C for 2 weeks and at 4°C for 6 months and also from field collected samples. This present protocol provides significant epidemiological, ethical and practical advantages over existing sampling methods and has the potential to be transferred to studies on other organisms, especially where specimens are unable to be seen by the naked eye, are difficult to handle and need to be obtained from a field environment.

  9. Infection with schistosome parasites in snails leads to increased predation by prawns: implications for human schistosomiasis control.

    Science.gov (United States)

    Swartz, Scott J; De Leo, Giulio A; Wood, Chelsea L; Sokolow, Susanne H

    2015-12-01

    Schistosomiasis - a parasitic disease that affects over 200 million people across the globe - is primarily transmitted between human definitive hosts and snail intermediate hosts. To reduce schistosomiasis transmission, some have advocated disrupting the schistosome life cycle through biological control of snails, achieved by boosting the abundance of snails' natural predators. But little is known about the effect of parasitic infection on predator-prey interactions, especially in the case of schistosomiasis. Here, we present the results of laboratory experiments performed on Bulinus truncatus and Biomphalaria glabrata snails to investigate: (i) rates of predation on schistosome-infected versus uninfected snails by a sympatric native river prawn, Macrobrachium vollenhovenii, and (ii) differences in snail behavior (including movement, refuge-seeking and anti-predator behavior) between infected and uninfected snails. In predation trials, prawns showed a preference for consuming snails infected with schistosome larvae. In behavioral trials, infected snails moved less quickly and less often than uninfected snails, and were less likely to avoid predation by exiting the water or hiding under substrate. Although the mechanism by which the parasite alters snail behavior remains unknown, these results provide insight into the effects of parasitic infection on predator-prey dynamics and suggest that boosting natural rates of predation on snails may be a useful strategy for reducing transmission in schistosomiasis hotspots. © 2015. Published by The Company of Biologists Ltd.

  10. Association between Micronutrients (Vitamin A, D, Iron and Schistosome-Specific Cytokine Responses in Zimbabweans Exposed to Schistosoma haematobium

    Directory of Open Access Journals (Sweden)

    Liam Reilly

    2012-01-01

    Full Text Available Micronutrients play an important role in the development of effective immune responses. This study characterised a populations exposed to schistosome infections in terms of the relationship between micronutrients and immune responses. Levels of retinol binding protein (RBP; vitamin A marker, vitamin D, ferritin and soluble transferrin receptor (sTfR, and C reactive protein (CRP were related to levels of schistosome specific cytokines (IFN-γ, IL-4/5/10 in 40 Zimbabweans (7–54 years exposed to Schistosoma haematobium infection. 67.2% of the participants were deficient in vitamin D. RBP levels were within normal ranges but declined with age. The two indicators of iron levels suggested that although levels of stored iron were within normal levels (normal ferritin levels, levels of functional iron (sTfR levels were reduced in 28.6% of the population. Schistosome infection alone was not associated with levels of any of the micronutrients, but altered the relationship between parasite-specific IL-4 and IL-5 and levels of ferritin and sTfR.

  11. School Water, Sanitation, and Hygiene, Soil-Transmitted Helminths, and Schistosomes: National Mapping in Ethiopia.

    Directory of Open Access Journals (Sweden)

    Jack E T Grimes

    2016-03-01

    Full Text Available It is thought that improving water, sanitation, and hygiene (WASH might reduce the transmission of schistosomes and soil-transmitted helminths, owing to their life cycles. However, few large-scale studies have yet assessed the real extent of associations between WASH and these parasites.In the 2013-2014 Ethiopian national mapping of infections with these parasites, school WASH was assessed alongside infection intensity in children, mostly between 10 and 15 years of age. Scores were constructed reflecting exposure to schistosomes arising from water collection for schools, from freshwater sources, and the adequacy of school sanitation and hygiene facilities. Kendall's τb was used to test the WASH scores against the school-level arithmetic mean intensity of infection with each parasite, in schools with at least one child positive for the parasite in question. WASH and parasitology data were available for 1,645 schools. More frequent collection of water for schools, from open freshwater sources was associated with statistically significantly higher Schistosoma mansoni infection intensity (Kendall's τb = 0.097, 95% confidence interval, CI: 0.011 to 0.18, better sanitation was associated with significantly lower Ascaris lumbricoides intensity (Kendall's τb = -0.067, 95% CI: -0.11 to -0.023 and borderline significant lower hookworm intensity (Kendall's τb = -0.039, 95% CI: -0.090 to 0.012, P = 0.067, and better hygiene was associated with significantly lower hookworm intensity (Kendall's τb = -0.076, 95% CI: -0.13 to -0.020. However, no significant differences were observed when comparing sanitation and infection with S. mansoni or Trichuris trichiura, or hygiene and infection with A. lumbricoides or T. trichiura.Improving school WASH may reduce transmission of these parasites. However, different forms of WASH appear to have different effects on infection with the various parasites, with our analysis finding the strongest associations between

  12. School Water, Sanitation, and Hygiene, Soil-Transmitted Helminths, and Schistosomes: National Mapping in Ethiopia.

    Science.gov (United States)

    Grimes, Jack E T; Tadesse, Gemechu; Mekete, Kalkidan; Wuletaw, Yonas; Gebretsadik, Abeba; French, Michael D; Harrison, Wendy E; Drake, Lesley J; Gardiner, Iain A; Yard, Elodie; Templeton, Michael R

    2016-03-01

    It is thought that improving water, sanitation, and hygiene (WASH) might reduce the transmission of schistosomes and soil-transmitted helminths, owing to their life cycles. However, few large-scale studies have yet assessed the real extent of associations between WASH and these parasites. In the 2013-2014 Ethiopian national mapping of infections with these parasites, school WASH was assessed alongside infection intensity in children, mostly between 10 and 15 years of age. Scores were constructed reflecting exposure to schistosomes arising from water collection for schools, from freshwater sources, and the adequacy of school sanitation and hygiene facilities. Kendall's τb was used to test the WASH scores against the school-level arithmetic mean intensity of infection with each parasite, in schools with at least one child positive for the parasite in question. WASH and parasitology data were available for 1,645 schools. More frequent collection of water for schools, from open freshwater sources was associated with statistically significantly higher Schistosoma mansoni infection intensity (Kendall's τb = 0.097, 95% confidence interval, CI: 0.011 to 0.18), better sanitation was associated with significantly lower Ascaris lumbricoides intensity (Kendall's τb = -0.067, 95% CI: -0.11 to -0.023) and borderline significant lower hookworm intensity (Kendall's τb = -0.039, 95% CI: -0.090 to 0.012, P = 0.067), and better hygiene was associated with significantly lower hookworm intensity (Kendall's τb = -0.076, 95% CI: -0.13 to -0.020). However, no significant differences were observed when comparing sanitation and infection with S. mansoni or Trichuris trichiura, or hygiene and infection with A. lumbricoides or T. trichiura. Improving school WASH may reduce transmission of these parasites. However, different forms of WASH appear to have different effects on infection with the various parasites, with our analysis finding the strongest associations between water and S

  13. Rigidity and resistance of larval- and adult schistosomes-medium interface

    Energy Technology Data Exchange (ETDEWEB)

    Migliardo, Federica, E-mail: fmigliardo@unime.it [Department of Physics and Earth Sciences, University of Messina, 98166 Messina (Italy); Tallima, Hatem; El Ridi, Rashika [Zoology Department, Faculty of Science, Cairo University, Cairo 12613 (Egypt)

    2014-03-28

    Graphical abstract: - Highlights: • Schistosoma larvae and worms are studied by neutron scattering. • Measurements on larvae were repeated after one day and by increasing temperature. • The flexibility properties of larvae and adult parasites are compared. • The parasite rigidity is related to their resistance to the hostile environment. • Insight into the parasite defense mechanisms to the immune system attack is achieved. - Abstract: Schistosomiasis is second only to malaria in prevalence and severity, and is still a major health problem in many tropical countries worldwide with about 200–300 million cases and with more than 800 million people at risk of infection. Based on these data, the World Health Organization recommends fostering research efforts for understanding at any level the mechanisms of the infection and then decreasing the social and economical impact of schistosomiasis. A key role is played by the parasite apical lipid membrane, which is entirely impervious to the surrounding elements of the immune system. We have previously demonstrated that the interaction between schistosomes and surrounding medium is governed by a parasite surface membrane sphingomyelin-based hydrogen barrier. In the present article, the elastic contribution to the total motion as a function of the exchanged wave-vector Q and the mean square displacement values for Schistosoma mansoni larvae and worms and Schistosomahaematobium worms have been evaluated by quasi elastic neutron scattering (QENS). The results point out that S. mansoni larvae show a smaller mean square displacement in comparison to S. mansoni and S. haematobium worms. These values increased by repeating the measurements after one day. These differences, which are analogous to those observed for the diffusion coefficient we previously evaluated, are interpreted in terms of rigidity of the parasite-medium interaction. S. mansoni larvae are the most rigid systems, while S. haematobium worms are the most

  14. 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.

  15. 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 FIT, 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.

  16. Pharmacological profiling an abundantly expressed schistosome serotonergic GPCR identifies nuciferine as a potent antagonist

    Directory of Open Access Journals (Sweden)

    John D. Chan

    2016-12-01

    Full Text Available 5-hydroxytryptamine (5-HT is a key regulator of muscle contraction in parasitic flatworms. In Schistosoma mansoni, the myoexcitatory action of 5-HT is effected through activation of a serotonergic GPCR (Sm.5HTRL, prioritizing pharmacological characterization of this target for anthelmintic drug discovery. Here, we have examined the effects of several aporphine alkaloids on the signaling activity of a heterologously expressed Sm.5HTRL construct using a cAMP biosensor assay. Four structurally related natural products – nuciferine, D-glaucine, boldine and bulbocapnine – were demonstrated to block Sm.5HTRL evoked cAMP generation with the potency of GPCR blockade correlating well with the ability of each drug to inhibit contractility of schistosomule larvae. Nuciferine was also effective at inhibiting both basal and 5-HT evoked motility of adult schistosomes. These data advance our understanding of structure-affinity relationships at Sm.5HTRL, and demonstrate the effectiveness of Sm.5HTRL antagonists as hypomotility-evoking drugs across different parasite life cycle stages.

  17. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  18. Potential schistosome-vector snails and associated trematodes in ricefields of Corrients province, Argentina: preliminary results

    Directory of Open Access Journals (Sweden)

    Alejandra Rumi

    1990-09-01

    Full Text Available Considering the possibility of introduction of schistosomiasis mansoni into Argentina as a consequence of dam construction on the Rio De La Plata basin, preliminary studies have been carried out on agrosystems such as ricefields in Corrientes province with the following purposes: 1 to survey and estimate the relative abundance of planorbids and identify potential vector species; 2 to identify environmental factors capable of influencing Biomphalaria population dynamics; and 3 to find out snail-parasite associations and estimate snail infection rates in order to detect possible competitive interactions between larval stages of native trematodes that could be used in biological control of Schistosoma mansoni. Three potential schistosome vectors were detected in ricefields, namely Biomphalaria straminea, B. tenagophila and B. peregrina, although B. orbignyi, a species refractory to infection with S. mansoni, proved the most frequent and abundant. Positive correlations (P0.05 was found in total iron, phosphates (SRP, pH and soil granulometry. Echinocercariae developed from rediae and belonging to Petasiger sp., Paryphostomum sp., and other undetermined species were found.

  19. Haematological and biochemical characteristics of the splenic effluent blood in schistosomal patients undergoing splenectomy

    Directory of Open Access Journals (Sweden)

    Andy Petroianu

    Full Text Available OBJECTIVE: To assess hematological and biochemical features of splenic effluent blood and their influence on the rise of hematological values after splenectomy. METHODS: we studied 20 patients undergoing surgical treatment for schistosomatic portal hypertension. We collected blood samples for CBC, coagulation, bilirubin and albumin in the splenic vein (perioperative and peripheral blood (immediately pre and postoperative periods. RESULTS: the splenic blood showed higher values of red blood cells, hemoglobin, hematocrit, platelet count, total leukocytes, neutrophils, lymphocytes, monocytes, eosinophils and basophils, as well as reduction of laboratory coagulation parameters in relation to peripheral blood collected preoperatively. In the postoperative peripheral blood there was an increase in the overall leukocytes and in their neutrophil component, and decreased levels of basophils, eosinophils and lymphocytes. The other postoperative variables of complete blood count and coagulation tests were not different compared with the splenic blood. The albumin values were lower postoperatively when compared to preoperative and splenic blood. There were higher values of direct bilirubin in the postoperative period when compared with the preoperative and splenic blood. Postoperative indirect bilirubin was lower compared to its value in the splenic blood. CONCLUSION: hematological and biochemical values of splenic effluent blood are higher than those found in peripheral blood in the presence of schistosomal splenomegaly. However, the splenic blood effluent is not sufficient to raise the blood levels found after splenectomy.

  20. Clinical-epidemiologic profile of the schistosomal myeloradiculopathy in Pernambuco, Brazil

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    Karina Conceição GM de Araújo

    2010-07-01

    Full Text Available This was a retrospective descriptive study on a series of cases of schistosomal myeloradiculopathy (SMR and the aim was to investigate the incidence of this disease and its clinical and epidemiological characteristics in cases diagnosed at three healthcare units in Pernambuco, Brazil between 1994-2006. The data were collected by reviewing the medical records from both the neurological and paediatric outpatient clinics and wards of the Hospital Clinics, Hospital of the Restoration and Pernambuco Mother and Child Institute. To gather the data, a spinal cord schistosomiasis evaluation protocol was used. The diagnoses were based on positive epidemiological evidence of schistosomiasis, clinical findings and laboratory tests (stool parasitological examination or rectal biopsies, magnetic resonance imaging findings and cerebrospinal fluid investigations. A total of 139 cases aged between 2-83 years were found. The most important determinants of SMR were male sex (66.2%, contact with fresh water (91%, origin in endemic regions (39.5%, lower-limb muscle weakness (100%, sensory level at the lower thoracic medulla (40.3%, myeloradicular form (76% and presence of eggs in the stool parasitological examination (48%. This sample indicates the need for intervention policies guided by diagnostic standardization, thereby avoiding disease under-notification.

  1. Portal blood flow volume measurement in schistosomal patients: evaluation of Doppler ultrasonography reproducibility

    Energy Technology Data Exchange (ETDEWEB)

    Leao, Alberto Ribeiro de Souza; Santos, Jose Eduardo Mourao; Moulin, Danilo Sales; Shigueoka, David Carlos; D' Ippolito, Giuseppe [Universidade Federal de Sao Paulo (UNIFESP/EPM), SP (Brazil). Escola Paulista de Medicina. Dept. de Diagnostico por Imagem]. E-mail: ar.leao@uol.com.br; Colleoni, Ramiro [Universidade Federal de Sao Paulo (UNIFESP/EPM), SP (Brazil). Escola Paulista de Medicina. Dept. de Gastroenterologia

    2008-09-15

    Objective: To evaluate the reproducibility of Doppler ultrasonography in the measurement of portal blood flow volume in schistosomal patients. Materials and methods: Prospective, transversal, observational and self-paired study evaluating 21 patients with hepatosplenic schistosomiasis submitted to Doppler ultrasonography performed by three independent observers for measurement of portal blood flow. Pairwise interobserver agreement was calculated by means of the intraclass correlation coefficient, paired t-test and Pearson's correlation coefficient. Results: Interobserver agreement was excellent. Intraclass correlation ranged from 80.6% to 93.0% (IC at 95% [65.3% ; 95.8%]), with the Pearson's correlation coefficient ranging between 81.6% and 92.7% with no statistically significant interobserver difference regarding the mean portal blood flow volume measured by Doppler ultrasonography (p = 0.954 / 0.758 / 0.749). Conclusion: Doppler ultrasonography has demonstrated to be a reliable method for measuring the portal blood flow volume in patients with portal hypertension secondary to schistosomiasis, with a good interobserver agreement. (author)

  2. Genetic dissimilarity between mates, but not male heterozygosity, influences divorce in schistosomes.

    Science.gov (United States)

    Beltran, Sophie; Cézilly, Frank; Boissier, Jérôme

    2008-10-08

    Correlational studies strongly suggest that both genetic similarity and heterozygosity can influence female mate choice. However, the influence of each variable has usually been tested independently, although similarity and heterozygosity might be correlated. We experimentally determined the relative influence of genetic similarity and heterozygosity in divorce and re-mating in the monogamous endoparasite Schistosoma mansoni. We performed sequential infections of vertebrate hosts with controlled larval populations of parasites, where sex and individual genetic diversity and similarity were predetermined before infection. Divorce rate increased significantly when females were given the opportunity to increase genetic dissimilarity through re-mating with a new partner, independently of the intensity of male-male competition. We found however no evidence for females attempting to maximize the level of heterozygosity of their reproductive partner through divorce. Female preference for genetically dissimilar males should result in more heterozygous offspring. Because genetic heterozygosity might partly determine the ability of parasites to counter host resistance, adaptive divorce could be an important factor in the evolutionary arms race between schistosomes and their hosts.

  3. Genetic dissimilarity between mates, but not male heterozygosity, influences divorce in schistosomes.

    Directory of Open Access Journals (Sweden)

    Sophie Beltran

    Full Text Available BACKGROUND: Correlational studies strongly suggest that both genetic similarity and heterozygosity can influence female mate choice. However, the influence of each variable has usually been tested independently, although similarity and heterozygosity might be correlated. We experimentally determined the relative influence of genetic similarity and heterozygosity in divorce and re-mating in the monogamous endoparasite Schistosoma mansoni. METHODOLOGY/PRINCIPAL FINDINGS: We performed sequential infections of vertebrate hosts with controlled larval populations of parasites, where sex and individual genetic diversity and similarity were predetermined before infection. Divorce rate increased significantly when females were given the opportunity to increase genetic dissimilarity through re-mating with a new partner, independently of the intensity of male-male competition. We found however no evidence for females attempting to maximize the level of heterozygosity of their reproductive partner through divorce. CONCLUSIONS/SIGNIFICANCE: Female preference for genetically dissimilar males should result in more heterozygous offspring. Because genetic heterozygosity might partly determine the ability of parasites to counter host resistance, adaptive divorce could be an important factor in the evolutionary arms race between schistosomes and their hosts.

  4. 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.

  5. 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

  6. Genetic evolution of pancreatic cancer: lessons learnt from the pancreatic cancer genome sequencing project

    Science.gov (United States)

    Iacobuzio-Donahue, Christine A

    2012-01-01

    Pancreatic cancer is a disease caused by the accumulation of genetic alterations in specific genes. Elucidation of the human genome sequence, in conjunction with technical advances in the ability to perform whole exome sequencing, have provided new insight into the mutational spectra characteristic of this lethal tumour type. Most recently, exomic sequencing has been used to clarify the clonal evolution of pancreatic cancer as well as provide time estimates of pancreatic carcinogenesis, indicating that a long window of opportunity may exist for early detection of this disease while in the curative stage. Moving forward, these mutational analyses indicate potential targets for personalised diagnostic and therapeutic intervention as well as the optimal timing for intervention based on the natural history of pancreatic carcinogenesis and progression. PMID:21749982

  7. 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.

  8. The carcinoGENOMICS project: Critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays

    NARCIS (Netherlands)

    Vinken, M.; Doktorova, T.; Ellinger-Ziegelbauer, H.; Ahr, H.-J.; Lock, E.; Carmichael, P.; Roggen, E.; Delft, J. van; Kleinjans, J.; Castell, J.; Bort, R.; Donato, T.; Ryan, M.; Corvi, R.; Keun, H.; Ebbels, T.; Athersuch, T.; Sansone, S.-A.; Rocca-Serra, P.; Stierum, R.; Jennings, P.; Pfaller, W.; Gmuender, H.; Vanhaecke, T.; Rogiers, V.

    2008-01-01

    Recent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animal experimentation. The Sixth Framework Program project carcinoGENOMICS was specifically raised to

  9. The carcinoGENOMICS project : critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays

    NARCIS (Netherlands)

    Vinken, Mathieu; Doktorova, Tatyana; Ellinger-Ziegelbauer, Heidrun; Ahr, Hans-Jürgen; Lock, Edward A; Carmichael, Paul; Roggen, Erwin; van Delft, Joost H; Kleinjans, Jos; Castell, José; Bort, Roque; Donato, Teresa; Ryan, Michael P; Corvi, Raffaella; Keun, Hector C; Ebbels, Timothy Mark David; Athersuch, Toby J; Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Stierum, Rob; Jennings, Paul; Pfaller, Walter; Gmuender, Hans; Vanhaecke, Tamara; Rogiers, Vera

    2008-01-01

    Recent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animal experimentation. The Sixth Framework Program project carcinoGENOMICS was specifically raised to

  10. 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.

  11. The iron distribution and magnetic properties of schistosome eggshells: implications for improved diagnostics.

    Directory of Open Access Journals (Sweden)

    Stephan Karl

    Full Text Available BACKGROUND: Schistosoma mansoni and Schistosoma japonicum are the most frequent causative agents of human intestinal schistosomiasis. Approximately 200 million people in the world are infected with schistosomes. Diagnosis of schistosomiasis is often difficult. High percentages of low level infections are missed in routine fecal smear analysis and current diagnostic methodologies are inadequate to monitor the progress of parasite control, especially in areas with low transmission. Improved diagnostic methods are urgently needed to evaluate the success of elimination programs. Recently, a magnetic fractionation method for isolation of parasite eggs from feces was described, which uses magnetic microspheres to form parasite egg - magnetic microsphere conjugates. This approach enables screening of larger sample volumes and thus increased diagnostic sensitivity. The mechanism of formation of the conjugates remains unexplained and may either be related to specific surface characteristics of eggs and microspheres or to their magnetic properties. METHODS/PRINCIPAL FINDINGS: Here, we investigated iron localization in parasite eggs, specifically in the eggshells. We determined the magnetic properties of the eggs, studied the motion of eggs and egg-microsphere conjugates in magnetic fields and determined species specific affinity of parasite eggs to magnetic microspheres. Our study shows that iron is predominantly localized in pores in the eggshell. Parasite eggs showed distinct paramagnetic behaviour but they did not move in a magnetic field. Magnetic microspheres spontaneously bound to parasite eggs without the presence of a magnetic field. S. japonicum eggs had a significantly higher affinity to bind microspheres than S. mansoni eggs. CONCLUSIONS/SIGNIFICANCE: Our results suggest that the interaction of magnetic microspheres and parasite eggs is unlikely to be magnetic in origin. Instead, the filamentous surface of the eggshells may be important in

  12. Regulation of schistosome egg production by HMG CoA reductase

    Energy Technology Data Exchange (ETDEWEB)

    VandeWaa, E.A.; Bennett, J.L.

    1986-03-05

    Hydroxymethylglutaryl coenzyme A reductase (HMG CoA reductase) catalyzes the conversion of HMG CoA to mevalonate in the synthesis of steroids, isoprenoids and terpenes. Mevinolin, an inhibitor of this enzyme, decreased egg production in Schistosoma mansoni during in vitro incubations. This was associated with a reduction in the incorporation of /sup 14/C-acetate into polyisoprenoids and a reduction in the formation of a lipid-linked oligosaccharide. In vivo, mevinolin in daily doses of 50 mg/kg (p.o., from days 30-48 post-infection) caused no change in gross liver pathology in S. mansoni infected mice. However, when parasites exposed to mevinolin or its vehicle in vivo were cultured in vitro, worms from mevinolin-treated mice produced six times more eggs than control parasites. When infected mice were dosed with 250 mg/kg mevinolin daily (p.o., from days 35-45 post-infection), liver pathology was reduced in comparison to control mice. Thus, during in vivo exposure to a high dose of the drug egg production is decreased, while at a lower dose it appears unaffected until the parasites are cultured in a drug-free in vitro system wherein egg production is stimulated to extraordinarily high levels. It may be that at low doses mevinolin, by inhibiting the enzyme, is blocking the formation of a product (such as an isoprenoid) which normally acts to down-regulate enzyme synthesis, resulting in enzyme induction. Induction of HMG CoA reductase is then expressed as increased egg production when the worms are removed from the drug. These data suggest that HMG CoA reductase plays a role in schistosome egg production.

  13. Epidermal keratinocytes initiate wound healing and pro-inflammatory immune responses following percutaneous schistosome infection.

    Science.gov (United States)

    Bourke, Claire D; Prendergast, Catriona T; Sanin, David E; Oulton, Tate E; Hall, Rebecca J; Mountford, Adrian P

    2015-03-01

    Keratinocytes constitute the majority of cells in the skin's epidermis, the first line of defence against percutaneous pathogens. Schistosome larvae (cercariae) actively penetrate the epidermis to establish infection, however the response of keratinocytes to invading cercariae has not been investigated. Here we address the hypothesis that cercariae activate epidermal keratinocytes to promote the development of a pro-inflammatory immune response in the skin. C57BL/6 mice were exposed to Schistosoma mansoni cercariae via each pinna and non-haematopoietic cells isolated from epidermal tissue were characterised for the presence of different keratinocyte sub-sets at 6, 24 and 96 h p.i. We identified an expansion of epidermal keratinocyte precursors (CD45(-), CD326(-), CD34(+)) within 24 h of infection relative to naïve animals. Following infection, cells within the precursor population displayed a more differentiated phenotype (α6integrin(-)) than in uninfected skin. Parallel immunohistochemical analysis of pinnae cryosections showed that this expansion corresponded to an increase in the intensity of CD34 staining, specifically in the basal bulge region of hair follicles of infected mice, and a higher frequency of keratinocyte Ki67(+) nuclei in both the hair follicle and interfollicular epidermis. Expression of pro-inflammatory cytokine and stress-associated keratin 6b genes was also transiently upregulated in the epidermal tissue of infected mice. In vitro exposure of keratinocyte precursors isolated from neonatal mouse skin to excretory/secretory antigens released by penetrating cercariae elicited IL-1α and IL-1β production, supporting a role for keratinocyte precursors in initiating cutaneous inflammatory immune responses. Together, these observations indicate that S.mansoni cercariae and their excretory/secretory products act directly upon epidermal keratinocytes, which respond by initiating barrier repair and pro-inflammatory mechanisms similar to those

  14. Introgressive hybridization of Schistosoma haematobium group species in Senegal: species barrier break down between ruminant and human schistosomes.

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    Bonnie L Webster

    Full Text Available BACKGROUND: Schistosomes are dioecious parasitic flatworms, which live in the vasculature of their mammalian definitive hosts. They are the causative agent of schistosomiasis, a disease of considerable medical and veterinary importance in tropical and subtropical regions. Schistosomes undergo a sexual reproductive stage within their mammalian host enabling interactions between different species, which may result in hybridization if the species involved are phylogenetically close. In Senegal, three closely related species in the Schistosoma haematobium group are endemic: S. haematobium, which causes urogenital schistosomiasis in humans, and S. bovis and S. curassoni, which cause intestinal schistosomiasis in cows, sheep and goats. METHODOLOGY/PRINCIPAL FINDINGS: Large-scale multi-loci molecular analysis of parasite samples collected from children and domestic livestock across Senegal revealed that interactions and hybridization were taking place between all three species. Evidence of hybridization between S. haematobium/S. curassoni and S. haematobium/S. bovis was commonly found in children from across Senegal, with 88% of the children surveyed in areas of suspected species overlap excreting hybrid miracidia. No S. haematobium worms or hybrids thereof were found in ruminants, although S. bovis and S. curassoni hybrid worms were found in cows. Complementary experimental mixed species infections in laboratory rodents confirmed that males and females of each species readily pair and produce viable hybrid offspring. CONCLUSIONS/SIGNIFICANCE: THESE DATA PROVIDE INDISPUTABLE EVIDENCE FOR: the high occurrence of bidirectional hybridization between these Schistosoma species; the first conclusive evidence for the natural hybridisation between S. haematobium and S. curassoni; and demonstrate that the transmission of the different species and their hybrids appears focal. Hybridization between schistosomes has been known to influence the disease epidemiology

  15. The impact of schistosomes and schistosomiasis on murine blood coagulation and fibrinolysis as determined by thromboelastography (TEG).

    Science.gov (United States)

    Da'dara, Akram A; de Laforcade, Armelle M; Skelly, Patrick J

    2016-05-01

    Schistosomes are parasitic platyhelminths that currently infect over 200 million people and cause the chronic debilitating disease schistosomiasis. While these large intravascular parasites can disturb blood flow, surprisingly they do not appear to provoke thrombus formation around them in vivo. In order to determine if the worms can alter their local environment to impede coagulation, we incubated adult worms (50 pairs) in murine blood (500 µl) for 1 h at 37 °C and, using thromboelastography (TEG), we compared the coagulation profile of the blood with control blood that never contained worms. Substantial differences were apparent between the two profiles. Blood that had been exposed to schistosomes clotted more slowly and yielded relatively poor, though stable, thrombi; all TEG measures of blood coagulation (R, K, α-angle, MA, G and TMA) differed significantly between conditions. No fibrinolysis (as determined by LY30 and LY60 values) was detected in either case. The observed TEG profile suggests that the worms are acting as local anti-coagulants. Blood recovered from schistosome-infected mice, however, does not behave in this way. At an early time point post infection (4-weeks), the TEG profile of infected murine blood is essentially the same as that of control blood. However at a later time point (7-weeks) infected murine blood clots significantly faster than control blood but these clots also break down faster. The R, K, α-angle, and TMA measures of coagulation are all significantly different between the control versus infected mice as are the LY30 and LY60 values. This profile is indicative of a hypercoagulable state with fibrinolysis and is akin to that seen in human patients with advanced schistosomiasis.

  16. Introgressive hybridization of Schistosoma haematobium group species in Senegal: species barrier break down between ruminant and human schistosomes.

    Science.gov (United States)

    Webster, Bonnie L; Diaw, Oumar T; Seye, Mohmoudane M; Webster, Joanne P; Rollinson, David

    2013-01-01

    Schistosomes are dioecious parasitic flatworms, which live in the vasculature of their mammalian definitive hosts. They are the causative agent of schistosomiasis, a disease of considerable medical and veterinary importance in tropical and subtropical regions. Schistosomes undergo a sexual reproductive stage within their mammalian host enabling interactions between different species, which may result in hybridization if the species involved are phylogenetically close. In Senegal, three closely related species in the Schistosoma haematobium group are endemic: S. haematobium, which causes urogenital schistosomiasis in humans, and S. bovis and S. curassoni, which cause intestinal schistosomiasis in cows, sheep and goats. Large-scale multi-loci molecular analysis of parasite samples collected from children and domestic livestock across Senegal revealed that interactions and hybridization were taking place between all three species. Evidence of hybridization between S. haematobium/S. curassoni and S. haematobium/S. bovis was commonly found in children from across Senegal, with 88% of the children surveyed in areas of suspected species overlap excreting hybrid miracidia. No S. haematobium worms or hybrids thereof were found in ruminants, although S. bovis and S. curassoni hybrid worms were found in cows. Complementary experimental mixed species infections in laboratory rodents confirmed that males and females of each species readily pair and produce viable hybrid offspring. THESE DATA PROVIDE INDISPUTABLE EVIDENCE FOR: the high occurrence of bidirectional hybridization between these Schistosoma species; the first conclusive evidence for the natural hybridisation between S. haematobium and S. curassoni; and demonstrate that the transmission of the different species and their hybrids appears focal. Hybridization between schistosomes has been known to influence the disease epidemiology and enhance phenotypic characteristics affecting transmission, morbidity and drug

  17. Impact of schistosome infection on Plasmodium falciparum Malariometric indices and immune correlates in school age children in Burma Valley, Zimbabwe.

    Directory of Open Access Journals (Sweden)

    Davison T Sangweme

    2010-11-01

    Full Text Available A group of children aged 6-17 years was recruited and followed up for 12 months to study the impact of schistosome infection on malaria parasite prevalence, density, distribution and anemia. Levels of cytokines, malaria specific antibodies in plasma and parasite growth inhibition capacities were assessed. Baseline results suggested an increased prevalence of malaria parasites in children co-infected with schistosomiasis (31% compared to children infected with malaria only (25% (p = 0.064. Moreover, children co-infected with schistosomes and malaria had higher sexual stage geometric mean malaria parasite density (189 gametocytes/µl than children infected with malaria only (73/µl gametocytes (p = 0.043. In addition, a larger percentage of co-infected children (57% had gametocytes as observed by microscopy compared to the malaria only infected children (36% (p = 0.06. There was no difference between the two groups in terms of the prevalence of anemia, which was approximately 64% in both groups (p = 0.9. Plasma from malaria-infected children exhibited higher malaria antibody activity compared to the controls (p = 0.001 but was not different between malaria and schistosome plus malaria infected groups (p = 0.44 and malaria parasite growth inhibition activity at baseline was higher in the malaria-only infected group of children than in the co-infected group though not reaching statistical significance (p = 0.5. Higher prevalence and higher mean gametocyte density in the peripheral blood may have implications in malaria transmission dynamics during co-infection with helminths.

  18. Interactions between natural populations of human and rodent schistosomes in the Lake Victoria region of Kenya: a molecular epidemiological approach.

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    Michelle L Steinauer

    2008-04-01

    Full Text Available Schistosoma mansoni exists in a complex environmental milieu that may select for significant evolutionary changes in this species. In Kenya, the sympatric distribution of S. mansoni with S. rodhaini potentially influences the epidemiology, ecology, and evolutionary biology of both species, because they infect the same species of snail and mammalian hosts and are capable of hybridization.Over a 2-year period, using a molecular epidemiological approach, we examined spatial and temporal distributions, and the overlap of these schistosomes within snails, in natural settings in Kenya. Both species had spatially and temporally patchy distributions, although S. mansoni was eight times more common than S. rodhaini. Both species were overdispersed within snails, and most snails (85.2% for S. mansoni and 91.7% for S. rodhaini only harbored one schistosome genotype. Over time, half of snails infected with multiple genotypes showed a replacement pattern in which an initially dominant genotype was less represented in later replicates. The other half showed a consistent pattern over time; however, the ratio of each genotype was skewed. Profiles of circadian emergence of cercariae revealed that S. rodhaini emerges throughout the 24-hour cycle, with peak emergence before sunrise and sometimes immediately after sunset, which differs from previous reports of a single nocturnal peak immediately after sunset. Peak emergence for S. mansoni cercariae occurred as light became most intense and overlapped temporally with S. rodhaini. Comparison of schistosome communities within snails against a null model indicated that the community was structured and that coinfections were more common than expected by chance. In mixed infections, cercarial emergence over 24 hours remained similar to single species infections, again with S. rodhaini and S. mansoni cercarial emergence profiles overlapping substantially.The data from this study indicate a lack of obvious spatial or

  19. Athlome Project Consortium: a concerted effort to discover genomic and other “omic” markers of athletic performance

    Science.gov (United States)

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

    2015-01-01

    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. PMID:26715623

  20. 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

  1. Dual targeting of insulin and venus kinase Receptors of Schistosoma mansoni for novel anti-schistosome therapy.

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    Mathieu Vanderstraete

    Full Text Available BACKGROUND: Chemotherapy of schistosomiasis relies on a single drug, Praziquantel (PZQ and mass-use of this compound has led to emergence of resistant strains of Schistosoma mansoni, therefore pointing out the necessity to find alternative drugs. Through their essential functions in development and metabolism, receptor tyrosine kinases (RTK could represent valuable drug targets for novel anti-schistosome chemotherapies. Taking advantage of the similarity between the catalytic domains of S. mansoni insulin receptors (SmIR1 and SmIR2 and Venus Kinase Receptors (SmVKR1 and SmVKR2, we studied the possibility to fight schistosomes by targeting simultaneously the four receptors with a single drug. METHODOLOGY/PRINCIPAL FINDINGS: Several commercial RTK inhibitors were tested for their potential to inhibit the kinase activities of SmIR1, SmIR2, SmVKR1 and SmVKR2 intracellular domains (ICD expressed in Xenopus oocytes. We measured the inhibitory effect of chemicals on meiosis resumption induced by the active ICD of the schistosome kinases in oocytes. The IR inhibitor, tyrphostin AG1024, was the most potent inhibitory compound towards SmIR and SmVKR kinases. In vitro studies then allowed us to show that AG1024 affected the viability of both schistosomula and adult worms of S. mansoni. At micromolar doses, AG1024 induced apoptosis and caused schistosomula death in a dose-dependent manner. In adult worms, AG1024 provoked alterations of reproductive organs, as observed by confocal laser scanner microscopy. With 5 µM AG1024, parasites were no more feeding and laying eggs, and they died within 48 h with 10 µM. CONCLUSION/SIGNIFICANCE: IRs and VKRs are essential in S. mansoni for key biological processes including glucose uptake, metabolism and reproduction. Our results demonstrate that inhibiting the kinase potential and function of these receptors by a single chemical compound AG1024 at low concentrations, leads to death of schistosomula and adult worms

  2. Dual targeting of insulin and venus kinase Receptors of Schistosoma mansoni for novel anti-schistosome therapy.

    Science.gov (United States)

    Vanderstraete, Mathieu; Gouignard, Nadège; Cailliau, Katia; Morel, Marion; Lancelot, Julien; Bodart, Jean-François; Dissous, Colette

    2013-01-01

    Chemotherapy of schistosomiasis relies on a single drug, Praziquantel (PZQ) and mass-use of this compound has led to emergence of resistant strains of Schistosoma mansoni, therefore pointing out the necessity to find alternative drugs. Through their essential functions in development and metabolism, receptor tyrosine kinases (RTK) could represent valuable drug targets for novel anti-schistosome chemotherapies. Taking advantage of the similarity between the catalytic domains of S. mansoni insulin receptors (SmIR1 and SmIR2) and Venus Kinase Receptors (SmVKR1 and SmVKR2), we studied the possibility to fight schistosomes by targeting simultaneously the four receptors with a single drug. Several commercial RTK inhibitors were tested for their potential to inhibit the kinase activities of SmIR1, SmIR2, SmVKR1 and SmVKR2 intracellular domains (ICD) expressed in Xenopus oocytes. We measured the inhibitory effect of chemicals on meiosis resumption induced by the active ICD of the schistosome kinases in oocytes. The IR inhibitor, tyrphostin AG1024, was the most potent inhibitory compound towards SmIR and SmVKR kinases. In vitro studies then allowed us to show that AG1024 affected the viability of both schistosomula and adult worms of S. mansoni. At micromolar doses, AG1024 induced apoptosis and caused schistosomula death in a dose-dependent manner. In adult worms, AG1024 provoked alterations of reproductive organs, as observed by confocal laser scanner microscopy. With 5 µM AG1024, parasites were no more feeding and laying eggs, and they died within 48 h with 10 µM. IRs and VKRs are essential in S. mansoni for key biological processes including glucose uptake, metabolism and reproduction. Our results demonstrate that inhibiting the kinase potential and function of these receptors by a single chemical compound AG1024 at low concentrations, leads to death of schistosomula and adult worms. Thus, AG1024 represents a valuable hit compound for further design of anti

  3. Dual Targeting of Insulin and Venus Kinase Receptors of Schistosoma mansoni for Novel Anti-schistosome Therapy

    Science.gov (United States)

    Vanderstraete, Mathieu; Gouignard, Nadège; Cailliau, Katia; Morel, Marion; Lancelot, Julien; Bodart, Jean-François; Dissous, Colette

    2013-01-01

    Background Chemotherapy of schistosomiasis relies on a single drug, Praziquantel (PZQ) and mass-use of this compound has led to emergence of resistant strains of Schistosoma mansoni, therefore pointing out the necessity to find alternative drugs. Through their essential functions in development and metabolism, receptor tyrosine kinases (RTK) could represent valuable drug targets for novel anti-schistosome chemotherapies. Taking advantage of the similarity between the catalytic domains of S. mansoni insulin receptors (SmIR1 and SmIR2) and Venus Kinase Receptors (SmVKR1 and SmVKR2), we studied the possibility to fight schistosomes by targeting simultaneously the four receptors with a single drug. Methodology/Principal Findings Several commercial RTK inhibitors were tested for their potential to inhibit the kinase activities of SmIR1, SmIR2, SmVKR1 and SmVKR2 intracellular domains (ICD) expressed in Xenopus oocytes. We measured the inhibitory effect of chemicals on meiosis resumption induced by the active ICD of the schistosome kinases in oocytes. The IR inhibitor, tyrphostin AG1024, was the most potent inhibitory compound towards SmIR and SmVKR kinases. In vitro studies then allowed us to show that AG1024 affected the viability of both schistosomula and adult worms of S. mansoni. At micromolar doses, AG1024 induced apoptosis and caused schistosomula death in a dose-dependent manner. In adult worms, AG1024 provoked alterations of reproductive organs, as observed by confocal laser scanner microscopy. With 5 µM AG1024, parasites were no more feeding and laying eggs, and they died within 48 h with 10 µM. Conclusion/Significance IRs and VKRs are essential in S. mansoni for key biological processes including glucose uptake, metabolism and reproduction. Our results demonstrate that inhibiting the kinase potential and function of these receptors by a single chemical compound AG1024 at low concentrations, leads to death of schistosomula and adult worms. Thus, AG1024

  4. Whole-genome sequence of Schistosoma haematobium.

    Science.gov (United States)

    Young, Neil D; Jex, Aaron R; Li, Bo; Liu, Shiping; Yang, Linfeng; Xiong, Zijun; Li, Yingrui; Cantacessi, Cinzia; Hall, Ross S; Xu, Xun; Chen, Fangyuan; Wu, Xuan; Zerlotini, Adhemar; Oliveira, Guilherme; Hofmann, Andreas; Zhang, Guojie; Fang, Xiaodong; Kang, Yi; Campbell, Bronwyn E; Loukas, Alex; Ranganathan, Shoba; Rollinson, David; Rinaldi, Gabriel; Brindley, Paul J; Yang, Huanming; Wang, Jun; Wang, Jian; Gasser, Robin B

    2012-01-15

    Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

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

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    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.

  6. Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium.

    Science.gov (United States)

    Zhang, Wenqian; Ng, Hui Wen; Shu, Mao; Luo, Heng; Su, ZhenQiang; Ge, Weigong; Perkins, Roger; Tong, Weida; Hong, Huixiao

    2015-12-01

    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 a means for assessing concerns regarding SNP array-based GWAS findings as well as for realistically bounding expectations for next generation sequencing (NGS)-based GWAS. We calculated and compared base composition, transitions to transversions ratio, minor allele frequency and heterozygous rate for SNPs from HapMap and 1KGP for the 622 common individuals. We analysed the genotype discordance between HapMap and 1KGP to assess consistency in the SNPs from the two references. In 1KGP, 90.58% of 36,817,799 SNPs detected were not measured in HapMap. More SNPs with minor allele frequencies less than 0.01 were found in 1KGP than HapMap. The two references have low disc ordance (generally smaller than 0.02) in genotypes of common SNPs, with most discordance from heterozygous SNPs. Our study demonstrated that SNP array-based GWAS findings were reliable and useful, although only a small portion of genetic variances were explained. NGS can detect not only common but also rare variants, supporting the expectation that NGS-based GWAS will be able to incorporate a much larger portion of genetic variance than SNP arrays-based GWAS.

  7. Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.

    Directory of Open Access Journals (Sweden)

    Paolo Fontana

    Full Text Available BACKGROUND: Large-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. METHODOLOGY: We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results. CONCLUSIONS: The extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage.

  8. 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)

  9. Clinical-epidemiological profile of children with schistosomal myeloradiculopathy attended at the Instituto Materno-Infantil de Pernambuco.

    Science.gov (United States)

    Araújo, Karina Conceição G M; Rosa e Silva, Cristiana da; Barbosa, Constança Simões; Ferrari, Teresa C A

    2006-09-01

    The most critical phase of exposure to schistosomal infection is the infancy, because of the more frequent contact with contaminated water and the immaturity of the immune system. One of the most severe presentations of this parasitosis is the involvement of the spinal cord, which prognosis is largely dependent on early diagnosis and treatment. Reports on this clinical form of schistosomiasis in children are rare in the literature. We present here the clinical-epidemiological profile of schistosomal myeloradiculopathy (SMR) from ten children who were admitted at the Instituto Materno-Infantil de Pernambuco over a five-year period. They were evaluated according to an investigation protocol. Most of these patients presented an acute neurological picture which included as the main clinical manifestations: sphincteral disorders, low back and lower limbs pain, paresthesia, lower limbs muscle weakness and absence of deep tendon reflex, and impairment of the gait. The diagnosis was presumptive in the majority of the cases. This study emphasizes the importance of considering the diagnosis of SMR in pediatric patients coming from endemic areas who present a low cord syndrome, in order to start the appropriate therapy and avoid future complications.

  10. Genetic differentiation of cercariae infrapopulations of the avian schistosome Trichobilharzia szidati based on RAPD markers and mitochondrial cox1 gene.

    Science.gov (United States)

    Korsunenko, Anna; Chrisanfova, Galina; Lopatkin, Anton; Beer, Sergey A; Voronin, Mikhail; Ryskov, Alexey P; Semyenova, Seraphima K

    2012-02-01

    Avian schistosome Trichobilharzia szidati is a member of the largest genus within the family Schistosomatidae (Trematoda). Population genetic structure of Trichobilharzia spp. schistosomes, causative agents of cercarial dermatitis in humans, has not been studied yet. The knowledge of the genetic structure of trichobilharzian populations is essential for understanding the host-parasite coevolutionary dynamics and epidemiology strategies. Here we examined genetic diversity in three geographically isolated local populations of T. szidati cercariae inhabiting Russia based on nuclear (randomly amplified polymorphic DNA, RAPD) and mt (cox1) markers. We analyzed T. szidati cercariae shed from seven naturally infected snails of Lymnaea stagnalis. Using three random primers, we demonstrated genetic variation among populations, thus posing genetic structure across geographic sites. Moreover, T. szidati cercariae have been genetically structured among hosts (infrapopulations). Molecular variance analysis was performed to test the significance of genetic differentiation within and between local populations. Of total parasitic diversity, 18.8% was partitioned between populations, whereas the higher contribution (48.9%) corresponds to the differences among individual cercariae within infrapopulations. In contrast to RAPD markers, a 1,125-bp fragment of cox1 mt gene failed to provide any significant within-species structure. The lack of geographic structuring was detected using unique haplotypes which were determined in the current work for Moscow and Western Siberian local populations as well as obtained previously for European isolates (Czech Republic and Germany). All T. szidati/Trichobilharzia ocellata haplotypes were found to be mixed across their geographical origin.

  11. Genome-wide linkage analysis of von Willebrand factor plasma levels: results from the GAIT project.

    Science.gov (United States)

    Souto, Juan Carlos; Almasy, Laura; Soria, Jose Manuel; Buil, Alfonso; Stone, William; Lathrop, Mark; Blangero, John; Fontcuberta, Jordi

    2003-03-01

    High plasma levels of von Willebrand factor (vWF) have been associated with the risk of thromboembolic disease. As a complex trait, this phenotype must be influenced by genetic and environmental factors. Among the genetic factors, only the ABO gene located on chromosome 9q34 has been clearly linked to the plasma levels of vWF. This locus explains about 30-40% of the genetic variability. Therefore, the source of the majority of the genetic component remains to be identified. To search for these unknown loci, we conducted a genomewide linkage screen for genes affecting normal variation in vWF levels in 21 Spanish families as part of the GAIT (Genetic Analysis of Idiopathic Thrombophilia) Project. The results showed that the strongest linkage signal (LOD =3.46, p = 0.00003) for vWF was found on chromosome 9q34 at the DNA marker D9S290, where the ABO gene is located. Additional suggestive linkage signals were found on chromosomes 2q23.2 (LOD = 1.65, p = 0.003) and 1p36.13 (LOD =1.32, p = 0.007). After refining the linkage analysis, conditional to the ABO genotype, three additional loci on chromosomes 5, 6 and 22 showed LOD scores higher than 1, suggesting the presence of other genes linked to vWF levels. Curiously, no linkage signals were detected in other chromosome regions previously associated with vWF levels (like the structural VWF gene on 12p13.2 or Lewis blood group gene on 19q13). These results indicate that these loci are not important genetic determinants of the normal variation of vWF levels. Our results indicate that the ABO locus is the major genetic determinant of the plasma levels of the vWF in Spanish population. It is possible that there are other potential regions on chromosomes 1, 2, 5, 6 and 22 that influence this thrombosis risk factor. However, the structural vWF gene itself has a very low influence (if any) on the plasma levels of vWF.

  12. Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects.

    Science.gov (United States)

    Sung, Yun J; Gu, C Charles; Tiwari, Hemant K; Arnett, Donna K; Broeckel, Ulrich; Rao, Dabeeru C

    2012-07-01

    Genotype imputation provides imputation of untyped single nucleotide polymorphisms (SNPs) that are present on a reference panel such as those from the HapMap Project. It is popular for increasing statistical power and comparing results across studies using different platforms. Imputation for African American populations is challenging because their linkage disequilibrium blocks are shorter and also because no ideal reference panel is available due to admixture. In this paper, we evaluated three imputation strategies for African Americans. The intersection strategy used a combined panel consisting of SNPs polymorphic in both CEU and YRI. The union strategy used a panel consisting of SNPs polymorphic in either CEU or YRI. The merge strategy merged results from two separate imputations, one using CEU and the other using YRI. Because recent investigators are increasingly using the data from the 1000 Genomes (1KG) Project for genotype imputation, we evaluated both 1KG-based imputations and HapMap-based imputations. We used 23,707 SNPs from chromosomes 21 and 22 on Affymetrix SNP Array 6.0 genotyped for 1,075 HyperGEN African Americans. We found that 1KG-based imputations provided a substantially larger number of variants than HapMap-based imputations, about three times as many common variants and eight times as many rare and low-frequency variants. This higher yield is expected because the 1KG panel includes more SNPs. Accuracy rates using 1KG data were slightly lower than those using HapMap data before filtering, but slightly higher after filtering. The union strategy provided the highest imputation yield with next highest accuracy. The intersection strategy provided the lowest imputation yield but the highest accuracy. The merge strategy provided the lowest imputation accuracy. We observed that SNPs polymorphic only in CEU had much lower accuracy, reducing the accuracy of the union strategy. Our findings suggest that 1KG-based imputations can facilitate discovery of

  13. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes [v1; ref status: indexed, http://f1000r.es/445

    Directory of Open Access Journals (Sweden)

    Jennifer Wyffels

    2014-08-01

    Full Text Available Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods and actinoptergii (ray-finned fish including teleosts taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase (http://skatebase.org serves as the skate genome project portal linking data, research tools, and teaching resources.

  14. A genetically distinct Schistosoma from Radix luteola from Nepal related to Schistosoma turkestanicum: A phylogenetic study of schistosome and snail host.

    Science.gov (United States)

    Devkota, Ramesh; Brant, Sara V; Loker, Eric S

    2016-12-01

    During a survey of freshwater snails in the Terai region of southern Nepal, 16 of 2588 specimens of Radix luteola from 4 different habitats were found to be shedding schistosome cercariae. None of the 1411 specimens of Radix acuminata we collected were positive for schistosomes. Analysis of 28S, cox1, 16S and 12S sequences indicated that all the R. luteola-derived schistosomes were genetically very similar to one another and, although unambiguously grouping most closely to the widespread Asian species Schistosoma turkestanicum, were clearly genetically distinct from it. We lack information from other life cycle stages to verify the specific identity of these cercariae, but it is possible they are of Schistosoma bomfordi or Schistosoma dattai, both species previously known only from northern India, the latter species known to infect R. luteola. This study provides sequence evidence for a third genetically distinct lymnaeid-transmitted Schistosoma lineage in Asia (to go along with S. turkestanicum and S. incognitum). As a close relative of S. turkestanicum, it provides the first direct molecular evidence to accompany morphological results from earlier studies for the presence of a S. turkestanicum species group in Asia. It increases to five the number of known or suspected mammalian schistosome species to be present in the Terai region of Nepal. Radix luteola and R. acuminata were identified and differentiated using conchological features and by molecular phylogenetic analyses of cox1 and 16S genes. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project

    OpenAIRE

    Salse, Jerome; Piégu, Benoît; Cooke, Richard; Delseny, Michel

    2002-01-01

    BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4-22 rice orthologs covering < or =3.2 cM (centiMorgan). Most regions are

  16. 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

  17. The kangaroo genome

    Science.gov (United States)

    Wakefield, Matthew J.; Graves, Jennifer A. Marshall

    2003-01-01

    The kangaroo genome is a rich and unique resource for comparative genomics. Marsupial genetics and cytology have made significant contributions to the understanding of gene function and evolution, and increasing the availability of kangaroo DNA sequence information would provide these benefits on a genomic scale. Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project. PMID:12612602

  18. the human genome project

    African Journals Online (AJOL)

    Enrique

    have resulted in the biological diversity, both past and present, on this planet. RAJ RAMESAR. MSc, PhD. Professor and Head. Division of Human Genetics. Faculty of Health Sciences. University of Cape Town. Raj Ramesar serves as Director of the MRC. Human Genetics Research Unit and. CANSA's Colorectal Cancer ...

  19. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    breaks (for example, VDJ recombination in the immune system in present. humans). The role of NHEJ in repairing radiation-induced double The var genes...there are also a number of pseudogenes and gene truncations breaks (for example, VDJ recombination in the immune system in present. humans). The role...protective efficacy of recombinant antigen constructs 16,17 Salvador I chromosomes can be separated by pulsed-field gel electrophoresis for karyotype and

  20. 'Death and axes': unexpected Ca²⁺ entry phenologs predict new anti-schistosomal agents.

    Directory of Open Access Journals (Sweden)

    John D Chan

    2014-02-01

    Full Text Available Schistosomiasis is a parasitic flatworm disease that infects 200 million people worldwide. The drug praziquantel (PZQ is the mainstay therapy but the target of this drug remains ambiguous. While PZQ paralyses and kills parasitic schistosomes, in free-living planarians PZQ caused an unusual axis duplication during regeneration to yield two-headed animals. Here, we show that PZQ activation of a neuronal Ca²⁺ channel modulates opposing dopaminergic and serotonergic pathways to regulate 'head' structure formation. Surprisingly, compounds with efficacy for either bioaminergic network in planarians also displayed antischistosomal activity, and reciprocally, agents first identified as antischistocidal compounds caused bipolar regeneration in the planarian bioassay. These divergent outcomes (death versus axis duplication result from the same Ca²⁺ entry mechanism, and comprise unexpected Ca²⁺ phenologs with meaningful predictive value. Surprisingly, basic research into axis patterning mechanisms provides an unexpected route for discovering novel antischistosomal agents.

  1. Susceptibility of Snails to Infection with Schistosomes is influenced by Temperature and Expression of Heat Shock Proteins

    Science.gov (United States)

    Knight, Matty; Elhelu, O; Smith, M; Haugen, B; Miller, A; Raghavan, N; Wellman, C; Cousin, C; Dixon, F; Mann, V; Rinaldi, G; Ittiprasert, W; Brindley, PJ

    2015-01-01

    The freshwater snail, Biomphalaria glabrata is the obligate intermediate host for the transmission of the parasitic trematode, Schistosoma mansoni the causative agent of the chronic debilitating neglected tropical disease, schistosomiasis. We showed previously that in juvenile snails, early and significant induction of stress manifested by the expression of stress proteins, Hsp 70, Hsp 90 and reverse transcriptase (RT) of the non- LTR retrotransposon, nimbus, is a characteristic feature of juvenile susceptible NMRI but not resistant BS-90 snails. These latter, however, could be rendered susceptible after mild heat shock at 32°C, revealing that resistance in the BS-90 resistant snail to schistosomes is a temperature dependent trait. Here we tested the hypothesis that maintenance of BS-90 resistant snails at the permissive temperature for several generations affects the resistance phenotype displayed at the non-permissive temperature of 25°C. The progeny of BS-90 snails bred and maintained through several generations (F1 to F4) at 32°C were susceptible to the schistosome infection when returned to room temperature, shedding cercariae at four weeks post-infection. Moreover, the study of expression levels of the heat shock protein (Hsp) 70 protein by ELISA and western blot analysis, showed that this protein is also differentially expressed between susceptible and resistant snails, with susceptible snails expressing more protein than their resistant counterparts after early exposure to wild-type but not to radiation-attenuated miracidia. These data suggested that in the face of global warming, the ability to sustain a reduction in schistosomiasis by using refractory snails as a strategy to block transmission of the disease might prove challenging since non-lethal elevation in temperature, affects snail susceptibility to S. mansoni. PMID:26504668

  2. Racial and ethnic differences in epilepsy classification among probands in the Epilepsy Phenome/Genome Project (EPGP).

    Science.gov (United States)

    Friedman, Daniel; Fahlstrom, Robyn

    2013-12-01

    Little is known about the ethnic and racial differences in the prevalence of generalized and focal epilepsy among patients with non-acquired epilepsies. In this study, we examined epilepsy classification and race/ethnicity in 813 probands from sibling or parent-child pairs with epilepsy enrolled in the Epilepsy Genome/Phenome Project (EPGP). Subjects were classified as generalized epilepsy (GE), non-acquired focal epilepsy (NAFE), mixed epilepsy syndrome (both generalized and focal), and unclassifiable, based on consensus review of semiology and available clinical, electrophysiology, and neuroimaging data. In this cohort, 628 (77.2%) subjects identified exclusively as Caucasian/white and 65 (8.0%) subjects reported African ancestry, including subjects of mixed-race. Of the Caucasian/white subjects, 357 (56.8%) had GE, 207 (33.0%) had NAFE, 32 (5.1%) had a mixed syndrome, and 32 (5.1%) were unclassifiable. Among subjects of African ancestry, 28 (43.1%) had GE, 27 (41.5%) had NAFE, 2 (3.1%) had a mixed syndrome, and 8 (12.3%) were unclassifiable. There was a higher proportion of subjects with GE compared to other syndromes among Caucasians/whites compared to subjects with African ancestry (OR 1.74, 95% CI: 1.04-2.92, two-tailed Fisher's exact test, p=0.036). There was no difference in the rate of GE among subjects reporting Hispanic ethnicity (7.6% of total) when adjusted for race (Caucasian/white vs non-Caucasian/white; OR 0.65, 95% CI: 0.40-1.06, p>0.05). The proportion of participants with unclassifiable epilepsy was significantly greater in those of African-American descent. In a group of patients with epilepsy of unknown etiology and an affected first degree relative, GE is more common among Caucasian/white subjects than among those with African ancestry. These findings suggest there may be geographical differences in the distribution of epilepsy susceptibility genes and an effect of genetic background on epilepsy phenotype. However, the results should be

  3. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

    Directory of Open Access Journals (Sweden)

    Santana Clara

    2009-10-01

    Full Text Available Abstract Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. Results A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. Conclusion The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.

  4. The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms.

    Science.gov (United States)

    Littlewood, D Timothy J; Lockyer, Anne E; Webster, Bonnie L; Johnston, David A; Le, Thanh Hoa

    2006-05-01

    Complete mitochondrial genome sequences for the schistosomes Schistosoma haematobium and Schistosoma. spindale have been characterized. S. haematobium is the causative agent of urinary schistosomiasis in humans and S. spindale uses ruminants as its definitive host; both are transmitted by freshwater snail intermediate hosts. Results confirm a major gene order rearrangement among schistosomes in all traditional Schistosoma species groups other than Schistosoma japonicum; i.e., species groups S. mansoni, S. haematobium, and S. indicum. These data lend support to the 'out of Asia' (East and Southeast Asia) hypothesis for Schistosoma. The gene order change involves translocation of atp6-nad2-trnA and a rearrangement of nad3-nad1 relative to other parasitic flatworm mt genomes so far sequenced. Gene order and tRNA secondary structure changes (loss and acquisition of the DHU and/or TPsiC arms of trnC, trnF, and trnR) between mitochondrial genomes of these and other (digenean and cestode) flatworms were inferred by character mapping onto a phylogeny estimated from nuclear small subunit rRNA gene sequences of these same species, in order to find additional rare genomic changes suitable as synapomorphies. Denser and wider taxon sampling of mt genomes across the Platyhelminthes will validate these putative characters.

  5. 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.

  6. Application of bioinformatics in cardiovascular genomics

    NARCIS (Netherlands)

    Tragante Do O, V.

    2014-01-01

    Genetic research made a remarkable progress in the past 20 years, with the Human Genome Project, which sequenced an entire genome; the HapMap project, that identified common genetic variation in hundreds of genomes from different populations; and the 1000 Genomes project, which identified common and

  7. Artesunate effect on schistosome thioredoxin glutathione reductase and cytochrome c peroxidase as new molecular targets in schistosoma mansoni-infected mice.

    Science.gov (United States)

    Abdin, Amany A; Ashour, Dalia S; Shoheib, Zeinab S

    2013-12-01

    To investigate the possible effect of artesunate (ART) on schistosome thioredoxin glutathione reductase (TGR) and cytochrome c peroxidase (CcP) in Schistosoma mansoni-infected mice. A total of 200 laboratory bred male Swiss albino mice were divided into 4 groups (50 mice in each group). Group I: infected untreated group (Control group) received a vehicle of 1% sodium carbonyl methylcellulose (CMC-Na); Group II: infected then treated with artesunate; Group III: infected then treated with praziquantel, and group IV: infected then treated with artesunate then praziquantel. Adult S. mansoni worms were collected by Animal Perfusion Method, tissue egg counted, TGR, and CcP mRNA Expression were estimated of in S. mansoni adult worms by semi-quantitative rt-PCR. Semi-quantitative rt-PCR values revealed that treatment with artesunate caused significant decrease in expression of schistosome TGR and CcP in comparison to the untreated group. In contrast, the treatment with praziquantel did not cause significant change in expression of these genes. The results showed more reduction in total worm and female worm count in combined ART-PZQ treated group than in monotherapy treated groups by either ART or PZQ. Moreover, complete disappearance (100%) of tissue eggs was recorded in ART-PZQ treated group with a respective reduction rate of 95.9% and 68.4% in ART- and PZQ-treated groups. The current study elucidated for the first time that anti-schistosomal mechanisms of artesunate is mediated via reduction in expression of schistosome TGR and CcP. Linking these findings, addition of artesunate to praziquantel could achieve complete cure outcome in treatment of schistosomiasis. Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  8. Differentiating Schistosoma haematobium from Schistosoma magrebowiei and other closely related schistosomes by polymerase chain reaction amplification of a species specific mitochondrial gene

    OpenAIRE

    Olaoluwa P Akinwale; Hock, Tang T.; Chia-Kwung, Fan; ZHENG Qi; Haimo, Shen; Ezeh, Charles; Gyang, Pam V

    2014-01-01

    Introduction: Schistosoma haematobium infection afflicts about 150 million people in 53 countries in Africa and the Middle East. In many endemic areas, S. haematobium is sympatric with Schistosoma bovis, Schistosoma mattheei, Schistosoma curassoni, Schistosoma intercalatum and Schistosoma magrebowiei, its closely related species. In addition, they also develop in the same intermediate snail hosts. Since these schistosome species often infect snails inhabiting the same bodies of water, examini...

  9. Impact of density of schistosomal antigen expression in urinary bladder tissue on the stratification, cell type, and staging, and prognosis of carcinoma of the bladder in Egyptian patients

    OpenAIRE

    Wishahi, Mohamed; Zakarya, Ahmed; Hamamm, Olfat; Abdel-Rasol, Mohamed; Badawy, Hisham; Elganzoury, Hossam; Ismail, Mohamed; Elkhouly, Amr; Meheina, Ahmed

    2014-01-01

    Background Infection with urinary schistosomiasis and its severity are oncogenic factors for developing carcinoma of the bladder, whether it is urothelial carcinoma (UC) of a transitional cell type (TCC) or non-urothelial of squamous cell carcinoma (SCC). In UC it is not defined whether it is schistosomal or not. This led to controversial results in expression of tumour markers, tumour prognosis, and response to therapy. Objectives We assessed the application by immunohistochemistry method (I...

  10. Molecular approaches to the identification of Bulinus species in south-west Nigeria and observations on natural snail infections with schistosomes.

    Science.gov (United States)

    Akinwale, O P; Kane, R A; Rollinson, D; Stothard, J R; Ajayi, M B; Akande, D O; Ogungbemi, M O; Duker, C; Gyang, P V; Adeleke, M A

    2011-09-01

    The current study considers the distribution of a small sample of 138 Bulinus snails, across 28 localities within eight Nigerian states. Snails were identified using a combination of molecular methods involving both DNA sequencing of a partial cytochrome oxidase subunit 1 (cox1) fragment and restriction profiles obtained from ribosomal internal transcribed spacer (its) amplicons. The results showed that the majority of Bulinus samples tested belonged to the species Bulinus truncatus while only two were Bulinus globosus. The use of RsaI restriction endonuclease to cleave the ribosomal its of Bulinus, as a method of species identification, was adopted for the majority of samples, this being a quicker and cheaper method better suited to small laboratory environments. Polymerase chain reaction (PCR) amplification of the schistosome Dra1 repeat within each of the collected Bulinus samples was employed to determine the extent and distribution of infected snails within the sample areas. Successful amplification of the Dra1 repeat demonstrated that 29.7% of snails were infected with schistosomes. Sequencing of the partial schistosome its from a small subset of snail samples suggested that some snails were either penetrated by both Schistosoma haematobium and Schistosoma bovis miracidia or hybrid miracidia formed from the two species.

  11. Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project.

    Science.gov (United States)

    Marano, Leonardo Arduino; Marcorin, Letícia; Castelli, Erick da Cruz; Mendes-Junior, Celso Teixeira

    2017-01-01

    The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing melanoma, it constitutes one of the best models to understand how natural selection acts on pigmentation. Here we employed a locally developed pipeline to obtain genotype and haplotype data for MC1R from the raw sequencing data provided by the 1000 Genomes FTP site. We also compared such genotype data to Phase 3 VCF to evaluate its quality and discover any polymorphic sites that may have been overlooked. In conclusion, either the VCF file or one of the presently described pipelines could be used to obtain reliable and accurate genotype calling from the 1000 Genomes Phase 3 data.

  12. Exploiting the genome

    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; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  13. Secretory glands in cercaria of the neuropathogenic schistosome Trichobilharzia regenti - ultrastructural characterization, 3-D modelling, volume and pH estimations

    Directory of Open Access Journals (Sweden)

    Koberna Karel

    2011-08-01

    Full Text Available Abstract Background Cercariae of schistosomes employ bioactive molecules for penetration into their hosts. These are released from specialized unicellular glands upon stimuli from host skin. The glands were previously well-described in the human pathogen Schistosoma mansoni. As bird schistosomes can also penetrate human skin and cause cercarial dermatitis, our aim was to characterize the architecture and ultrastructure of glands in the neurotropic bird schistosome Trichobilharzia regenti and compare it with S. mansoni. In the context of different histolytic enzymes used by these two species, we focused also on the estimations of gland volumes and pH in T. regenti. Results The architecture and 3-D models of two types of acetabular penetration glands, their ducts and of the head gland are shown here. We characterized secretory vesicles in all three gland types by means of TEM and confirmed accuracy of the models obtained by confocal microscopy. The results of two independent approaches showed that the glands occupy ca. one third of cercarial body volume (postacetabular glands ca. 15%, circumacetabular 12% and head gland 6%. The inner environment within the two types of acetabular glands differed significantly as evidenced by dissimilar ability to bind fluorescent markers and by pH value which was higher in circumacetabular (7.44 than in postacetabular (7.08 glands. Conclusions As far as we know, this is the first presentation of a 3-D model of cercarial glands and the first exact estimation of the volumes of the three gland types in schistosomes. Our comparisons between T. regenti and S. mansoni implied that the architecture and ultrastructure of the glands is most likely conserved within the family. Only minor variations were found between the two species. It seems that the differences in molecular composition have no effect on general appearance of the secretory cells in TEM. Fluorescent markers employed in this study, distinguishing between

  14. 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

  15. 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.

  16. Database management research for the Human Genome Project: Progress report, 7/1/96-3/15/97

    Energy Technology Data Exchange (ETDEWEB)

    Goodman, N.

    1997-03-01

    Progress is reported on the development of software that works in conjunction with database management systems (DBMSs) in ways that are useful for genomics. This new release of LabBase has two major advantages over the previous version, namely it runs on the Sybase relational DBMS rather than ObjectStore and offers more complete data modeling features than the previous version so is suitable for more kinds of genetic databases.

  17. Affinities between Asian non-human Schistosoma species, the S. indicum group, and the African human schistosomes.

    Science.gov (United States)

    Agatsuma, T; Iwagami, M; Liu, C X; Rajapakse, R P V J; Mondal, M M H; Kitikoon, V; Ambu, S; Agatsuma, Y; Blair, D; Higuchi, T

    2002-03-01

    Schistosoma species have traditionally been arranged in groups based on egg morphology, geographical origins, and the genus or family of snail intermediate host. One of these groups is the 'S. indicum group' comprising species from Asia that use pulmonate snails as intermediate hosts. DNA sequences were obtained from the four members of this group (S. indicum, S. spindale, S. nasale and S. incognitum) to provide information concerning their phylogenetic relationships with other Asian and African species and species groups. The sequences came from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. Tree analyses using both distance and parsimony methods showed the S. indicum group not to be monophyletic. Schistosoma indicum, S. spindale and S. nasale were clustered among African schistosomes, while S. incognitum was placed as sister to the African species (using ITS2 and 28S nucleotide sequences and CO1 amino acid sequences), or as sister to all other species of Schistosoma (CO1 nucleotide sequences). Based on the present molecular data, a scenario for the evolution of the S. indicum group is discussed.

  18. Differentiating Schistosoma haematobium from related animal schistosomes by PCR amplifying inter-repeat sequences flanking newly selected repeated sequences.

    Science.gov (United States)

    Abbasi, Ibrahim; Hamburger, Joseph; Kariuki, Curtis; Mungai, Peter L; Muchiri, Eric M; King, Charles H

    2012-12-01

    In schistosomiasis elimination programs, successful discrimination of Schistosoma haematobium from the related animal Schistosoma parasites will be essential for accurate detection of human parasite transmission. Polymerase chain reaction assays employing primers from two newly selected repeated sequences, named Sh73 and Sh77, did not discriminate S. haematobium when amplifying Sh73-77 intra- or inter-repeats. However, amplification between Sh73 and the previously described DraI repeat exhibited discriminative banding patterns for S. haematobium and Schistosoma bovis (sensitivity 1 pg and 10 pg, respectively). It also enabled banding pattern discrimination of Schistosoma curassoni and Schistosoma intercalatum, but Schistosoma mattheei and Schistosoma margrebowiei did not yield amplicons. Similar inter-repeat amplification between Sh77 and DraI yielded amplicons with discriminative banding for S. haematobium, and S. bovis; however, S. mattheei was detected only at low sensitivity (1 ng). The Sh73/DraI assay detected snails infected with S. haematobium, S. bovis, or both, and should prove useful for screening snails where discrimination of S. haematobium from related schistosomes is required.

  19. Vaccination of goats against the trematode Schistosoma bovis with a recombinant homologous schistosome-derived glutathione S-transferase.

    Science.gov (United States)

    Boulanger, D; Trottein, F; Mauny, F; Bremond, P; Couret, D; Pierce, R J; Kadri, S; Godin, C; Sellin, E; Lecocq, J P

    1994-08-01

    We assayed the vaccine potentialities of a recombinant S. bovis-derived glutathione S-transferase (rSb28GST), member of a molecular family already shown to have protective capacities in the S. mansoni and S. japonicum models. Injection of the rSb28GST in Freund's Complete Adjuvant resulted in good specific IgG responses allowing all the animals to display high antibody titres on the day of experimental challenge with S. bovis cercariae. No statistically significant differences were observed in the faecal egg output. Although tissue egg counts in vaccinated animals were lower than in controls, the difference was not statistically significant, apart from the number of eggs trapped in the liver (P bovis, by affecting worm viability but not fecundity. These results also point to the striking differences in the effect of vaccination according to animal species. Because it has the capacity to prevent growth impairment due to schistosome pathogenicity, the molecule can be proposed as a valuable tool in the development of vaccine-based control programs in endemic areas.

  20. Information and dialogue conference on the human genome project for the minority communities in the state of Louisiana

    Energy Technology Data Exchange (ETDEWEB)

    None

    1999-04-17

    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.

  1. 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.

  2. Citrus Genomics

    Science.gov (United States)

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  3. National Human Genome Research Institute

    Science.gov (United States)

    ... Barb Biesecker, highlights a recent dog genome project Reddit AMA and provides a reminder to learn your family health history on Thanksgiving. Reddit "Ask Me Anything" Recap: The NHGRI Dog Genome ...

  4. 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...

  5. 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

  6. Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project.

    Science.gov (United States)

    Das, Ranajit; Upadhyai, Priyanka

    2017-12-28

    The utilization of biological data to infer the geographic origins of human populations has been a long standing quest for biologists and anthropologists. Several biogeographical analysis tools have been developed to infer the geographical origins of human populations utilizing genetic data. However due to the inherent complexity of genetic information these approaches are prone to misinterpretations. The Geographic Population Structure (GPS) algorithm is an admixture based tool for biogeographical analyses and has been employed for the geo-localization of various populations worldwide. Here we sought to dissect its sensitivity and accuracy for localizing highly admixed groups. Given the complex history of population dispersal and gene flow in the Indian subcontinent, we have employed the GPS tool to localize five South Asian populations, Punjabi, Gujarati, Tamil, Telugu and Bengali from the 1000 Genomes project, some of whom were recent migrants to USA and UK, using populations from the Indian subcontinent available in Human Genome Diversity Panel (HGDP) and those previously described as reference. Our findings demonstrate reasonably high accuracy with regards to GPS assignment even for recent migrant populations sampled elsewhere, namely the Tamil, Telugu and Gujarati individuals, where 96%, 87% and 79% of the individuals, respectively, were positioned within 600 km of their native locations. While the absence of appropriate reference populations resulted in moderate-to-low levels of precision in positioning of Punjabi and Bengali genomes. Our findings reflect that the GPS approach is useful but likely overtly dependent on the relative proportions of admixture in the reference populations for determination of the biogeographical origins of test individuals. We conclude that further modifications are desired to make this approach more suitable for highly admixed individuals.

  7. Discovery of Western European R1b1a2 Y chromosome variants in 1000 genomes project data: an online community approach.

    Directory of Open Access Journals (Sweden)

    Richard A Rocca

    Full Text Available The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076. Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data.

  8. 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.

  9. Whole genome analysis of a Vietnamese trio

    Indian Academy of Sciences (India)

    2015-02-04

    Feb 4, 2015 ... We used standard and high-quality methods and software/ pipelines that had been used in the 1000 Genomes Project and other human genome projects to analyse our KHV trio genomic data. 3.1 Data production. The genomic DNA used in this study was from an anony- mous Kinh Vietnamese (KHV) trio ...

  10. Helminth genomics: The implications for human health.

    Directory of Open Access Journals (Sweden)

    Paul J Brindley

    2009-10-01

    Full Text Available More than two billion people (one-third of humanity are infected with parasitic roundworms or flatworms, collectively known as helminth parasites. These infections cause diseases that are responsible for enormous levels of morbidity and mortality, delays in the physical development of children, loss of productivity among the workforce, and maintenance of poverty. Genomes of the major helminth species that affect humans, and many others of agricultural and veterinary significance, are now the subject of intensive genome sequencing and annotation. Draft genome sequences of the filarial worm Brugia malayi and two of the human schistosomes, Schistosoma japonicum and S. mansoni, are now available, among others. These genome data will provide the basis for a comprehensive understanding of the molecular mechanisms involved in helminth nutrition and metabolism, host-dependent development and maturation, immune evasion, and evolution. They are likely also to predict new potential vaccine candidates and drug targets. In this review, we present an overview of these efforts and emphasize the potential impact and importance of these new findings.

  11. Helminth Genomics: The Implications for Human Health

    Science.gov (United States)

    Brindley, Paul J.; Mitreva, Makedonka; Ghedin, Elodie; Lustigman, Sara

    2009-01-01

    More than two billion people (one-third of humanity) are infected with parasitic roundworms or flatworms, collectively known as helminth parasites. These infections cause diseases that are responsible for enormous levels of morbidity and mortality, delays in the physical development of children, loss of productivity among the workforce, and maintenance of poverty. Genomes of the major helminth species that affect humans, and many others of agricultural and veterinary significance, are now the subject of intensive genome sequencing and annotation. Draft genome sequences of the filarial worm Brugia malayi and two of the human schistosomes, Schistosoma japonicum and S. mansoni, are now available, among others. These genome data will provide the basis for a comprehensive understanding of the molecular mechanisms involved in helminth nutrition and metabolism, host-dependent development and maturation, immune evasion, and evolution. They are likely also to predict new potential vaccine candidates and drug targets. In this review, we present an overview of these efforts and emphasize the potential impact and importance of these new findings. PMID:19855829

  12. Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma

    Science.gov (United States)

    2011-01-01

    Blood flukes within the genus Schistosoma still remain a major cause of disease in the tropics and subtropics and the study of their evolution has been an area of major debate and research. With the advent of modern molecular and genomic approaches deeper insights have been attained not only into the divergence and speciation of these worms, but also into the historic movement of these parasites from Asia into Africa, via migration and dispersal of definitive and snail intermediate hosts. This movement was subsequently followed by a radiation of Schistosoma species giving rise to the S. mansoni and S. haematobium groups, as well as the S. indicum group that reinvaded Asia. Each of these major evolutionary events has been marked by distinct changes in genomic structure evident in differences in mitochondrial gene order and nuclear chromosomal architecture between the species associated with Asia and Africa. Data from DNA sequencing, comparative molecular genomics and karyotyping are indicative of major constitutional genomic events which would have become fixed in the ancestral populations of these worms. Here we examine how modern genomic techniques may give a more in depth understanding of the evolution of schistosomes and highlight the complexity of speciation and divergence in this group. PMID:21736723

  13. The Schistosoma indicum species group in Nepal: presence of a new lineage of schistosome and use of the Indoplanorbis exustus species complex of snail hosts✯

    OpenAIRE

    Devkota, Ramesh; Brant, Sara V.; Loker, Eric S.

    2015-01-01

    From 2007–2014, 19,360 freshwater snails from the Terai and hilly regions of Nepal were screened for cercariae of mammalian schistosomes. Based on analysis of mitochondrial cytochrome oxidase I (cox1), 12S, 16S and 28S sequences (3,675 bp) of the cercariae recovered, we provide, to our knowledge, the first report of the Schistosoma indicum species group in Nepal. Five samples of Schistosoma nasale, nine of Schistosoma spindale and 17 of Schistosoma sp. were recovered, all from the snail Indop...

  14. The fishes of Genome 10K

    KAUST Repository

    Bernardi, Giacomo

    2012-09-01

    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  15. In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the fucosyltransferase multigene family.

    Science.gov (United States)

    Peterson, Nathan A; Anderson, Tavis K; Yoshino, Timothy P

    2013-01-01

    Fucosylated glycans of the parasitic flatworm Schistosoma mansoni play key roles in its development and immunobiology. In the present study we used a genome-wide homology-based bioinformatics approach to search for genes that contribute to fucosylated glycan expression in S. mansoni, specifically the α2-, α3-, and α6-fucosyltransferases (FucTs), which transfer L-fucose from a GDP-L-fucose donor to an oligosaccharide acceptor. We identified and in silico characterized several novel schistosome FucT homologs, including six α3-FucTs and six α6-FucTs, as well as two protein O-FucTs that catalyze the unrelated transfer of L-fucose to serine and threonine residues of epidermal growth factor- and thrombospondin-type repeats. No α2-FucTs were observed. Primary sequence analyses identified key conserved FucT motifs as well as characteristic transmembrane domains, consistent with their putative roles as fucosyltransferases. Most genes exhibit alternative splicing, with multiple transcript variants generated. A phylogenetic analysis demonstrated that schistosome α3- and α6-FucTs form monophyletic clades within their respective gene families, suggesting multiple gene duplications following the separation of the schistosome lineage from the main evolutionary tree. Quantitative decreases in steady-state transcript levels of some FucTs during early larval development suggest a possible mechanism for differential expression of fucosylated glycans in schistosomes. This study systematically identifies the complete repertoire of FucT homologs in S. mansoni and provides fundamental information regarding their genomic organization, genetic variation, developmental expression, and evolutionary history.

  16. In Silico Analysis of the Fucosylation-Associated Genome of the Human Blood Fluke Schistosoma mansoni: Cloning and Characterization of the Fucosyltransferase Multigene Family

    Science.gov (United States)

    Peterson, Nathan A.; Anderson, Tavis K.; Yoshino, Timothy P.

    2013-01-01

    Fucosylated glycans of the parasitic flatworm Schistosoma mansoni play key roles in its development and immunobiology. In the present study we used a genome-wide homology-based bioinformatics approach to search for genes that contribute to fucosylated glycan expression in S. mansoni, specifically the α2-, α3-, and α6-fucosyltransferases (FucTs), which transfer L-fucose from a GDP-L-fucose donor to an oligosaccharide acceptor. We identified and in silico characterized several novel schistosome FucT homologs, including six α3-FucTs and six α6-FucTs, as well as two protein O-FucTs that catalyze the unrelated transfer of L-fucose to serine and threonine residues of epidermal growth factor- and thrombospondin-type repeats. No α2-FucTs were observed. Primary sequence analyses identified key conserved FucT motifs as well as characteristic transmembrane domains, consistent with their putative roles as fucosyltransferases. Most genes exhibit alternative splicing, with multiple transcript variants generated. A phylogenetic analysis demonstrated that schistosome α3- and α6-FucTs form monophyletic clades within their respective gene families, suggesting multiple gene duplications following the separation of the schistosome lineage from the main evolutionary tree. Quantitative decreases in steady-state transcript levels of some FucTs during early larval development suggest a possible mechanism for differential expression of fucosylated glycans in schistosomes. This study systematically identifies the complete repertoire of FucT homologs in S. mansoni and provides fundamental information regarding their genomic organization, genetic variation, developmental expression, and evolutionary history. PMID:23696810

  17. The occurrence of schistosomin, an antagonist of female gonadotropic hormones, is a general phenomenon in haemolymph of schistosome-infected freshwater snails.

    Science.gov (United States)

    De Jong-Brink, M; Elsaadany, M; Soto, M S

    1991-12-01

    In haemolymph of Lymnaea stagnalis, parasitized with the digenetic trematode parasite Trichobilharzia ocellata, a neuropeptide (schistosomin) occurs which antagonizes female gonadotropic hormones, e.g. calfluxin (CaFl). By means of an ultracytochemical hormone-assay, the CaFl assay, it was demonstrated that the occurrence of schistosomin is a general phenomenon in schistosome-infected freshwater snails. Haemolymph of the schistosomiasis-transmitting snail species Biomphalaria glabrata and B. pfeifferi, parasitized with Schistosoma mansoni, also appeared to contain an antagonizing factor, i.e. schistosomin. In contrast, in haemolymph of L. stagnalis parasitized with Diplostomum spathaceum (Diplostomatidae) no schistosomin could be found. This suggests that schistosomin may only occur in snails infected with parasites belonging to the Schistosomatidae. The effect of schistosomin is rather specific. Haemolymph of B. glabrata parasitized with S. mansoni had not the capacity to inhibit the response to CaFl in the target organs for CaFl, the albumen glands of L. stagnalis and Bulinus truncatus. The same holds true for haemolymph of infected L. stagnalis: it did not inhibit the CaFl response in glands of B. glabrata and B. truncatus and even not in those of a related species (L. ovata). Schistosomins in haemolymph of infected B. glabrata and B. pfeifferi, on the other hand, seem more related. Both appeared to inhibit the hormone response in glands of the two Biomphalaria species studied. The results indicate that schistosomin in haemolymph of schistosome-infected pulmonate snails, although functionally related, may differ structurally.

  18. Cigarette smoking induced liver insult concomitant with inflammatory mediators in serum crevicular fluid and bronchio alveolar lavage of schistosomal diabetic subjects with history of bronchial asthma.

    Science.gov (United States)

    El-Dardiry, Samia A; Shafik, Sherine R; Wagih, Ayman; Amir, El-Amir M; Kassem, Gamal K; Atef, Ghada; El-Toukhy, Heba

    2007-08-01

    Forty five smokers were classified into schistosomal cases with type-2 diabetis mellitus (GI) and with associated history of bronchial asthma (GII) and without T-2 DM (GIII). A control group (GIV) of non-diabetic non schistosomal age matched subjects who quitted smoking for >6 months were included. Assessed parameters included indices of glycemic status (glycated hemoglobin), angiogenesis (vascular endothelial growth factor) hepatic and bronchoalveolar disposition (Liver function test, metallothionein, serum levels of cotinine, cadmium selenium, copper & zinc) and bronchoalveolar lavage) (BAL) levels of surfactant proteins A & D, zinc and copper oxidative stress and fibrogenesis (total antioxidant capacity thiobarbituric acid reactive substance) and vasculopathy (angiotensin converting enzyme, P-selectin, nitrate) and periodontitis (collagenase and elastase in GCF) impact of cigarette smoking associated with trace element disbalance and enzymatic changes in crevicular fluid on altered parameters collaborative out-come. The study reflected the collaborative outcome of immune mediated mechanisms initiated by liver affection, glycemic status and history of predisposed bronchial integrity induced by oxidative stress.

  19. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  20. Genome-tools: a flexible package for genome sequence analysis.

    Science.gov (United States)

    Lee, William; Chen, Swaine L

    2002-12-01

    Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools.

  1. Experimental pulmonary schistosomiasis: lack of morphological evidence of modulation in schistosomal pulmonary granulomas Esquistossomose pulmonar experimental: falta de evidência morfológica de modulação nos granulomas esquistosomóticos pulmonares

    OpenAIRE

    Maura R. F. Souza Vidal; Barbosa Jr.,Aryon A.; Zilton A. ANDRADE

    1993-01-01

    Numerous pulmonary schistosome egg granulomas were present in mice submitted to partial portal vein ligation (Warren's model). The granulomas were characterized by cellular aggregations formed within alveolar tissue. Main cellular types were macrophages (epithelioid cells), eosinophils, plasma cells and lymphocytes. These cells were supported by scanty fibrous stroma and exhibited close membrane contact points amongst themselves, but without forming specialized adhesion apparatus. When granul...

  2. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.

    Directory of Open Access Journals (Sweden)

    Guillaume Lettre

    2011-02-01

    Full Text Available Coronary heart disease (CHD is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C, hypertension, smoking, and type-2 diabetes in individuals of African ancestry, we performed a genome-wide association study (GWAS in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1, we could leverage the distinct linkage disequilibrium (LD patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia.

  3. The promise of insect genomics

    DEFF Research Database (Denmark)

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

    2007-01-01

    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts...

  4. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  5. 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 HapMap and 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of PHapMap 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.

  6. Ethical issues and GenomEUtwin

    NARCIS (Netherlands)

    Harris, J.R.; Willemsen, G.; Aitlahti, T.; Petrini, C.; Evans, A.; Silander, K.; Cirrincione, L.; Kyvik, K.

    2003-01-01

    The post-genomic era is witnessing a proliferation of large-scale and population based genetic and genomic research projects. Many countries have or are establishing research biobanks and, as with GenomEUtwin, there is great interest in building multinational projects that link genotypic and

  7. Evolution of schistosomiasis-induced pathology after therapy and interruption of exposure to schistosomes: a review of ultrasonographic studies.

    Science.gov (United States)

    Richter, J

    2000-10-23

    urogenital lesions led to complications many years after exposure. Contrary to hepatosplenic and urinary pathology, knowlegde on the evolution of other organic abnormalities is very limited: studies on the evolution of biliary abnormalities or intestinal pathology have not been published. Genital pathology may be induced by all Schistosoma spp. Post-therapy evolution of genital schistosomiasis is largely ignored. In some European travellers partial regression of prostatic fibrosis has been described. Schistosomal adnexitis leading to infertility and/or ectopic pregnancy has been reported occurring many years after interruption of exposure. Ultrasonography (US) has never been used to study the influence of schistosomiasis on pregnancy. Concluding, current knowlegde on the evolution of pathology after treatment and/or interruption of exposure is still fragmentary. Frequently, fibrosis reverses after therapy, but advanced pathology may persist for long. Therefore, the possibility of severe clinical complications has to be taken into account, even if the infection is inactive since many years. In interventions aimed at controlling schistosomiasis-related morbidity, evolution of pathology must be monitored by US in representative patient cohorts. Further systematic US-studies are needed not only on the evolution of hepatosplenic and urinary pathology but also on that of intestinal, biliary and genital pathology induced by schistosomiasis, as well as on the influence of schistosomiasis on the outcome of pregnancy.

  8. Trichobilharzia anseri n. sp. (Schistosomatidae: Digenea), a new visceral species of avian schistosomes isolated from greylag goose (Anser anser L.) in Iceland and France.

    Science.gov (United States)

    Jouet, D; Kolářová, L; Patrelle, C; Ferté, H; Skírnisson, K

    2015-08-01

    Parasitological investigations carried out on birds in Iceland and France highlight the presence of four species of avian schistosomes from greylag geese (Anser anser L.): the european nasal species Trichobilharzia regenti and three visceral species, among which an unknown species isolated from blood vessels of the large intestine and liver. Morphological and molecular analyzes of different parasite stages (eggs, adults) revealed new species of Trichobilharzia genus – Trichobilharzia anseri sp. nov. Studies on host-parasite relationship under natural conditions, showed that the life-cycle includes the snail Radix balthica (syn. R. peregra) as intermediate host. The cercariae, already isolated in Iceland from two ponds of the Reykjavik capital area – the Family park and Tjörnin Lake – are the same as those isolated in 1999 by Kolářová et al. during the first study on Icelandic parasitic agents of cercarial dermatitis. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. DNA barcoding of schistosome cercariae reveals a novel sub-lineage within Schistosoma rodhaini from Ngamba Island Chimpanzee Sanctuary, Lake Victoria.

    Science.gov (United States)

    Standley, C J; Stothard, J R

    2012-10-01

    While Schistosoma rodhaini is typically considered a parasite of small mammals and is very scantly distributed in the Lake Victoria basin, it is known to hybridize with the more widespread Schistosoma mansoni, the causative agent of intestinal schistosomiasis. As part of broader parasitological and malacological surveys for S. mansoni across Lake Victoria, schistosome cercariae were harvested from a field-caught Biomphalaria choanomphala taken on Ngamba Island Chimpanzee Sanctuary, Uganda. Upon DNA barcoding, these cercariae were found to be a mixture of both S. rodhaini and S. mansoni, with further phylogenetic analysis revealing a hitherto unknown sub-lineage within S. rodhaini. Despite repeated sampling for eggs and miracidia from both chimpanzees and staff on Ngamba Island Sanctuary, detection of S. rodhaini within local definitive hosts awaits additional efforts, which should be mindful of a potential host role of spotted-necked otters.

  10. Differences in the egg morphology and certain biological characteristics of some African and Middle Eastern schistosomes, genus Schistosoma, with terminal-spined eggs*

    Science.gov (United States)

    Pitchford, R. J.

    1965-01-01

    There is some confusion regarding the differentiation of African and Middle Eastern schistosomes with terminal-spined eggs. In an attempt to clarify the situation, the author has separated the members of the genus Schistosoma that have terminal-spined eggs into three broad groups and five species on the basis of egg morphology and certain biological characteristics. The groups are: the haematobium group, with one species (S. haematobium); the bovis group, with three species (S. bovis, S. mattheei and S. leiperi); and the intercalatum group, with one species (S. intercalatum). Further species separation is not thought to be justified yet, and reasons are given for considering S. capense and S. curassoni as synonymous with S. haematobium and S. mattheei respectively. PMID:14292062

  11. DIFFERENCES IN THE EGG MORPHOLOGY AND CERTAIN BIOLOGICAL CHARACTERISTICS OF SOME AFRICAN AND MIDDLE EASTERN SCHISTOSOMES, GENUS SCHISTOSOMA, WITH TERMINAL-SPINED EGGS.

    Science.gov (United States)

    PITCHFORD, R J

    1965-01-01

    There is some confusion regarding the differentiation of African and Middle Eastern schistosomes with terminal-spined eggs. In an attempt to clarify the situation, the author has separated the members of the genus Schistosoma that have terminal-spined eggs into three broad groups and five species on the basis of egg morphology and certain biological characteristics.THE GROUPS ARE: the haematobium group, with one species (S. haematobium); the bovis group, with three species (S. bovis, S. mattheei and S. leiperi); and the intercalatum group, with one species (S. intercalatum). Further species separation is not thought to be justified yet, and reasons are given for considering S. capense and S. curassoni as synonymous with S. haematobium and S. mattheei respectively.

  12. Differences in the gene expression profiles of haemocytes from schistosome-susceptible and -resistant biomphalaria glabrata exposed to Schistosoma mansoni excretory-secretory products.

    Directory of Open Access Journals (Sweden)

    Zahida Zahoor

    Full Text Available During its life cycle, the helminth parasite Schistosoma mansoni uses the freshwater snail Biomphalaria glabrata as an intermediate host to reproduce asexually generating cercariae for infection of the human definitive host. Following invasion of the snail, the parasite develops from a miracidium to a mother sporocyst and releases excretory-secretory products (ESPs that likely influence the outcome of host infection. To better understand molecular interactions between these ESPs and the host snail defence system, we determined gene expression profiles of haemocytes from S. mansoni-resistant or -susceptible strains of B. glabrata exposed in vitro to S. mansoni ESPs (20 μg/ml for 1 h, using a 5K B. glabrata cDNA microarray. Ninety-eight genes were found differentially expressed between haemocytes from the two snail strains, 57 resistant specific and 41 susceptible specific, 60 of which had no known homologue in GenBank. Known differentially expressed resistant-snail genes included the nuclear factor kappa B subunit Relish, elongation factor 1α, 40S ribosomal protein S9, and matrilin; known susceptible-snail specific genes included cathepsins D and L, and theromacin. Comparative analysis with other gene expression studies revealed 38 of the 98 identified genes to be uniquely differentially expressed in haemocytes in the presence of ESPs, thus identifying for the first time schistosome ESPs as important molecules that influence global snail host-defence cell gene expression profiles. Such immunomodulation may benefit the schistosome, enabling its survival and successful development in the snail host.

  13. Comparative analysis of rs12979860 SNP of the IFNL3 gene in children with hepatitis C and ethnic matched controls using 1000 Genomes Project data.

    Science.gov (United States)

    Indolfi, Giuseppe; Mangone, Giusi; Bartolini, Elisa; Nebbia, Gabriella; Calvo, Pier Luigi; Moriondo, Maria; Tovo, Pier-Angelo; de Martino, Maurizio; Azzari, Chiara; Resti, Massimo

    2014-01-01

    The rs12979860 single nucleotide polymorphism located on chromosome 19q13.13 near the interferon L3 gene (formerly and commonly known as interleukin 28B gene) has been associated in adults with both spontaneous and treatment induced clearance of hepatitis C virus. Although the exact mechanism of these associations remains unclear, it suggests that variation in genes involved in the immune response against the virus favours viral clearance. Limited and preliminary data are available on this issue in children. The aim of the present study was to evaluate, in a representative cohort of children with perinatal infection, the potential association between rs12979860 single nucleotide polymorphism and the outcome of hepatitis C virus infection. Alleles and genotypes frequencies were evaluated in 30 children who spontaneously cleared the virus and in 147 children with persistent infection and were compared with a population sample of ethnically matched controls with unknown hepatitis C status obtained using the 1000 Genomes Project data. The C allele and the C/C genotype showed greater frequencies in the clearance group (76.7% and 56.7%, respectively) when compared with both children with viral persistence (C allele 56.5%, p = 0.004; C/C genotype 32.7%, p = 0.02) and with the ethnically matched individuals (C allele 59.7%, p = 0.02; C/C genotype 34.7%, p = 0.03). Children with the C/C genotype were 2 times more likely to clear hepatitis C virus relative to children with the C/T and T/T genotypes combined (odds ratio: 2.7; 90% confidence intervals: 1.3-5.8). The present study provides the evidence that the rs12979860 single nucleotide polymorphism influences the natural history of hepatitis C virus in children.

  14. Comparative analysis of rs12979860 SNP of the IFNL3 gene in children with hepatitis C and ethnic matched controls using 1000 Genomes Project data.

    Directory of Open Access Journals (Sweden)

    Giuseppe Indolfi

    Full Text Available The rs12979860 single nucleotide polymorphism located on chromosome 19q13.13 near the interferon L3 gene (formerly and commonly known as interleukin 28B gene has been associated in adults with both spontaneous and treatment induced clearance of hepatitis C virus. Although the exact mechanism of these associations remains unclear, it suggests that variation in genes involved in the immune response against the virus favours viral clearance. Limited and preliminary data are available on this issue in children. The aim of the present study was to evaluate, in a representative cohort of children with perinatal infection, the potential association between rs12979860 single nucleotide polymorphism and the outcome of hepatitis C virus infection. Alleles and genotypes frequencies were evaluated in 30 children who spontaneously cleared the virus and in 147 children with persistent infection and were compared with a population sample of ethnically matched controls with unknown hepatitis C status obtained using the 1000 Genomes Project data. The C allele and the C/C genotype showed greater frequencies in the clearance group (76.7% and 56.7%, respectively when compared with both children with viral persistence (C allele 56.5%, p = 0.004; C/C genotype 32.7%, p = 0.02 and with the ethnically matched individuals (C allele 59.7%, p = 0.02; C/C genotype 34.7%, p = 0.03. Children with the C/C genotype were 2 times more likely to clear hepatitis C virus relative to children with the C/T and T/T genotypes combined (odds ratio: 2.7; 90% confidence intervals: 1.3-5.8. The present study provides the evidence that the rs12979860 single nucleotide polymorphism influences the natural history of hepatitis C virus in children.

  15. How well do HapMap haplotypes identify common haplotypes of genes? A comparison with haplotypes of 334 genes resequenced in the environmental genome project.

    Science.gov (United States)

    Taylor, Jack A; Xu, Zong-Li; Kaplan, Norman L; Morris, Richard W

    2006-01-01

    One of the goals of the International HapMap Project is the identification of common haplotypes in genes. However, HapMap uses an incomplete catalogue of single nucleotide polymorphisms (SNPs) and might miss some common haplotypes. We examined this issue using data from the Environmental Genome Project (EGP) which resequenced 335 genes in 90 people, and thus, has a nearly complete catalogue of gene SNPs. The EGP identified a total of 45,243 SNPs, of which 10,780 were common SNPs (minor allele frequency >or=0.1). Using EGP common SNP genotype data, we identified 1,459 haplotypes with frequency >or=0.05 and we use these as "benchmark" haplotypes. HapMap release 16 had genotype information for 1,573 of 10,780 (15%) EGP common SNPs. Using these SNPs, we identified common HapMap haplotypes (frequency >or=0.05) in each of the four HapMap ethnic groups. To compare common HapMap haplotypes to EGP benchmark haplotypes, we collapsed benchmark haplotypes to the set of 1,573 SNPs. Ninety-eight percent of the collapsed benchmark haplotypes could be found as common HapMap haplotypes in one or more of the four HapMap ethnic groups. However, collapsing benchmark haplotypes to the set of SNPs available in HapMap resulted in a loss of haplotype information: 545 of 1,459 (37%) benchmark haplotypes were uniquely identified, and only 25% of genes had all their benchmark haplotypes uniquely identified. We resampled the EGP data to examine the effect of increasing the number of HapMap SNPs to 5 million, and estimate that approximately 40% of common SNPs in genes will be sampled and that half of the genes will have sufficient SNPs to identify all common haplotypes. This inability to distinguish common haplotypes of genes may result in loss of power when examining haplotype-disease association. (Cancer Epidemiol Biomarkers Prev 2006;15(1):133-7).

  16. From genomes to vaccines via the proteome

    Directory of Open Access Journals (Sweden)

    R Alan Wilson

    2004-08-01

    Full Text Available An effective vaccine against schistosomiasis mansoni would be a valuable control tool and the high levels of protection elicited in rodents and primates by radiation-attenuated cercariae provide proof of principle. A major obstacle to vaccine development is the difficulty of identifying the antigens that mediate protection, not least because of the size of the genome at 280Mb DNA encoding 14,000 to 20,000 genes. The technologies collectively called proteomics, including 2D electrophoresis, liquid chromatography and mass spectrometry, now permit any protein to be identified provided there is extensive DNA data, and preferably a genome sequence. Applied to soluble (cytosolic proteins from schistosomes, proteomics reveals the great similarity in composition between life cycle stages, with several WHO vaccine candidates amongst the most abundant constituents. The proteomic approach has been successfully applied to identify the secretions used by cercaria to penetrate host skin, the gut secretions of adult worms and the proteins exposed on the tegument surface. Soluble proteins can also be separated by 2D electrophoresis before western blotting to identify the full range of antigenic targets present in a parasite preparation. The next step is to discover which target proteins represent the weak points in the worm's defences.

  17. The TIGR Rice Genome Annotation Resource: improvements and new features

    National Research Council Canada - National Science Library

    Ouyang, Shu; Zhu, Wei; Hamilton, John; Lin, Haining; Campbell, Matthew; Childs, Kevin; Thibaud-Nissen, Françoise; Malek, Renae L; Lee, Yuandan; Zheng, Li; Orvis, Joshua; Haas, Brian; Wortman, Jennifer; Buell, C Robin

    2007-01-01

    In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation...

  18. Genomic Testing

    Science.gov (United States)

    ... Counseling Genomic Testing Pathogen Genomics Epidemiology Resources Genomic Testing Recommend on Facebook Tweet Share Compartir Fact Sheet: ... Page The Need for Reliable Information on Genetic Testing In 2008, the former Secretary’s Advisory Committee on ...

  19. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  20. The complete mitochondrial genome of Orientobilharzia turkestanicum supports its affinity with African Schistosoma spp.

    Science.gov (United States)

    Wang, Yu; Wang, Chun-Ren; Zhao, Guang-Hui; Gao, Jun-Feng; Li, Ming-Wei; Zhu, Xing-Quan

    2011-12-01

    Orientobilharzia turkestanicum is a blood fluke of many mammals and causes orientobilharziasis that is also a neglected parasitic zoonosis because the cercaria of O. turkestanicum can infect humans and cause cercarial dermatitis. The present study determined the complete sequence of mt genome of O. turkestanicum and revised its phylogenetic position based on mt gene content and arrangement. The complete mtDNA sequence of O. turkestanicum was 14,755 bp in length, which is slightly larger than the mtDNA genomes of three species of the blood flukes, Schistosoma mekongi (14,072 bp), Schistosoma japonicum (14,085 bp) and Schistosoma mansoni (14,415 bp), but smaller than Schistosoma haematobium (15,003 bp) and Schistosoma spindale (16,901 bp). The mt genome of O. turkestanicum contains 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks an atp8 gene, consistent with that of Schistosoma species. The mt genome arrangement of O. turkestanicum contains an AT-rich region and two non-coding regions (NCRs), including long non-coding region (LNR) and short non-coding region (SNR). Phylogenetic analysis based on amino acids sequences showed that O. turkestanicum belonged to the genus Schistosoma, and is phylogenetically closer to the African schistosome group (S. haematobium, S. spindale and S. mansoni) than to the Asian group (S. mekongi and S. japonicum). But the arrangement of mtDNA protein-coding genes for O. turkestanicum is the same as Asian group, and distinct from the African species. Combining content and arrangement of mtDNA for O. turkestanicum, we conclude that O. turkestanicum should be considered a member of the Schistosoma genus, which shares a closer affinity to the African schistosomes than the Asian species, and gene order of mt genome in O. turkestanicum would be considered sympleisiomorphic (perhaps retained from the ancestor). Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Decoding the human genome

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  2. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  3. 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.

    Directory of Open Access Journals (Sweden)

    Andrew R Wood

    Full Text Available 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 <5% and rare variants (<1% can enhance previously identified associations and identify novel loci, we selected 93 quantitative circulating factors where data was available from the InCHIANTI population study. These phenotypes included cytokines, binding proteins, hormones, vitamins and ions. We selected these phenotypes because many have known strong genetic associations and are potentially important to help understand disease processes. We performed a genome-wide scan for these 93 phenotypes in InCHIANTI. We identified 21 signals and 33 signals that reached P<5×10(-8 based on HapMap and 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P<5×10(-11 respectively. Imputation of 1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P<5×10(-8 in both analyses (17 of which represent well replicated signals in the NHGRI catalogue, six were captured by the same index SNP, five were nominally more strongly associated in 1000 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

  4. Genomics in health and disease | Shawky | Egyptian Journal of ...

    African Journals Online (AJOL)

    Genomics in health and disease. ... The completion of the Human Genome Project signaled that the genome revolution was here to stay and symbolized its promise that knowing the DNA sequence of our genome and those of hundreds of other ... Key Words: Genomics, genetics, gene regulation, mutation, genetic testing.

  5. Environmental Medicine Genome Bank (EMGB): Current Composition

    National Research Council Canada - National Science Library

    Sonna, Larry

    2000-01-01

    The USARIEM Environmental Medicine Genome Bank (EMGB) project is an ongoing effort to identify and characterize genes relevant to environmental injuries and illnesses and to human physical performance...

  6. The Schistosoma indicum species group in Nepal: presence of a new lineage of schistosome and use of the Indoplanorbis exustus species complex of snail hosts.

    Science.gov (United States)

    Devkota, Ramesh; Brant, Sara V; Loker, Eric S

    2015-11-01

    From 2007-2014, 19,360 freshwater snails from the Terai and Hilly regions of Nepal were screened for cercariae of mammalian schistosomes. Based on analysis of mitochondrial cytochrome oxidase I, 12S, 16S and 28S sequences (3,675bp) of the cercariae recovered, we provide, to our knowledge, the first report of the Schistosoma indicum species group in Nepal. Five samples of Schistosoma nasale, nine of Schistosoma spindale and 17 of Schistosoma sp. were recovered, all from the snail Indoplanorbis exustus. The last-mentioned lineage failed to group in any of our analyses with S. nasale, S. spindale or S. indicum. It diverged in cox1 sequence from them by 16%, 13% and 13%, respectively, levels of difference comparable to well-studied species pairs of Schistosoma. Analysis of cox1, 16S and internal transcribed spacer 1 sequences (1,874bp) for Nepalese specimens of I. exustus was also surprising in revealing the presence of four genetically distinct clades. They diverged from one another at levels comparable to those noted for species pairs in the sister genus Bulinus. There was no obvious pattern of use by Nepalese Schistosoma of the Indoplanorbis clades. We found high support for a close relationship between S. indicum and Schistosoma haematobium groups, but failed to retrieve support for a clean separation of the two, with a tendency for S. nasale to fall as the most basal representative. If this pattern holds, hypotheses for the origin of the Asian Indoplanorbis-transmitted S. indicum group from the Bulinus-transmitted S. haematobium group may require modification, including consideration of more contemporaneous origins of the two groups. The Indian subcontinent is under-studied with respect to schistosome diversity and our current knowledge of the S. indicum and I. exustus species groups is inadequate. Further study is warranted given the ability of indicum group species to cause veterinary problems and cercarial dermatitis, with a worrisome potential in the future to

  7. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.

    Science.gov (United States)

    Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M; Bhak, Jong

    2016-11-24

    Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

  8. Comparative RNA genomics

    DEFF Research Database (Denmark)

    Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.

    2018-01-01

    small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs...

  9. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  10. CD209a Synergizes with Dectin-2 and Mincle to Drive Severe Th17 Cell-Mediated Schistosome Egg-Induced Immunopathology

    Directory of Open Access Journals (Sweden)

    Parisa Kalantari

    2018-01-01

    Full Text Available The immunopathology caused by schistosome helminths varies greatly in humans and among mouse strains. A severe form of parasite egg-induced hepatic granulomatous inflammation, seen in CBA mice, is driven by Th17 cells stimulated by IL-1β and IL-23 produced by dendritic cells that express CD209a (SIGNR5, a C-type lectin receptor (CLR related to human DC-SIGN. Here, we show that CD209a-deficient CBA mice display decreased Th17 responses and are protected from severe immunopathology. In vitro, CD209a augments the egg-induced IL-1β and IL-23 production initiated by the related CLRs Dectin-2 and Mincle. While Dectin-2 and Mincle trigger an FcRγ-dependent signaling cascade that involves the tyrosine kinase Syk and the trimolecular Card9-Bcl10-Malt1 complex, CD209a promotes the sustained activation of Raf-1. Our findings demonstrate that CD209a drives severe Th17 cell-mediated immunopathology in a helminthic disease based on synergy between DC-SIGN- and Dectin-2-related CLRs.

  11. Murine eosinophils labeled with indium-111 oxine: localization to delayed hypersensitivity reactions against a schistosomal antigen and to lymphokine in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Rand, T.H.; Clanton, J.A.; Runge, V.; English, D.; Colley, D.G.

    1983-04-01

    We have evaluated a method for quantitation of eosinophil migration to stimuli in vivo. Upon transfusion into normal syngeneic mice, 111In-labeled eosinophils had an intravascular half-life of 9.5 hr and distributed predominantly into spleen, bone marrow, and liver. In either Schistosoma mansoni-infected mice or recipients of lymphoid cells from infected mice, intradermal (ear pinna) injection of the schistosomal egg antigenic preparation (SEA) elicited time-dependent accumulation of 111In-labeled eosinophils detectable by either gamma scintillation counting of tissue samples or by nuclear medicine external imaging. Intradermal administration of a lymphokine fraction (containing eosinophil stimulation promoter activity) similarly caused accumulation of 111In-labeled eosinophils. Both reactions depended on the concentration of stimulus (SEA or lymphokine). 111In-labeled neutrophils or macrophages or 125I-albumin did not preferentially accumulate at the reactions examined to the extent found with 111In-labeled eosinophils, indicating that localization of label depends on an active process and is due to eosinophils rather than a contaminating cell type. The method was used to estimate how long eosinotactic lymphokine remained at dermal sites: 60% of initial activity was present 12 hr after injection. The model is discussed with regard to the role of lymphokines in hypersensitivity reactions with eosinophil involvement, such as the granulomatous response to S. mansoni eggs.

  12. Genome-wide association of major depression: description of samples for the GAIN Major Depressive Disorder Study: NTR and NESDA biobank projects.

    Science.gov (United States)

    Boomsma, Dorret I; Willemsen, Gonneke; Sullivan, Patrick F; Heutink, Peter; Meijer, Piet; Sondervan, David; Kluft, Cornelis; Smit, Guus; Nolen, Willem A; Zitman, Frans G; Smit, Johannes H; Hoogendijk, Witte J; van Dyck, Richard; de Geus, Eco J C; Penninx, Brenda W J H

    2008-03-01

    To identify the genomic regions that confer risk and protection for major depressive disorder (MDD) in humans, large-scale studies are needed. Such studies should collect multiple phenotypes, DNA, and ideally, biological material that allows gene expression analysis, transcriptomic, proteomic, and metabolomic studies. In this paper, we briefly review linkage studies of MDD and then describe the large-scale nationwide biological sample collection in Dutch twin families from the Netherlands Twin Register (NTR) and in participants in the Netherlands Study of Depression and Anxiety (NESDA). Within these studies, 1,862 participants with a diagnosis of MDD and 1,857 controls at low liability for MDD have been selected for genome-wide genotyping by the US Foundation for the National Institutes of Health Genetic Association Information Network. Stage 1 genome-wide association results are scheduled to be accessible before the end of 2007. Genome-wide association results are open-access and can be viewed at the dbGAP web portal (http://www.ncbi.nlm.nih.gov). Approved users can download the genotype and phenotype data, which have been made available as of 9 October 2007.

  13. Genome-wide association of major depression: description of samples for the GAIN Major Depressive Disorder Study: NTR and NESDA biobank projects.

    NARCIS (Netherlands)

    Boomsma, D.I.; Willemsen, G.; Sullivan, P.F.; Heutink, P.; Meijer, P.; Sondervan, D.; Kluft, C.; Smit, A.B.; Nolen, W.A.; Zitman, F.G.; Smit, J.H.; Hoogendijk, W.J.G.; van Dyck, R.; de Geus, E.J.C.; Penninx, B.W.J.H.

    2008-01-01

    To identify the genomic regions that confer risk and protection for major depressive disorder (MDD) in humans, large-scale studies are needed. Such studies should collect multiple phenotypes, DNA, and ideally, biological material that allows gene expression analysis, transcriptomic, proteomic, and

  14. Genome-wide association of major depression: Description of samples for the GAIN Major Depressive Disorder Study: NTR and NESDA biobank projects

    NARCIS (Netherlands)

    Boomsma, D.I.; Willemsen, G.; Sullivan, P.F.; Heutink, P.; Meijer, P.; Sondervan, D.; Kluft, C.; Smit, G.; Nolen, W.A.; Zitman, F.G.; Smit, J.H.; Hoogendijk, W.J.; Dyck, R. van; Geus, E.J.C. de; Penninx, B.W.J.H.

    2008-01-01

    To identify the genomic regions that confer risk and protection for major depressive disorder (MDD) in humans, large-scale studies are needed. Such studies should collect multiple phenotypes, DNA, and ideally, biological material that allows gene expression analysis, transcriptomic, proteomic, and

  15. Database management research for the Human Genome Project. Final progress report for period: 02/01/99 - 06/14/00

    Energy Technology Data Exchange (ETDEWEB)

    Bult, Carol J.

    1999-11-01

    The MouseBLAST server allows researchers to search a sequence within mouse/rodent sequence databases to find matching sequences that may be associated with mouse genes. Query results may be linked to gene detail records in the Mouse Genome Database (MGD). Searches are performed using WU-BLAST 2.0. All sequence databases are updated on a weekly basis.

  16. Comparative Genomics

    Indian Academy of Sciences (India)

    tory motifs and other non-coding DNA motifs, and genome flux and dynamics. Finally the article describes how the information one can extract from a comparative analysis of genomes depends to a large extent, on the specific aspect of the genomes that is being compared and the phylogenetic distances of the organisms ...

  17. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  18. Human genome. 1993 Program report

    Energy Technology Data Exchange (ETDEWEB)

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  19. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  20. Comparative Genomics in Homo sapiens.

    Science.gov (United States)

    Oti, Martin; Sammeth, Michael

    2018-01-01

    Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

  1. Genome annotation for clinical genomic diagnostics: strengths and weaknesses.

    Science.gov (United States)

    Steward, Charles A; Parker, Alasdair P J; Minassian, Berge A; Sisodiya, Sanjay M; Frankish, Adam; Harrow, Jennifer

    2017-05-30

    The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.

  2. eGenomics: Cataloguing Our Complete Genome Collection III

    Directory of Open Access Journals (Sweden)

    Dawn Field

    2007-01-01

    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  3. Genome Improvement at JGI-HAGSC

    Energy Technology Data Exchange (ETDEWEB)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  4. Vestibular Evoked Myogenic Potential (VEMP Triggered by Galvanic Vestibular Stimulation (GVS: A Promising Tool to Assess Spinal Cord Function in Schistosomal Myeloradiculopathy.

    Directory of Open Access Journals (Sweden)

    Júlia Fonseca de Morais Caporali

    2016-04-01

    Full Text Available Schistosomal myeloradiculopathy (SMR, the most severe and disabling ectopic form of Schistosoma mansoni infection, is caused by embolized ova eliciting local inflammation in the spinal cord and nerve roots. The treatment involves the use of praziquantel and long-term corticotherapy. The assessment of therapeutic response relies on neurological examination. Supplementary electrophysiological exams may improve prediction and monitoring of functional outcome. Vestibular evoked myogenic potential (VEMP triggered by galvanic vestibular stimulation (GVS is a simple, safe, low-cost and noninvasive electrophysiological technique that has been used to test the vestibulospinal tract in motor myelopathies. This paper reports the results of VEMP with GVS in patients with SMR.A cross-sectional comparative study enrolled 22 patients with definite SMR and 22 healthy controls that were submitted to clinical, neurological examination and GVS. Galvanic stimulus was applied in the mastoid bones in a transcranial configuration for testing VEMP, which was recorded by electromyography (EMG in the gastrocnemii muscles. The VEMP variables of interest were blindly measured by two independent examiners. They were the short-latency (SL and the medium-latency (ML components of the biphasic EMG wave.VEMP showed the components SL (p = 0.001 and ML (p<0.001 delayed in SMR compared to controls. The delay of SL (p = 0.010 and of ML (p = 0.020 was associated with gait dysfunction.VEMP triggered by GVS identified alterations in patients with SMR and provided additional functional information that justifies its use as a supplementary test in motor myelopathies.

  5. Gonad RNA-specific qRT-PCR analyses identify genes with potential functions in schistosome reproduction such as SmFz1 and SmFGFRs

    Science.gov (United States)

    Hahnel, Steffen; Quack, Thomas; Parker-Manuel, Sophia J.; Lu, Zhigang; Vanderstraete, Mathieu; Morel, Marion; Dissous, Colette; Cailliau, Katia; Grevelding, Christoph G.

    2014-01-01

    In the search for new strategies to fight schistosomiasis, the unique reproductive biology of Schistosoma mansoni has come into the focus of research. The development of the gonads and the ability of egg production are fundamental not only for continuing the life cycle but also for pathogenicity. Previous studies of schistosome biology demonstrated an influence of pairing on gonad development of the female and on gene expression profiles in both genders. Due to the limited access to specific tissues, however, most of these studies were done at the level of whole worms neglecting individual tissues that may be targets of pairing-dependent processes. Recently, we established a protocol allowing the isolation of testes and ovaries from adult S. mansoni. Here, we describe tissue-specific qRT-PCR analyses comparing transcript levels of selected genes on the basis of RNA from gonads and whole worms. Gene expression in ovary and testes was in some cases found to be significantly influenced by pairing, which was not traceable in whole worms. Among the candidate genes identified as regulated by pairing in gonads were the frizzled homolog SmFz1 and the two fibroblast growth factor receptor homologs SmFGFR-A and SmFGFR-B. First functional characterizations were done, including comparative qRT-PCR analyses, in situ-localization experiments, heterologous expression in Xenopus oocytes (SmFGFR-A/B), and inhibitor studies using the Fz/Dvl-pathway inhibitor 3289-8625, or BIBF1120 blocking FGFR-signaling. Besides confirming gonad localization and receptor functions, inhibitor-induced phenotypes were observed in vitro such as decreased egg production as well as drastic effects on gonad differentiation, morphology, embryogenesis, and survival of adult worms. In summary, these results emphasise the usefulness of tissue-specific qRT-PCRs for selection of candidate genes with important roles in reproduction, allowing subsequent studies to determine their suitability as drug targets. PMID

  6. Prevalence and effect of schistosome and soil-transmitted helminth infection on labour input in rice-growing communities of Ogun State, Nigeria

    Directory of Open Access Journals (Sweden)

    Sammy Olufemi Sam-Wobo

    2013-06-01

    Full Text Available Schistosomiasis and soil-transmitted helminthiasis (STH are public health problems in communities which lack basic social amenities with poor hygienic conditions. Studies were carried out to determine the prevalence and effect of schistosomes and soil-transmitted helminths infection on labour input on rice production in 9 rice-growing communities of Ogun State. Parasitological examinations of urine and faecal samples, and structured questionnaires were conducted on 243 consented individuals from May 2009 to March 2010. The results showed an overall prevalence of 17% for Ascaris lumbricoides, 12% for hookworms, 2% for Trichuris trichiura, 1% for Schistosoma haematobium and 1% for Schistosoma mansoni. A. lumbricoides and hookworms were more prevalent in Agbajege (25%, and varied in the other 8 communities. T. trichiura was prevalent in three communities, Agbajege (5%, Akodu (4.2%, and Moloko-Asipa (4.8 %; S. haematobium was prevalent only in Ayedere (2.6% and Lufoko (8%, while S. mansoni was prevalent only in Moloko-Asipa (9.5%. Infections among the gender were varied as 26.3 % of males and 33.8 % of females had an overall prevalence of: A. lumbricoides (16.8%, hookworms (11.8%, T. trichiura (1.6%, S. haematobium (1.1% and S. mansoni (1.1%. On frequency of infection to incapacitation per year, 45% of respondents were incapacitated 1-2 times, 27% 3-4 times and 19% were incapacitated more than 4 times. Understanding the effect of these two diseases will not only improve the health status of residents but also increase their productivity and ensure food security.

  7. Gonad RNA-specific qRT-PCR analyses identify genes with potential functions in schistosome reproduction such as SmFz1 and SmFGFRs

    Directory of Open Access Journals (Sweden)

    Steffen eHahnel

    2014-06-01

    Full Text Available In the search for new strategies to fight schistosomiasis, the unique reproductive biology of Schistosoma mansoni has come into the focus of research. The development of the gonads and the ability of egg production are fundamental not only for continuing the life cycle but also for pathogenicity.Previous studies of schistosome biology demonstrated an influence of pairing on gonad development of the female and on gene expression profiles in both genders. Due to the limited access to specific tissues, however, most of these studies were done at the level of whole worms neglecting individual tissues that may be targets of pairing-dependent processes.Recently, we established a protocol allowing the isolation of testes and ovaries from adult S. mansoni. Here, we describe tissue-specific qRT-PCR analyses comparing transcript levels of selected genes on the basis of RNA from gonads and whole worms. Gene expression in ovary and testes was in some cases found to be significantly influenced by pairing, which was not traceable in whole worms. Among the candidate genes identified as regulated by pairing in gonads were the frizzled homolog SmFz1 and the two fibroblast growth factor receptor homologs SmFGFR-A and SmFGFR-B. First functional characterizations were done, including comparative qRT-PCR analyses, in situ-localization experiments, heterologous expression in Xenopus oocytes (SmFGFR-A/B, and inhibitor studies using the Fz/Dvl-pathway inhibitor 3289-8625, or BIBF1120 blocking FGFR-signaling. Besides confirming gonad localization and receptor functions, inhibitor-induced phenotypes were observed in vitro such as decreased egg production as well as drastic effects on gonad differentiation, morphology, embryogenesis, and survival of adult worms.In summary, these results emphasise the usefulness of tissue specific qRT-PCRs for selection of candidate genes with important roles in reproduction, allowing subsequent studies to determine their suitability as

  8. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies.

    Science.gov (United States)

    Ruperao, Pradeep; Chan, Chon-Kit Kenneth; Azam, Sarwar; Karafiátová, Miroslava; Hayashi, Satomi; Cížková, Jana; Saxena, Rachit K; Simková, Hana; Song, Chi; Vrána, Jan; Chitikineni, Annapurna; Visendi, Paul; Gaur, Pooran M; Millán, Teresa; Singh, Karam B; Taran, Bunyamin; Wang, Jun; Batley, Jacqueline; Doležel, Jaroslav; Varshney, Rajeev K; Edwards, David

    2014-08-01

    With the expansion of next-generation sequencing technology and advanced bioinformatics, there has been a rapid growth of genome sequencing projects. However, while this technology enables the rapid and cost-effective assembly of draft genomes, the quality of these assemblies usually falls short of gold standard genome assemblies produced using the more traditional BAC by BAC and Sanger sequencing approaches. Assembly validation is often performed by the physical anchoring of genetically mapped markers, but this is prone to errors and the resolution is usually low, especially towards centromeric regions where recombination is limited. New approaches are required to validate reference genome assemblies. The ability to isolate individual chromosomes combined with next-generation sequencing permits the validation of genome assemblies at the chromosome level. We demonstrate this approach by the assessment of the recently published chickpea kabuli and desi genomes. While previous genetic analysis suggests that these genomes should be very similar, a comparison of their chromosome sizes and published assemblies highlights significant differences. Our chromosomal genomics analysis highlights short defined regions that appear to have been misassembled in the kabuli genome and identifies large-scale misassembly in the draft desi genome. The integration of chromosomal genomics tools within genome sequencing projects has the potential to significantly improve the construction and validation of genome assemblies. The approach could be applied both for new genome assemblies as well as published assemblies, and complements currently applied genome assembly strategies. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  9. The Human Genome Project as a case study in the debate about the relationship between theology and natural science

    OpenAIRE

    Johan Buitendag

    2005-01-01

    The author presents a review article on the book, Brave new world? Theology, ethics and the human genome, edited by Celia Deane-Drummond and published in 2003 by T&T Clark International in London. After a rather elaborate exposition, he appraises the collection of essays in terms of the dialogue between theology and the natural sciences. As an acid test, he assesses the challenge Kant, however, dealt with, namely to combine and to separate the right things. Kant pushed this to extremes and en...

  10. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  11. Genome Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genome Imprinting - The Silencing of Genes and Genomes. H A Ranganath M T Tanuja. General Article Volume 5 Issue 9 September 2000 pp 49-57. Fulltext. Click here to view fulltext PDF. Permanent link:

  12. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  13. Genomic footprinting.

    Science.gov (United States)

    Vierstra, Jeff; Stamatoyannopoulos, John A

    2016-03-01

    The advent of DNA footprinting with DNase I more than 35 years ago enabled the systematic analysis of protein-DNA interactions, and the technique has been instrumental in the decoding of cis-regulatory elements and the identification and characterization of transcription factors and other DNA-binding proteins. The ability to analyze millions of individual genomic cleavage events via massively parallel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the potential for global analysis of transcription factor occupancy in a single experiment. Genomic footprinting has opened unique vistas on the organization, function and evolution of regulatory DNA; however, the technology is still nascent. Here we discuss both prospects and challenges of genomic footprinting, as well as considerations for its application to complex genomes.

  14. A Taste of Algal Genomes from the Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  15. WGM Resonators for Proteomic Analysis Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Due to the extensive amounts of data generated from the genome sequencing projects, the focus of genomics has shifted from elucidating DNA sequence to the...

  16. Mapping the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.

    1989-06-01

    The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.

  17. Solution NMR in structural genomics.

    Science.gov (United States)

    Yee, Adelinda; Gutmanas, Aleksandras; Arrowsmith, Cheryl H

    2006-10-01

    Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure.

  18. Public health genomics: origins and basic concepts

    Directory of Open Access Journals (Sweden)

    Ron Zimmern

    2006-12-01

    Full Text Available Knowledge and technologies arising from the Human Genome Project promise in time to offer new opportunities for the treatment and prevention of disease. The enterprise of public health genomics aims to bridge the gap between advances in basic research and their responsible and effective implementation in clinical services and public health programmes. Public health genomics stresses the importance of understanding how genes and environment act together to influence health; avoiding genetic exceptionalism; appreciating the social and political context of genomic advances; and encouraging critical evaluation of proposed new tests and interventions. New international networks and collaborations are being established to develop public health genomics and further its aims.

  19. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  20. Human genetics and genomics a decade after the release of the draft sequence of the human genome

    OpenAIRE

    Naidoo Nasheen; Pawitan Yudi; Soong Richie; Cooper David N; Ku Chee-Seng

    2011-01-01

    Abstract Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with...

  1. HGVA: the Human Genome Variation Archive.

    Science.gov (United States)

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-05-23

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1.

    Science.gov (United States)

    Hufnagel, Peter; Rabus, Ralf

    2006-01-01

    The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium 'Aromatoleum' sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot >or=95, ProFound >or=2.2, MetaScore >or=97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research. Copyright (c) 2006 S. Karger AG, Basel.

  3. Genomic Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genomic Imprinting - Some Interesting Implications for the Evolution of Social Behaviour. Raghavendra Gadagkar. General Article Volume 5 Issue 9 September 2000 pp 58-68 ...

  4. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  5. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    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). One of its projects, 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) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 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.

  6. Fueling Future with Algal Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-07-05

    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  7. Imaging genomics.

    Science.gov (United States)

    Thompson, Paul M; Martin, Nicholas G; Wright, Margaret J

    2010-08-01

    Imaging genomics is an emerging field that is rapidly identifying genes that influence the brain, cognition, and risk for disease. Worldwide, thousands of individuals are being scanned with high-throughput genotyping (genome-wide scans), and new imaging techniques [high angular resolution diffusion imaging and resting state functional magnetic resonance imaging (MRI)] that provide fine-grained measures of the brain's structural and functional connectivity. Along with clinical diagnosis and cognitive testing, brain imaging offers highly reproducible measures that can be subjected to genetic analysis. Recent studies of twin, pedigree, and population-based datasets have discovered several candidate genes that consistently show small to moderate effects on brain measures. Many studies measure single phenotypes from the images, such as hippocampal volume, but voxel-wise genomic methods can plot the profile of genetic association at each 3D point in the brain. This exploits the full arsenal of imaging statistics to discover and replicate gene effects. Imaging genomics efforts worldwide are now working together to discover and replicate many promising leads. By studying brain phenotypes closer to causative gene action, larger gene effects are detectable with realistic sample sizes obtainable from meta-analysis of smaller studies. Imaging genomics has broad applications to dementia, mental illness, and public health.

  8. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  9. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  10. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  11. Snake Genome Sequencing: Results and Future Prospects

    Science.gov (United States)

    Kerkkamp, Harald M. I.; Kini, R. Manjunatha; Pospelov, Alexey S.; Vonk, Freek J.; Henkel, Christiaan V.; Richardson, Michael K.

    2016-01-01

    Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression. PMID:27916957

  12. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  13. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  14. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  15. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  16. Lessons from Structural Genomics*

    Science.gov (United States)

    Terwilliger, Thomas C.; Stuart, David; Yokoyama, Shigeyuki

    2010-01-01

    A decade of structural genomics, the large-scale determination of protein structures, has generated a wealth of data and many important lessons for structural biology and for future large-scale projects. These lessons include a confirmation that it is possible to construct large-scale facilities that can determine the structures of a hundred or more proteins per year, that these structures can be of high quality, and that these structures can have an important impact. Technology development has played a critical role in structural genomics, the difficulties at each step of determining a structure of a particular protein can be quantified, and validation of technologies is nearly as important as the technologies themselves. Finally, rapid deposition of data in public databases has increased the impact and usefulness of the data and international cooperation has advanced the field and improved data sharing. PMID:19416074

  17. Lessons from structural genomics.

    Science.gov (United States)

    Terwilliger, Thomas C; Stuart, David; Yokoyama, Shigeyuki

    2009-01-01

    A decade of structural genomics, the large-scale determination of protein structures, has generated a wealth of data and many important lessons for structural biology and for future large-scale projects. These lessons include a confirmation that it is possible to construct large-scale facilities that can determine the structures of a hundred or more proteins per year, that these structures can be of high quality, and that these structures can have an important impact. Technology development has played a critical role in structural genomics, the difficulties at each step of determining a structure of a particular protein can be quantified, and validation of technologies is nearly as important as the technologies themselves. Finally, rapid deposition of data in public databases has increased the impact and usefulness of the data and international cooperation has advanced the field and improved data sharing.

  18. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2013-11-12

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  19. Fueling the Future with Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 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 will lead 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.

  20. Genome Imprinting

    Indian Academy of Sciences (India)

    because of their maternal 'or paternal origin. Human homologies for the type of situation described above are naturally occurring placental malformation, the hydatidiform ..... drome, familial glomus tumors, psoriasis, neural tube defects, congenital heart disease and narcolepsy. Since genome imprint- ing is implicated in the ...

  1. CucCAP - Developing genomic resources for the cucurbit community

    Science.gov (United States)

    The U.S. cucurbit community has initiated a USDA-SCRI funded cucurbit genomics project, CucCAP: Leveraging applied genomics to increase disease resistance in cucurbit crops. Our primary objectives are: develop genomic and bioinformatic breeding tool kits for accelerated crop improvement across the...

  2. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  3. RPAN: rice pan-genome browser for ∼3000 rice genomes.

    Science.gov (United States)

    Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

    2017-01-25

    A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Project 2010 Project Management

    CERN Document Server

    Happy, Robert

    2010-01-01

    The ideal on-the-job reference guide for project managers who use Microsoft Project 2010. This must-have guide to using Microsoft Project 2010 is written from a real project manager's perspective and is packed with information you can use on the job. The book explores using Project 2010 during phases of project management, reveals best practices, and walks you through project flow from planning through tracking to closure. This valuable book follows the processes defined in the PMBOK Guide, Fourth Edition , and also provides exam prep for Microsoft's MCTS: Project 2010 certification.: Explains

  5. [Evaluation of effectiveness of comprehensive schistosomiasis control project in Yunnan Province from 2004 to 2013].

    Science.gov (United States)

    Zhang, Yun; Feng, Xi-guang; Wu, Ming-shou; Xiong, Meng-tao; Shen, Mei-fen; Sun, Jia-yu

    2015-04-01

    To evaluate the effect of comprehensive schistosomiasis control project in Yunnan Province after its implementation for ten years, so as to provide the evidence for formulating the future prevention and control strategy. The data of the schistosomiasis comprehensive control project and the endemic situation were collected and analyzed to evaluate the control effect of the project in Yunnan Province from 2004 to 2013. After the comprehensive control project implementation for ten years, the Oncomelania hupensis snail area in Yunnan Province decreased from 4,364.79 hm2 in 2004 to 1,528.50 hm2 in 2013, with a reduction rate of 64.98%, and the occurrence rate of frames with snails and the density of living snails decreased from 4.71% and 0.26 snails/0.1 m2 in 2004 to 1.35% and 0.04 snails/0.1 m2 in 2013, with the reduction rates of 71.34% and 84.62%, respectively. The schistosome infected snails were found only in 2011 and 2013 since 2008. In 2013, the infection rates of human (0.0021%) and cattle (0.0209%) decreased by 99.84% and 99.44%, respectively, compared to those in 2004, and no acute schistosome infection cases were found since 2008. The 212 villages with relatively serious endemic situation (Type One, Type Two and Type Three) all declined to the slight endemic villages (Type Four and Type Five), therefore, they reached the criteria of schistosomiasis transmission controlled or interrupted. The awareness rates of schistosomiasis control among villagers and students in endemic areas were above 90% and 98%, respectively. The effect of the comprehensive schistosomiasis control project is significant in Yunnan Province, but the task to consolidate and enlarge the control results still remains a challenge.

  6. Beyond editing to writing large genomes.

    Science.gov (United States)

    Chari, Raj; Church, George M

    2017-08-30

    Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.

  7. [The human variome project and its progress].

    Science.gov (United States)

    Gao, Shan; Zhang, Ning; Zhang, Lei; Duan, Guang-You; Zhang, Tao

    2010-11-01

    The main goal of post genomics is to explain how the genome, the map of which has been constructed in the Human Genome Project, affacts activities of life. This leads to generate multiple "omics": structural genomics, functional genomics, proteomics, metabonomics, et al. In Jun. 2006, Melbourne, Australia, Human Genome Variation Society (HGVS) initiated the Human Variome Project (HVP) to collect all the sequence variation and polymorphism data worldwidely. HVP is to search and determine those mutations related with human diseases by association study between genetype and phenotype on the scale of genome level and other methods. Those results will be translated into clinical application. Considering the potential effects of this project on human health, this paper introduced its origin and main content in detail and discussed its meaning and prospect.

  8. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  9. Scaffolder - software for manual genome scaffolding

    Directory of Open Access Journals (Sweden)

    Barton Michael D

    2012-05-01

    Full Text Available Abstract Background The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regions together and fill gaps. This scaffolding step is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together these considerations may make reproducing or editing an existing genome scaffold difficult. Methods The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format which is both human and machine-readable. Command line binaries and extensive documentation are available. Results This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax. This syntax further allows unknown regions to be specified and additional sequence to be used to fill known gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with large FASTA nucleotide sequences. Conclusions Scaffolder is easy-to-use genome scaffolding software which promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs.

  10. Functional genomics of tomato: Opportunities and challenges in post ...

    Indian Academy of Sciences (India)

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum ...

  11. Materials Genome Initiative

    Science.gov (United States)

    Vickers, John

    2015-01-01

    The Materials Genome Initiative (MGI) project element is a cross-Center effort that is focused on the integration of computational tools to simulate manufacturing processes and materials behavior. These computational simulations will be utilized to gain understanding of processes and materials behavior to accelerate process development and certification to more efficiently integrate new materials in existing NASA projects and to lead to the design of new materials for improved performance. This NASA effort looks to collaborate with efforts at other government agencies and universities working under the national MGI. MGI plans to develop integrated computational/experimental/ processing methodologies for accelerating discovery and insertion of materials to satisfy NASA's unique mission demands. The challenges include validated design tools that incorporate materials properties, processes, and design requirements; and materials process control to rapidly mature emerging manufacturing methods and develop certified manufacturing processes

  12. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)

    Energy Technology Data Exchange (ETDEWEB)

    Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2010-01-01

    Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  14. Primate comparative genomics: lemur biology and evolution.

    Science.gov (United States)

    Horvath, Julie E; Willard, Huntington F

    2007-04-01

    Comparative genome sequencing projects are providing insight into aspects of genome biology that raise new questions and challenge existing paradigms. Placement in the phylogenetic tree can often be a major determinant of which organism to choose for study. Lemurs hold a key position at the base of the primate evolutionary tree and will be highly informative for the genomics community by offering comparisons of primate-specific characteristics and processes. Combining research in chromosome evolution, genome evolution and behavior with lemur comparative genomic sequencing will offer insights into many levels of primate evolution. We discuss the current state of lemur cytogenetic and phylogenetic analyses, and suggest how focusing more genomic efforts on lemurs will be beneficial to understanding human and primate evolution, as well as disease, and will contribute to conservation efforts.

  15. Open Access Data Sharing in Genomic Research

    Directory of Open Access Journals (Sweden)

    Stacey Pereira

    2014-08-01

    Full Text Available The current emphasis on broad sharing of human genomic data generated in research in order to maximize utility and public benefit is a significant legacy of the Human Genome Project. Concerns about privacy and discrimination have led to policy responses that restrict access to genomic data as the means for protecting research participants. Our research and experience show, however, that a considerable number of research participants agree to open access sharing of their genomic data when given the choice. General policies that limit access to all genomic data fail to respect the autonomy of these participants and, at the same time, unnecessarily limit the utility of the data. We advocate instead a more balanced approach that allows for individual choice and encourages informed decision making, while protecting against the misuse of genomic data through enhanced legislation.

  16. Expanding Genomics of Mycorrhizal Symbiosis

    Directory of Open Access Journals (Sweden)

    Alan eKuo

    2014-11-01

    Full Text Available The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant and soil health, and carbon and nutrient cycles. The symbiosis evolved repeatedly and independently as multiple morphological types (e.g. arbuscular [AM], ectomycorrhizal [ECM] in multiple fungal clades (e.g. phyla Glomeromycota, Ascomycota, Basidiomycota. The accessibility and culturability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first 3 mycorrhizal fungal genomes, representing 3 fungal phyla and 2 mycorrhizal types. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant-degrading enzymes (PDEs and expansion of lineage-specific gene families, including short secreted protein (SSP effectors and other symbiosis genes. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of gene families in contrast to Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other 2 fungi, the symbiosis can involve similar solutions as loss of PDEs and mycorrhiza-induced SSPs. The mycorrhizal community is building on these studies with 3 large-scale initiatives. The Mycorrhizal Genomics Initiative (MGI is sequencing 35 genomes of multiple fungal clades and mycorrhizal types for phylogenomic and population analyses. 17 MGI species whose symbiosis is reconstitutable in vitro are targeted for comprehensive transcriptomics of mycorrhiza formation. MGI genomes are seeding a set of 50+ reference fungal genomes for annotating metatranscriptomes sampled from 7 diverse well-described soil sites. These 3 projects address fundamental questions about the nature and role of a

  17. Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest.

    Science.gov (United States)

    Haury, David L.

    This ERIC Digest identifies how the human genome project fits into the "National Science Education Standards" and lists Human Genome Project Web sites found on the World Wide Web. It is a resource companion to "Learning about the Human Genome. Part 1: Challenge to Science Educators" (Haury 2001). The Web resources and…

  18. Human genetics and genomics a decade after the release of the draft sequence of the human genome

    Science.gov (United States)

    2011-01-01

    Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

  19. THE HUMAN GENOME PROJECT IN CLINICAL PERSPECTIVE ...

    African Journals Online (AJOL)

    Enrique

    the fragile X syndrome: an atypically. X-linked disorder due to a dynamic mutation of the FMR1 gene and the commonest cause of inherited men- tal retardation (see the article by Dr. Karen Fieggen, (p.29 of this issue). • the 22q deletion syndrome: a chro- mosomal microdeletion disorder which is the second most common.

  20. THE HUMAN GENOME PROJECT IN CLINICAL PERSPECTIVE ...

    African Journals Online (AJOL)

    Enrique

    quently, however, diseases are caused by defects in many genes or in a gene controlling a complex pathway combining both genetic and environmental fac- tors (e.g. spina bifida or .... ularly in the field of epigenetic (non- ... effects of changes (mutations) in the sequence: ... most normal human variation lies, as well as the ...

  1. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  2. Bioprospecting in the genomic age.

    Science.gov (United States)

    Hicks, Michael A; Prather, Kristala L J

    2014-01-01

    The genomic revolution promises great advances in the search for useful biocatalysts. Function-based metagenomic approaches have identified several enzymes with properties that make them useful candidates for a variety of bioprocesses. As DNA sequencing costs continue to decline, the volume of genomic data, along with their corresponding predicted protein sequences, will continue to increase dramatically, necessitating new approaches to leverage this information for gene-based bioprospecting efforts. Additionally, as new functions are discovered and correlated with this sequence information, the knowledge of the often complex relationship between a protein's sequence and function will improve. This in turn will lead to better gene-based bioprospecting approaches and facilitate the tailoring of desired properties through protein engineering projects. In this chapter, we discuss a number of recent advances in bioprospecting within the context of the genomic age. © 2014 Elsevier Inc. All rights reserved.

  3. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content.

    Science.gov (United States)

    Elliott, Tyler A; Gregory, T Ryan

    2015-09-26

    Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60,000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of 'complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future. © 2015 The Author(s).

  4. Bacterial genome reengineering.

    Science.gov (United States)

    Zhou, Jindan; Rudd, Kenneth E

    2011-01-01

    The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer design tool with a model organism database increases the level of quality control. Computer-assisted design of gene primer pairs relies upon having highly accurate genomic DNA sequence information that exactly matches the DNA of the cells being used in the laboratory to ensure predictable DNA hybridizations. It is equally crucial to have confidence that the predicted start codons define the locations of genes accurately. Annotations in the EcoGene database are queried by PrimerPair to eliminate pseudogenes, IS elements, and other problematic genes before the design process starts. These projects progressively familiarize users with the EcoGene content, scope, and application interfaces that are useful for genome reengineering projects. The first protocol leads to the design of a pair of primer sequences that were used to clone and express a single gene. The N-terminal protein sequence was experimentally verified and the protein was detected in the periplasm. This is followed by instructions to design PCR primer pairs for cloning gene fragments encoding 50 periplasmic proteins without their signal peptides. The design process begins with the user simply designating one pair of forward and reverse primer endpoint positions relative to all start and stop codon positions. The gene name, genomic coordinates, and primer DNA sequences are reported to the user. When making chromosomal deletions, the integrity of the provisional primer design is checked to see whether it will generate any unwanted double deletions with adjacent genes. The bad designs are recalculated and replacement primers are provided alongside the

  5. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  6. Experimental pulmonary schistosomiasis: lack of morphological evidence of modulation in schistosomal pulmonary granulomas Esquistossomose pulmonar experimental: falta de evidência morfológica de modulação nos granulomas esquistosomóticos pulmonares

    Directory of Open Access Journals (Sweden)

    Maura R. F. Souza Vidal

    1993-10-01

    Full Text Available Numerous pulmonary schistosome egg granulomas were present in mice submitted to partial portal vein ligation (Warren's model. The granulomas were characterized by cellular aggregations formed within alveolar tissue. Main cellular types were macrophages (epithelioid cells, eosinophils, plasma cells and lymphocytes. These cells were supported by scanty fibrous stroma and exhibited close membrane contact points amongst themselves, but without forming specialized adhesion apparatus. When granulomas involved arterial structures, proliferation of cndothelial and smooth muscle cells occurred and fibrosis associated with angiogenesis became more evident. Granulomas formed around mature eggs in the pulmonary alveolar tissue presented approximately the same size and morphology regardless of the time of infection, the latter being 10, 18 and 25 weeks after cercarial exposure. This persistence of morphological appearance suggests that pulmonary granulomas do not undergo immunological modulation, as is the case with the granulomas in the liver and, to a lesser extent, in the intestines. Probably, besides general immunological factors, local (stromal factors play an important role in schistosomal granuloma modulation.Em camundongos submetidos à ligadura parcial da veia porta e infecção pelo Schistosoma mansoni, os granulomas periovulares apareceram em grande número nos pulmões, comprovando a validade do modelo de Warren. Histologicamente os granulomas eram representados por agregados celulares compactos no seio de escasso estroma. Os macrófagos (células epitelióides e eosinófilos eram os elementos celulares predominantes, vindo em seguida os linfóticos e plasmócitos. Ultraestruturalmenle, as células do granuloma exibiam íntimo contacto de suas membranas, com varios pontos de adesão, mas sem formar estruturas juncionais mais específicas. Os granulomas formados em torno a ovos maduros tinham tamanho, forma e composição celular similares ap

  7. TCGA's Pan-Cancer Efforts and Expansion to Include Whole Genome Sequence - TCGA

    Science.gov (United States)

    Carolyn Hutter, Ph.D., Program Director of NHGRI's Division of Genomic Medicine, discusses the expansion of TCGA's Pan-Cancer efforts to include the Pan-Cancer Analysis of Whole Genomes (PAWG) project.

  8. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Recent genomic heritage in Scotland.

    Science.gov (United States)

    Amador, Carmen; Huffman, Jennifer; Trochet, Holly; Campbell, Archie; Porteous, David; Wilson, James F; Hastie, Nick; Vitart, Veronique; Hayward, Caroline; Navarro, Pau; Haley, Chris S

    2015-06-06

    The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at ~700 K SNPs are currently available for 10,000 participants. The cohort was designed as a resource for genetic and health related research and the study of complex traits. In this study we developed a suite of analyses to disentangle the genomic differentiation within GS:SFHS individuals to describe and optimise the sample and methods for future analyses. We combined the genotypic information of GS:SFHS with 1092 individuals from the 1000 Genomes project and estimated their genomic relationships. Then, we performed Principal Component Analyses of the resulting relationships to investigate the genomic origin of different groups. We characterised two groups of individuals: those with a few sparse rare markers in the genome, and those with several large rare haplotypes which might represent relatively recent exogenous ancestors. We identified some individuals with likely Italian ancestry and a group with some potential African/Asian ancestry. An analysis of homozygosity in the GS:SFHS sample revealed a very similar pattern to other European populations. We also identified an individual carrying a chromosome 1 uniparental disomy. We found evidence of local geographic stratification within the population having impact on the genomic structure. These findings illuminate the history of the Scottish population and have implications for further analyses such as the study of the contributions of common and rare variants to trait heritabilities and the evaluation of genomic and phenotypic prediction of disease.

  10. Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni.

    Science.gov (United States)

    Hahnel, Steffen; Wheeler, Nic; Lu, Zhigang; Wangwiwatsin, Arporn; McVeigh, Paul; Maule, Aaron; Berriman, Matthew; Day, Timothy; Ribeiro, Paula; Grevelding, Christoph G

    2018-01-01

    Schistosomes are blood-dwelling trematodes with global impact on human and animal health. Because medical treatment is currently based on a single drug, praziquantel, there is urgent need for the development of alternative control strategies. The Schistosoma mansoni genome project provides a platform to study and connect the genetic repertoire of schistosomes to specific biological functions essential for successful parasitism. G protein-coupled receptors (GPCRs) form the largest superfamily of transmembrane receptors throughout the Eumetazoan phyla, including platyhelminths. Due to their involvement in diverse biological processes, their pharmacological importance, and proven druggability, GPCRs are promising targets for new anthelmintics. However, to identify candidate receptors, a more detailed understanding of the roles of GPCR signalling in schistosome biology is essential. An updated phylogenetic analysis of the S. mansoni GPCR genome (GPCRome) is presented, facilitated by updated genome data that allowed a more precise annotation of GPCRs. Additionally, we review the current knowledge on GPCR signalling in this parasite and provide new insights into the potential roles of GPCRs in schistosome reproduction based on the findings of a recent tissue-specific transcriptomic study in paired and unpaired S. mansoni. According to the current analysis, GPCRs contribute to gonad-specific functions but also to nongonad, pairing-dependent processes. The latter may regulate gonad-unrelated functions during the multifaceted male-female interaction. Finally, we compare the schistosome GPCRome to that of another parasitic trematode, Fasciola, and discuss the importance of GPCRs to basic and applied research. Phylogenetic analyses display GPCR diversity in free-living and parasitic platyhelminths and suggest diverse functions in schistosomes. Although their roles need to be substantiated by functional studies in the future, the data support the selection of GPCR candidates

  11. Birth of an 'Asian cool' reference genome: AK1.

    Science.gov (United States)

    Kim, Changhoon

    2016-12-01

    The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine. [BMB Reports 2016; 49(12): 653-654].

  12. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Sieprawska-Lupa, Magdalena [University of Georgia, Athens, GA; Goltsman, Eugene [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Whitman, W. B. [University of Georgia, Athens, GA; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  13. The Protein Data Bank and structural genomics.

    Science.gov (United States)

    Westbrook, John; Feng, Zukang; Chen, Li; Yang, Huanwang; Berman, Helen M

    2003-01-01

    The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projects--developing and maintaining the Target Registration Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture data from standard structure determination applications.

  14. Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.

    Science.gov (United States)

    Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario

    2017-01-01

    The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.

  15. Personal genomes, participatory genomics and the anonymity ...

    Indian Academy of Sciences (India)

    2014-12-02

    Dec 2, 2014 ... GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology. (CSIR-IGIB), Mall Road, New Delhi ... also towards understanding the genomic biology. Neverthe- ..... Erwin C. 2008 Legal update: living with the genetic information nondiscrimination act.

  16. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  17. Data management in structural genomics: an overview.

    Science.gov (United States)

    Haquin, Sabrina; Oeuillet, Eric; Pajon, Anne; Harris, Mark; Jones, Alwyn T; van Tilbeurgh, Herman; Markley, John L; Zolnai, Zolt; Poupon, Anne

    2008-01-01

    Data management has been identified as a crucial issue in all large-scale experimental projects. In this type of project, many different persons manipulate multiple objects in different locations; thus, unless complete and accurate records are maintained, it is extremely difficult to understand exactly what has been done, when it was done, who did it, and what exact protocol was used. All of this information is essential for use in publications, reusing successful protocols, determining why a target has failed, and validating and optimizing protocols. Although data management solutions have been in place for certain focused activities (e.g., genome sequencing and microarray experiments), they are just emerging for more widespread projects, such as structural genomics, metabolomics, and systems biology as a whole. The complexity of experimental procedures, and the diversity and high rate of development of protocols used in a single center, or across various centers, have important consequences for the design of information management systems. Because procedures are carried out by both machines and hand, the system must be capable of handling data entry both from robotic systems and by means of a user-friendly interface. The information management system needs to be flexible so it can handle changes in existing protocols or newly added protocols. Because no commercial information management systems have had the needed features, most structural genomics groups have developed their own solutions. This chapter discusses the advantages of using a LIMS (laboratory information management system), for day-to-day management of structural genomics projects, and also for data mining. This chapter reviews different solutions currently in place or under development with emphasis on three systems developed by the authors: Xtrack, Sesame (developed at the Center for Eukaryotic Structural Genomics under the US Protein Structural Genomics Initiative), and HalX (developed at the

  18. Genome-wide comparative analysis of four Indian Drosophila species.

    Science.gov (United States)

    Mohanty, Sujata; Khanna, Radhika

    2017-12-01

    Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

  19. Target selection for structural genomics: an overview.

    Science.gov (United States)

    Marsden, Russell L; Orengo, Christine A

    2008-01-01

    The success of the whole genome sequencing projects brought considerable credence to the belief that high-throughput approaches, rather than traditional hypothesis-driven research, would be essential to structurally and functionally annotate the rapid growth in available sequence data within a reasonable time frame. Such observations supported the emerging field of structural genomics, which is now faced with the task of providing a library of protein structures that represent the biological diversity of the protein universe. To run efficiently, structural genomics projects aim to define a set of targets that maximize the potential of each structure discovery whether it represents a novel structure, novel function, or missing evolutionary link. However, not all protein sequences make suitable structural genomics targets: It takes considerably more effort to determine the structure of a protein than the sequence of its gene because of the increased complexity of the methods involved and also because the behavior of targeted proteins can be extremely variable at the different stages in the structural genomics "pipeline." Therefore, structural genomics target selection must identify and prioritize the most suitable candidate proteins for structure determination, avoiding "problematic" proteins while also ensuring the ultimate goals of the project are followed.

  20. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  1. Big Data Analysis of Human Genome Variations

    KAUST Repository

    Gojobori, Takashi

    2016-01-25

    Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a phylogenetic tree of about 5,000 human individuals at the genome level. As a result, we were able to identify clusters of ethnic groups, with detectable admixture, that were not possible by an analysis of each of the three data sets. Here, we report the outcome of this kind of big data analyses and discuss evolutionary significance of human genomic variations. Note that the present study was conducted in collaboration with Katsuhiko Mineta and Kosuke Goto at KAUST.

  2. [Survey on Schistosomes of man and livestock in Senegal using specific identification given by chetotaxy of cercaria. I. New arguments for the validation of S. curassoni Brumpt, 1931, parasite of man and domestic Bovidae].

    Science.gov (United States)

    Albaret, J L; Picot, H; Diaw, O T; Bayssade-Dufour, C; Vassiliades, G; Adamson, M; Luffau, G; Chabaud, A G

    1985-01-01

    Study of Senegal cercariae emitted by naturally infected snails or by snails experimentally infected using eggs from human urine or from sheep liver, and study of the corresponding eggs. The relative position of the dorsal sensillae of cercariae is described by an "AD index" and the ratio length/width of eggs by an "L/l index." At the present time, we have not finished the epidemiological studies, certain experiments are imperfect and the isoenzyme analysis of the corresponding adults is incomplete. Nevertheless information given by the indices AD and L/l agree and lead us to admit the existence of a Schistosome different to mattheei, haematobium and bovis and which, following Brumpt and Gretillat we refer to as Schistosoma curassoni. If one relies on the indices, the study indicates that: a) S. mattheei has not been found in Senegal, b) S. bovis is quite rare, c) S. haematobium apparently exists in pure infections in Casamance and in mixed infections with S. curassoni in man in the north and in the east, d) S. curassoni is apparently the dominant species in domestic ruminants and in man in the north and in the east, e) Bulinus umbilicatus is the principal vector of S. curassoni and S. haematobium.

  3. Lesions of the enteric nervous system and the possible role of mast cells in the pathogenic mechanisms of migration of schistosome eggs in the small intestine of cattle during Schistosoma bovis infection.

    Science.gov (United States)

    Balemba, O B; Mbassa, G K; Assey, R J; Kahwa, C K; Makundi, A E; Hay-Schmidt, A; Dantzer, V; Semuguruka, W D

    2000-06-10

    The enteric nervous system in the small intestine of cattle during Schistosoma bovis infection was studied by histological stains and immunohistochemical methods. Lesions due to migration of schistosoma eggs were located mainly in the mucous and the submucous layer overlaying the submucous vascular arcades. Granulomas destroyed ganglia, neurons, nerves fibre strands and nerve fibres. Ganglia situated within or near granulomas were infiltrated by mast cells, eosinophils, lymphocytes, globule leukocytes, neutrophils and macrophages. Mast cells were in close contact with degenerating neuronal perikarya. Whereas vasoactive intestinal peptide-like immunoreactivity in the nerves and neurons in the ganglia within and around granulomas was increased, the neurofilament-like immunoreactivity was reduced. Compared to the myenteric and external submucous plexuses, the internal submucous and mucous plexuses were the most damaged. These changes imply reduced functional capacity in the nervous tissue which might cause reduced motility, malabsorption and partly account for the loss of body weight and condition and failure to thrive which occur in schistosomosis. Biotinylated affinity purified swine anti-rabbit and mouse anti-rabbit immunoglobulins reacted nonspecifically with a subset of mast cells. The reaction revealed many mast cells in early forming granulomas and around schistosome egg tracts and infiltration of mast cells into the ganglia of intestinal nerve plexuses. The observation shows a localized, Type I hypersensitivity reaction suggesting for the release of mast cell-derived chemical mediators in the intestinal reaction to trap or evict S. bovis eggs and to cause diarrhoea.

  4. The genome of Brugia malayi – all worms are not created equal

    OpenAIRE

    Scott, Alan; Ghedin, Elodie

    2008-01-01

    Filarial nematode parasites, the causative agents of elephantiasis and river blindness, undermine the livelihoods of over one hundred millions people in the developing world. Recently, the Filarial Genome Project reported the draft sequence of the ~95 Mb genome of the human filarial parasite Brugia malayi - the first parasitic nematode genome to be sequenced. Comparative genome analysis with the prevailing model nematode Caenorhabditis elegans revealed similarities and differences in genome s...

  5. A Snapshot of the Emerging Tomato Genome Sequence

    Directory of Open Access Journals (Sweden)

    Lukas A. Mueller

    2009-03-01

    Full Text Available The genome of tomato ( L. is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States as part of the larger “International Solanaceae Genome Project (SOL: Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN. Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L. sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

  6. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. © 2015 Hilton and Gersbach; Published by Cold Spring Harbor Laboratory Press.

  7. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Pan-Tetris: an interactive visualisation for Pan-genomes.

    Science.gov (United States)

    Hennig, André; Bernhardt, Jörg; Nieselt, Kay

    2015-01-01

    Large-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes. We introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table. The main features of Pan-Tetris are a standard coordinate based presentation of multiple genomes complemented by easy to use tools compensating for algorithmic weaknesses in the pan-genome generation workflow. We demonstrate an application of Pan-Tetris to the pan-genome of Staphylococcus aureus. Pan-Tetris is currently the only interactive pan-genome visualisation tool. Pan-Tetris is available from http://bit.ly/1vVxYZT.

  9. Bacterial genomes: habitat specificity and uncharted organisms.

    Science.gov (United States)

    Dini-Andreote, Francisco; Andreote, Fernando Dini; Araújo, Welington Luiz; Trevors, Jack T; van Elsas, Jan Dirk

    2012-07-01

    The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

  10. HLA diversity in the 1000 genomes dataset.

    Directory of Open Access Journals (Sweden)

    Pierre-Antoine Gourraud

    Full Text Available The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation by sequencing at a level that should allow the genome-wide detection of most variants with frequencies as low as 1%. However, in the major histocompatibility complex (MHC, only the top 10 most frequent haplotypes are in the 1% frequency range whereas thousands of haplotypes are present at lower frequencies. Given the limitation of both the coverage and the read length of the sequences generated by the 1000 Genomes Project, the highly variable positions that define HLA alleles may be difficult to identify. We used classical Sanger sequencing techniques to type the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genes in the available 1000 Genomes samples and combined the results with the 103,310 variants in the MHC region genotyped by the 1000 Genomes Project. Using pairwise identity-by-descent distances between individuals and principal component analysis, we established the relationship between ancestry and genetic diversity in the MHC region. As expected, both the MHC variants and the HLA phenotype can identify the major ancestry lineage, informed mainly by the most frequent HLA haplotypes. To some extent, regions of the genome with similar genetic or similar recombination rate have similar properties. An MHC-centric analysis underlines departures between the ancestral background of the MHC and the genome-wide picture. Our analysis of linkage disequilibrium (LD decay in these samples suggests that overestimation of pairwise LD occurs due to a limited sampling of the MHC diversity. This collection of HLA-specific MHC variants, available on the dbMHC portal, is a valuable resource for future analyses of the role of MHC in population and disease studies.

  11. Aspergillus and Penicillium in the Post-genomic Era

    DEFF Research Database (Denmark)

    Genome sequencing has affected studies into the biology of all classes of organisms and this is certainly true for filamentous fungi. The level with which biological systems can be studied since the availability of genomes and post-genomic technologies is beyond what most people could have imagined...... and a whole genus genome sequencing project in progress for Aspergillus. This book highlights some of the changes in the studies into these fungi, since the availability of genome sequences. The contributions vary from insights in the taxonomy of these genera, use of genomics for forward genetics and genomic...

  12. Using Ancient Samples in Projection Analysis

    Directory of Open Access Journals (Sweden)

    Melinda A. Yang

    2016-01-01

    Full Text Available Projection analysis is a tool that extracts information from the joint allele frequency spectrum to better understand the relationship between two populations. In projection analysis, a test genome is compared to a set of genomes from a reference population. The projection’s shape depends on the historical relationship of the test genome’s population to the reference population. Here, we explore in greater depth the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model, or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model. We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present-day population or not. Second, we compute projections for several published ancient genomes. We compare two Neanderthals and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these five ancient genomes to assess how well the observed projections are recovered.

  13. Expansion of the Genomic Encyclopedia of Bacteria and Archaea

    OpenAIRE

    Rinke, Christian

    2011-01-01

    To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed to systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99percent of microorganisms elude current culturing attempts, severely limiting the ability to r...

  14. The SickKids Genome Clinic: developing and evaluating a pediatric model for individualized genomic medicine.

    Science.gov (United States)

    Bowdin, S C; Hayeems, R Z; Monfared, N; Cohn, R D; Meyn, M S

    2016-01-01

    Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genomic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to anticipate, diagnose and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific and clinical paradigms. The potential benefits of pre-symptomatic identification of at-risk individuals, improved diagnostics, individualized therapy, accurate prognosis and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models and increased health care costs. Here we review the challenges, opportunities and limits of integrating genomic analysis into pediatric clinical practice and describe a model for implementing individualized genomic medicine. Our multidisciplinary team of bioinformaticians, health economists, health services and policy researchers, ethicists, geneticists, genetic counselors and clinicians has designed a 'Genome Clinic' research project that addresses multiple challenges in pediatric genomic medicine--ranging from development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference and the ethics of consent. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  15. A snapshot of the emerging tomato genome sequence

    NARCIS (Netherlands)

    Mueller, L.A.; Klein Lankhorst, R.M.; Tanksley, S.D.; Peters, R.M.; Staveren, van M.J.; Datema, E.; Fiers, M.W.E.J.; Ham, van R.C.H.J.; Szinay, D.; Jong, de J.H.S.G.M.

    2009-01-01

    The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL):

  16. MIPS: a database for genomes and protein sequences.

    Science.gov (United States)

    Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

    2002-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

  17. Partnering for functional genomics research conference: Abstracts of poster presentations

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-06-01

    This reports contains abstracts of poster presentations presented at the Functional Genomics Research Conference held April 16--17, 1998 in Oak Ridge, Tennessee. Attention is focused on the following areas: mouse mutagenesis and genomics; phenotype screening; gene expression analysis; DNA analysis technology development; bioinformatics; comparative analyses of mouse, human, and yeast sequences; and pilot projects to evaluate methodologies.

  18. Whole-genome sequence-based analysis of thyroid function

    DEFF Research Database (Denmark)

    Taylor, Peter N.; Porcu, Eleonora; Chew, Shelby

    2015-01-01

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome seque...

  19. Integrated Genome-Based Studies of Shewanella Ecophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jizhong [Univ. of Oklahoma, Norman, OK (United States); He, Zhili [Univ. of Oklahoma, Norman, OK (United States)

    2014-04-08

    As a part of the Shewanella Federation project, we have used integrated genomic, proteomic and computational technologies to study various aspects of energy metabolism of two Shewanella strains from a systems-level perspective.

  20. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular

  1. 10. international mouse genome conference

    Energy Technology Data Exchange (ETDEWEB)

    Meisler, M.H.

    1996-12-31

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  2. Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study

    NARCIS (Netherlands)

    P.S. de Vries (Paul); M. Sabater-Lleal (Maria); D.I. Chasman (Daniel); S. Trompet (Stella); T.S. Ahluwalia (Tarunveer Singh); A. Teumer (Alexander); M.E. Kleber (Marcus); M.-H. Chen (Ming-Huei); J.J. Wang (Jie Jin); J. Attia (John); R.E. Marioni (Riccardo); M. Steri (Maristella); Weng, L.-C. (Lu-Chen); R. Pool (Reńe); V. Grossmann (Vera); J. Brody (Jennifer); C. Venturini (Cristina); T. Tanaka (Toshiko); L.M. Rose (Lynda); C. Oldmeadow (Christopher); J. Mazur (Johanna); S. Basu (Saonli); M. Frånberg (Mattias); Q. Yang (Qiong); S. Ligthart (Symen); J.J. Hottenga (Jouke Jan); A. Rumley (Ann); Mulas, A. (Antonella); A.J. de Craen (Anton); A. Grotevendt (Anne); K.D. Taylor (Kent D.); G. Delgado; A. Kifley (Annette); L.M. Lopez (Lorna); T.L. Berentzen (Tina L.); M. Mangino (Massimo); S. Bandinelli (Stefania); Morrison, A.C. (Alanna C.); A. Hamsten (Anders); G.H. Tofler (Geoffrey); M.P.M. de Maat (Moniek); G. Draisma (Gerrit); G.D. Lowe (Gordon D.); M. Zoledziewska (Magdalena); N. Sattar (Naveed); Lackner, K.J. (Karl J.); U. Völker (Uwe); McKnight, B. (Barbara); J. Huang (Jian); E.G. Holliday (Elizabeth); McEvoy, M.A. (Mark A.); J.M. Starr (John); P.G. Hysi (Pirro); D.G. Hernandez (Dena); W. Guan (Weihua); F. Rivadeneira Ramirez (Fernando); W.L. McArdle (Wendy); P.E. Slagboom (Eline); Zeller, T. (Tanja); B.M. Psaty (Bruce); A.G. Uitterlinden (André); E.J.C. de Geus (Eco); D.J. Stott (David J.); H. Binder (Harald); A. Hofman (Albert); O.H. Franco (Oscar); J.I. Rotter (Jerome I.); L. Ferrucci (Luigi); Spector, T.D. (Tim D.); I.J. Deary (Ian J.); W. März (Winfried); A. Greinacher (Andreas); P.S. Wild (Philipp S.); F. Cucca (Francesco); D.I. Boomsma (Dorret); Watkins, H. (Hugh); Tang, W. (Weihong); P.M. Ridker (Paul); J.W. Jukema; R.J. Scott (Rodney J.); P. Mitchell (Paul); T. Hansen (T.); O'Donnell, C.J. (Christopher J.); Smith, N.L. (Nicholas L.); D.P. Strachan (David P.); A. Dehghan (Abbas)

    2017-01-01

    textabstractAn increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap

  3. Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

    NARCIS (Netherlands)

    de Vries, Paul S; Sabater-Lleal, Maria; Chasman, Daniel I; Trompet, Stella; Ahluwalia, Tarunveer S; Teumer, Alexander; Kleber, Marcus E; Chen, Ming-Huei; Wang, Jie Jin; Attia, John R; Marioni, Riccardo E; Steri, Maristella; Weng, Lu-Chen; Pool, Rene; Grossmann, Vera; Brody, Jennifer A; Venturini, Cristina; Tanaka, Toshiko; Rose, Lynda M; Oldmeadow, Christopher; Mazur, Johanna; Basu, Saonli; Frånberg, Mattias; Yang, Qiong; Ligthart, Symen; Hottenga, Jouke J; Rumley, Ann; Mulas, Antonella; De Craen, Anton J M; Grotevendt, Anne; Taylor, Kent D; Delgado, Graciela E; Kifley, Annette; Lopez, Lorna M; Berentzen, Tina L; Mangino, Massimo; Bandinelli, Stefania; Morrison, Alanna C; Hamsten, Anders; Tofler, Geoffrey; de Maat, Moniek P M; Draisma, Harmen H M; Lowe, Gordon D; Zoledziewska, Magdalena; Sattar, Naveed; Lackner, Karl J; Völker, Uwe; McKnight, Barbara; Huang, Jie; Holliday, Elizabeth G; McEvoy, Mark A; Starr, John M; Hysi, Pirro G; Hernandez, Dena G; Guan, Weihua; Rivadeneira, Fernando; McArdle, Wendy L; Slagboom, P. Eline; Zeller, Tanja; Psaty, Bruce M; Uitterlinden, André G; de Geus, Eco J C; Stott, David J; Binder, Harald; Hofman, Albert; Franco, Oscar H; Rotter, Jerome I; Ferrucci, Luigi; Spector, Tim D; Deary, Ian J; März, Winfried; Greinacher, Andreas; Wild, Philipp S; Cucca, Francesco; Boomsma, Dorret I; Watkins, Hugh; Tang, Weihong; Ridker, Paul M; Jukema, Jan W; Scott, Rodney J; Mitchell, Paul; Hansen, Torben; O'Donnell, Christopher J; Smith, Nicholas L; Strachan, David P; Dehghan, Abbas

    2017-01-01

    An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In

  4. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

    Directory of Open Access Journals (Sweden)

    Martijn Staats

    Full Text Available Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes, but at least generating vital comparative genomic data for testing (phylogenetic, demographic and genetic hypotheses, that become increasingly more

  5. ISOL@: an Italian SOLAnaceae genomics resource

    Science.gov (United States)

    Chiusano, Maria Luisa; D'Agostino, Nunzio; Traini, Alessandra; Licciardello, Concetta; Raimondo, Enrico; Aversano, Mario; Frusciante, Luigi; Monti, Luigi

    2008-01-01

    Background Present-day ‘-omics’ technologies produce overwhelming amounts of data which include genome sequences, information on gene expression (transcripts and proteins) and on cell metabolic status. These data represent multiple aspects of a biological system and need to be investigated as a whole to shed light on the mechanisms which underpin the system functionality. The gathering and convergence of data generated by high-throughput technologies, the effective integration of different data-sources and the analysis of the information content based on comparative approaches are key methods for meaningful biological interpretations. In the frame of the International Solanaceae Genome Project, we propose here ISOLA, an Italian SOLAnaceae genomics resource. Results ISOLA (available at ) represents a trial platform and it is conceived as a multi-level computational environment. ISOLA currently consists of two main levels: the genome and the expression level. The cornerstone of the genome level is represented by the Solanum lycopersicum genome draft sequences generated by the International Tomato Genome Sequencing Consortium. Instead, the basic element of the expression level is the transcriptome information from different Solanaceae species, mainly in the form of species-specific comprehensive collections of Expressed Sequence Tags (ESTs). The cross-talk between the genome and the expression levels is based on data source sharing and on tools that enhance data quality, that extract information content from the levels' under parts and produce value-added biological knowledge. Conclusions ISOLA is the result of a bioinformatics effort that addresses the challenges of the post-genomics era. It is designed to exploit ‘-omics’ data based on effective integration to acquire biological knowledge and to approach a systems biology view. Beyond providing experimental biologists with a preliminary annotation of the tomato genome, this effort aims to produce a trial

  6. Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development

    Science.gov (United States)

    Collins, James J.; Hou, Xiaowen; Romanova, Elena V.; Lambrus, Bramwell G.; Miller, Claire M.; Saberi, Amir; Sweedler, Jonathan V.; Newmark, Phillip A.

    2010-01-01

    Bioactive peptides (i.e., neuropeptides or peptide hormones) represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites. PMID:20967238

  7. Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

    Directory of Open Access Journals (Sweden)

    James J Collins

    Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

  8. Gramene database: Navigating plant comparative genomics resources

    Directory of Open Access Journals (Sweden)

    Parul Gupta

    2016-11-01

    Full Text Available Gramene (http://www.gramene.org is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

  9. Genomic approaches in aquaculture and fisheries

    DEFF Research Database (Denmark)

    Cancela, M. Leonor; Bargelloni, Luca; Boudry, Pierre

    2010-01-01

    . Improving state-of-the-art genomics research in various aquaculture systems, as well as its industrial applications, remains one of the major challenges in this area and should be the focus of well developed strategies to be implemented in the next generation of projects. This chapter will first provide......Despite the enormous input into the worldwide development of fish and shellfish farming in the recent decades, in part as an attempt to minimize the impact of fishing on already overexploited natural populations, the application of genomics to aquaculture and fisheries remains poorly developed...... an overview of the genomic tools and resources available, then discuss the application of genomic approaches to the improvement of fish and shellfish farming (e.g. breeding, reproduction, growth, nutrition and product quality), including the evaluation of stock diversity and the use of selection procedures...

  10. Functional genomics strategies with transposons in rice

    NARCIS (Netherlands)

    Greco, R.

    2003-01-01

    Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

  11. Translating Genomic Discoveries to Cure Ultrahypermutant ...

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

    Translating Genomic Discoveries to Cure Ultrahypermutant Mismatch Repair Deficient Brain Tumours. Malignant brain tumours are the most common cause of death among children with cancer, but there is no known cure. This project will advance research in this important field. Inherited mutations and childhood cancer.

  12. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  13. Directed genome engineering for genome optimization.

    Science.gov (United States)

    D'Halluin, Kathleen; Ruiter, Rene

    2013-01-01

    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  14. Plant Functional Genomics

    National Research Council Canada - National Science Library

    Chris Somerville; Shauna Somerville

    1999-01-01

    Nucleotide sequencing of the Arabidopsis genome is nearing completion, sequencing of the rice genome has begun, and large amounts of expressed sequence tag information are being obtained for many other plants...

  15. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  16. Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

  17. Fish genomes : a powerful tool to uncover new functional elements in vertebrates

    NARCIS (Netherlands)

    Stupka, Elia

    2011-01-01

    This thesis spans several years of work dedicated to understanding fish genomes. In the first chapter it describes the genome of the first fish for which the entire genome was sequenced through a large-scale international project, Fugu rubripes. the pufferfish. In particular, it highlights how this

  18. Whole-genome sequence variation, population structure and demographic history of the Dutch population

    NARCIS (Netherlands)

    The Genome of the Netherlands Consortium; T. Marschall (Tobias); A. Schönhuth (Alexander)

    2014-01-01

    htmlabstractWhole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch

  19. Analysis of pan-genome content and its application in microbial identification

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana

    the application of PanFunPro to a set of more than 2000 genomes; this paper aims to define set of protein families, which are conserved among all the genomes. Papers V demonstrates comparative genomics analysis of proteomes, belonging to Vibrio genus. In the last project, described in Chapter 5, both BLAST...

  20. 75 FR 13558 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-03-22

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research... individual intramural programs and projects conducted by the National Human Genome Research Institute...

  1. 76 FR 65204 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2011-10-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute, including...

  2. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-05-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research... individual intramural programs and projects conducted by the National Human Genome Research Institute...

  3. 77 FR 64816 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2012-10-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute, including...

  4. 75 FR 60467 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2010-09-30

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute, including...

  5. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus,...

  6. Whole Genome Selection

    Science.gov (United States)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  7. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human...

  8. Projects Work!

    Science.gov (United States)

    Textor, Martin R.

    2005-01-01

    The great educational value of projects is emphasized by contrasting negative aspects of the life of today's children with the goals of project work. This is illustrated by a project "Shopping." It is shown what children are learning in such projects and what the advantages of project work are. Relevant topic areas, criteria for selecting a…

  9. Leveraging rural energy investment for parasitic disease control: schistosome ova inactivation and energy co-benefits of anaerobic digesters in rural China.

    Science.gov (United States)

    Remais, Justin; Chen, Lin; Seto, Edmund

    2009-01-01

    Cooking and heating remain the most energy intensive activities among the world's poor, and thus improved access to clean energies for these tasks has been highlighted as a key requirement of attaining the major objectives of the UN Millennium Development Goals. A move towards clean energy technologies such as biogas systems (which produce methane from human and animal waste) has the potential to provide immediate benefits for the control of neglected tropical diseases. Here, an assessment of the parasitic disease and energy benefits of biogas systems in Sichuan Province, China, is presented, highlighting how the public health sector can leverage the proliferation of rural energy projects for infectious disease control. First, the effectiveness of biogas systems at inactivating and removing ova of the human parasite Schistosoma japonicum is experimentally evaluated. Second, the impact of biogas infrastructure on energy use and environmental quality as reported by surveyed village populations is assessed, as is the community acceptance of the technology. No viable eggs were recovered in the effluent collected weekly from biogas systems for two months following seeding with infected stool. Less than 1% of ova were recovered viable from a series of nylon bags seeded with ova, a 2-log removal attributable to biochemical inactivation. More than 90% of Ascaris lumbricoides ova (used as a proxy for S. japonicum ova) counted at the influent of two biogas systems were removed in the systems when adjusted for system residence time, an approximate 1-log removal attributable to sedimentation. Combined, these inactivation/removal processes underscore the promise of biogas infrastructure for reducing parasite contamination resulting from nightsoil use. When interviewed an average of 4 years after construction, villagers attributed large changes in fuel usage to the installation of biogas systems. Household coal usage decreased by 68%, wood by 74%, and crop waste by 6%. With

  10. Leveraging rural energy investment for parasitic disease control: schistosome ova inactivation and energy co-benefits of anaerobic digesters in rural China.

    Directory of Open Access Journals (Sweden)

    Justin Remais

    Full Text Available Cooking and heating remain the most energy intensive activities among the world's poor, and thus improved access to clean energies for these tasks has been highlighted as a key requirement of attaining the major objectives of the UN Millennium Development Goals. A move towards clean energy technologies such as biogas systems (which produce methane from human and animal waste has the potential to provide immediate benefits for the control of neglected tropical diseases. Here, an assessment of the parasitic disease and energy benefits of biogas systems in Sichuan Province, China, is presented, highlighting how the public health sector can leverage the proliferation of rural energy projects for infectious disease control.First, the effectiveness of biogas systems at inactivating and removing ova of the human parasite Schistosoma japonicum is experimentally evaluated. Second, the impact of biogas infrastructure on energy use and environmental quality as reported by surveyed village populations is assessed, as is the community acceptance of the technology. No viable eggs were recovered in the effluent collected weekly from biogas systems for two months following seeding with infected stool. Less than 1% of ova were recovered viable from a series of nylon bags seeded with ova, a 2-log removal attributable to biochemical inactivation. More than 90% of Ascaris lumbricoides ova (used as a proxy for S. japonicum ova counted at the influent of two biogas systems were removed in the systems when adjusted for system residence time, an approximate 1-log removal attributable to sedimentation. Combined, these inactivation/removal processes underscore the promise of biogas infrastructure for reducing parasite contamination resulting from nightsoil use. When interviewed an average of 4 years after construction, villagers attributed large changes in fuel usage to the installation of biogas systems. Household coal usage decreased by 68%, wood by 74%, and crop waste

  11. The Hydra genome: insights, puzzles and opportunities for developmental biologists.

    Science.gov (United States)

    Steele, Robert E

    2012-01-01

    The sequencing of a Hydra genome marked the beginning of a new era in the use of Hydra as a developmental model. Analysis of the genome sequence has led to a number of interesting findings, has required revisiting of previous work, and most importantly presents new opportunities for understanding the developmental biology of Hydra. This review will de-scribe the history of the Hydra genome project, a selection of results from it that are relevant to developmental biologists, and some future research opportunities provided by Hydra genomics.

  12. Complete genome sequence of Methanoculleus marisnigri type strain JR1

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Sieprawska-Lupa, Magdalena [University of Georgia, Athens, GA; Goltsman, Eugene [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Brettin, Tom [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Whitman, W. B. [University of Georgia, Athens, GA; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2009-01-01

    Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

  13. Complete genome sequence of Thermomonospora curvata type strain (B9)

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Olga [Los Alamos National Laboratory (LANL); Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California

    2011-01-01

    Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    Energy Technology Data Exchange (ETDEWEB)

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Comparative genomics of Lactobacillus

    Science.gov (United States)

    Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

    2011-01-01

    Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein‐encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group‐specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

  16. Chromium and Genomic Stability

    Science.gov (United States)

    Wise, Sandra S.; Wise, John Pierce

    2014-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as highly toxic and carcinogenic with no nutritional value. Recent data indicate that it causes genomic instability and also has no role in promoting genomic stability. PMID:22192535

  17. Ethical aspects of genome diversity research: genome research into cultural diversity or cultural diversity in genome research?

    Science.gov (United States)

    Ilkilic, Ilhan; Paul, Norbert W

    2009-03-01

    The goal of the Human Genome Diversity Project (HGDP) was to reconstruct the history of human evolution and the historical and geographical distribution of populations with the help of scientific research. Through this kind of research, the entire spectrum of genetic diversity to be found in the human species was to be explored with the hope of generating a better understanding of the history of humankind. An important part of this genome diversity research consists in taking blood and tissue samples from indigenous populations. For various reasons, it has not been possible to execute this project in the planned scope and form to date. Nevertheless, genomic diversity research addresses complex issues which prove to be highly relevant from the perspective of research ethics, transcultural medical ethics, and cultural philosophy. In the article at hand, we discuss these ethical issues as illustrated by the HGDP. This investigation focuses on the confrontation of culturally diverse images of humans and their cosmologies within the framework of genome diversity research and the ethical questions it raises. We argue that in addition to complex questions pertaining to research ethics such as informed consent and autonomy of probands, genome diversity research also has a cultural-philosophical, meta-ethical, and phenomenological dimension which must be taken into account in ethical discourses. Acknowledging this fact, we attempt to show the limits of current guidelines used in international genome diversity studies, following this up by a formulation of theses designed to facilitate an appropriate inquiry and ethical evaluation of intercultural dimensions of genome research.

  18. Selecting targets from eukaryotic parasites for structural genomics and drug discovery.

    Science.gov (United States)

    Phan, Isabelle Q H; Stacy, Robin; Myler, Peter J

    2014-01-01

    The selection of targets is the first step for any structural genomics project. The application of structural genomics approaches to drug discovery also starts with the selection of targets. Here, three protocols are described that were developed to select targets from eukaryotic pathogens. These protocols could also be applied to other drug discovery projects.

  19. Selecting targets from eukaryotic parasites for structural genomics and drug discovery

    Science.gov (United States)

    Phan, Isabelle Q. H.; Stacy, Robin; Myler, Peter J.

    2015-01-01

    The selection of targets is the first step for any structural genomics project. The application of structural genomics approaches to drug discovery also starts with the selection of targets. Here, three protocols are described that were developed to select targets from eukaryotic pathogens. These protocols could also be applied to other drug discovery projects. PMID:24590708

  20. The Human Variome Project.

    Science.gov (United States)

    Burn, John; Watson, Michael

    2016-06-01

    The practical realization of genomics has meant a growing realization that variant interpretation is a major barrier to practical use of DNA sequence data. The late Professor Dick Cotton devoted his life to innovation in molecular genetics and was a prime mover in the international response to the need to understand the "variome." His leadership resulted in the launch first of the Human Genetic Variation Society and then, in 2006, an international agreement to launch the Human Variome Project (HVP), aimed at data integration enabled by standards and infrastructure of the databases of variants being identified in families with a range of inherited disorders. The project attracted a network of affiliates across 81 countries and earned formal recognition by UNESCO, which now hosts its biennial meetings. It has also signed a Memorandum of Understanding with the World Health Organization. Future progress will depend on longer term secure funding and integration with the efforts of the genomics community where the rapid advances in sequencing technology have enabled variant capture on a previously unimaginable scale. Efforts are underway to integrate the efforts of HVP with those of the Global Alliance for Genomics and Health to provide a lasting legacy of Dick Cotton's vision. © 2016 WILEY PERIODICALS, INC.