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Sample records for belize high genetic

  1. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

    Full Text Available Abstract Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity

  2. Belize.

    Science.gov (United States)

    1987-08-01

    In 1986, the population of Belize stood at 166,000, with an annual growth rate of 1%. The infant mortality rate was 56/1000, and life expectancy is 60 years. Of the work force of 50,000, 30% are engaged in agriculture, 27% are employed in industry and commerce, 25% are in the services sector, and 16% are government employees. Belize is a parliamentary democracy. Independence was achieved in 1981. The country's gross domestic product was US$156 million in 1985, with an annual growth rate of 1.5%. Per capita income is US$938. Forestry was the major economic activity until the timber supply began to dwindle. Sugar is now the principal export, although efforts are underway to expand the production of citrus, rice, beef, bananas, and tropical fruit. Domestic industry is constrained by the relatively high cost of labor and a small domestic market. Membership in the Caribbean community provides Belize with assured access to a large market for potential grain and livestock surpluses and should help stimulate the growth of commercial agriculture. Belize also expects to benefit from its designation for the Caribbean Basin Initiative, a US Government program designed to stimulate investment in Caribbean nations by providing duty free access to the US market for most Caribbean products. Economic growth has been hindered by the lack of infrastructure, especially roads, electricity, and port facilities. The Government recognizes the need to develop the country, and 54% of its 1986-87 budget of US$106.8 million is earmarked for development spending.

  3. Batrachochytrium dendrobatidis shows high genetic diversity and ecological niche specificity among haplotypes in the Maya Mountains of Belize.

    Directory of Open Access Journals (Sweden)

    Kristine Kaiser

    Full Text Available The amphibian pathogen Batrachochytrium dendrobatidis (Bd has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd.

  4. Chicxulub High-Altitude Ballistic Ejecta from Central Belize

    Science.gov (United States)

    Pope, K. O.; Ocampo, A. C.

    2000-01-01

    Chicxulub ejecta are found in central Belize, 475 km southeast of the impact crater center. These deposits are ballistic ejecta launched along high-altitude trajectories above the atmosphere and deposited as a discontinuous sheet on the terminal Cretaceous land surface.

  5. Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee

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    Hunter, M.E.; Auil-Gomez, N. E.; Tucker, K.P.; Bonde, R.K.; Powell, J.; McGuire, P.M.

    2010-01-01

    The Antillean subspecies of the West Indian manatee Trichechus manatus is found throughout Central and South America and the Caribbean. Because of severe hunting pressure during the 17th through 19th centuries, only small populations of the once widespread aquatic mammal remain. Fortunately, protections in Belize reduced hunting in the 1930s and allowed the country's manatee population to become the largest breeding population in the Wider Caribbean. However, increasing and emerging anthropogenic threats such as coastal development, pollution, watercraft collision and net entanglement represent challenges to this ecologically important population. To inform conservation and management decisions, a comprehensive molecular investigation of the genetic diversity, relatedness and population structure of the Belize manatee population was conducted using mitochondrial and microsatellite DNA. Compared with other mammal populations, a low degree of genetic diversity was detected (HE=0.455; NA=3.4), corresponding to the small population size and long-term exploitation. Manatees from the Belize City Cayes and Southern Lagoon system were genetically different, with microsatellite and mitochondrial FST values of 0.029 and 0.078, respectively (P≤0.05). This, along with the distinct habitats and threats, indicates that separate protection of these two groups would best preserve the region's diversity. The Belize population and Florida subspecies appear to be unrelated with microsatellite and mitochondrial FST values of 0.141 and 0.63, respectively (P≤0.001), supporting the subspecies designations and suggesting low vagility throughout the northern Caribbean habitat. Further monitoring and protection may allow an increase in the Belize manatee genetic diversity and population size. A large and expanding Belize population could potentially assist in the recovery of other threatened or functionally extinct Central American Antillean manatee populations.

  6. The relic Criollo cacao in Belize- genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

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    Cacao (Theobroma cacao L.) is native to the South American rainforest but it was domesticated in Mesoamerica. The relic Criollo cocoa in Belize has been well known in the premium chocolate market for its high-quality. Knowledge of genetic diversity in this variety is essential for efficient conserva...

  7. High prevalence of soil-transmitted helminths in Southern Belize-highlighting opportunity for control interventions

    Institute of Scientific and Technical Information of China (English)

    Rina Girard Kaminsky; Steven K Ault; Phillip Castillo; Kenton Serrano; Guillermo Troya

    2014-01-01

    Objective: To assess prevalence and intensity of soil-transmitted helminths (STH) in school age children of two southern districts as baseline information prior to implement a deworming program against intestinal parasites as part of an integrated country development plan. Methods:Children randomly selected from urban and rural schools in Southern Belize provided one stool sample each, analysed by the Kato-Katz method to assess prevalence and intensity of STH infections. Epi Info software was used for data analysis;Chi-square test and Fischer exact test were applied to compare group proportions;P Results:A total of 500 children from 10 schools participated in the study from May to December 2005. Prevalence of STH ranged between 40%and 82%among schools, with a median of 59.2%;the majority of light intensity, and with 2.2%high intensity infection. Trichuris and Ascaris infections presented similar frequency in children aged from 6 to 9 years old;hookworm infections tended to be more frequent in the older group 10 to 12 years old. Statistical significances (P≤0.01) were found in children in rural schools infected with any species of STH, in moderate Trichuris infections, in hookworm infections in rural areas with strong Mayan presence and in Ascaris infections in children of Mayan origin. Conclusions:High prevalence of STH in Southern Belize provided sound ground for implementing an integrated deworming control program.

  8. Nano particles as the primary cause for long-term sunlight suppression at high southern latitudes following the Chicxulub impact - evidence from ejecta deposits in Belize and Mexico

    DEFF Research Database (Denmark)

    Vajda, Vivi; Ocampo, Adriana; Ferrow, Embaie;

    2015-01-01

    Life on Earth was sharply disrupted 66 Ma ago as an asteroid hit the sea-floor in what is today Yucatan Peninsula, Mexico. Approximately 600 km3 of sedimentary rock were vapourized, ejected into the atmosphere and subsequently deposited globally as an ejecta apron and fallout layer. Proximal ejecta...... deposits occur in Belize and southern Mexico where the so called Albion island spheroid bed is superimposed on the target rock (the Barton Creek Formation). We analysed the spheroid bed via Mössbauer spectroscopy, petrology, XRD, and palynology at several sites ~ 350-500 km distance from the crater centre....... Our results show that the relative concentrations of Fe in nano-phase goethite (α-FeOOH) are very high in the spheroid bed samples from Albion Island (Belize) and from Ramonal South (Mexico), but are low to absent in the spheroid bed at Ramonal North, and in the Cretaceous target rock. Moreover, our...

  9. Chicxulub Impact Ejecta in Belize

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    Ocampo, A.; Pope, K.; Fischer, A.; Alvarez, W.; Fouke, B.; Asaro, F.; Webster, C., Jr.; Vega, F.; Smith, J.; Fritsche, A. E.

    1997-01-01

    Chicxulub ejecta deposits in Belize provide the closest exposures of ejecta to the crater and the only exposures of proximal ejecta deposited in a terrestrial environment. A quarry on Albion Island in northern Belize exposes Late Cretaceous, possibly Maastrichtian, carbonate platform sediments that were folded, eroded, and subaerially weathered prior to the deposition of coarse ejecta from Chicxulub. These ejecta deposits are composed of a basal, about 1-m-thick clay and dolomite Spheroid Bed overlain by a about 15-m-thick coarse Diamictite Bed. Many and perhaps most of the clay spheroids are altered glass. Many dolomite spheroids have concentric layers and angular cores are probably of accretionary lapilli origin. A slight Ir concentration (111-152 ppt) was detected in the base of the Spheroid Bed. The Diamictite Bed contains about 10% altered glass, rare shocked quartz, 3-8 m diameter boulders and striated and polished cobbles, one with a penetrating rock chip that plastically deformed the cobble. Ejecta deposits extend to the surface at Albion and the maximum thickness in this area is not known. Ejecta deposits are exposed in several roadside quarries in the Cayo District of central Belize. The Late Cretaceous here is also represented by carbonate platform sediments. The upper surface of the carbonate platform is a highly irregular and extensively recrystallized horizon possibly representing deep karst weathering. Approximately 30 in of diamictite overlies this horizon with a texture similar to the Diamictite Bed at the Albion quarry, but with a more diverse lithology. In three locations the Cayo diamictites, contain red clay layers with abundant polished and striated limestone pebbles and cobbles called Pook's Pebbles, several of which have penetrating rock chips and ablated surfaces. We interpret the Albion Spheroid Bed as a deposit from the impact vapor plume and the Albion and Cayo diamictites as the result of a turbulent flow that contained debris derived

  10. Short communication: high prevalence of drug resistance in HIV type 1-infected children born in Honduras and Belize 2001 to 2004.

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    Parham, Leda; de Rivera, Ivette Lorenzana; Murillo, Wendy; Naver, Lars; Largaespada, Natalia; Albert, Jan; Karlsson, Annika C

    2011-10-01

    Antiretroviral therapy has had a great impact on the prevention of mother-to-child transmission (MTCT) of HIV-1. However, development of drug resistance, which could be subsequently transmitted to the child, is a major concern. In Honduras and Belize the prevalence of drug resistance among HIV-1-infected children remains unknown. A total of 95 dried blood spot samples was obtained from HIV-1-infected, untreated children in Honduras and Belize born during 2001 to 2004, when preventive antiretroviral therapy was often suboptimal and consisted of monotherapy with nevirapine or zidovudine. Partial HIV-1 pol gene sequences were successfully obtained from 66 children (Honduras n=55; Belize n=11). Mutations associated with drug resistance were detected in 13% of the Honduran and 27% of the Belizean children. Most of the mutations detected in Honduras (43%) and all mutations detected in Belize were associated with resistance to nonnucleoside reverse transcriptase inhibitors, which was expected from the wide use of nevirapine to prevent MTCT during the study period. In addition, although several mothers reported that they had not received antiretroviral therapy, mutations associated with resistance to nucleoside reverse transcriptase inhibitors and protease inhibitors were found in Honduras. This suggests prior and unreported use of these drugs, or that these women had been infected with resistant virus. The present study demonstrates, for the first time, the presence of drug resistance-associated mutations in HIV-1-infected Honduran and Belizean children.

  11. THE FISHES OF THE PELICAN CAYS, BELIZE

    Science.gov (United States)

    Smith, C. Lavett, James C. Tyler, William P. Davis, Robert S. Jones, David G. Smith and Carole C. Baldwin. Submitted. Fishes of the Pelican Cays, Belize. Atoll Res. Bull. 108 p. (ERL,GB 1204). The fishes of the Pelican Cays, Belize, were sampled using a combination of sma...

  12. Holocene cemented beach deposits in Belize

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    Gischler, Eberhard; Lomando, Anthony J.

    1997-06-01

    Two types of cemented beach deposits occur on reef islands off the coast of Belize. These are (1) intertidal beachrock that is dominantly cemented by marine aragonite and high-magnesium-calcite cements, and (2) supratidal cayrock that is cemented mainly by vadose low-magnesium-calcite cements. Besides differences in position relative to present sea level and resulting early diagenesic features, beachrock and cayrock can be distinguished on the basis of differences in composition, texture, geographical position, and age. Whereas the composition of beachrock is similar to that of the adjacent marginal reef sediments, cayrock is enriched in benthic foraminifera. Intertidal beachrock is moderately to well sorted and well cemented, while supratidal cayrock is very well sorted, poorly cemented and friable. Beachrock occurs preferentially on windward beaches of sand-shingle Gays on the middle and southern barrier reefs and on the isolated platforms Glovers and Lighthouse Reefs. Cayrock only occurs on larger mangrove-sand Gays of the isolated platforms Turneffe Islands, Lighthouse Reef, and the northern barrier reef. 14C-dating of ten whole-rock and mollusk shell samples produced calibrated dates between AD 345 and AD 1435 for beachrock and between BC 1085 and AD 1190 for cayrock. The large-scale distribution of beachrock in Belize supports the contention that physical processes such as water agitation rather than biological processes control beachrock formation and distribution. Only on windward sides of cays that are close to the reef crest, where large amounts of seawater flush the beaches, considerable amounts of cements can be precipitated to produce beachrock. Cayrock forms due to cementation in the vadose zone and is only preserved on larger, stable mangrove-sand cays.

  13. The Epidemiology of Malaria in Belize, 1989-1999

    Science.gov (United States)

    2003-02-01

    responsible for transmission were the same as those in Canada (Faust 1949). Malaria was highly endemic in the South at the time of the civil war. Returning...in reaching inaccessible areas, by the speed in which they change, and by other situations such as natural disasters and civil strife. Remote sensing...and broadleaf forests. Culturally diverse, Belize is home to many ethnicities such as three Mayan groups, Afro- Belizeans or creoles, Spanish-speaking

  14. Chicxulub Impact Ejecta From Albion Island, Belize

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    Ocampo, A.; Pope, K.; Fischer, A.; Alvarez, W.; Fouke, B.; Webster, C.; Vega, F.; Smit, J.; Fritsche, A.; Claeys, P.

    1999-01-01

    Impact ejecta from the Albion Formation are exposed in northern Belize. The ejecta come from the outer portion of the continuous ejecta blanket of the Chicxulub crater, which is located 360 km to the northwest.

  15. Belize--a last stronghold for manatees in the Caribbean

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    O'Shea, T.J.; Salisbury, C.A.

    1991-01-01

    Belize is a small country but it offers a safe haven for the largest number of manatees in the Caribbean. The authors' survey in 1989 revealed that there has been no apparent decline since the last study in 1977. However, there is no evidence for population growth either and as the Belize economy develops threats from fisheries, human pressure and declining habitat quality will increase. Recommendations are made to ensure that Belize safeguards its manatee populations.

  16. Chicxulub Ejecta Blanket Deposits From Belize

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    Ocampo, A.

    1995-01-01

    The Chicxulub impact into a thick sequence of carbonates and sulfates released over a trillion tons of volatiles. The importance of the explosive release of such a large mass of volatiles has been greatly underestimated in studies of ejecta depositional processes. Proximal Chicxulub ejecta blanket deposits recent discovered on Albion Island in Belize provide a key to understanding the role of volatile-rich target material during large impact events.

  17. Holocene coral patch reef ecology and sedimentary architecture, Northern Belize, Central America

    Energy Technology Data Exchange (ETDEWEB)

    Mazzullo, S.J.; Anderson-Underwood, K.E.; Burke, C.D.; Bischoff, W.D. (Wichita State Univ., KS (United States))

    1992-12-01

    Coral patch reefs are major components of Holocene platform carbonate facies systems in tropical and subtropical areas. The biotic composition, growth and relationship to sea level history, and diagenetic attributes of a representative Holocene patch reef ([open quotes]Elmer Reef[close quotes]) in the Mexico Rocks complex in northern Belize are described and compared to those of Holocene patch reefs in southern Belize. Elmer Reef has accumulated in shallow (2.5 m) water over the last 420 yr, under static sea level conditions. Rate of vertical construction is 0.3-0.5 m/100 yr, comparable to that of patch reefs in southern Belize. A pronounced coral zonation exists across Elmer Reef, with Monastrea annularis dominating on its crest and Acropora cervicornis occurring on its windward and leeward flanks. The dominance of Montastrea on Elmer Reef is unlike that of patch reefs in southern Belize, in which this coral assumes only a subordinate role in reef growth relative to that of Acropora palmata. Elmer Reef locally is extensively biodegraded and marine, fibrous aragonite and some bladed high-magnesium calcite cements occur throughout the reef section, partially occluding corallites and interparticle pores in associated sands. Patch reefs in southern Belize have developed as catch-up and keep-up reefs in a transgressive setting. In contrast, the dominant mode of growth of Elmer Reef, and perhaps other patch reefs in Mexico Rocks, appears to be one of lateral rather than vertical accretion. This style of growth occurs in a static sea level setting where there is only limited accommodation space because of the shallowness of the water, and such reefs are referred to as [open quotes]expansion reefs[close quotes]. 39 refs., 8 figs., 2 tabs.

  18. Area Handbook Series: Guyana and Belize: Country Studies

    Science.gov (United States)

    1993-01-01

    coat and dark blue trousers. Women had sever- al uniforms, including a khaki blouse and slacks worn with a fa- tigue hat and a light khaki blouse and...Europeans Belize: 198 Guyana: xx, 37, 43 Exclusive Economic Zone, 147 executive blanch (ste also executive presi- dent; president): of Belize, 244

  19. Economics of an ecotourism operation in Belize

    Science.gov (United States)

    Kangas, Patrick; Shave, Mary; Shave, Paul

    1995-09-01

    The economic inputs and outputs for the Possum Point Biological Station in Belize during 1990 1992 are described to illustrate some aspects of an ecotourism operation. Eight hundred fifty-four people in 59 groups visited Possum Point during the study period to tour rain forests, estuaries, and coral reefs. The economic input to Possum Point from these groups increased from 74,552 in 1990 to 166,268 in 1992. Outputs were for license fees, capital improvements, goods and services, labor, fossil fuels, and development of a historic sugar mill site. An annual donation was also made to a scholarship fund for local Belizean students. The net cash balance of income and outputs changed from negative (-6678) in 1990 to positive (+4811) in 1992, suggesting development of the economic operation. Possum Point meets the economic criteria for ecotourism by feeding back some tourist monies for community and environmental support, particularly donations for the sugar mill site and the scholarship fund. Most of the outputs from Possum Point (about 80%) were retained in the local economy through employment and purchases, which have a positive influence on the local community. We conclude that ecotourism operations, such as Possum Point, offer important sustainable development opportunities for Belize.

  20. Belize: Reflections on Police Training and Professionalization

    Directory of Open Access Journals (Sweden)

    Carlos Barrachina

    2013-06-01

    Full Text Available This article looks to analyze the preparation process the Belizean police force goes through with the objective of training the officers for duty. It also has the purpose of detailing the entrails the officers have to confront in their way up the corporate ladder as they develop into a professional police officer. Seen from a regional objectivity, Belize has been singled out to be in the center of numerous regional and hemispherical security problems; it is facing several of the same security challenges as its neighbors and explains the use of armed forces at the service of the public safety and the necessity to upgrade their law enforcement tactics and practices. The country also participates in many several mutual support instruments designed to assist and receive preparation and instruction from other nation’s police bodies. An example of that international aid came in a report from 2008 entitled "Review of the Belize Department" written by a Jamaican consultant in which the Police Plan elaborated in 2006 was analyzed and critiqued pointed out the strong and weak points of that project.

  1. Body condition of Morelet’s Crocodiles (Crocodylus moreletii) from northern Belize

    Science.gov (United States)

    Mazzotti, Frank J.; Cherkiss, Michael S.; Brandt, Laura A.; Fujisaki, Ikuko; Hart, Kristen; Jeffery, Brian; McMurry, Scott T.; Platt, Steven G.; Rainwater, Thomas R.; Vinci, Joy

    2012-01-01

    Body condition factors have been used as an indicator of health and well-being of crocodilians. We evaluated body condition of Morelet's Crocodiles (Crocodylus moreletii) in northern Belize in relation to biotic (size, sex, and habitat) and abiotic (location, water level, and air temperature) factors. We also tested the hypothesis that high water levels and warm temperatures combine or interact to result in a decrease in body condition. Size class, temperature, and water level explained 20% of the variability in condition of Morelet's Crocodiles in this study. We found that adult crocodiles had higher condition scores than juveniles/subadults but that sex, habitat, and site had no effect. We confirmed our hypothesis that warm temperatures and high water levels interact to decrease body condition. We related body condition of Morelet's Crocodiles to natural fluctuations in air temperatures and water levels in northern Belize, providing baseline conditions for population and ecosystem monitoring.

  2. Investigating the Maya Polity at Lower Barton Creek Cayo, Belize

    Science.gov (United States)

    Kollias, George Van, III

    The objectives of this research are to determine the importance of Lower Barton Creek in both time and space, with relation to other settlements along the Belize River Valley. Material evidence recovered from field excavations and spatial information developed from Lidar data were employed in determining the socio-political nature and importance of this settlement, so as to orient its existence within the context of ancient socio-political dynamics in the Belize River Valley. Before the investigations detailed in this thesis no archaeological research had been conducted in the area, the site of Lower Barton Creek itself was only recently identified via the 2013 West-Central Belize LiDAR Survey (WCBLS 2013). Previously, the southern extent of the Barton Creek area represented a major break in our knowledge not only of the Barton Creek area, but the southern extent of the Belize River Valley. Conducting research at Lower Barton Creek has led to the determination of the polity's temporal existence and allowed for a greater and more complex understanding of the Belize River Valley's interaction with regions abutting the Belize River Valley proper.

  3. Deforestation Along the Maya Mountain Massif Belize-Guatemala Border

    Science.gov (United States)

    Chicas, S. D.; Omine, K.; Arevalo, B.; Ford, J. B.; Sugimura, K.

    2016-06-01

    In recent years trans-boundary incursions from Petén, Guatemala into Belize's Maya Mountain Massif (MMM) have increased. The incursions are rapidly degrading cultural and natural resources in Belize's protected areas. Given the local, regional and global importance of the MMM and the scarcity of deforestation data, our research team conducted a time series analysis 81 km by 12 km along the Belize-Guatemalan border adjacent to the protected areas of the MMM. Analysis drew on Landsat imagery from 1991 to 2014 to determine historic deforestation rates. The results indicate that the highest deforestation rates in the study area were -1.04% and -6.78% loss of forested area per year in 2012-2014 and 1995-1999 respectively. From 1991 to 2014, forested area decreased from 96.9 % to 85.72 % in Belize and 83.15 % to 31.52 % in Guatemala. During the study period, it was clear that deforestation rates fluctuated in Belize's MMM from one time-period to the next. This seems linked to either a decline in deforestation rates in Guatemala, the vertical expansion of deforestation in Guatemalan forested areas and monitoring. The results of this study urge action to reduce incursions and secure protected areas and remaining forest along the Belize-Guatemalan border.

  4. Women and development in Northern Belize.

    Science.gov (United States)

    Brockmann, C T

    1985-07-01

    Northern Belize, composed of Orange Walk and Corozal districts, is the sugar-producing region of Belize, a newly independent country on the Caribbean coast of Central America, and because of the extensive involvement in the modern sugar industry, existing status differentials in Orange Walk have increased. Town farmers have increased their sugarcane license sizes more than villagers and also are much more likely to meet or exceed their delivery quotas than villagers. There has been the differentiation of a new middle socioeconomic stratum in Orange Walk, with a much higher proportion of villagers remaining in the lower stratum than townspeople. With greater involvement in the market economy, there has been a decline in the social integration of groups in the district as well as less symbiosis between husband and wife and among related male age mates. Some people now consistently work for others; there was an egalitarian labor exchange before. With the decline in subsistence production, the extensive reciprocity in food among related women diminishes. Women have participated in the overall changes in Orange Walk, yet their position vis-a-vis men has become weaker. Women are most likely to hold licenses in the communities that participated earliest in the sugar industry and that are the most traditional. With greater market involvement, women become less likely to hold licenses. Women's licenses have not increased to the same degree as those of men. And, with the income from sugar and wage labor, the family income is more and more viewed as belonging to men, rather than being the result of a joint family enterprise. Women become dependent on what men give them, with less control and security. With declining subsistence production, women have a reduced basis of involvement in traditional reciprocal food exchanges with other households. They lose some independent sources of money income with the result of increasing undernutrition for young children. The economic

  5. Organochlorine contaminants in Morelet's crocodile (Crocodylus moreletii) eggs from Belize.

    Science.gov (United States)

    Wu, T H; Rainwater, T R; Platt, S G; McMurry, S T; Anderson, T A

    2000-03-01

    Non-viable eggs of Morelet's crocodile (Crocodylus moreletii) were collected from Gold Button (GBL) and New River lagoons (NRL) in northern Belize and screened for organochlorine (OC) compounds using gas chromatography (GC) with electron capture detection (ECD). All egg samples from both lagoons (n = 24) tested positive for one or more OCs. Primary contaminants were p,p-DDE and methoxychlor, detected in 100% and 29% of the eggs examined, respectively. Concentrations of individual OC contaminants ranged from 1 ppb (ng chemical/g egg) to > 0.5 ppm (microgram chemical/g egg). Total concentrations of OCs (sum of all OCs) for one egg collected from a nest at GBL reached as high as 0.7 ppm. Sediment samples from both lagoons also tested positive for OCs (lindane, aldrin, methoxychlor, heptachlor epoxide, p,p-DDT, among others). Nest media (soil and plant material) collected from crocodile nests at GBL were positive for p,p-DDT, methoxychlor, aldrin, endosulfan II, and endrin aldehyde. Based on the 24 egg samples analyzed to date, crocodiles from both lagoons are being exposed to OCs. Such exposure may present a health threat to populations of crocodiles in Central America.

  6. Comparison of experimental hut entrance and exit behavior between Anopheles darlingi from the Cayo District, Belize, and Zungarococha, Peru.

    Science.gov (United States)

    Sachs, Paige; Diaz Rodriguez, Gloria Alicia; Briceno, Ireneo; King, Russell; Achee, Nicole L; Grieco, John P

    2013-12-01

    Anopheles darlingi is a major vector for malaria in Central and South America. Behavioral, ecological, genetic, and morphologic variability has been observed across its wide distribution. Recent studies have documented that 2 distinct genotypes exist for An. darlingi: a northern lineage (Belize, Guatemala, Colombia, Venezuela, and Panama) and a southern lineage (Amazonia and southern Brazil). In order to determine if these genotypes exhibited different behavioral traits, entrance and exit movement patterns between 2 field populations of An. darlingi that represented each genotype were evaluated using experimental huts. The Belize population exhibited bimodal entrance, with peak entry occurring between 7:00-8:00 p.m. and 5:00-6:00 a.m. and peak exiting occurring between 7:00-8:00 p.m. The Peru population exhibited unimodal entrance, with peak entry occurring between 10:00-11:00 p.m. and peak exiting occurring between 11:00-12:00 a.m. with a secondary smaller peak at 2:30 a.m. Entrance and exit behavioral patterns were significantly different between the Belize and Peru populations of An. darlingi (log-rank [Mantel-Cox] P < 0.001). Information from the present study will be used in the future to determine if there is a correlation between genotype and host-seeking behavior and can be used in the present for regional vector risk assessment.

  7. Thinking positively: The genetics of high intelligence.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Trzaskowski, Maciej; McMillan, Andrew; Krapohl, Eva; Simpson, Michael A; Reichenberg, Avi; Cederlöf, Martin; Larsson, Henrik; Lichtenstein, Paul; Plomin, Robert

    2015-01-01

    High intelligence (general cognitive ability) is fundamental to the human capital that drives societies in the information age. Understanding the origins of this intellectual capital is important for government policy, for neuroscience, and for genetics. For genetics, a key question is whether the genetic causes of high intelligence are qualitatively or quantitatively different from the normal distribution of intelligence. We report results from a sibling and twin study of high intelligence and its links with the normal distribution. We identified 360,000 sibling pairs and 9000 twin pairs from 3 million 18-year-old males with cognitive assessments administered as part of conscription to military service in Sweden between 1968 and 2010. We found that high intelligence is familial, heritable, and caused by the same genetic and environmental factors responsible for the normal distribution of intelligence. High intelligence is a good candidate for "positive genetics" - going beyond the negative effects of DNA sequence variation on disease and disorders to consider the positive end of the distribution of genetic effects.

  8. DEFORESTATION ALONG THE MAYA MOUNTAIN MASSIF BELIZE-GUATEMALA BORDER

    Directory of Open Access Journals (Sweden)

    S. D. Chicas

    2016-06-01

    Full Text Available In recent years trans-boundary incursions from Petén, Guatemala into Belize’s Maya Mountain Massif (MMM have increased. The incursions are rapidly degrading cultural and natural resources in Belize’s protected areas. Given the local, regional and global importance of the MMM and the scarcity of deforestation data, our research team conducted a time series analysis 81 km by 12 km along the Belize-Guatemalan border adjacent to the protected areas of the MMM. Analysis drew on Landsat imagery from 1991 to 2014 to determine historic deforestation rates. The results indicate that the highest deforestation rates in the study area were −1.04% and −6.78% loss of forested area per year in 2012-2014 and 1995-1999 respectively. From 1991 to 2014, forested area decreased from 96.9 % to 85.72 % in Belize and 83.15 % to 31.52 % in Guatemala. During the study period, it was clear that deforestation rates fluctuated in Belize's MMM from one time-period to the next. This seems linked to either a decline in deforestation rates in Guatemala, the vertical expansion of deforestation in Guatemalan forested areas and monitoring. The results of this study urge action to reduce incursions and secure protected areas and remaining forest along the Belize-Guatemalan border.

  9. Predicting Citizen Satisfaction with Government Services in Belize

    Science.gov (United States)

    2015-03-26

    thousand per citizen (CIA: The World Factbook, 2014). The largest sector of Belize’s economy is tourism , which accounts for 33.2% of the GDP and 30.1...of the employed workforce (World Travel & Tourism Council, 2012). The rest of Belize’s economy consists of agricultural exports such as bananas...of Belize is English, which negated the requirement for language translation and back- translation of the survey instrument; however, due to a

  10. A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca, Pumas (Puma concolor, and Ocelots (Leopardus pardalis in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone.

    Directory of Open Access Journals (Sweden)

    Claudia Wultsch

    Full Text Available With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca, pumas (Puma concolor, and ocelots (Leopardus pardalis. We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09, followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16, and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08. We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.

  11. A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone.

    Science.gov (United States)

    Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

    2016-01-01

    With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.

  12. Jaguar conservation in southern Belize: Conflicts, perceptions, and prospects among mayan hunters

    Directory of Open Access Journals (Sweden)

    Michael K Steinberg

    2016-01-01

    Full Text Available Belize has emerged as an international leader in jaguar conservation through the creation of numerous protected areas that contain prime cat habitat and by strengthening conservation laws. For example, in 1984, Belize created the Cockscomb Basin Jaguar Preserve, the first special jaguar protection area in the Americas. In 1995, the government expanded Cockscomb by creating the adjacent Chiquibul National Park. In 2010, the government continued this commitment to jaguar conservation by creating the Labouring Creek Jaguar Corridor Wildlife Sanctuary in central Belize. As a result of these protected areas, Belize has been rightfully lauded as a leader in nature-based tourism and protected areas creation in Central America. However, outside national parks and communities that directly benefit from ecotourism, it is less clear how supportive rural residents are of cat conservation. It is also not clear if jaguars persist outside protected areas in locations such as southern Belize, where the environment has been significantly altered by human activities. Through interviews with Mayan hunters, this paper investigates the attitudes towards jaguars, human-jaguar conflicts, and potential community-based jaguar conservation in two Mayan villages in the Toledo District in southern Belize. Also, using indirect methods, the paper documents the presence/absence and other temporal/spatial aspects of jaguars in a heavily altered landscape in southern Belize.

  13. Paleoecology of mangroves along the Sibun River, Belize

    Science.gov (United States)

    Monacci, Natalie M.; Meier-Grünhagen, Ursula; Finney, Bruce P.; Behling, Hermann; Wooller, Matthew J.

    2011-09-01

    This study examines a sediment core (SR-63) from a mangrove ecosystem along the Sibun River in Belize, which is subject to both changes in sea-level and in the characteristics of the river's drainage basin. Radiocarbon dates from the core show a decreased sedimentation rate from ~ 6 ka to 1 cal ka BP and a marked change in lithology from primarily mangrove peat to fluvial-derived material at ~ 2.5 cal ka BP. Changes in the sedimentation rates observed in mangrove ecosystems offshore have previously been attributed to changes in relative sea-level and the rate of sea-level rise. Pollen analyses show a decreased abundance of Rhizophora (red mangrove) pollen and an increased abundance of Avicennia (black mangrove) pollen and non-mangrove pollen coeval with the decreased sedimentation rates. Elemental ratios ([N:C] a) and stable isotope analyses (δ 15N and δ 13C) show that changes in the composition of the organic material are also coeval with the change in lithology. The decrease in sedimentation rate at the site of core SR-63 and at offshore sites supports the idea that regional changes in hydrology occurred during the Holocene in Belize, influencing both mainland and offshore mangrove ecosystems.

  14. Metals and organochlorine pesticides in caudal scutes of crocodiles from Belize and Costa Rica.

    Science.gov (United States)

    Rainwater, Thomas R; Wu, Ted H; Finger, Adam G; Cañas, Jaclyn E; Yu, Lu; Reynolds, Kevin D; Coimbatore, Gopal; Barr, Brady; Platt, Steven G; Cobb, George P; Anderson, Todd A; McMurry, Scott T

    2007-02-01

    Despite high animal diversity in the Neotropics and the largely unregulated use and disposal of pesticides and industrial chemicals in Central America, few data exist regarding accumulation of environmental contaminants in Central American wildlife. In this study we examined accumulation of metals and organochlorine (OC) pesticides in caudal scutes of crocodiles from Belize and Costa Rica. Scutes from Morelet's crocodiles (Crocodylus moreletii) from two sites in northern Belize were analyzed for metals, and scutes from American crocodiles (C. acutus) from one site in Costa Rica were analyzed for metals and OC pesticides. All scutes (n=25; one scute from each of 25 individuals) contained multiple contaminants. Mercury was the predominant metal detected, occurring in all scutes examined from both species. Other metals detected include cadmium, copper, lead, and zinc. American crocodile scutes from Costa Rica contained multiple OC pesticides, including endrin, methoxychlor, p,p'-DDE, and p,p'-DDT, all of which occurred in 100% of scutes analyzed (n=6). Mean metal and OC concentrations varied in relation to those previously reported in crocodilian scutes from other localities in North, Central, and South America. OC concentrations in American crocodile scutes were generally higher than those previously reported for other Costa Rican wildlife. Currently, caudal scutes may serve as general, non-lethal indicators of contaminant accumulation in crocodilians and their areas of occurrence. However, a better understanding of the relationships between pollutant concentrations in scutes, internal tissues, and environmental matrices at sample collection sites are needed to improve the utility of scutes in future ecotoxicological investigations.

  15. Metals and organochlorine pesticides in caudal scutes of crocodiles from Belize and Costa Rica

    Energy Technology Data Exchange (ETDEWEB)

    Rainwater, Thomas R. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States)]. E-mail: thomas.rainwater@tiehh.ttu.edu; Wu, Ted H. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Finger, Adam G. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Canas, Jaclyn E. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Yu Lu [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Reynolds, Kevin D. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Coimbatore, Gopal [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Barr, Brady [National Geographic Channel, 1145 17th St. NW Washington, DC 20036 (United States); Platt, Steven G. [Department of Biology, Box C-64, Sul Ross State University, Alpine, TX 79832 (United States); Cobb, George P. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); Anderson, Todd A. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States); McMurry, Scott T. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States)

    2007-02-01

    Despite high animal diversity in the Neotropics and the largely unregulated use and disposal of pesticides and industrial chemicals in Central America, few data exist regarding accumulation of environmental contaminants in Central American wildlife. In this study we examined accumulation of metals and organochlorine (OC) pesticides in caudal scutes of crocodiles from Belize and Costa Rica. Scutes from Morelet's crocodiles (Crocodylus moreletii) from two sites in northern Belize were analyzed for metals, and scutes from American crocodiles (C. acutus) from one site in Costa Rica were analyzed for metals and OC pesticides. All scutes (n = 25; one scute from each of 25 individuals) contained multiple contaminants. Mercury was the predominant metal detected, occurring in all scutes examined from both species. Other metals detected include cadmium, copper, lead, and zinc. American crocodile scutes from Costa Rica contained multiple OC pesticides, including endrin, methoxychlor, p,p'-DDE, and p,p'-DDT, all of which occurred in 100% of scutes analyzed (n = 6). Mean metal and OC concentrations varied in relation to those previously reported in crocodilian scutes from other localities in North, Central, and South America. OC concentrations in American crocodile scutes were generally higher than those previously reported for other Costa Rican wildlife. Currently, caudal scutes may serve as general, non-lethal indicators of contaminant accumulation in crocodilians and their areas of occurrence. However, a better understanding of the relationships between pollutant concentrations in scutes, internal tissues, and environmental matrices at sample collection sites are needed to improve the utility of scutes in future ecotoxicological investigations.

  16. Evolution in the Caribbean Classroom: A critical analysis of the role of biology teachers and science standards in shaping evolution instruction in Belize

    Science.gov (United States)

    Nunez, Elvis Enrique; Pringle, Rose M.; Showalter, Kevin Tyler

    2012-10-01

    A survey of the literature on evolution instruction provides evidence that teachers' personal views and understandings can shape instructional approaches and content delivered in science classrooms regardless of established science standards. This study is the first to quantify evolutionary worldviews of in-service teachers in the Caribbean, specifically in Belize, an English-speaking nation with a high school system guided by a regional biology syllabus and strict standardized tests. Using the Measure of Acceptance of the Theory of Evolution (MATE) instrument and knowledge test, we investigated (1) the current level of acceptance and understanding of evolution as given by 97% of high school biology teachers in Belize; (2) the factors associated with acceptance and understanding of evolutionary theory. With an average MATE score of 64.4 and a mean knowledge score of 47.9%, Belizean teachers were classified as having both 'Low Acceptance' and 'Low Understanding' of evolutionary theory. A positive correlation was found between teacher acceptance and understanding of evolution. A review of the Caribbean Secondary Examination Certificate biology syllabus suggests that evolution plays a minimal role in the high school biology classroom. We believe that Belize presents a unique opening for future training on evolution instruction since 57% of the biology teachers self-proclaim to be unprepared to teach evolution. The results of this study have implications for policy, practice and research with teachers' acceptance, understanding and confidence in teaching evolution serving as important predictors for instructional approaches used in the biology classroom.

  17. Geochemistry of crude oils, seepage oils and source rocks from Belize and Guatemala

    DEFF Research Database (Denmark)

    Petersen, H.I.; Holland, B.; Nytoft, H.P.;

    2012-01-01

    Mountains fault block in central Belize which separates the Corozal Basin in northern Belize from the Belize Basin to the south. Numerous petroleum seeps have been reported in both of these basins. Small-scale oil production takes place in the Corozal Basin and the North and South Petén Basins....... For this study, samples of crude oil, seepage oil and potential source rocks were collected from both countries and were investigated by organic geochemical analyses and microscopy. The oil samples consisted of non-biodegraded crude oils and slightly to severely biodegraded seepage oils, both of which were...... generated from source rocks with similar thermal maturities. The crude oils were generated from marine carbonate source rocks and could be divided into three groups: Group 1 oils come from the North Petén Basin (Guatemala) and the western part of the Corozal Basin (Belize), and have a typical carbonate...

  18. Assessment of undiscovered, conventional oil and gas resources of Mexico, Guatemala, and Belize, 2012

    Science.gov (United States)

    Schenk, Christopher J.; Brownfield, Michael E.; Charpentier, Ronald R.; Cook, Troy A.; Klett, Timothy R.; Pitman, Janet K.; Pollastro, Richard M.; Weaver, Jean N.

    2012-01-01

    Using a geology-based assessment methodology, the U.S. Geological Survey estimated means of 19 billion barrels of oil and 83 trillion cubic feet of undiscovered natural gas resources in 10 geologic provinces of Mexico, Guatemala, and Belize.

  19. Accretionary Lapilli (Carbonate Spherules) at the Cretaceous-Paleogene ('KT') Boundary in Belize (Central America)

    Science.gov (United States)

    King, D. T.; Petruny, L. W.

    2013-08-01

    The Chicxulub impact event produced accretionary lapilli (or carbonate spherules) that fell across a wide area. This paper compares Chicxulub ('KT') accretionary lapilli from two sites in Belize: Albion Island and Armenia.

  20. Modern tree species composition reflects ancient Maya "forest gardens" in northwest Belize.

    Science.gov (United States)

    Ross, Nanci J

    2011-01-01

    Ecology and ethnobotany were integrated to assess the impact of ancient Maya tree-dominated home gardens (i.e., "forest gardens"), which contained a diversity of tree species used for daily household needs, on the modern tree species composition of a Mesoamerican forest. Researchers have argued that the ubiquity of these ancient gardens throughout Mesoamerica led to the dominance of species useful to Maya in the contemporary forest, but this pattern may be localized depending on ancient land use. The tested hypothesis was that species composition would be significantly different between areas of dense ancient residential structures (high density) and areas of little or no ancient settlement (low density). Sixty-three 400-m2 plots (31 high density and 32 low density) were censused around the El Pilar Archaeological Reserve in northwestern Belize. Species composition was significantly different, with higher abundances of commonly utilized "forest garden" species still persisting in high-density forest areas despite centuries of abandonment. Subsequent edaphic analyses only explained 5% of the species composition differences. This research provides data on the long-term impacts of Maya forests gardens for use in development of future conservation models. For Mesoamerican conservation programs to work, we must understand the complex ecological and social interactions within an ecosystem that developed in intimate association with humans.

  1. Coral zonation and diagenesis of an emergent Pleistocene patch reef, Belize, Central America

    Energy Technology Data Exchange (ETDEWEB)

    Lighty, R.G.; Russell, K.L.

    1985-01-01

    Transect mapping and petrologic studies reveal a new depositional model and limited diagenesis of a well-exposed Pleistocene reef outcrop at Ambergris Cay, northern Belize. This emergent shelf-edge reef forms a rocky wave-washed headland at the northern terminus of the present-day 250 km long flourishing Belize Barrier Reef. Previously, the Belize reef outcrop was thought to extend southward in the subsurface beneath the modern barrier reef as a Pleistocene equivalent. The authors study indicate that this outcrop is a large, coral patch reef and not part of a barrier reef trend. Sixteen transects 12.5 m apart described in continuous cm increments from fore reef to back reef identified: extensive deposits of broken Acropora cervicornis; small thickets of A. palmata with small, oriented branches; and muddy skeletal sediments with few corals or reef rubble. Thin section and SEM studies show three phases of early submarine cementation: syntaxial and rosette aragonite; Mg-calcite rim cement and peloids; and colloidal Mg-calcite geopetal fill. Subaerial exposure in semi-arid northern Belize caused only minor skeletal dissolution, some precipitation of vadose whisker calcite, and no meteoric phreatic diagenesis. Facies geometry, coral assemblages, lack of rubble deposits, coralline algal encrustations and Millepora framework, and recognition of common but discrete submarine cements, all indicate that this Pleistocene reef was an isolated, coral-fringed sediment buildup similar to may large patch reefs existing today in moderate-energy shelf environments behind the modern barrier reef in central and southern Belize.

  2. 76 FR 63985 - Notice of Receipt of Cultural Property Request From the Government of the Republic of Belize

    Science.gov (United States)

    2011-10-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF STATE Notice of Receipt of Cultural Property Request From the Government of the Republic of Belize Belize, concerned that its cultural heritage is in jeopardy from pillage, made a request to the Government of the United States under Article 9 of the 1970...

  3. Genetic engineering for high methionine grain legumes.

    Science.gov (United States)

    Müntz, K; Christov, V; Saalbach, G; Saalbach, I; Waddell, D; Pickardt, T; Schieder, O; Wüstenhagen, T

    1998-08-01

    Methionine (Met) is the primary limiting essential amino acid in grain legumes. The imbalance in amino acid composition restricts their biological value (BV) to 55 to 75% of that of animal protein. So far improvement of the BV could not be achieved by conventional breeding. Therefore, genetic engineering was employed by several laboratories to resolve the problem. Three strategies have been followed. A) Engineering for increased free Met levels; B) engineering of endogenous storage proteins with increased numbers of Met residues; C) transfer of foreign genes encoding Met-rich proteins, e.g. the Brazil nut 2S albumin (BNA) and its homologue from sunflower, into grain legumes. The latter strategy turned out to be most promising. In all cases the gene was put under the control of a developmentally regulated seed specific promoter and transferred into grain legumes using the bacterial Agrobacterium tumefaciens-system. Integration into and copy numbers in the plant genome as well as Mendelian inheritance and gene dosage effects were verified. After correct precursor processing the mature 2S albumin was intracellularly deposited in protein bodies which are part of the vacuolar compartment. The foreign protein amounted to 5 to 10% of the total seed protein in the best transgenic lines of narbon bean (Vicia narbonensis L., used in the authors' laboratories), lupins (Lupinus angustifolius L., used in CSIRO, Australia), and soybean (Glycine max (L.) Merr., used by Pioneer Hi-Bred, Inc., USA). In the narbon bean the increase of Met was directly related to the amount of 2S albumin in the transgenic seeds, but in soybean it remained below the theoretically expected value. Nevertheless, trangenic soybean reached 100%, whereas narbon bean and lupins reached approximately 80% of the FAO-standard for nutritionally balanced food proteins. These results document that the Met problem of grain legumes can be resolved by genetic engineering.

  4. Winter habitat occurrence patterns of temperate migrant birds in Belize

    Science.gov (United States)

    Dawson, D.K.; Robbins, C.S.; Sauer, J.R.

    1992-01-01

    We used mist nets and point counts to sample bird populations in 61 sites in Belize during January-March of 1987-1991. Sites were classified as forest, second growth, woody agricultural crops (citrus, mango, cacao, and cashew), or non-woody agricultural crops (rice and sugar cane). We evaluated patterns of occurence of wintering temperate migrant bird species in these habitats. Mist net captures of 22 of 31 migrant species differed significantly among habitats. Of these, 13 species were captured more frequently in the agricultural habitats. American Redstart (Setophaga ruticilla), Black-and-white Warbler (Mniotilta varia), and Magnolia Warbler (Dendroica magnolia) were among the species captured most frequently in woody agricultural habitats; captures of Common Yellowthroat (Geothlypis trichas), Indigo Bunting (Passerina cyanea), and Northern (lcterus galbula) and Orchard orioles (I. spur/anus) were highest in the non-woody agricultural sites. We relate these occurrence patterns to trends in breeding populations in North America. While count data provide a wide picture of winter habitat distribution of migrants, more intensive work is necessary to assess temporal and geographic variation of migrant bird use of agricultural habitats.

  5. Mercury in Morelet's crocodile eggs from northern Belize.

    Science.gov (United States)

    Rainwater, T R; Adair, B M; Platt, S G; Anderson, T A; Cobb, G P; McMurry, S T

    2002-04-01

    Recent studies have examined mercury accumulation in crocodilians. However, though most researchers have focused on tissue concentrations, few have examined mercury levels in crocodilian eggs. In July 1995, we analyzed mercury in 31 nonviable Morelet's crocodile ( Crocodylus moreletii) eggs collected from eight nests across three localities in northern Belize. All eggs were found to contain mercury. Based on an individual egg basis, mean concentration of mercury for all three localities was among the lowest reported for any crocodilian species. When localities were examined separately, mean concentrations for Laguna Seca and Gold Button Lagoon were comparable to those observed in other studies, and the mean for Sapote Lagoon was the lowest ever reported. Based on mean nest concentrations, mercury in eggs from Laguna Seca was approximately two- and tenfold higher than for Gold Button Lagoon and Sapote Lagoon, respectively. Variability in mercury concentrations among localities is likely the result of site-specific differences in mercury input, bioavailabilty, and bioaccumulation. Mercury concentrations were relatively uniform in eggs from the same nest and among nests from the same localities. The presence of mercury in Morelet's crocodile eggs suggests exposure in adult females, developing embryos, and neonates. However, crocodiles in these areas show no overt signs of mercury toxicity, and no indication of population decline is evident. A paucity of data on the effects of mercury on crocodilians precludes meaningful speculation as to the biological significance of tissue and egg concentrations. Controlled laboratory studies and long-term population monitoring are needed to address these questions.

  6. Supporting School Counseling in Belize: Establishing a Middle School Career Development Program

    Directory of Open Access Journals (Sweden)

    Theresa COOGAN

    2016-03-01

    Full Text Available Within the education field, international partnerships to address career development have been successful around the world (Brown, Bim Rose, & Hughes, 2005; Nazali, 2007; Prideaux, Patton, & Creed, 2002; Repetto, 2001. Career development programming impacts the educational development for children and adolescents (Gottfredson, 1981; Gottfredson & Lapan, 1997; NCDA, 2011. School Counselors are often an untapped resource in the schools to design, implement and evaluate school-wide programs centered on career development. This article explores the benefits of career development and the creation of a career development school-wide program for the 6th grade level in Belize. This is accomplished through an international partnership between the Ministry of Education in Belize and a University in the Northeastern United States. This article explains the school counselors role as well as best practices for international partnerships when creating a full-year, school-wide career program at the middle school level in Belize.

  7. Pathoecology and paleodiet in Postclassic: Historic Maya from northern coastal Belize

    Directory of Open Access Journals (Sweden)

    Christine White

    2006-12-01

    Full Text Available This paper examines the synergism among diet, disease, and ecology at two related coastal Maya sites in Belize (Marco Gonzalez and San Pedro for the Postclassic and Historic periods (1350-1650 AD, which immediately follow the Classic period collapse. Stable carbon- and nitrogen-isotope ratios in collagen and stable carbon-isotope ratios in structural carbonate were analysed for bones from 65 humans and a wide variety of faunal species. There are no apparent differences in whole diets or degree of carnivory between individuals with lesions indicative of anemia and those without, but those with lesions appear to have consumed significantly more C4 foods and protein from lower trophic levels. Non-specific infection (periostitis and vitamin C deficiency (scurvy are also present in high frequencies and appear to co-occur with lesions indicative of anemia, particularly in childhood. Individuals with scurvy also appear to have consumed significantly more C4 foods than normal individuals. Spondyloarthropathy is common in adults. These findings are discussed in light of: (1 the debate on how anemia versus scurvy are manifest and diagnosed, (2 Spanish ethnohistoric descriptions of the poor state of Maya health at the time of contact, and (3 the Osteological Paradox. We suggest that although this coastal environment exacerbated morbidity because of possible parasitic infection, the inhabitants were probably able to survive physiological stresses better than either their inland contemporaries or their modern counterparts.

  8. Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay.

    Science.gov (United States)

    Rützler, Klaus; Piantoni, Carla; Van Soest, Rob W M; Díaz, M Cristina

    2014-05-29

    The Caribbean barrier reef near Carrie Bow Cay, Belize, has been a focus of Smithsonian Institution (Washington) reef and mangrove investigations since the early 1970s. Systematics and biology of sponges (Porifera) were addressed by several researchers but none of the studies dealt with cryptic habitats, such as the shaded undersides of coral rubble, reef crevices, and caves, although a high species diversity was recognized and samples were taken for future reference and study. This paper is the result of processing samples taken between 1972 and 2012. In all, 122 species were identified, 14 of them new (including one new genus). The new species are Tetralophophora (new genus) mesoamericana, Geodia cribrata, Placospongia caribica, Prosuberites carriebowensis, Timea diplasterina, Timea oxyasterina, Rhaphidhistia belizensis, Wigginsia curlewensis, Phorbas aurantiacus, Myrmekioderma laminatum, Niphates arenata, Siphonodictyon occultum, Xestospongia purpurea, and Aplysina sciophila. We determined that about 75 of the 122 cryptic sponge species studied (61%) are exclusive members of the sciophilic community, 47 (39 %) occur in both, light-exposed and shaded or dark habitats. Since we estimate the previously known sponge population of Carrie Bow reefs and mangroves at about 200 species, the cryptic fauna makes up 38 % of total diversity.

  9. Taphonomy of coral reefs from Southern Lagoon of Belize

    Energy Technology Data Exchange (ETDEWEB)

    Westphall, M.J.; Ginsburg, R.N.

    1985-02-01

    The Southern Lagoon of the Belize barrier complex, an area of some 600 km/sup 2/, contains a tremendous number of lagoon reefs, which range in size from patches several meters across to rhomboidal-shaped structures several kilometers in their long dimension. These lagoon reefs are remarkable because they have Holocene sediment accumulations in excess of 13 m consisting almost entirely of coral debris and lime mud and sand, and rise up to 30 m above the surrounding lagoon floor with steeply sloping sides (50-80/sup 0/), yet are totally uncemented. The reef-building biota and their corresponding deposits were studied at a representative reef, the rhomboidal complex of Channel Cay. As with many of the reefs in this area, the steeply sloping flanks of Channel Cay are covered mainly by the branched staghorn coral Acropora cervicornis and ribbonlike and platy growth of Agaricia spp. The living corals are not cemented to the substrate, but are merely intergrown. Fragmented pieces of corals accumulate with an open framework below the living community; this open framework is subsequently infilled by lime muds and sands produced mainly from bioerosion. Results from probing and coring suggest that the bafflestone fabric of coral debris and sediment extends at least 13 m into the subsurface. Radiocarbon-age estimates indicate these impressive piles of coral rubble and sediment have accumulated in the past 9000 yr (giving a minimum accumulation rate of 1.4 m/1000 yr) and illustrate the potential for significant carbonate buildups without the need for early lithification.

  10. A Multi-Tier Social-Ecological System Analysis of Protected Areas Co-Management in Belize

    Directory of Open Access Journals (Sweden)

    Kenrick W. Williams

    2016-01-01

    Full Text Available Co-management of protected areas has been recognized as a viable option to sustainably manage ecosystems. This collaborative approach actively engages civil society in the protected areas governance processes. Attempts at co-management, however, have not been uniformly successful; whereas the governance of some initiatives succeed and become strong and sustainable, others become weak or fail over time. In this paper, we provide a nuanced application of Ostrom’s multi-tier SES framework to carry out a systematic analysis of representative cases of co-management in Belize. This novel approach allows us to avoid the common problem of overstating the explanatory power of individual variables, while enabling us to tease out the interrelationships among critical process and contextual variables that may influence co-management outcomes. Our findings show that strong co-management is associated with a multiplicity of variables, including information sharing, conflict resolution, investments, self-organization, and networking. Contextual conditions inclusive of strong leadership, social capital, and high levels of dependence on resources for daily livelihoods seem to have influenced these processes over time. The presence of cross-scale and cross-level networks also seems to be important in influencing co-management outcomes. Our study contributes to the further development of Ostrom’s multi-tier SES framework by proposing the addition of five new third-tier variables. We advance some key lessons in the analysis of co-management outcomes and offer some policy recommendations to improve protected areas co-management policy and practice in Belize.

  11. The Rotifer fauna of Guatemala and Belize: survey and biogeographical affinities.

    Science.gov (United States)

    García-Morales, Alma Estrella; Elías-Gutiérrez, Manuel

    2007-06-01

    Rotifer samples were obtained from 29 localities in northern Guatemala and central-southern Belize during March 2000 and June 2001. A total of 119 species were identified. Ten selected taxa are illustrated and commented: Euchlanis semicarinata, Lepadella apsicora, L. cryphaea, Lecane curvicornis f. lofuana, L. whitfordi, Monommata maculata, Scaridium bostjani, Trichocerca elongata f. braziliensis, and Z. hollaerti. The species Lepadella rhomboidula is a first record for the American Continent. The species are 71% cosmopolitan, 6 % tropicopolitan, and 4.2 % restricted to the subtropics. The Guatemala species number range was Petén-Itza lake (53 taxa), and Raxruja pool (three). La Democracia pool (49 taxa), and the Blue Hole sink-hole (six species) were the extremes in Belize. In total, 68 of the recorded taxa are new for Guatemala and 91 for Belize. Additionally, 47 species are registered by the first time in Central America. A comparison between these two countries and Mexico revealed that the south part of the latter conform a cluster with them, emphasizing the transitional character of this region between the Nearctics and the Neotropics. Furthermore, Guatemala and Belize have differences in species assemblages, as a response to the nature of their particular environments and topographical accidents.

  12. The impacts of tourism on coral reef conservation awareness and support in coastal communities in Belize

    Science.gov (United States)

    Diedrich, A.

    2007-12-01

    Marine recreational tourism is one of a number of threats to the Belize Barrier Reef but, conversely, represents both a motivation and source of resources for its conservation. The growth of tourism in Belize has resulted in the fact that many coastal communities are in varying stages of a socio-economic shift from dependence on fishing to dependence on tourism. In a nation becoming increasingly dependent on the health of its coral reef ecosystems for economic prosperity, a shift from extractive uses to their preservation is both necessary and logical. Through examining local perception data in five coastal communities in Belize, each attracting different levels of coral reef related tourism, this analysis is intended to explore the relationship between tourism development and local coral reef conservation awareness and support. The results of the analysis show a positive correlation between tourism development and coral reef conservation awareness and support in the study communities. The results also show a positive correlation between tourism development and local perceptions of quality of life, a trend that is most likely the source of the observed relationship between tourism and conservation. The study concludes that, because the observed relationship may be dependent on continued benefits from tourism as opposed to a perceived crisis in coral reef health, Belize must pay close attention to tourism impacts in the future. Failure to do this could result in a destructive feedback loop that would contribute to the degradation of the reef and, ultimately, Belize’s diminished competitiveness in the ecotourism market.

  13. Attitudes toward Spanish and Code-Switching in Belize: Stigmatization and Innovation in the Spanish Classroom

    Science.gov (United States)

    Balam, Osmer; de Prada Pérez, Ana

    2017-01-01

    Through the analysis of survey and interview data, we investigated the attitudes and perceptions of 32 multilingual teachers of Spanish in Belize, a code-switching (CS) context where Spanish is in intense contact with English and Belizean Kriol. More specifically, we examined teachers' and students' attitudes toward Spanish and CS and teachers'…

  14. Student Identities and the Tourist Gaze in International Service-Learning: A University Project in Belize

    Science.gov (United States)

    Prins, Esther; Webster, Nicole

    2010-01-01

    This qualitative study explores how 11 university students in a U.S. service-learning course in Belize understood and represented their identities during the project, particularly their use of "the tourist" as a construct to interpret their experiences. Drawing on literature in international service-learning (ISL) and tourism studies,…

  15. Cutaneous leishmaniasis in three Dutch military cohorts following jungle training in Belize

    NARCIS (Netherlands)

    P.P.A.M. van Thiel; J.E. Zeegelaar; T. van Gool; W.R. Faber; P.A. Kager

    2011-01-01

    Skin lesions occur frequently in travelers to tropical countries. Military personnel acquire skin lesions regularly during jungle training as did Dutch troops who trained in the jungle of Belize in 1998, 2004 and 2009, in an area endemic for cutaneous leishmaniasis. Demographic and clinical data wer

  16. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  17. Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

    DEFF Research Database (Denmark)

    Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong

    2011-01-01

    Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). The pathogen is highly adaptable and to get an overview of the genetic variation in the Nordic countries, Denmark, Finland, Norway and Sweden we have analyzed 200 isolates from...

  18. Child health outcomes among Central American refugees and immigrants in Belize.

    Science.gov (United States)

    Moss, N; Stone, M C; Smith, J B

    1992-01-01

    The purpose of this study was to investigate the effect of international migration, including refugee status, upon child health outcomes. Data were drawn from a survey conducted in 1989 in three settlements in Belize, Central America, that have a high proportion of refugees and economic immigrants living side-by-side with the local population. In two of the settlements, the entire population of mothers with children under 6 was interviewed; in the third settlement a two-thirds random sample was interviewed. Health history data were obtained for 255 children of 134 mothers, from whom sociodemographic data were also collected. The majority of children were born to Salvadoran or Guatemalan mothers, but native and naturalized Belizeans in the survey communities were included for comparison purposes. Migration, the exposure variable, was characterized by mother's residency/refugee legal status, nationality, and duration of time in country. Socioeconomic and proximate control variables were included as suggested by the Mosley-Chen framework. Despite normal birthweight averaging 3374 g, a large proportion of children are at the lowest percentiles of the weight-for-age curves (44% below the tenth percentile for the international reference population). A high incidence of diarrheal and respiratory illnesses (30% and 47% of children, respectively, having frequent episodes), and 50% of children with measles vaccination appropriate for age, indicate a population with high potential morbidity. Logistic regression was used to model the effects of migration on weight-for-age and frequency of diarrheal and respiratory tract episodes independent of socioeconomic and proximate factors, as suggested by the Mosley-Chen framework.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Holocene lagoonal development in the isolated carbonate platforms off Belize

    Science.gov (United States)

    Gischler, Eberhard

    2003-06-01

    Thirty-one vibracores were taken in interior lagoons of Glovers Reef, Lighthouse Reef, and Turneffe Islands—three isolated carbonate platforms offshore Belize, Central America. Holocene facies successions overlying the Pleistocene limestone bedrock begin with soils, followed by mangrove peats, and marine carbonate sediments of lagoonal origin. The soils formed on top of subaerially exposed Pleistocene limestone before the Holocene transgression. Mangrove peats developed during initial flooding of the platforms (Glovers ca. 8.5 ky, Lighthouse ca. 7 ky, Turneffe ca. 6 ky BP). As water depths increased, reefs colonized platform margins, lagoonal circulation improved thereby promoting carbonate production. The basal lagoonal carbonate sediments are characterized by shell beds and/or Halimeda packstones-grainstones. Mollusk-dominated wackestones and packstones follow upsection in Glovers and Lighthouse Reefs. At present, open circulation prevails in Glovers and Lighthouse lagoons. In contrast, organic-rich Halimeda wackestones and packstones dominate the Turneffe Islands Holocene succession. The main lagoon area of Turneffe is enclosed by mangroves, and restricted circulation prevails. Factors that explain the differences in geomorphology, circulation, and facies are variations in depth of antecedent topography and degree of exposure to waves and currents. The thickness of Holocene lagoon sediments may exceed the maximum core length of 6 m in all atolls. Holocene sedimentation rates average 0.6 m/ky, with highest rates in Turneffe (0.82 m/ky), followed by Lighthouse (0.53 m/ky), and Glovers (0.46 m/ky). Like in many other isolated carbonate platforms and atolls, lagoon floor sedimentation did not keep pace with rising sea level, leading to unfilled accommodation space. At present, Glovers has an 18 m deep lagoon, while Lighthouse and the main Turneffe lagoon are 8 m deep. It is unlikely that the lagoons will be completely filled during the Holocene sea level highstand

  20. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian;

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups....

  1. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  2. Energy Transition Initiative: Island Energy Snapshot - Belize; U.S. Department of Energy (DOE), NREL (National Renewable Energy Laboratory)

    Energy Technology Data Exchange (ETDEWEB)

    None

    2015-03-01

    This profile provides a snapshot of the energy landscape of Belize, a Central American country bordering Mexico to the north, Guatemala to the west and south, and the Caribbean Sea to the east. Although not an island nation, Belize is included in this energy snapshot series because it is a member of the Caribbean Community (CARICOM), an alliance of 15 Caribbean nations in the region.

  3. Porewater biogeochemistry and soil metabolism in dwarf red mangrove habitats (Twin Cays, Belize)

    Science.gov (United States)

    Lee, R.Y.; Porubsky, W.P.; Feller, Ilka C.; McKee, K.L.; Joye, S.B.

    2008-01-01

    Seasonal variability in biogeochemical signatures was used to elucidate the dominant pathways of soil microbial metabolism and elemental cycling in an oligotrophic mangrove system. Three interior dwarf mangrove habitats (Twin Cays, Belize) where surface soils were overlain by microbial mats were sampled during wet and dry periods of the year. Porewater equilibration meters and standard biogeochemical methods provided steady-state porewater profiles of pH, chloride, sulfate, sulfide, ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, nitrogen, and phosphorus, reduced iron and manganese, dissolved inorganic carbon, methane and nitrous oxide. During the wet season, the salinity of overlying pond water and shallow porewaters decreased. Increased rainwater infiltration through soils combined with higher tidal heights appeared to result in increased organic carbon inventories and more reducing soil porewaters. During the dry season, evaporation increased both surface water and porewater salinities, while lower tidal heights resulted in less reduced soil porewaters. Rainfall strongly influenced inventories of dissolved organic carbon and nitrogen, possibly due to more rapid decay of mangrove litter during the wet season. During both times of year, high concentrations of reduced metabolites accumulated at depth, indicating substantial rates of organic matter mineralization coupled primarily to sulfate reduction. Nitrous oxide and methane concentrations were supersaturated indicating considerable rates of nitrification and/or incomplete denitrification and methanogenesis, respectively. More reducing soil conditions during the wet season promoted the production of reduced manganese. Contemporaneous activity of sulfate reduction and methanogenesis was likely fueled by the presence of noncompetitive substrates. The findings indicate that these interior dwarf areas are unique sites of nutrient and energy regeneration and may be critical to the overall persistence

  4. Is Echinometra viridis facilitating a phase shift on an Acropora cervicornis patch reef in Belize?

    Science.gov (United States)

    Stefanic, C. M.; Greer, L.; Norvell, D.; Benson, W.; Curran, H.

    2012-12-01

    Coral reef health is in rapid decline across the Caribbean due to a number of anthropogenic and natural disturbances. A phase shift from coral- to macroalgae-dominant reefs is pervasive and has been well documented. Acropora cervicornis (Staghorn Coral) has been particularly affected by this shift due to mass mortality of this species since the 1980s. In recent years few Caribbean A. cervicornis refugia have been documented. This study characterizes the relationship between coral and grazing urchins on a rare patch reef system dominated by A. cervicornis off the coast of Belize. To assess relative abundance of live A. cervicornis and the urchin Echinometra viridis, photographs and urchin abundance data were collected from 132 meter square quadrats along five transects across the reef. Photographs were digitized and manually segmented using Adobe Illustrator, and percent live coral cover and branch tip densities were calculated using Matlab. Mean percent live coral cover across all transects was 24.4 % with a high of 65% live coral per meter square. Average urchin density was 18.5 per quadrat, with an average density per transect ranging from 22.1 to 0.5 per quadrat. Up to over 400 live A. cervicornis branch tips per quadrat were observed. Data show a positive correlation between E. viridis abundance and live A. cervicornis, suggesting that these urchins are facilitating recovery or persistence of this endangered coral species. These results suggest the relationship between E. viridis and A. cervicornis could be a key element in a future reversal of the coral to macroalgae phase shift on some Caribbean coral reefs.

  5. Temperature Regimes Impact Coral Assemblages along Environmental Gradients on Lagoonal Reefs in Belize

    Science.gov (United States)

    Townsend, Joseph E.; Courtney, Travis A.; Aichelman, Hannah E.; Davies, Sarah W.; Lima, Fernando P.; Castillo, Karl D.

    2016-01-01

    Coral reefs are increasingly threatened by global and local anthropogenic stressors such as rising seawater temperature, nutrient enrichment, sedimentation, and overfishing. Although many studies have investigated the impacts of local and global stressors on coral reefs, we still do not fully understand how these stressors influence coral community structure, particularly across environmental gradients on a reef system. Here, we investigate coral community composition across three different temperature and productivity regimes along a nearshore-offshore gradient on lagoonal reefs of the Belize Mesoamerican Barrier Reef System (MBRS). A novel metric was developed using ultra-high-resolution satellite-derived estimates of sea surface temperatures (SST) to classify reefs as exposed to low (lowTP), moderate (modTP), or high (highTP) temperature parameters over 10 years (2003 to 2012). Coral species richness, abundance, diversity, density, and percent cover were lower at highTP sites relative to lowTP and modTP sites, but these coral community traits did not differ significantly between lowTP and modTP sites. Analysis of coral life history strategies revealed that highTP sites were dominated by hardy stress-tolerant and fast-growing weedy coral species, while lowTP and modTP sites consisted of competitive, generalist, weedy, and stress-tolerant coral species. Satellite-derived estimates of Chlorophyll-a (chl-a) were obtained for 13-years (2003–2015) as a proxy for primary production. Chl-a concentrations were highest at highTP sites, medial at modTP sites, and lowest at lowTP sites. Notably, thermal parameters correlated better with coral community traits between site types than productivity, suggesting that temperature (specifically number of days above the thermal bleaching threshold) played a greater role in defining coral community structure than productivity on the MBRS. Dominance of weedy and stress-tolerant genera at highTP sites suggests that corals utilizing

  6. Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae):implications for its conservation

    Institute of Scientific and Technical Information of China (English)

    Yuan HUANG; Chang-Qin ZHANG; De-Zhu LI

    2009-01-01

    Omphalogramma souliei Franch. Is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. Souliei in NW Yunnan, China. The genetic diversity at the species level is low with P= 42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenog-amy predominated and autogamy played an assistant role in O. Souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.

  7. Survey, Settlement, and Population History at the Ancient Maya Site of Pacbitun, Belize

    DEFF Research Database (Denmark)

    Healy, Paul F.; Helmke, Christophe G.B.; Awe, Jaime J.

    2007-01-01

    Survey and excavations of mounds on the outskirts of the site of Pacbitun in western Belize provide insights to the ancient Maya settlement pattern at this medium-sized regional center. This research employed two methods: analysis of structural remains from four separate 1000 m transect surveys...... to have been about 5000-6000 persons. This population estimate is compared with several coeval lowland Maya centers, and found to be reasonable for a medium-sized, Late Classic Maya center....

  8. Forest to agriculture conversion in southern Belize: Implications for migrant land birds

    Science.gov (United States)

    Spruce, J.P.; Dowell, B.A.; Robbins, C.S.; Sader, S.A.; Doyle, Jamie K.; Schelhas, John

    1993-01-01

    Central America offers a suite of neotropical habitats vital to overwintering migrant land birds. The recent decline of many forest dwelling avian migrants is believed to be related in part to neotropical deforestation and land use change. However, spatio-temporal trends in neotropical habitat availability and avian migrant habitat use are largely unknown. Such information is needed to assess the impact of agriculture conversion on migrant land birds. In response, the USDI Fish and Wildlife Service and the University of Maine began a cooperative study in 1988 which applies remote sensing and field surveys to determine current habitat availability and avian migrant habitat use. Study sites include areas in Belize, Costa Rica, Guatemala and southern Mexico. Visual assessment of Landsat TM imagery indicates southern Belize forests are fragmented by various agricultural systems. Shifting agriculture is predominant in some areas, while permanent agriculture (citrus and mixed animal crops) is the primary system in others. This poster focuses on efforts to monitor forest to agriculture conversion in southern Belize using remote sensing, field surveys and GIS techniques. Procedures and avian migrant use of habitat are summarized.

  9. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  10. Linear extension rates and gross carbonate production of Acropora cervicornis at Coral Gardens, Belize.

    Science.gov (United States)

    Peeling, E.; Greer, L.; Lescinsky, H.; Humston, R.; Wirth, K. R.; Baums, I. B.; Curran, A.

    2014-12-01

    Branching Acropora coral species have fast growth and carbonate production rates, and thus have functioned as important reef-building species throughout the Pleistocene and Holocene. Recently, net carbonate production (kg CaCO3 m-2 year-1) has been recognized as an important measure of reef health, especially when monitoring endangered species, such as Acropora cervicornis. This study examines carbonate production in a thriving population of A. cervicornis at the Coral Gardens reef in Belize. Photographic surveys were conducted along five transects of A. cervicornis-dominated reefs from 2011-2014. Matching photographs from 2013 and 2014 were scaled to 1 m2 and compared to calculate 84 individual A. cervicornis linear extension rates across the reef. Linear extension rates averaged 12.4 cm/yr and were as high as 17 cm/yr in some areas of the reef. Carbonate production was calculated two ways. The first followed the standard procedure of multiplying percent live coral cover, by the linear extension rate and skeletal density. The second used the number of live coral tips per square meter in place of percent live coral multiplied by the average cross-sectional area of the branches. The standard method yielded a carbonate production rate of 113 kg CaCO3 m-2 year-1 for the reef, and the tip method yielded a rate of 6 kg m-2 year-1. We suggest that the tip method is a more accurate measure of production, because A. cervicornis grows primarily from the live tips, with only limited radial growth and resheeting over dead skeleton. While this method omits the contributions of radial growth and resheeting, and is therefore somewhat of an underestimate, our future work will quantify these aspects of growth in a more complete carbonate budget. Still, our estimate suggests a carbonate production rate per unit area of A. cervicornis that is on par with other Caribbean coral species, rather than two orders of magnitude higher as reported by Perry et al (2013). Although gross coral

  11. UNDERSTANDING THE HIGH MIND: HUMANS ARE STILL EVOLVING GENETICALLY

    Directory of Open Access Journals (Sweden)

    Blum K et al

    2011-01-01

    Full Text Available The total population of the United States at the turn of the 21 st century was 281,421,906. The total number of people above the age of 12 years old was estimated at 249 million. The National Institutes on Drug Abuse and the Substance Abuse and Mental Health Services Administration (SAMHSA have surveyed persons age 12 and older and found that in the year 2001, a total of 104 million people have used illegal drugs in their life (ever used, 32 million used a psychoactive drug in the past year (2000-2001 and 18 million used a psychoactive drug in the past 30 days. Interestingly this does not include Alcohol. We must ask then, who are the people that could just say NO? When almost half-of the US population have indulged in illegal drug practices, when our presidential candidates are forced to dodge the tricky question of their past history involving illegal drug use, and when almost every American has sloshed down a martini or two in their life time, there must be a reason, there must be a need, there must be a natural response for humans to imbibe at such high rates. There is even a more compelling question surrounding the millions who seek out high risk novelty. Why do millions have this innate drive in face of putting themselves in harms-way? Why are millions paying the price of their indiscretions in our jails, in hospitals, in wheel chairs and are lying dead in our cemeteries. What price must we pay for pleasure seeking or just plain getting “HIGH”? Maybe the answer lies within our brain. Maybe it is in our genome? Utilization of the candidate vs the common variant approach may be parsimonious as it relates to unraveling the addiction riddle. In this commentary we have discussed evidence, theories and conjecture about the “High Mind” and its relationship to evolutionary genetics and drug seeking behavior as impacted by genetic polymorphisms. We consider the meaning of recent findings in genetic research including an exploration of the

  12. High-throughput neuroimaging-genetics computational infrastructure.

    Science.gov (United States)

    Dinov, Ivo D; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D; Franco, Joseph; Toga, Arthur W

    2014-01-01

    Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize

  13. High-Throughput Neuroimaging-Genetics Computational Infrastructure

    Directory of Open Access Journals (Sweden)

    Ivo D Dinov

    2014-04-01

    Full Text Available Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate and disseminate novel scientific methods, computational resources and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval and aggregation. Computational processing involves the necessary software, hardware and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical and phenotypic data and meta-data. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI and the Laboratory of Neuro Imaging (LONI at University of Southern California (USC. INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer’s and Parkinson’s data, we provide several examples of translational applications using this infrastructure.

  14. COSMIC: somatic cancer genetics at high-resolution

    Science.gov (United States)

    Forbes, Simon A.; Beare, David; Boutselakis, Harry; Bamford, Sally; Bindal, Nidhi; Tate, John; Cole, Charlotte G.; Ward, Sari; Dawson, Elisabeth; Ponting, Laura; Stefancsik, Raymund; Harsha, Bhavana; Kok, Chai Yin; Jia, Mingming; Jubb, Harry; Sondka, Zbyslaw; Thompson, Sam; De, Tisham; Campbell, Peter J.

    2017-01-01

    COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website. PMID:27899578

  15. The genetic architecture of adaptations to high altitude in Ethiopia.

    Science.gov (United States)

    Alkorta-Aranburu, Gorka; Beall, Cynthia M; Witonsky, David B; Gebremedhin, Amha; Pritchard, Jonathan K; Di Rienzo, Anna

    2012-01-01

    Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

  16. a Review of Late Holocene Fluvial Systems in the Karst Maya Lowlands with Focus on the Rio Bravo, Belize

    Science.gov (United States)

    Beach, T.; Luzzadder-Beach, S.; Krause, S.; Doyle, C.

    2015-12-01

    The Maya Lowlands is mostly an internally draining karst region with about 400 m of regional relief. Fluvial and fluviokarst systems drain the edges of this landscape either from low limestone uplands or igneous and metamorphic complexes. Thus far most fluvial research has focused around archaeology projects, and here we review the extant research conducted across the region and new research on the transboundary Rio Bravo watershed of Belize and Guatemala. The Rio Bravo drains a largely old growth tropical forest today, but was partly deforested around ancient Maya cities and farms from 3,000 to 1000 BP. Several studies estimate that 30 to 40 percent of forest survived through the Maya period. Work here has focused on soils and sediment movement along slope catenas, in floodplain sites, and on contributions from groundwater with high dissolved loads of sulfate and calcium. We review radiocarbon dates and present new dates and soil stratigraphy from these sequences to date slope and floodplain movement, and we estimate ancient land use from carbon isotopic and pollen evidence. Aggradation in this watershed occurred by flooding, gypsum precipitation, upland erosion, and ancient Maya canal building and filling for wetland farming. Soil erosion and aggradation started at least by 3,000 BP and continued through the ancient Maya period, though reduced locally by soil conservation, post urban construction, and source reduction, especially in Maya Classic period from 1700 to 1000 BP.

  17. High Performance Data mining by Genetic Neural Network

    Directory of Open Access Journals (Sweden)

    Dadmehr Rahbari

    2013-10-01

    Full Text Available Data mining in computer science is the process of discovering interesting and useful patterns and relationships in large volumes of data. Most methods for mining problems is based on artificial intelligence algorithms. Neural network optimization based on three basic parameters topology, weights and the learning rate is a powerful method. We introduce optimal method for solving this problem. In this paper genetic algorithm with mutation and crossover operators change the network structure and optimized that. Dataset used for our work is stroke disease with twenty features that optimized number of that achieved by new hybrid algorithm. Result of this work is very well incomparison with other similar method. Low present of error show that our method is our new approach to efficient, high-performance data mining problems is introduced.

  18. Natural Hazard Mitigation Strategies in the Continental Caribbean: The Case of Belize

    Directory of Open Access Journals (Sweden)

    Kareem M. Usher

    2008-02-01

    Full Text Available La petite nation de Belize est nichée au cœur de l’Amérique Centrale, bordée au nord par le Mexique, à l'ouest et au sud par le Guatemala ; la mer Caraïbe constituant sa frontière orientale. Situé sur la trajectoire des cyclones tropicaux atlantiques, le pays est exposé aux catastrophes atmosphériques. Parmi les plus notables dans l’histoire de Bélize : l'ouragan de 1931 et l'ouragan Hattie qui ont fait 275 victimes et causé des dommages évalués à plus de 1 milliard de dollars. En réponse, le pays a mis en place diverses politiques responsables et inédites visant la réduction des risques afin de sauvegarder sa population et de protéger l’essor du tourisme. Malgré ces efforts, la majorité des populations côtières demeure vulnérable aux ouragans et aux inondationsThe small nation of Belize is nestled on the Central American Continent bounded on its north by Mexico, the west and south by Guatemala and the Caribbean Sea on its eastern border.  Located in the path of Atlantic Tropical Cyclones, the country is susceptible to atmospheric disasters.  Most notably are the Hurricane of 1931 and Hurricane Hattie which claimed 275 lives and caused damages in excess of US$1 Billion. Consequently, Belize has implemented several responsible and original mitigation policies to safeguard its population and protect the bourgeoning tourism industry. In spite of those efforts, most of its coastal populations remain vulnerable to hurricanes and floods.

  19. A multiproxy peat record of Holocene mangrove palaeoecology from Twin Cays, Belize

    OpenAIRE

    2007-01-01

    The extent and function of coastal mangrove ecosystems are likely to be influenced by future changes in sea level. Multiple proxies of past mangrove ecosystems preserved in a 780 cm long peat core (TCC2) taken from Twin Cays, Belize, record palaeoecological changes since ~8000 cal. yr BP. The proxies included pollen and the stable-isotope (C, N and O) compositions of mangrove leaf fragments. Rhizophora mangle (red mangrove) has been dominant at this site on Twin Cays for over ~8000 years. Var...

  20. Preliminary study of pesticide drift into the Maya Mountain protected areas of Belize.

    Science.gov (United States)

    Kaiser, Kristine

    2011-01-01

    In Belize, Central America, many farms surrounding the Protected Areas of the Maya Mountains rely heavily on the application of agrochemicals. The purpose of this study was to test whether orographic drift of glyphosate and organophosphates into the nearby Maya Mountain Protected Areas occurred by collecting phytotelmic water from seven sites over 3 years. Regardless of location within the Maya Mountain Protected Areas, glyphosate was present; organophosphates were more common at ridge sites. Although glyphosate concentrations were low, due to the number of threatened species and the human use of stream water outside the Maya Mountain Protected Areas, better understanding of these effects is warranted.

  1. A new species of the alpheid shrimp genus Triacanthoneus Anker, 2010 (Crustacea: Alpheidae) from Belize.

    Science.gov (United States)

    Alvarez, Fernando; Iliffe, Thomas M; Villalobos, José Luis

    2014-02-24

    A new species of the alpheid shrimp genus Triacanthoneus Anker, 2010, is described based on material collected in a marine cave off Caye Chapel, Belize. Triacanthoneus chapelianus sp. nov. is the fifth species in the genus and can be distinguished from the other four species by the position of the dorsolateral teeth on the carapace, which in the new species have an anterior (= submarginal) position, and by the configuration of the posterior margin of the telson, with a notch in the middle portion and two pairs of spines and one pair of plumose setae. A key to the five species of Triacanthoneus is provided.

  2. The genetic architecture of adaptations to high altitude in Ethiopia.

    Directory of Open Access Journals (Sweden)

    Gorka Alkorta-Aranburu

    Full Text Available Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

  3. Awareness of Societal Issues among High School Biology Teachers Teaching Genetics

    Science.gov (United States)

    Lazarowitz, Reuven; Bloch, Ilit

    2005-01-01

    The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when…

  4. High School Students' Use of Meiosis When Solving Genetics Problems.

    Science.gov (United States)

    Wynne, Cynthia F.; Stewart, Jim; Passmore, Cindy

    2001-01-01

    Paints a different picture of students' reasoning with meiosis as they solved complex, computer-generated genetics problems, some of which required them to revise their understanding of meiosis in response to anomalous data. Students were able to develop a rich understanding of meiosis and can utilize that knowledge to solve genetics problems.…

  5. Assessing the suitability of Holocene environments along the central Belize coast, Central America, for the reconstruction of hurricane records

    Science.gov (United States)

    Adomat, Friederike; Gischler, Eberhard

    2017-01-01

    Since the Belize coast was repeatedly affected by hurricanes and the paleohurricane record for this region is poor, sediment cores from coastal lagoon environments along the central Belize coast have been examined in order to identify storm deposits. The paleohurricane record presented in this study spans the past 8000 years and exhibits three periods with increased evidences of hurricane strikes occurring at 6000-4900, 4200-3600 and 2200-1500 cal yr BP. Two earlier events around 7100 and 7900 cal yr BP and more recent events around 180 cal yr BP and during modern times have been detected. Sand layers, redeposited corals and lagoon shell concentrations have been used as proxies for storm deposition. Additionally, hiatuses and reversed ages may indicate storm influence. While sand layers and corals represent overwash deposits, the lagoon shell concentrations, which mainly comprise the bivalve Anomalocardia cuneimeris and cerithid gastropods, have been deposited due to changes in lagoon salinity during and after storm landfalls. Comparison with other studies reveals similarities with one record from Belize, but hardly any matches with other published records. The potential for paleotempestology reconstructions of the barrier-lagoon complexes along the central Belize coast differs depending on geomorphology, and deposition of washovers in the lagoon basins is limited, probably due to the interplay of biological, geological and geomorphological processes.

  6. Assessing the suitability of Holocene environments along the central Belize coast, Central America, for the reconstruction of hurricane records

    Science.gov (United States)

    Adomat, Friederike; Gischler, Eberhard

    2016-03-01

    Since the Belize coast was repeatedly affected by hurricanes and the paleohurricane record for this region is poor, sediment cores from coastal lagoon environments along the central Belize coast have been examined in order to identify storm deposits. The paleohurricane record presented in this study spans the past 8000 years and exhibits three periods with increased evidences of hurricane strikes occurring at 6000-4900, 4200-3600 and 2200-1500 cal yr BP. Two earlier events around 7100 and 7900 cal yr BP and more recent events around 180 cal yr BP and during modern times have been detected. Sand layers, redeposited corals and lagoon shell concentrations have been used as proxies for storm deposition. Additionally, hiatuses and reversed ages may indicate storm influence. While sand layers and corals represent overwash deposits, the lagoon shell concentrations, which mainly comprise the bivalve Anomalocardia cuneimeris and cerithid gastropods, have been deposited due to changes in lagoon salinity during and after storm landfalls. Comparison with other studies reveals similarities with one record from Belize, but hardly any matches with other published records. The potential for paleotempestology reconstructions of the barrier-lagoon complexes along the central Belize coast differs depending on geomorphology, and deposition of washovers in the lagoon basins is limited, probably due to the interplay of biological, geological and geomorphological processes.

  7. Scholar-Practitioner Inquiry as International Action Research: Surveying Leadership Perceptions of Principals in the Toledo District of Belize

    Science.gov (United States)

    Hickey, Wesley D.; Gill, Peggy B.; Brown, Lakesha

    2011-01-01

    The scholar-practitioner approach to leadership has the potential for effectiveness in developing countries through contextual understanding of unique circumstances. The purpose of this study was to survey leadership perceptions of principals in the Toledo District of Belize. This data, in the tradition of scholar-practitioner involvement, was…

  8. A genetically encoded, high-signal-to-noise maltose sensor

    Energy Technology Data Exchange (ETDEWEB)

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  9. A comprehensive platform for highly multiplexed mammalian functional genetic screens

    Directory of Open Access Journals (Sweden)

    Cheung-Ong Kahlin

    2011-05-01

    Full Text Available Abstract Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray based deconvolution methods.

  10. Fish-assemblage variation between geologically defined regions and across a longitudinal gradient in the Monkey River Basin, Belize

    Science.gov (United States)

    Esselman, P.C.; Freeman, Mary C.; Pringle, C.M.

    2006-01-01

    Linkages between geology and fish assemblages have been inferred in many regions throughout the world, but no studies have yet investigated whether fish assemblages differ across geologies in Mesoamerica. The goals of our study were to: 1) compare physicochemical conditions and fish-assemblage structure across 2 geologic types in headwaters of the Monkey River Basin, Belize, and 2) describe basin-scale patterns in fish community composition and structure for the benefit of conservation efforts. We censused headwater-pool fishes by direct observation, and assessed habitat size, structure, and water chemistry to compare habitat and fish richness, diversity, evenness, and density between streams in the variably metamorphosed sedimentary geologic type typical of 80% of Belize's Maya Mountains (the Santa Rosa Group), and an anomalous extrusive geologic formation in the same area (the Bladen Volcanic Member). We also collected species-presence data from 20 sites throughout the basin for analyses of compositional patterns from the headwaters to the top of the estuary. Thirty-nine fish species in 21 families were observed. Poeciliids were numerically dominant, making up 39% of individuals captured, followed by characins (25%), and cichlids (20%). Cichlidae was the most species-rich family (7 spp.), followed by Poeciliidae (6 spp.). Habitat size and water chemistry differed strongly between geologic types, but habitat diversity did not. Major fish-assemblage differences also were not obvious between geologies, despite a marked difference in the presence of the aquatic macrophyte, Marathrum oxycarpum (Podostemaceae), which covered 37% of the stream bottom in high-nutrient streams draining the Santa Rosa Group, and did not occur in the low-P streams draining the Bladen Volcanic Member. Correlation analyses suggested that distance from the sea and amount of cover within pools are important to fish-assemblage structure, but that differing abiotic factors may influence

  11. Evidence of multiple paternity in Morelet's Crocodile (Crocodylus moreletii) in Belize, CA, inferred from microsatellite markers.

    Science.gov (United States)

    McVay, John D; Rodriguez, David; Rainwater, Thomas R; Dever, Jennifer A; Platt, Steven G; McMurry, Scott T; Forstner, Michael R J; Densmore, Llewellyn D

    2008-12-01

    Microsatellite data were generated from hatchlings collected from ten nests of Morelet's Crocodile (Crocodylus moreletii) from New River Lagoon and Gold Button Lagoon in Belize to test for evidence of multiple paternity. Nine microsatellite loci were genotyped for 188 individuals from the 10 nests, alongside 42 nonhatchlings from Gold Button Lagoon. Then mitochondrial control region sequences were generated for the nonhatchlings and for one individual from each nest to test for presence of C. acutus-like haplotypes. Analyses of five of the nine microsatellite loci revealed evidence that progeny from five of the ten nests were sired by at least two males. These data suggest the presence of multiple paternity as a mating strategy in the true crocodiles. This information may be useful in the application of conservation and management techniques to the 12 species in this genus, most of which are threatened or endangered.

  12. Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize.

    Science.gov (United States)

    Rainwater, Thomas R; Selcer, Kyle W; Nespoli, Lisa M; Finger, Adam G; Ray, David A; Platt, Steven G; Smith, Philip N; Densmore, Llewellyn D; Anderson, Todd A; McMurry, Scott T

    2008-05-01

    Vitellogenin induction has been widely used as a biomarker of endocrine disruption in wildlife, but few studies have investigated its use in wild reptiles living in contaminated habitats. This study examined vitellogenin induction in Morelet's crocodiles (Crocodylus moreletii) from wetlands in northern Belize contaminated with organochlorine (OC) pesticides. Vitellogenin was measured in 381 crocodile plasma samples using a vitellogenin ELISA previously developed for this species. Vitellogenin was detected in nine samples, all from adult females sampled during the breeding season. Males and juvenile females did not contain detectable levels of vitellogenin; however, many of these animals contained OC pesticides in their caudal scutes, confirming contaminant exposure. The lack of a vitellogenic response in these animals may be attributable to several factors related to the timing and magnitude of exposure to endocrine-disrupting chemicals and should not be interpreted as an absence of other contaminant-induced biological responses.

  13. Screening of anti-bacterial activity of medicinal plants from Belize (Central America).

    Science.gov (United States)

    Camporese, A; Balick, M J; Arvigo, R; Esposito, R G; Morsellino, N; De Simone, F; Tubaro, A

    2003-07-01

    Twenty-one extracts from seven herbal drugs, Aristolochia trilobata (Aristolochiaceae) leaves and bark, Bursera simaruba (Burseraceae) bark, Guazuma ulmifolia (Sterculiaceae) bark, Hamelia patens (Rubiaceae) leaves and Syngonium podophyllum (Araceae) leaves and bark, used in traditional medicine of Belize (Central America) as deep and superficial wound healers, were evaluated for their anti-bacterial properties. Activity was tested against standard strains of Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 25923 and Enterococcus faecalis ATCC 29212. Almost all the extracts were able to inhibit the growth of one or more of the bacterial strains, except that of Enterococcus faecalis. For the first time an anti-microbial activity is reported for Aristolochia trilobata as well as for Syngonium podophyllum. The hexane extracts of Aristolochia trilobata leaves and bark were the most active extracts against Staphylococcus aureus (MIC=0.31 and 0.625mg/ml, respectively).

  14. Identifying and assessing ecotourism visitor impacts at selected protected areas in Costa Rica and Belize

    Science.gov (United States)

    Farrell, T.A.; Marion, J.L.

    2001-01-01

    Protected area visitation is an important component of ecotourism, and as such, must be sustainable. However, protected area visitation may degrade natural resources, particularly in areas of concentrated visitor activities like trails and recreation sites. This is an important concern in ecotourism destinations such as Belize and Costa Rica, because they actively promote ecotourism and emphasize the pristine qualities of their natural resources. Research on visitor impacts to protected areas has many potential applications in protected area management, though it has not been widely applied in Central and South America. This study targeted this deficiency through manager interviews and evaluations of alternative impact assessment procedures at eight protected areas in Belize and Costa Rica. Impact assessment procedures included qualitative condition class systems, ratings systems, and measurement-based systems applied to trails and recreation sites. The resulting data characterize manager perceptions of impact problems, document trail and recreation site impacts, and provide examples of inexpensive, efficient and effective rapid impact assessment procedures. Interview subjects reported a variety of impacts affecting trails, recreation sites, wildlife, water, attraction features and other resources. Standardized assessment procedures were developed and applied to record trail and recreation site impacts. Impacts affecting the study areas included trail proliferation, erosion and widening, muddiness on trails, vegetation cover loss, soil and root exposure, and tree damage on recreation sites. The findings also illustrate the types of assessment data yielded by several alternative methods and demonstrate their utility to protected area managers. The need for additional rapid assessment procedures for wildlife, water, attraction feature and other resource impacts was also identified.

  15. Hydrological and Oceanographic Considerations for Integrated Coastal Zone Management in Southern Belize.

    Science.gov (United States)

    Heyman; Kjerfve

    1999-09-01

    / The objectives of this study are to: (1) characterize the meteorology and hydrology of the Maya Mountain-Marine Area Transect in southern Belize, (2) employ a simple water balance model to examine the discharge rates of seven watersheds to Port Honduras, (3) test the validity of the hydrological model, (4) explore the implications of potential landscape and hydrological alterations, and (5) examine the value of protected areas. The southern coastal portion of the study area is classified as wet tropical forest and the remainder as moist tropical forest. Rainfall is 3000-4000 mm annually. Resulting annual freshwater discharge directly into Port Honduras is calculated at 2.5 x 10(9) m3, a volume equal to the basin. During the rainy season, June-September, 84% of the annual discharge occurs, which causes the bay to become brackish. Port Honduras serves as an important nursery ground for many species of commercially important fish and shellfish. The removal of forest cover in the uplands, as a result of agriculture, aquaculture, and village development, is likely to significantly accelerate erosion. Increased erosion would reduce soil fertility in the uplands and negatively affect mangrove, seagrass, and coral reef productivity in the receiving coastal embayment. Alternatively, the conservation of an existing protected areas corridor, linking the Maya Mountains to the Caribbean Sea, is likely to enhance regional sustainable economic development. This study aims to support environmental management at the scale of the "ecoscape"-a sensible ecological unit of linked watersheds and coastal and marine environments.KEY WORDS: Ecosystem management; Coastal zone management; Belize; Hydrologyhttp://link.springer-ny.com/link/service/journals/00267/bibs/24n2p229.html

  16. Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA.

    Science.gov (United States)

    Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

    2014-11-01

    There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids.

  17. High genetic polymorphism of relapsing P. vivax isolates in northwest Colombia

    OpenAIRE

    Restrepo, Eliana; Imwong, Mallika; Rojas,Winston; Carmona-Fonseca, Jaime; Maestre, Amanda

    2011-01-01

    Genetic diversity of Plasmodium populations has been more extensively documented in Colombia for Plasmodium falciparum than for Plasmodium vivax. Recently, highly variable microsatellite markers have been described and used in population-level studies of genetic variation of P. vivax throughout the world. We applied this approach to understand the genetic structure of P. vivax populations and to identify recurrence-associated haplotypes. In this, three microsatellite markers of P. vivax were ...

  18. High-Speed General Purpose Genetic Algorithm Processor.

    Science.gov (United States)

    Hoseini Alinodehi, Seyed Pourya; Moshfe, Sajjad; Saber Zaeimian, Masoumeh; Khoei, Abdollah; Hadidi, Khairollah

    2016-07-01

    In this paper, an ultrafast steady-state genetic algorithm processor (GAP) is presented. Due to the heavy computational load of genetic algorithms (GAs), they usually take a long time to find optimum solutions. Hardware implementation is a significant approach to overcome the problem by speeding up the GAs procedure. Hence, we designed a digital CMOS implementation of GA in [Formula: see text] process. The proposed processor is not bounded to a specific application. Indeed, it is a general-purpose processor, which is capable of performing optimization in any possible application. Utilizing speed-boosting techniques, such as pipeline scheme, parallel coarse-grained processing, parallel fitness computation, parallel selection of parents, dual-population scheme, and support for pipelined fitness computation, the proposed processor significantly reduces the processing time. Furthermore, by relying on a built-in discard operator the proposed hardware may be used in constrained problems that are very common in control applications. In the proposed design, a large search space is achievable through the bit string length extension of individuals in the genetic population by connecting the 32-bit GAPs. In addition, the proposed processor supports parallel processing, in which the GAs procedure can be run on several connected processors simultaneously.

  19. Genetic versus antigenic differences among highly pathogenic H5N1 avian influenza A viruses

    NARCIS (Netherlands)

    Peeters, Ben; Reemers, Sylvia; Dortmans, Jos; Vries, de Erik; Jong, de Mart; Zande, van de Saskia; Rottier, Peter J.M.; Haan, de Cornelis A.M.

    2017-01-01

    Highly pathogenic H5N1 avian influenza A viruses display a remarkable genetic and antigenic diversity. We examined to what extent genetic distances between several H5N1 viruses from different clades correlate with antigenic differences and vaccine performance. H5-specific antisera were generated, an

  20. Capacity building and policy development in Belize marine protected areas, an example for Caribbean integrated coastal management

    OpenAIRE

    Crabbe, M James C

    2014-01-01

    Sustainability science can, through capacity building, allow for integrated stakeholder management of the vital Caribbean marine ecosystems. We did a capacity building exercise in two major coral reef areas in Southern Belize. The key outcome was a six-month personal/professional action plan developed by each participant about tactics for leading, educating and supporting issues regarding sustainable development and tactics for collaboration to influence policy decisions. Our results can be a...

  1. Simulating the Upper Ocean Circulation on the Belize Shelf: An Application of a Triply Nested-Grid Ocean Circulation Model

    Institute of Scientific and Technical Information of China (English)

    SHENG Jinyu; TANG Liqun; WANG Liang

    2005-01-01

    We present a three-level nested-grid ocean circulation modeling system for the Belize shelf of the western Caribbean Sea. The nested-grid system has three subcomponents: a coarse-resolution outer model of the western Caribbean Sea; an intermediate-resolution middle model of the southern Meso-American Barrier Reef System; and a fine-resolution inner model of the Belize shelf. The two-way nesting technique based on the semi-prognostic method is used to exchange information between the three subcomponents. We discuss two applications of the nested-grid system in this study. In the first application we simulate the seasonal mean circulation in the region, with the nested system forced by monthly mean surface fluxes and boundary forcing. The model results reproduce the general circulation features on the western Caribbean Sea and meso-scale circulation features on the Belize shelf. In the second application, we simulate the storm-induced circulation during Hurricane Mitch in 1998, with the nested-grid system forced by the combination of monthly mean forcing and idealized wind stress associated with the storm. The model results demonstrate that the storm-induced currents transport a large amount of estuarinc waters from coastal regions of Honduras and Guatemala to offshore reef atolls.

  2. High performance genetic algorithm for VLSI circuit partitioning

    Science.gov (United States)

    Dinu, Simona

    2016-12-01

    Partitioning is one of the biggest challenges in computer-aided design for VLSI circuits (very large-scale integrated circuits). This work address the min-cut balanced circuit partitioning problem- dividing the graph that models the circuit into almost equal sized k sub-graphs while minimizing the number of edges cut i.e. minimizing the number of edges connecting the sub-graphs. The problem may be formulated as a combinatorial optimization problem. Experimental studies in the literature have shown the problem to be NP-hard and thus it is important to design an efficient heuristic algorithm to solve it. The approach proposed in this study is a parallel implementation of a genetic algorithm, namely an island model. The information exchange between the evolving subpopulations is modeled using a fuzzy controller, which determines an optimal balance between exploration and exploitation of the solution space. The results of simulations show that the proposed algorithm outperforms the standard sequential genetic algorithm both in terms of solution quality and convergence speed. As a direction for future study, this research can be further extended to incorporate local search operators which should include problem-specific knowledge. In addition, the adaptive configuration of mutation and crossover rates is another guidance for future research.

  3. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Directory of Open Access Journals (Sweden)

    Annika M E Noreen

    Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  4. "Doing the Lesson" or "Doing Science": Argument in High School Genetics.

    Science.gov (United States)

    Jimenez-Aleixandre, M. Pilar; Rodriguez, Anxela Bugallo; Duschl, Richard A.

    2000-01-01

    Focuses on student capacity to develop and assess arguments during a high school genetics instructional sequence, and on the location distinction in argumentation discourse between "doing science" vs. "doing school" or "doing the lesson". (Contains 37 references.) (Author/YDS)

  5. High genetic diversity and population structure in the endangered Canarian endemic Ruta oreojasme (Rutaceae).

    Science.gov (United States)

    Meloni, Marilena; Reid, Andrea; Caujapé-Castells, Juli; Soto, Moisés; Fernández-Palacios, José María; Conti, Elena

    2015-10-01

    Insular species are expected to have low genetic diversity, for their populations are often small and isolated, and characterized by restricted gene flow and increased incidence of inbreeding. However, empirical results do not always match this expectation. For example, population genetic analyses of several Canarian endemics, based mainly on allozymes, show levels of genetic diversity exceptionally high for insular species. To investigate whether genetic variation in rare species endemic to Canary Islands is low, as predicted by theoretical expectations, or high, as documented in some previous studies, we analysed genetic diversity of the endangered Ruta oreojasme, a rare endemic of the island of Gran Canaria, using microsatellite markers, which are more variable than allozymes. Our analyses identified very high levels of genetic diversity (A = 7.625, P = 0.984, H o = 0.558, H e = 0.687) for R. oreojasme. Even though the distribution of the species is restricted to the South of Gran Canaria, only one population shows low genetic diversity, isolation and signs of a recent bottleneck/founder event. Some intrinsic characteristics of R. oreojasme (hermaphroditism, proterandry and polyploidy), the relative climatic stability of the Canarian archipelago during Quaternary glacials/interglacials, the size of most populations (thousands of individuals), its age, and the relative proximity of the archipelago to the mainland might have contributed to the high diversity that characterises this endemic. As expected, given the marked topographic complexity of Gran Canaria, we found marked genetic structure in R. oreojasme populations. Our results support the observation that Canarian endemics are characterised by unexpectedly high genetic diversity and provides important insights for potential applications to the conservation of R. oreojasme.

  6. High local genetic diversity of canine parvovirus from Ecuador.

    Science.gov (United States)

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a.

  7. The role of sponges in the Mesoamerican Barrier-Reef Ecosystem, Belize.

    Science.gov (United States)

    Rützler, Klaus

    2012-01-01

    Over the past four decades, sponge research has advanced by leaps and bounds through endeavours such as the Caribbean Coral Reef Ecosystems (CCRE) programme at the U.S. National Museum of Natural History in Washington, D.C. Since its founding in the early 1970s, the programme has been dedicated to a detailed multidisciplinary study of a section of the Mesoamerican Barrier Reef, the Atlantic's largest reef complex, and has generated data far beyond the capability of lone investigators and brief expeditions. This reef complex extends 250 km southward from Yucatan, Mexico, into the Gulf of Honduras, most of it lying 20-40 km off the coast of Belize. A relatively unspoiled ecosystem, it features a great variety of habitats in close proximity, ranging from mangrove islands, seagrass meadows, and patch reefs in its lagoon to the barrier reef along the margin of the continental shelf. Among its varied macrobenthos, sponges stand out for their ubiquity, range of colours, rich species and biomass, and ecological importance; they populate rocky substrates, some sandy bottoms, and the subtidal stilt roots and peat banks of mangroves. Working from a field station established in 1972 on Carrie Bow Cay, a sand islet atop the reef off southern Belize, experts in numerous disciplines from both the Museum and academic institutions throughout the world have explored the area's biodiversity in the broadest sense and community development over time. At last count, 113 researchers (88 working on site) have focused on the biological and geological role of Porifera in Carrie Bow's reef communities, with the results reported in 125 scientific papers to date. The majority of these sponge studies have centred on systematics and faunistics, including quantitative distribution among the various habitats. Taxonomic approaches have ranged from basic morphology to fine structure, DNA barcoding, and ecological manipulations and culminated in a mini-workshop involving several experts on Caribbean

  8. Genetic consequences of forest fragmentation for a highly specialized arboreal mammal--the edible dormouse.

    Directory of Open Access Journals (Sweden)

    Joanna Fietz

    Full Text Available Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis, a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident.

  9. Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.

    Science.gov (United States)

    Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

    2014-10-01

    Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks.

  10. Algal growth and species composition under experimental control of herbivory, phosphorus and coral abundance in Glovers Reef, Belize.

    Science.gov (United States)

    McClanahan, T R; Cokos, B A; Sala, E

    2002-06-01

    The proliferation of algae on disturbed coral reefs has often been attributed to (1) a loss of large-bodied herbivorous fishes, (2) increases in sea water nutrient concentrations, particularly phosphorus, and (3) a loss of hard coral cover or a combination of these and other factors. We performed replicated small-scale caging experiments in the offshore lagoon of Glovers Reef atoll, Belize where three treatments had closed-top (no large-bodied herbivores) and one treatment had open-top cages (grazing by large-bodied herbivores). Closed-top treatments simulated a reduced-herbivory situation, excluding large fishes but including small herbivorous fishes such as damselfishes and small parrotfishes. Treatments in the closed-top cages included the addition of high phosphorus fertilizer, live branches of Acropora cervicornis and a third unmanipulated control treatment. Colonization, algal biomass and species composition on dead A. palmata "plates" were studied weekly for 50 days in each of the four treatments. Fertilization doubled the concentration of phosphorus from 0.35 to 0.77 microM. Closed-top cages, particularly the fertilizer and A. cervicornis additions, attracted more small-bodied parrotfish and damselfish than the open-top cages such that there was moderate levels of herbivory in closed-top cages. The open-top cages did, however, have a higher abundance of the chemically and morphologically defended erect algal species including Caulerpa cupressoides, Laurencia obtusa, Dictyota menstrualis and Lobophora variegata. The most herbivore-resistant calcareous green algae (i.e. Halimeda) were, however, uncommon in all treatments. Algal biomass increased and fluctuated simultaneously in all treatments over time, but algal biomass, as measured by wet, dry and decalcified weight, did not differ greatly between the treatments with only marginally higher biomass (p cervicornis suppressed algal colonization compared to the unmanipulated controls. Instead, the herbivore

  11. Essay contest reveals misconceptions of high school students in genetics content.

    Science.gov (United States)

    Mills Shaw, Kenna R; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

    2008-03-01

    National educational organizations have called upon scientists to become involved in K-12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education.

  12. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques.

    Science.gov (United States)

    Onda, Yoshihiko; Mochida, Keiichi

    2016-08-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.

  13. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Science.gov (United States)

    Noreen, Annika M E; Webb, Edward L

    2013-01-01

    Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  14. Conflict factors in cooperation for shared watersheds: Rio Hondo case (Mexico-Guatemala- Belize

    Directory of Open Access Journals (Sweden)

    David Nemesio Olvera Alarcón

    2011-07-01

    Full Text Available The Hondo transboundary river basin is a territory shared by Mexico, Guatemala and Belize. There is not enough information about mechanisms of cooperation in water issues in the river basin and the reasons that prevent this process. Nevertheless, we know about the existence of factors of conflicts that limit the cooperation. This article describes the factor of conflicts and their bonds with the cooperation around the water. The construction of the analysis was based in the grounded theory, with the use of the semi–structured interviews and the participant observation as tools of data collection. The data obtained was analyzed by a codification of information based on: the anthropic conflicts, their relation with the cooperation and the institutional paper as part of the factors of conflict. For the location of key stakeholders and the elaboration of interviews, it was necessary to take advantage of a hemerographic analysis and the existing relations as a result of a previous work in 2003, besides applying the technique of “snow ball” to identify new key stakeholders. The paper tries to highlight how existing potential anthropic conflicts in the river basin may affect processes and attempts for cooperation in water issues.

  15. An Iterative Approach to Ground Penetrating Radar at the Maya Site of Pacbitun, Belize

    Directory of Open Access Journals (Sweden)

    Sheldon Skaggs

    2016-09-01

    Full Text Available Ground penetrating radar (GPR surveys provide distinct advantages for archaeological prospection in ancient, complex, urban Maya sites, particularly where dense foliage or modern debris may preclude other remote sensing or geophysical techniques. Unidirectional GPR surveys using a 500 MHz shielded antenna were performed at the Middle Preclassic Maya site of Pacbitun, Belize. The survey in 2012 identified numerous linear and circular anomalies between 1 m and 2 m deep. Based on these anomalies, one 1 m × 4 m unit and three smaller units were excavated in 2013. These test units revealed a curved plaster surface not previously found at Pacbitun. Post-excavation, GPR data were reprocessed to best match the true nature of excavated features. Additional GPR surveys oriented perpendicular to the original survey confirmed previously detected anomalies and identified new anomalies. The excavations provided information on the sediment layers in the survey area, which allowed better identification of weak radar reflections of the surfaces of a burnt, Middle Preclassic temple in the northern end of the survey area. Additional excavations of the area in 2014 and 2015 revealed it to be a large square structure, which was named El Quemado.

  16. Mangrove ecosystem dynamics and elemental cycling at Twin Cays, Belize, during the Holocene

    Science.gov (United States)

    Wooller, Matthew J.; Behling, Hermann; Smallwood, Barbara J.; Fogel, Marilyn

    2004-10-01

    Existing at the transition between the terrestrial environment and hydrosphere, mangroves are sensitive to environmental change (e.g. sea-level rise). We present pollen and stable isotope data from a core (TCC1) of continuous (10 m) mangrove peat from Twin Cays, 12 km off of the coast of Belize, Central America. Radiocarbon dates on fragments of mangrove leaves preserved in TCC1 show that the core provides an 8600 14C year record of mangrove ecosystem changes. Variation in the stable carbon and nitrogen isotope composition (13C = -30 to -25; 15N = -6 to 2) of mangrove leaves imply that the stand structure and nutrient status of the mangroves at the site have changed during the Holocene. Pollen data from the same core show that the floral composition of the site has changed at points during the Holocene, most notably a brief (240 years) switch at 3860 14C yr BP to dominance by a species of Myrsine (not currently present at the site). Our results are consistent with significant environmental changes (either marked disturbance from hurricanes or fluctuations in sea-level) through the Holocene. Copyright

  17. Holocene Palaeosalinity in a Maya Wetland, Belize, Inferred from the Microfaunal Assemblage

    Science.gov (United States)

    Alcala-Herrera, Javier A.; Jacob, John S.; Castillo, Maria Luisa Machain; Neck, Raymond W.

    1994-01-01

    A 5.4-m sequence of peat and marl overlying a basal clay in a northern Belize wetland was studied to assess salinity changes over the past 7000 yr. The distribution of ostracods, gastropods, and foraminifers revealed initially freshwater conditions in a terrestrial wetland, changing to at least mesohaline conditions by about 5600 yr B.P. The mesohaline conditions corresponded to the formation of an open-water lagoon (and precipitation of a lacustrine marl) that was contemporaneous with rapidly rising sea level in the area. A mangrove peat filled the lagoon by 4800 yr B.P. probably as a result of increasingly shallow waters as sea level rise slowed and marl precipitation continued. A new lagoon began to form sometime after 3400 yr B.P. Freshwater ostracods and gastropods found in the marl of this lagoon suggest that it formed under near-limnetic conditions. Freshwater input likely resulted from massive deforestation by the Maya that began by 4400 yr B.P. Subsidence of the mangrove peat likely permitted the formation of a lagoon. A peat has filled the lagoon since at least 500 yr B.P.

  18. Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize

    Energy Technology Data Exchange (ETDEWEB)

    Rainwater, Thomas R. [Institute of Environmental and Human Health and Department of Environmental Toxicology, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)], E-mail: thomas.rainwater@gmail.com; Selcer, Kyle W. [Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA 15282 (United States)], E-mail: selcer@duq.edu; Nespoli, Lisa M. [Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA 15282 (United States)], E-mail: nespoli345@duq.edu; Finger, Adam G. [Institute of Environmental and Human Health and Department of Environmental Toxicology, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)], E-mail: agfinger@tiehh.ttu.edu; Ray, David A. [Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 (United States)], E-mail: david.ray@mail.wvu.edu; Platt, Steven G. [Department of Biology, P.O. Box C-64, Sul Ross State University, Alpine, TX 79832 (United States)], E-mail: splatt@sulross.edu; Smith, Philip N. [Institute of Environmental and Human Health and Department of Environmental Toxicology, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)], E-mail: philip.smith@tiehh.ttu.edu; Densmore, Llewellyn D. [Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 (United States)], E-mail: lou.densmore@ttu.edu; Anderson, Todd A. [Institute of Environmental and Human Health and Department of Environmental Toxicology, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)], E-mail: todd.anderson@tiehh.ttu.edu; McMurry, Scott T. [Institute of Environmental and Human Health and Department of Environmental Toxicology, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)], E-mail: scott.mcmurry@tiehh.ttu.edu

    2008-05-15

    Vitellogenin induction has been widely used as a biomarker of endocrine disruption in wildlife, but few studies have investigated its use in wild reptiles living in contaminated habitats. This study examined vitellogenin induction in Morelet's crocodiles (Crocodylus moreletii) from wetlands in northern Belize contaminated with organochlorine (OC) pesticides. Vitellogenin was measured in 381 crocodile plasma samples using a vitellogenin ELISA previously developed for this species. Vitellogenin was detected in nine samples, all from adult females sampled during the breeding season. Males and juvenile females did not contain detectable levels of vitellogenin; however, many of these animals contained OC pesticides in their caudal scutes, confirming contaminant exposure. The lack of a vitellogenic response in these animals may be attributable to several factors related to the timing and magnitude of exposure to endocrine-disrupting chemicals and should not be interpreted as an absence of other contaminant-induced biological responses. - Wild crocodiles living in habitats polluted with organochlorine pesticides did not exhibit contaminant-induced vitellogenin induction in blood plasma.

  19. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    Science.gov (United States)

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  20. High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort

    OpenAIRE

    Santos, Susana; Marques, Vanda; Pires, Marina; Silveira, Leonor; Oliveira, Helena; Lança, Vasco; Brito, Dulce; Madeira, Hugo; Esteves, J Fonseca; Freitas, António; Carreira, Isabel M; Gaspar, Isabel M; Monteiro, Carolino; Alexandra R. Fernandes

    2012-01-01

    Background Hypertrophic Cardiomyopathy (HCM) is a complex myocardial disorder with a recognized genetic heterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis that should be considered of most importance for basic research and clinical medicine. Methodology In this report, we evaluated High Resolution Melting (HRM) robustness, regarding HCM genetic testing, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associa...

  1. Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

    Directory of Open Access Journals (Sweden)

    Robin Cristofari

    Full Text Available How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the

  2. High Genetic Diversity in a Rare, Narrowly Endemic Primrose Species: Primula interjacens by ISSR Analysis

    Institute of Scientific and Technical Information of China (English)

    XUEDa-Wei; GEXue-Jun; HAOGang; ZHANGChang-Qin

    2004-01-01

    Prirnula interjacens Chen (Primulaceae) is a rare and narrow endemic species of centralsouth of Yunnan Province in China. This species consists of two varieties: P.interjacens var. interjacens known with only one population, and P.interjacens var. epilosa with two populations. Intersimple sequence repeat (ISSR) marker was used to detect the genetic diversity of the three extant populations. We expected a low genetic diversity level, but our results revealed a high level of intraspecific genetic diversity (at population level: P=59.75%, HE=0.2368, and Hpop=0.3459; at species level: P=75.47%, HT= 0.320 5, and Hsp = 0.4618), probably resulting from floral heteromorphism and preferring outcrossing. A moderate level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (26.13%) and Shannon's diversity index (25.09%). Although P./ntedacens var. intedacens and P. interjacens var. epilosa were morphologically distinct, UPGMA cluster analysis showed that the two varieties had no distinct genetic differentiation and may be treated as a single taxon. Conservation measures are suggested, including in situ and ex situ strategies, based on the observed population genetic information.

  3. A late Holocene paleoenvironmental reconstruction from Agua Caliente, southern Belize, linked to regional climate variability and cultural change at the Maya polity of Uxbenká

    Science.gov (United States)

    Walsh, Megan K.; Prufer, Keith M.; Culleton, Brendan J.; Kennett, Douglas J.

    2014-07-01

    We report high-resolution macroscopic charcoal, pollen and sedimentological data for Agua Caliente, a freshwater lagoon located in southern Belize, and infer a late Holocene record of human land-use/climate interactions for the nearby prehistoric Maya center of Uxbenká. Land-use activities spanning the initial clearance of forests for agriculture through the drought-linked Maya collapse and continuing into the historic recolonization of the region are all reflected in the record. Human land alteration in association with swidden agriculture is evident early in the record during the Middle Preclassic starting ca. 2600 cal yr BP. Fire slowly tapered off during the Late and Terminal Classic, consistent with the gradual political demise and depopulation of the Uxbenká polity sometime between ca. 1150 and 950 cal yr BP, during a period of multiple droughts evident in a nearby speleothem record. Fire activity was at its lowest during the Maya Postclassic ca. 950-430 cal yr BP, but rose consistent with increasing recolonization of the region between ca. 430 cal yr BP and present. These data suggest that this environmental record provides both a proxy for 2800 years of cultural change, including colonization, growth, decline, and reorganization of regional populations, and an independent confirmation of recent paleoclimate reconstructions from the same region.

  4. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  5. A Summary of the 1999-2002 Seasons of Archaeological Investigations at Pook's Hill, Cayo District, Belize

    DEFF Research Database (Denmark)

    Helmke, Christophe G.B.

    2006-01-01

    The following is a synopsis of the 1999 through 2002 seasons of archaeological investigations conducted at the site of Pook's Hill. The site's location and description precede an outline of the research objectives that have guided the investigations. Results of the first four seasons of investiga...... wider Late to Terminal Classic social processes in central Belize and the eastern Maya Lowlands generally........ Our investigations have revealed thar there is a notable diachronic and spatial patterning in ritual practices at Pook's Hill, as reflected in the material precipitates of such actions. Further study should offer insight into whether local and idiosyncratic patterns are manifest, or if it reflects...

  6. Diet items of manatee Trichechus manatus manatus in three priority sites for the species in Mexico and Belize

    OpenAIRE

    Flores-Cascante, Lavinia; Morales-Vela, Benjamín; Castelblanco-Martínez, Nataly; Padilla-Saldívar, Janneth; Auil, Nicole

    2013-01-01

    Manatees (Trichechus manatus manatus) are herbivorous mammals with opportunistic habits that feed on approximately 60 species of plants. The focus of this paper was to identify diet elements of the manatee by fecal analysis in two sites in Mexico (Jonuta, Tabasco and Bahía de la Ascensión, Quintana Roo) and one site in Belize (Southern Lagoon). Samples were obtained from wild manatees and captive manatees temporarily captured for health assessment and sampling during 2004-2006. A total of 24 ...

  7. Identification of patients at high risk of psychological distress after BRCA1 genetic testing.

    Science.gov (United States)

    Ertmański, Sławomir; Metcalfe, Kelly; Trempała, Janusz; Głowacka, Maria Danuta; Lubiński, Jan; Narod, Steven A; Gronwald, Jacek

    2009-06-01

    To predict which women might suffer from abnormally high levels of anxiety and depression after receiving a positive genetic BRCA1 test result, series of pregenetic testing and postgenetic testing psychological measurements were performed. Of 3524 women who returned the psychological test sheets before receiving their genetic test result, 111 women were found to carry a BRCA1 mutation. We found that overall, anxiety does not increase in women who receive a positive BRCA1 genetic test result; however, women who experience high levels of anxiety before genetic testing continue to experience high levels of anxiety up to 1 year posttesting. There were differences in cancer-related distress in affected and unaffected women. BRCA1 carriers with a previous diagnosis of cancer had significantly higher levels of cancer-related distress at 1 month posttest than those without cancer. Our findings suggest that healthcare providers should consider including a brief pretest psychological assessment before initiating genetic testing for BRCA1 and BRCA2.

  8. Parameters inversion of high central core rockfill dams based on a novel genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHOU Wei; LI ShaoLin; MA Gang; CHANG XiaoLin; MA Xing; ZHANG Chao

    2016-01-01

    Parameters identification of rockfill materials is a crucial issue for high rockfill dams.Because of the scale effect,random sampling and sample disturbance,it is difficult to obtain the actual mechanical properties of rockfill from laboratory tests.Parameters inversion based on in situ monitoring data has been proven to be an efficient method for identifying the exact parameters of the rockfill.In this paper,we propose a modified genetic algorithm to solve the high-dimension multimodal and nonlinear optimal parameters inversion problem.A novel crossover operator based on the sum of differences in gene fragments (SoDX) is proposed,inspired by the cloning of superior genes in genetic engineering.The crossover points are selected according to the difference in the gene fragments,defining the adaptive length.The crossover operator increases the speed and accuracy of algorithm convergence by reducing the inbreeding and enhancing the global search capability of the genetic algorithm.This algorithm is compared with two existing crossover operators.The modified genetic algorithm is then used in combination with radial basis function neural networks (RBFNN) to perform the parameters back analysis of a high central earth core rockfill dam.The settlements simulated using the identified parameters show good agreement with the monitoring data,illustrating that the back analysis is reasonable and accurate.The proposed genetic algorithm has considerable superiority for nonlinear multimodal parameter identification problems.

  9. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    Science.gov (United States)

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  10. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  11. The Source of Volcanic Ash in Late Classic Maya Pottery at El Pilar, Belize

    Science.gov (United States)

    Catlin, B. L.; Ford, A.; Spera, F. J.

    2007-12-01

    The presence of volcanic ash used as temper in Late Classic Maya pottery (AD 600-900) at El Pilar has been long known although the volcano(s) contributing ash have not been identified. We use geochemical fingerprinting, comparing compositions of glass shards in potsherds with volcanic sources to identify the source(s). El Pilar is located in the Maya carbonate lowlands distant from volcanic sources. It is unlikely Maya transported ash from distant sites: ash volumes are too large, the terrain too rugged, and no draft animals were available. Ash layer mining is unlikely because mine sites have not been found despite intensive surveys. Nearest volcanic sources to El Pilar, Belize and Guatemala, are roughly 450 km to the south and east. The ash found in potsherds has a cuspate morphology. This suggests ash was collected during, or shortly after, an ash airfall event following eruption. Analyses of n=333 ash shards from 20 ceramic (pottery) sherds was conducted by electron microprobe for major elements, and LA-ICPMS for trace elements and Pb isotopes. These analyses can be compared to volcanic materials from candidate volcanoes in the region. The 1982 El Chichon eruption caused airfall deposition (clay according to heating schedules used by Maya potters. Two important changes are that Na is rapidly lost preferentially to K and that the Si/Ca ratio decreases due to Ca diffusion from matrix into glass during firing. One expects that ratios of the refractory trace elements such as La/Yb and Zr/Hf are less susceptible to modification. Further experiments of trace element mobility during firing are underway.

  12. Lobster and Conch Fisheries of Belize: a History of Sequential Exploitation

    Directory of Open Access Journals (Sweden)

    Miriam Huitric

    2005-06-01

    Full Text Available This article presents a historical review of the lobster and conch fisheries in Belize, Central America. In terms of yield and value, these are the main wild-caught targets of the national fisheries, a small-scale commercial fishery of around 3000 fishermen. Data were collected during interviews with key informants involved with the fisheries and through literature and archive research. The goal was to study how the fishing industry has responded to environmental signals from these resources and from their ecosystems and ecosystem dynamics. National yields for both lobster and conch have been relatively stable, however, individuals’ yields have been declining despite increased effort since the 1980s. This study concludes that the use of fossil fuel-based technology and organizational change, with the establishment of fishermen's cooperatives, have masked environmental signals. This masking, together with economic incentives, has led to the “pathology of resource use.” As a symptom of this pathology, four forms of sequential exploitation in these fisheries were identified. A major conclusion is that social resilience may not confer ecological resilience. The development of the cooperatives was needed in order to improve equity in the industry. Before their impacts could be assessed, this organizational change, together with new technology, led to very important and rapid changes in the industry. Together with existing regulations that allow de facto open access to lobster and conch, these changes resulted in a short-term boom that has resulted in the pathology of resource use, with over-capitalization and dependence on maintained yields, regardless of environmental feedback.

  13. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

    Science.gov (United States)

    Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

    2015-12-01

    It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.

  14. Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

    Science.gov (United States)

    Brutsaert, Tom

    2016-01-01

    Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise.

  15. [Recent progress in gene mapping through high-throughput sequencing technology and forward genetic approaches].

    Science.gov (United States)

    Lu, Cairui; Zou, Changsong; Song, Guoli

    2015-08-01

    Traditional gene mapping using forward genetic approaches is conducted primarily through construction of a genetic linkage map, the process of which is tedious and time-consuming, and often results in low accuracy of mapping and large mapping intervals. With the rapid development of high-throughput sequencing technology and decreasing cost of sequencing, a variety of simple and quick methods of gene mapping through sequencing have been developed, including direct sequencing of the mutant genome, sequencing of selective mutant DNA pooling, genetic map construction through sequencing of individuals in population, as well as sequencing of transcriptome and partial genome. These methods can be used to identify mutations at the nucleotide level and has been applied in complex genetic background. Recent reports have shown that sequencing mapping could be even done without the reference of genome sequence, hybridization, and genetic linkage information, which made it possible to perform forward genetic study in many non-model species. In this review, we summarized these new technologies and their application in gene mapping.

  16. Efficient micropropagation and assessment of genetic fidelity of Boerhaavia diffusa L- High trade medicinal plant.

    Science.gov (United States)

    Patil, Kapil S; Bhalsing, Sanjivani R

    2015-07-01

    Boerhaavia diffusa L is a medicinal herb with immense pharmaceutical significance. The plant is used by many herbalist, Ayurvedic and pharmaceutical industries for production biopharmaceuticals. It is among the 46 medicinal plant species in high trade sourced mainly from wastelands and generally found in temperate regions of the world. However, the commercial bulk of this plant shows genetic variations which are the main constraint to use this plant as medicinal ingredient and to obtain high value products of pharmaceutical interest from this plant. In this study, we have regenerated the plant of Boerhaavia diffusa L through nodal explants and evaluated genetic fidelity of the micropropagated plants of Boerhaavia diffusa L with the help of random amplified polymorphic DNA (RAPD) markers. The results obtained using RAPD showed monomorphic banding pattern revealing genetic stability among the mother plant and in vitro regenerated plants of Boerhaavia diffusa L.

  17. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

    Science.gov (United States)

    Jacquiod, Samuel; Demanèche, Sandrine; Franqueville, Laure; Ausec, Luka; Xu, Zhuofei; Delmont, Tom O; Dunon, Vincent; Cagnon, Christine; Mandic-Mulec, Ines; Vogel, Timothy M; Simonet, Pascal

    2014-11-20

    A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.

  18. Utilizing high-fidelity crucial conversation simulation in genetic counseling training.

    Science.gov (United States)

    Holt, R Lynn; Tofil, Nancy M; Hurst, Christina; Youngblood, Amber Q; Peterson, Dawn Taylor; Zinkan, J Lynn; White, Marjorie Lee; Clemons, Jason L; Robin, Nathaniel H

    2013-06-01

    Genetics professionals are often required to deliver difficult news to patients and families. This is a challenging task, but one that many genetics trainees have limited opportunity to master during training. This is true for several reasons, including relative scarcity of these events and an understandable hesitation of supervisors allowing a trainee to provide such high stakes information. Medical simulation is effective in other health care disciplines giving trainees opportunities of "hands on" education in similar high stakes situations. We hypothesized that crucial conversations simulation would be effective for genetics trainees to gain experience in communication and counseling skills in a realistic clinical scenario. To test this hypothesis, we designed a prenatal counseling scenario requiring disclosure of an abnormal amniocentesis result and discussion of pregnancy management options; we challenged participants to address common counseling questions. Three medical genetics resident physicians and five genetic counseling students participated. Genetics and simulation experts observed the session via live video feed from a different room. A behavioral checklist was completed in real time assessing trainee's performance and documenting medical information discussed. Debriefing immediately followed the session and included simulation and genetics experts and the actor parents. Participants completed open-ended post evaluations. There was a trend towards participants being more likely to discuss issues the child could have while an infant/toddler rather than issues that could emerge as the child with Down Syndrome transitions to adulthood and end of life (P=.069). All participants found the simulation helpful, notably that it was more realistic than role-playing with colleagues.

  19. Population genetic structure of a centipede species with high levels of developmental instability.

    Science.gov (United States)

    Fusco, Giuseppe; Leśniewska, Małgorzata; Congiu, Leonardo; Bertorelle, Giorgio

    2015-01-01

    European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe.

  20. Unravelling the genetic basis of hereditary disorders by high-throughput exome sequencing strategies

    NARCIS (Netherlands)

    Jazayeri, Omid

    2016-01-01

    The research presented in this thesis focuses on using Whole Exome Sequencing (WES) to unravel the genetic basis of human hereditary disorders with different inheritance patterns. We set out to apply WES as a diagnostic approach for establishing a molecular diagnosis in a highly heterogeneous group

  1. A botanical inventory of forest on karstic limestone and metamorphic substrate in the Chiquibul Forest, Belize, with focus on woody taxa

    DEFF Research Database (Denmark)

    Baden, Maria; Särkinen, Tiina; Conde, Dalia Amor

    2016-01-01

    The Chiquibul Forest Reserve and National Park in Belize is a priority conservation area within the ‘Maya Forest’ in Central America. Although taxonomic data are essential for the development of conservation plans in the region, there is limited knowledge of the existing species in the area. Here...

  2. Multilocus spacer analysis revealed highly homogeneous genetic background of Asian type of Borrelia miyamotoi.

    Science.gov (United States)

    Mukhacheva, Tatyana A; Salikhova, Irina I; Kovalev, Sergey Y

    2015-04-01

    Borrelia miyamotoi, a member of the relapsing fever group borreliae, was first isolated in Japan and subsequently found in Ixodes ticks in North America, Europe and Russia. Currently, there are three types of B. miyamotoi: Asian or Siberian (transmitted mainly by Ixodes persulcatus), European (Ixodesricinus) and American (Ixodesscapularis and Ixodespacificus). Despite the great genetic distances between B. miyamotoi types, isolates within a type are characterised by an extremely low genetic variability. In particular, strains of B. miyamotoi of Asian type, isolated in Russia from the Baltic sea to the Far East, have been shown to be identical based on the analysis of several conventional genetic markers, such as 16S rRNA, flagellin, outer membrane protein p66 and glpQ genes. Thus, protein or rRNA - coding genes were shown not to be informative enough in studying genetic diversity of B. miyamotoi within a type. In the present paper, we have attempted to design a new multilocus technique based on eight non-coding intergenic spacers (3686bp in total) and have applied it to the analysis of intra-type genetic variability of В. miyamotoi detected in different regions of Russia and from two tick species, I. persulcatus and Ixodespavlovskyi. However, even though potentially the most variable loci were selected, no genetic variability between studied DNA samples was found, except for one nucleotide substitution in two of them. The sequences obtained were identical to those of the reference strain FR64b. Analysis of the data obtained with the GenBank sequences indicates a highly homogeneous genetic background of B. miyamotoi from the Baltic Sea to the Japanese Islands. In this paper, a hypothesis of clonal expansion of B. miyamotoi is discussed, as well as possible mechanisms for the rapid dissemination of one B. miyamotoi clone over large distances.

  3. A scalable pipeline for highly effective genetic modification of a malaria parasite

    KAUST Repository

    Pfander, Claudia

    2011-10-23

    In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (>77% A+T content) in a bacteriophage N15-based vector that can be modified efficiently using the lambda Red method of recombineering. We built a pipeline for generating P. berghei genetic modification vectors at genome scale in serial liquid cultures on 96-well plates. Vectors have long homology arms, which increase recombination frequency up to tenfold over conventional designs. The feasibility of efficient genetic modification at scale will stimulate collaborative, genome-wide knockout and tagging programs for P. berghei. © 2011 Nature America, Inc. All rights reserved.

  4. A scalable pipeline for highly effective genetic modification of a malaria parasite.

    Science.gov (United States)

    Pfander, Claudia; Anar, Burcu; Schwach, Frank; Otto, Thomas D; Brochet, Mathieu; Volkmann, Katrin; Quail, Michael A; Pain, Arnab; Rosen, Barry; Skarnes, William; Rayner, Julian C; Billker, Oliver

    2011-10-23

    In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (>77% A+T content) in a bacteriophage N15-based vector that can be modified efficiently using the lambda Red method of recombineering. We built a pipeline for generating P. berghei genetic modification vectors at genome scale in serial liquid cultures on 96-well plates. Vectors have long homology arms, which increase recombination frequency up to tenfold over conventional designs. The feasibility of efficient genetic modification at scale will stimulate collaborative, genome-wide knockout and tagging programs for P. berghei.

  5. Attitudes towards genetics: a case study among Brazilian high school students.

    Science.gov (United States)

    Massarani, Luisa; Moreira, Ildeu de Castro

    2005-04-01

    The objective of our study was to investigate young people's attitudes towards modern genetics and biotechnology. Quantitative and qualitative studies were conducted among high school students in Rio de Janeiro. These included a survey of students in nine public and private schools as well as focus groups for a complementary analysis of their attitudes and perceptions with respect to these subjects. We observe that, in general, students are relatively well informed about some of the main issues related to the applications of genetics. In their assessment of the utility, the potential risks, and the need for encouragement of the different techniques used in genetic manipulation, they were able to make clear distinctions between the different purposes of each technique. Most students believed that transgenic food could be useful and that it should be encouraged, but they were also aware that there were risks involved. Furthermore, the students were strongly supportive of the labeling of transgenic food.

  6. A common genetic influence on human intensity ratings of sugars and high-potency sweeteners.

    Science.gov (United States)

    Hwang, Liang-Dar; Zhu, Gu; Breslin, Paul A S; Reed, Danielle R; Martin, Nicholas G; Wright, Margaret J

    2015-08-01

    The perception of sweetness varies among individuals but the sources of this variation are not fully understood. Here, in a sample of 1,901 adolescent and young adults (53.8% female; 243 MZ and 452 DZ twin pairs, 511 unpaired individuals; mean age 16.2±2.8, range 12–26 years), we studied the variation in the perception of sweetness intensity of two monosaccharides and two high-potency sweeteners: glucose, fructose, neohesperidine dihydrochalcone (NHDC), and aspartame. Perceived intensity for all sweeteners decreased with age (2–5% per year) and increased with the history of otitis media (6–9%). Males rated aspartame slightly stronger than females (7%). We found similar heritabilities for sugars (glucose: h2=0.31, fructose: h2=0.34) and high-potency sweeteners (NHDC: h2=0.31, aspartame: h2=0.30); all were in the modest range. Multivariate modeling showed that a common genetic factor accounted for >75% of the genetic variance in the four sweeteners, suggesting that individual differences in perceived sweet intensity, which are partly due to genetic factors, may be attributed to a single set of genes. This study provided evidence of the shared genetic pathways between the perception of sugars and high-potency sweeteners.

  7. High-throughput genetic analysis using time-resolved fluorometry and closed-tube detection.

    Science.gov (United States)

    Nurmi, J; Kiviniemi, M; Kujanpää, M; Sjöroos, M; Ilonen, J; Lövgren, T

    2001-12-15

    Robust methods for genetic analysis are required for efficient exploitation of the constantly accumulating genetic information. We describe a closed-tube genotyping method suitable for high-throughput screening of genetic markers. The method is based on allele-specific probes labeled with an environment-sensitive lanthanide chelate, the fluorescence intensity of which is significantly increased upon PCR amplification of a complementary target. Genomic DNA samples were analyzed in an insulin gene single nucleotide polymorphism (SNP) assay using universal amplification primers and probes that recognized the two different alleles. The feasibility of dry reagent based all-in-one PCR assays was tested using another diabetes-related genetic marker, human leukocyte antigen DQB1 allele *0302 as a model analyte in a dual-color, closed-tube end-point assay. There was a 100% correlation between the novel SNP assay and a conventional PCR restriction fragment length polymorphism assay. It was also demonstrated that using real-time monitoring, accurate genotyping results can be obtained despite strongly cross-reacting probes, minimizing the time and effort needed for optimization of probe sequence. Throughput can be maximized by using predried PCR mixtures that are stable for at least 6 months. This homogenous, all-in-one dry reagent assay chemistry permits cost-effective genetic screening on a large scale.

  8. High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus).

    Science.gov (United States)

    Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha

    2013-09-01

    Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.

  9. Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.

    Science.gov (United States)

    Fu, Yong-Bi

    2014-03-13

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data.

  10. Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Duster, T.

    1998-11-01

    The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as families at risk for two of the most common autosomal recessive diseases, sickle cell disease (SC) and cystic fibrosis (CF), encounter genetic testing. Each of these diseases is found primarily in a different ethnic/racial group (CF in Americans of North European descent and SC in Americans of West African descent). This has permitted them to have a certain additional lens on the role of culture in integrating genetic testing into family life and reproductive planning. A third type of genetic disorder, the thalassemias was added to the sample in order to extent the comparative frame and to include other ethnic and racial groups.

  11. Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea).

    Science.gov (United States)

    Santamaria, Carlos A; Mateos, Mariana; DeWitt, Thomas J; Hurtado, Luis A

    2016-03-01

    Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark-based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross

  12. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  13. Genetic diversity of high-elevation populations of an endangered medicinal plant.

    Science.gov (United States)

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2014-11-21

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G'st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks.

  14. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

    Science.gov (United States)

    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

    2016-03-01

    Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.

  15. The role of minerals in food selection in a black howler monkey (Alouatta pigra) population in Belize following a major hurricane.

    Science.gov (United States)

    Behie, Alison M; Pavelka, Mary S M

    2012-11-01

    As plants may contain low levels of some minerals including sodium, copper, and phosphorous, herbivores may become deficient in these nutrients. In 2001, Hurricane Iris hit the Monkey River Forest in Belize causing substantial damage to the food supply of the black howler monkey population (Alouatta pigra) living there. This included an 18-month absence in fruit production and a complete loss of figs that are high in calcium. In this article, we describe the post-hurricane diet of this monkey population and compare the mineral content of food items to each other and to recommendations for non-human primates [NRC 2003]. We also investigate food selection in relation to potentially limiting minerals. Behavioral data from four groups of howlers (2002-2006) and samples of all ingested food items were collected and a sample of 99 plant from 18 food species was analyzed for mineral content. Unexpectedly, the post-hurricane diet contained more mature leaves than new leaves despite the availability of new leaves. Leaves contained higher amounts of minerals than reproductive parts and with the exception of Cecropia peltata stems, plant parts were low in sodium. Cecropia peltata is a pioneer species that grows following habitat disturbance thus the ingestion of these stems may be a potential mechanism to avoid sodium deficiency in this damaged forest. Calcium and zinc were found above recommended values in most food items; however, both positively predicted food selection, which may reflect a difference between their abundance and their bioavailability. However, as mature leaves contained more calcium than other plant parts, their high post-hurricane consumption may also be a response to the absence of figs and the need to find an alternate calcium source. This study highlights how habitat disturbance may affect mineral abundance and the dietary choices of primates.

  16. Combined analysis of six lipoprotein lipase genetic variants on triglycerides, high-density lipoprotein, and ischemic heart disease

    DEFF Research Database (Denmark)

    Wittrup, Hans H; Andersen, Rolf V; Tybjaerg-Hansen, Anne;

    2006-01-01

    Genetic variants in lipoprotein lipase may affect triglycerides, high-density lipoprotein (HDL), and risk of ischemic heart disease (IHD).......Genetic variants in lipoprotein lipase may affect triglycerides, high-density lipoprotein (HDL), and risk of ischemic heart disease (IHD)....

  17. Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

    Directory of Open Access Journals (Sweden)

    Aline Finger

    Full Text Available Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

  18. High Altitude Pulmonary Edema in an Experienced Mountaineer. Possible Genetic Predisposition

    Directory of Open Access Journals (Sweden)

    Kenneth S. Whitlow,

    2014-11-01

    Full Text Available High altitude pulmonary edema (HAPE is a form of high altitude illness characterized by cough, dyspnea upon exertion progressing to dyspnea at rest and eventual death, seen in patients who ascend over 2,500 meters, particularly if that ascent is rapid. This case describes a patient with no prior history of HAPE and extensive experience hiking above 2,500 meters who developed progressive dyspnea and cough while ascending to 3,200 meters. His risk factors included rapid ascent, high altitude, male sex, and a possible genetic predisposition for HAPE. [West J Emerg Med. 2014;15(7:–0.

  19. High Altitude Pulmonary Edema in an Experienced Mountaineer. Possible Genetic Predisposition

    Science.gov (United States)

    Whitlow, Kenneth S.; Davis, Babette W.

    2014-01-01

    High altitude pulmonary edema (HAPE) is a form of high altitude illness characterized by cough, dyspnea upon exertion progressing to dyspnea at rest and eventual death, seen in patients who ascend over 2,500 meters, particularly if that ascent is rapid. This case describes a patient with no prior history of HAPE and extensive experience hiking above 2,500 meters who developed progressive dyspnea and cough while ascending to 3,200 meters. His risk factors included rapid ascent, high altitude, male sex, and a possible genetic predisposition for HAPE. PMID:25493133

  20. High acceptance of an early dyslexia screening test involving genetic analyses in Germany.

    Science.gov (United States)

    Wilcke, Arndt; Müller, Bent; Schaadt, Gesa; Kirsten, Holger; Boltze, Johannes

    2016-02-01

    Dyslexia is a developmental disorder characterized by severe problems in the acquisition of reading and writing skills. It has a strong neurobiological basis. Genetic influence is estimated at 50-70%. One of the central problems with dyslexia is its late diagnosis, normally not before the end of the 2nd grade, resulting in the loss of several years for early therapy. Currently, research is focusing on the development of early tests for dyslexia, which may be based on EEG and genetics. Our aim was to determine the acceptance of such a future test among parents. We conducted a representative survey in Germany with 1000 parents of children aged 3-7 years, with and without experience of dyslexia. 88.7% of the parents supported the introduction of an early test for dyslexia based on EEG and genetics; 82.8% would have their own children tested, and 57.9% were willing to pay for the test if health insurance did not cover the costs. Test acceptance was significantly higher if parents had prior experience with dyslexia. The perceived benefits of such a test were early recognition and remediation and, preventing deficits. Concerns regarded the precision of the test, its potentially stigmatizing effect and its costs. The high overall support for the test leads to the conclusion that parents would accept a test for dyslexia based on EEG and genetics.

  1. High genetic polymorphism of relapsing P. vivax isolates in northwest Colombia.

    Science.gov (United States)

    Restrepo, Eliana; Imwong, Mallika; Rojas, Winston; Carmona-Fonseca, Jaime; Maestre, Amanda

    2011-07-01

    Genetic diversity of Plasmodium populations has been more extensively documented in Colombia for Plasmodium falciparum than for Plasmodium vivax. Recently, highly variable microsatellite markers have been described and used in population-level studies of genetic variation of P. vivax throughout the world. We applied this approach to understand the genetic structure of P. vivax populations and to identify recurrence-associated haplotypes. In this, three microsatellite markers of P. vivax were amplified and the combined size of the fragments was used to establish genotypes. Patients from an ongoing treatment efficacy trial who were kept either in endemic or non-endemic regions in the northwest of Colombia were included in the study. In total 58 paired clinical isolates, were amplified. A total of 54 haplotypes were observed among the two regions. Some haplotypes were exclusive to the endemic region where the highest degree of polymorphism was detected. In addition, we confirmed the different genotypes of recurrent-relapsing and primary infection isolates suggesting the activation of heterologous hypnozoite populations. We conclude that analysis of the three microsatellites is a valuable tool to establish the genetic characteristics of P. vivax populations in Colombia.

  2. Receipt of genetic counseling recommendations among black women at high risk for BRCA mutations.

    Science.gov (United States)

    Thompson, Hayley S; Sussner, Katarina; Schwartz, Marc D; Edwards, Tiffany; Forman, Andrea; Jandorf, Lina; Brown, Karen; Bovbjerg, Dana H; Valdimarsdottir, Heiddis B

    2012-11-01

    Low use of BRCA counseling and testing services among black women has been reported in several studies, even though such services may play an important role in reducing racial disparities in breast cancer. Surprisingly, little is known about the extent to which black women at high risk for BRCA mutations actually receive recommendations for BRCA counseling. Thus, a primary goal of the current study was to identify sociodemographic and clinical factors associated with the receipt of physician recommendation for genetic counseling based on the self-report of black women at high risk for BRCA mutations. In this cross-sectional study, participants were 125 black women with a family history suggestive of a hereditary breast and/or ovarian cancer syndrome. Participants were asked about their receipt of genetic counseling recommendation or referral. Physician recommendation was reported by over two-thirds of the sample. Multivariate analyses revealed that older age and study recruitment source, specifically community-based recruitment, were significantly and independently associated with lower likelihood of physician recommendation. Findings highlight the need for additional research to identify subgroups of high-risk black women among whom physician recommendation of genetic counseling is low but would benefit from such counseling.

  3. Feeding preferences of West Indian manatees in Florida, Belize, and Puerto Rico as indicated by stable isotope analysis

    Science.gov (United States)

    Alves-Stanley, Christy D.; Worthy, Graham A.J.; Bonde, Robert K.

    2010-01-01

    The endangered West Indian manatee Trichechus manatus has 2 recognized subspecies: the Florida T. m. latirostris and Antillean T. m. manatus manatee, both of which are found in freshwater, estuarine, and marine habitats. A better understanding of manatee feeding preferences and habitat use is essential to establish criteria on which conservation plans can be based. Skin from manatees in Florida, Belize, and Puerto Rico, as well as aquatic vegetation from their presumed diet, were analyzed for stable carbon and nitrogen isotope ratios. This is the first application of stable isotope analysis to Antillean manatees. Stable isotope ratios for aquatic vegetation differed by plant type (freshwater, estuarine, and marine), collection location, and in one instance, season. Carbon and nitrogen isotope ratios for manatee skin differed between collection location and in one instance, season, but did not differ between sex or age class. Signatures in the skin of manatees sampled in Belize and Puerto Rico indicated a diet composed primarily of seagrasses, whereas those of Florida manatees exhibited greater regional variation. Mixing model results indicated that manatees sampled from Crystal River and Homosassa Springs (Florida, USA) ate primarily freshwater vegetation, whereas manatees sampled from Big Bend Power Plant, Ten Thousand Islands, and Warm Mineral Springs (Florida) fed primarily on seagrasses. Possible diet-tissue discrimination values for 15N were estimated to range from 1.0 to 1.5 per mil. Stable isotope analysis can be used to interpret manatee feeding behavior over a long period of time, specifically the use of freshwater vegetation versus seagrasses, and can aid in identifying critical habitats and improving conservation efforts.

  4. Effects of natural environmental conditions on faecal glucocorticoid metabolite concentrations in jaguars (Panthera onca) in Belize.

    Science.gov (United States)

    Mesa-Cruz, J Bernardo; Brown, Janine L; Kelly, Marcella J

    2014-01-01

    In situ studies that rely on non-invasive faecal hormone monitoring are subject to problems due to potential changes in hormone concentrations in samples exposed to field conditions. In this study, we conducted an environmental validation for measurement of faecal glucocorticoid metabolites (FGMs) in jaguars (Panthera onca). We collected fresh faeces (e.g. no older than 8 h) from jaguars (six males and four females), housed at the Belize Zoo, and exposed them randomly to two environmental conditions: shade and sun. A control (first sub-sample) was immediately frozen, after which sub-samples were frozen daily over a 5 day period in both the dry and wet seasons. We quantified FGMs using a cortisol enzyme immunoassay (EIA) and a corticosterone radioimmunoassay (RIA), both capable of identifying relevant metabolites. Results indicated that FGMs assessed with the cortisol EIA were stable for 5 days during the dry season but for <1 day during the wet season, while FGMs assessed with the corticosterone RIA were stable for 5 days during both the dry and wet seasons. Exposure of jaguar faeces to sun or shade had no effect on FGM concentrations, despite significant differences in weather parameters. Analysis of faecal morphology proved unreliable in identifying faecal age. We conclude that the corticosterone RIA is suitable for assessing FGMs in free-ranging Belizean jaguars by surveying the same transects every 3-4 days in both seasons. The cortisol EIA can be used during the dry season, but there are possible shifts in metabolite immunoactivity in wet conditions. Assessment of adrenal activity in jaguars ranging areas of varying human disturbance is a timely application of this methodology in Belize.

  5. High prevalence and genetic heterogeneity of rodent-borne Bartonella species on Heixiazi Island, China.

    Science.gov (United States)

    Li, Dong-Mei; Hou, Yong; Song, Xiu-Ping; Fu, Ying-Qun; Li, Gui-Chang; Li, Ming; Eremeeva, Marina E; Wu, Hai-Xia; Pang, Bo; Yue, Yu-Juan; Huang, Ying; Lu, Liang; Wang, Jun; Liu, Qi-Yong

    2015-12-01

    We performed genetic analysis of Bartonella isolates from rodent populations from Heixiazi Island in northeast China. Animals were captured at four sites representing grassland and brushwood habitats in 2011 and examined for the prevalence and genetic diversity of Bartonella species, their relationship to their hosts, and geographic distribution. A high prevalence (57.7%) and a high diversity (14 unique genotypes which belonged to 8 clades) of Bartonella spp. were detected from 71 rodents comprising 5 species and 4 genera from 3 rodent families. Forty-one Bartonella isolates were recovered and identified, including B. taylorii, B. japonica, B. coopersplainsensis, B. grahamii, B. washoensis subsp. cynomysii, B. doshiae, and two novel Bartonella species, by sequencing of four genes (gltA, the 16S rRNA gene, ftsZ, and rpoB). The isolates of B. taylorii and B. grahamii were the most prevalent and exhibited genetic difference from isolates identified elsewhere. Several isolates clustered with strains from Japan and far-eastern Russia; strains isolated from the same host typically were found within the same cluster. Species descriptions are provided for Bartonella heixiaziensis sp. nov. and B. fuyuanensis sp. nov.

  6. High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort

    Directory of Open Access Journals (Sweden)

    Santos Susana

    2012-03-01

    Full Text Available Abstract Background Hypertrophic Cardiomyopathy (HCM is a complex myocardial disorder with a recognized genetic heterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis that should be considered of most importance for basic research and clinical medicine. Methodology In this report, we evaluated High Resolution Melting (HRM robustness, regarding HCM genetic testing, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associated sarcomere genes, as well as 24 genes with lower reported HCM-phenotype association. We analyzed 80 Portuguese individuals with clinical phenotype of HCM allowing simultaneously a better characterization of this disease in the Portuguese population. Results HRM technology allowed us to identify 60 mutated alleles in 72 HCM patients: 49 missense mutations, 3 nonsense mutations, one 1-bp deletion, one 5-bp deletion, one in frame 3-bp deletion, one insertion/deletion, 3 splice mutations, one 5'UTR mutation in MYH7, MYBPC3, TNNT2, TNNI3, CSRP3, MYH6 and MYL2 genes. Significantly 22 are novel gene mutations. Conclusions HRM was proven to be a technique with high sensitivity and a low false positive ratio allowing a rapid, innovative and low cost genotyping of HCM. In a short return, HRM as a gene scanning technique could be a cost-effective gene-based diagnosis for an accurate HCM genetic diagnosis and hopefully providing new insights into genotype/phenotype correlations.

  7. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    Science.gov (United States)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  8. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

    Directory of Open Access Journals (Sweden)

    Ellis Nathan A

    2008-02-01

    Full Text Available Abstract Background Genetic isolates such as the Ashkenazi Jews (AJ potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups. Results A small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P Conclusion LD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure.

  9. Development and Validation of the Learning Progression-Based Assessment of Modern Genetics in a High School Context

    Science.gov (United States)

    Todd, Amber; Romine, William L.; Cook Whitt, Katahdin

    2017-01-01

    We describe the development, validation, and use of the "Learning Progression-Based Assessment of Modern Genetics" (LPA-MG) in a high school biology context. Items were constructed based on a current learning progression framework for genetics (Shea & Duncan, 2013; Todd & Kenyon, 2015). The 34-item instrument, which was tied to…

  10. Genetic Evidence for Multiple Sources of the Non-Native Fish Cichlasoma urophthalmus (Günther; Mayan Cichlids) in Southern Florida

    Science.gov (United States)

    Harrison, Elizabeth; Trexler, Joel C.; Collins, Timothy M.; Vazquez-Domínguez, Ella; Razo-Mendivil, Ulises; Matamoros, Wilfredo A.; Barrientos, Christian

    2014-01-01

    The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, where all individuals were fixed for the mitochondrial haplotype found in the introduced population, and a more diverse but also relatively small number of individuals from Belize. The Florida cytochrome b haplotype appears to be absent from Belize (0 out of 136 fish screened from Belize had this haplotype). Genetic structure within the Florida population was minimal, indicating a panmictic population, while Mexican and Central American samples displayed more genetic subdivision. Individuals from the Upper Yucatán Peninsula and the Petén region of Guatemala were more genetically similar to each other than to fish from nearby sites and movement of Mayan Cichlids between these regions occurred thousands of generations ago, suggestive of pre-Columbian human transportation of Mayan Cichlids through this region. Mayan Cichlids present a rare example of cytonuclear disequilibrium and reduced genetic diversity in the introduced population that persists more than 30 years (at least 7–8 generations) after introduction. We suggest that hybridization occurred in ornamental fish farms in Florida and may contribute their establishment in the novel habitat. Hybridization prior to release may contribute to other successful invasions. PMID:25184569

  11. Genetic evidence for multiple sources of the non-native fish Cichlasoma urophthalmus (Günther; Mayan Cichlids) in southern Florida.

    Science.gov (United States)

    Harrison, Elizabeth; Trexler, Joel C; Collins, Timothy M; Vazquez-Domínguez, Ella; Razo-Mendivil, Ulises; Matamoros, Wilfredo A; Barrientos, Christian

    2014-01-01

    The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, where all individuals were fixed for the mitochondrial haplotype found in the introduced population, and a more diverse but also relatively small number of individuals from Belize. The Florida cytochrome b haplotype appears to be absent from Belize (0 out of 136 fish screened from Belize had this haplotype). Genetic structure within the Florida population was minimal, indicating a panmictic population, while Mexican and Central American samples displayed more genetic subdivision. Individuals from the Upper Yucatán Peninsula and the Petén region of Guatemala were more genetically similar to each other than to fish from nearby sites and movement of Mayan Cichlids between these regions occurred thousands of generations ago, suggestive of pre-Columbian human transportation of Mayan Cichlids through this region. Mayan Cichlids present a rare example of cytonuclear disequilibrium and reduced genetic diversity in the introduced population that persists more than 30 years (at least 7-8 generations) after introduction. We suggest that hybridization occurred in ornamental fish farms in Florida and may contribute their establishment in the novel habitat. Hybridization prior to release may contribute to other successful invasions.

  12. High-Voltage Electroporation of Bacteria: Genetic Transformation of Campylobacter jejuni with Plasmid DNA

    Science.gov (United States)

    Miller, Jeff F.; Dower, William J.; Tompkins, Lucy S.

    1988-02-01

    Electroporation permits the uptake of DNA by mammalian cells and plant protoplasts because it induces transient permeability of the cell membrane. We investigated the utility of high-voltage electroporation as a method for genetic transformation of intact bacterial cells by using the enteric pathogen Campylobacter jejuni as a model system. This report demonstrates that the application of high-voltage discharges to bacterial cells permits genetic transformation. Our method involves exposure of a Campylobacter cell suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a brief period of time (resistance-capacitance time constant = 2.4-26 msec) in the presence of plasmid DNA. Electrical transformation of C. jejuni results in frequencies as high as 1.2 × 106 transformants per μ g of DNA. We have investigated the effects of pulse amplitude and duration, cell growth conditions, divalent cations, and DNA concentration on the efficiency of transformation. Transformants of C. jejuni obtained by electroporation contained structurally intact plasmid molecules. In addition, evidence is presented that indicates that C. jejuni possesses DNA restriction and modification systems. The use of electroporation as a method for transforming other bacterial species and guidelines for its implementation are also discussed.

  13. Abandoning the common law: medical negligence, genetic tests and wrongful life in the Australian High Court.

    Science.gov (United States)

    Faunce, Thomas; Jefferys, Susannah

    2007-05-01

    The Australian High Court recently found that the common law could allow parents to claim tortious damages when medical negligence was proven to have led to the birth of an unplanned, but healthy, baby (Cattanach v Melchior (2003) 215 CLR 1). In Harriton v Stephens (2006) 80 ALJR 791; [2006] HCA 15 and Waller v James; Waller v Hoolahan (2006) 80 ALJR 846; [2006] HCA 16 the High Court in a six-to-one decision (Kirby J dissenting) decided that no such claim could be made by a child when medical negligence in failing to order an in utero genetic test caused the child severe disability. In an era when almost all pregnancies will soon require patented fetal genetic tests as part of the professional standard of care, the High Court, by barring so-called "wrongful life" (better termed "wrongful suffering") claims, may have created a partial immunity from suit for their corporate manufacturers and the doctors who administer them. What lessons can be learnt from this case about how the Australian High Court is, or should be, approaching medical negligence cases and its role as guardian of the Australian common law?

  14. Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae (Muller, 1774 in Portugal.

    Directory of Open Access Journals (Sweden)

    Cidália Gomes

    Full Text Available The Asian clam, Corbicula fluminea, is an invasive alien species (IAS originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers, morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity.

  15. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans.

    Directory of Open Access Journals (Sweden)

    Hafid Laayouni

    Full Text Available Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.

  16. A High Precision Comprehensive Evaluation Method for Flood Disaster Loss Based on Improved Genetic Programming

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yuliang; LU Guihua; JIN Juliang; TONG Fang; ZHOU Ping

    2006-01-01

    Precise comprehensive evaluation of flood disaster loss is significant for the prevention and mitigation of flood disasters. Here, one of the difficulties involved is how to establish a model capable of describing the complex relation between the input and output data of the system of flood disaster loss. Genetic programming (GP) solves problems by using ideas from genetic algorithm and generates computer programs automatically. In this study a new method named the evaluation of the grade of flood disaster loss (EGFD) on the basis of improved genetic programming (IGP) is presented (IGPEGFD). The flood disaster area and the direct economic loss are taken as the evaluation indexes of flood disaster loss. Obviously that the larger the evaluation index value, the larger the corresponding value of the grade of flood disaster loss is. Consequently the IGP code is designed to make the value of the grade of flood disaster be an increasing function of the index value. The result of the application of the IGP-EGFD model to Henan Province shows that a good function expression can be obtained within a bigger searched function space; and the model is of high precision and considerable practical significance.Thus, IGP-EGFD can be widely used in automatic modeling and other evaluation systems.

  17. Comparison of Fluorescence In Situ Hybridization and Chromogenic In Situ Hybridization for Low and High Throughput HER2 Genetic Testing

    DEFF Research Database (Denmark)

    Poulsen, Tim S; Espersen, Maiken Lise Marcker; Kofoed, Vibeke;

    2013-01-01

    results show that the differences between the HER2 genetic assays do not have an effect on the analytic performance and the CISH technology is superior to high throughput HER2 genetic testing due to scanning speed, while the IQ-FISH may still be a choice for fast low throughput HER2 genetic testing.......The purpose was to evaluate and compare 5 different HER2 genetic assays with different characteristics that could affect the performance to analyze the human epidermal growth factor 2 (HER2) gene copy number under low and high throughput conditions. The study included 108 tissue samples from breast...... cancer patients with HER2 immunohistochemistry (IHC) results scored as 0/1+, 2+, and 3+. HER2 genetic status was analysed using chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). Scoring results were documented through digital image analysis. The cancer region...

  18. Using spatial metrics and surveys for the assessment of trans-boundary deforestation in protected areas of the Maya Mountain Massif: Belize-Guatemala border.

    Science.gov (United States)

    Chicas, S D; Omine, K; Ford, J B; Sugimura, K; Yoshida, K

    2017-02-01

    Understanding the trans-boundary deforestation history and patterns in protected areas along the Belize-Guatemala border is of regional and global importance. To assess deforestation history and patterns in our study area along a section of the Belize-Guatemala border, we incorporated multi-temporal deforestation rate analysis and spatial metrics with survey results. This multi-faceted approach provides spatial analysis with relevant insights from local stakeholders to better understand historic deforestation dynamics, spatial characteristics and human perspectives regarding the underlying causes thereof. During the study period 1991-2014, forest cover declined in Belize's protected areas: Vaca Forest Reserve 97.88%-87.62%, Chiquibul National Park 99.36%-92.12%, Caracol Archeological Reserve 99.47%-78.10% and Colombia River Forest Reserve 89.22%-78.38% respectively. A comparison of deforestation rates and spatial metrics indices indicated that between time periods 1991-1995 and 2012-2014 deforestation and fragmentation increased in protected areas. The major underlying causes, drivers, impacts, and barriers to bi-national collaboration and solutions of deforestation along the Belize-Guatemala border were identified by community leaders and stakeholders. The Mann-Whitney U test identified significant differences between leaders and stakeholders regarding the ranking of challenges faced by management organizations in the Maya Mountain Massif, except for the lack of assessment and quantification of deforestation (LD, SH: 18.67, 23.25, U = 148, p > 0.05). The survey results indicated that failure to integrate buffer communities, coordinate among managing organizations and establish strong bi-national collaboration has resulted in continued ecological and environmental degradation. The information provided by this research should aid managing organizations in their continued aim to implement effective deforestation mitigation strategies.

  19. Genetic dissection of the mouse brain using high-field magnetic resonance microscopy.

    Science.gov (United States)

    Badea, A; Johnson, G A; Williams, R W

    2009-05-01

    Magnetic resonance (MR) imaging has demonstrated that variation in brain structure is associated with differences in behavior and disease state. However, it has rarely been practical to prospectively test causal models that link anatomical and functional differences in humans. In the present study we have combined classical mouse genetics with high-field MR to systematically explore and test such structure-functional relations across multiple brain regions. We segmented 33 regions in two parental strains-C57BL/6J (B) and DBA/2J (D)-and in nine BXD recombinant inbred strains. All strains have been studied extensively for more than 20 years using a battery of genetic, functional, anatomical, and behavioral assays. We compared levels of variation within and between strains and sexes, by region, and by system. Average within-strain variation had a coefficient of variation (CV) of 1.6% for the whole brain; while the CV ranged from 2.3 to 3.6% for olfactory bulbs, cortex and cerebellum, and up to approximately 18% for septum and laterodorsal thalamic nucleus. Variation among strain averages ranged from 6.7% for cerebellum, 7.6% for whole brain, 9.0% for cortex, up to approximately 26% for the ventricles, laterodorsal thalamic nucleus, and the interpeduncular nucleus. Heritabilities averaged 0.60+/-0.18. Sex differences were not significant with the possible (and unexpected) exception of the pons ( approximately 20% larger in males). A correlation matrix of regional volumes revealed high correlations among functionally related parts of the CNS (e.g., components of the limbic system), and several high correlations between regions that are not anatomically connected, but that may nonetheless be functionally or genetically coupled.

  20. No beneficial effect of preimplantation genetic screening in women of advanced maternal age with a high risk for embryonic aneuploidy

    NARCIS (Netherlands)

    Twisk, Moniek; Mastenbroek, Sebastiaan; Hoek, Annemieke; Heineman, Maas-Jan; van der Veen, Fulco; Bossuyt, Patrick M.; Repping, Sjoerd; Korevaar, Johanna C.

    2008-01-01

    Human preimplantation embryos generated through in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) treatments show a variable rate of numerical chromosome abnormalities or aneuploidies. Preimplantation genetic screening (PGS) has been designed to screen for aneuploidies in high

  1. Ancient Maya Regional Settlement and Inter-Site Analysis: The 2013 West-Central Belize LiDAR Survey

    Directory of Open Access Journals (Sweden)

    Arlen F. Chase

    2014-09-01

    Full Text Available During April and May 2013, a total of 1057 km2 of LiDAR was flown by NCALM for a consortium of archaeologists working in West-central Belize, making this the largest surveyed area within the Mayan lowlands. Encompassing the Belize Valley and the Vaca Plateau, West-central Belize is one of the most actively researched parts of the Maya lowlands; however, until this effort, no comprehensive survey connecting all settlement had been conducted. Archaeological projects have investigated at least 18 different sites within this region. Thus, a large body of archaeological research provides both the temporal and spatial parameters for the varied ancient Maya centers that once occupied this area; importantly, these data can be used to help interpret the collected LiDAR data. The goal of the 2013 LiDAR campaign was to gain information on the distribution of ancient Maya settlement and sites on the landscape and, particularly, to determine how the landscape was used between known centers. The data that were acquired through the 2013 LiDAR campaign have significance for interpreting both the composition and limits of ancient Maya political units. This paper presents the initial results of these new data and suggests a developmental model for ancient Maya polities.

  2. High genetic variation in marginal fragmented populations at extreme climatic conditions of the Patagonian Cypress Austrocedrus chilensis.

    Science.gov (United States)

    Arana, María Verónica; Gallo, Leonardo A; Vendramin, Giovanni G; Pastorino, Mario J; Sebastiani, Federico; Marchelli, Paula

    2010-03-01

    Knowledge about current patterns of genetic structure of populations together with the evolutionary history of a species helps to understand and predict the adaptation of populations to future climate change. We assayed variation at nuclear microsatellite markers among peripheral vs. continuous populations of the temperate South American species Austrocedrus chilensis, to investigate the role of historical vs. demographical forces in shaping population genetic structure. This species occurs in continuous populations in the west and central distribution range, but becomes highly fragmented at the eastern limit, which comprised ice-free areas during Quaternary glaciations and has extreme climatic conditions at present times. Bayesian analysis methods identified two contrasting patterns of genetic structure; (I) populations from humid, mesic and peri-glacial regions formed a single deme with relatively low genetic differentiation and high admixture levels whereas (II) a highly heterogeneous genetic structure with low level of admixture was found in the steppe, towards the east and northeast limit of the distribution range. In the steppe, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. In addition, several small steppe populations showed high genetic diversity and divergent gene pools, suggesting that they constitute ancient refuges from pre-Holocene glaciations with just a subgroup of them contributing significantly to post-glacial spread. These results are discussed in relation to patterns of genetic variation found for other temperate species and the contribution of the particular southern Andes topography and climate to post-glacial spread.

  3. Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study

    Science.gov (United States)

    Athanasiadis, Georgios; Jørgensen, Frank G.; Cheng, Jade Y.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas

    2016-01-01

    Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies. PMID:27571202

  4. Metabolic safety-margins do not differ between cows of high and low genetic merit for milk production

    DEFF Research Database (Denmark)

    Knight, Christopher Harold; Alamer, Mohammed A; Sorensen, Annette;

    2004-01-01

    Three galactopoietic stimuli, frequent milking (4X), bovine somatotrophin (bST) and thyroxine (T4) were used in an additive stair-step design to achieve maximum output (metabolic capacity) in six peak-lactation cows of high genetic merit (HT) and six of low genetic merit (LT). A further six of ea...... the commonly held belief that selective breeding of dairy cows for high milk production has rendered them markedly more susceptible to metabolic disturbances....

  5. A comparison of genetic variants between proficient low- and high-risk sport participants.

    Science.gov (United States)

    Thomson, Cynthia J; Power, Rebecca J; Carlson, Scott R; Rupert, Jim L; Michel, Grégory

    2015-01-01

    Athletes participating in high-risk sports consistently report higher scores on sensation-seeking measures than do low-risk athletes or non-athletic controls. To determine whether genetic variants commonly associated with sensation seeking were over-represented in such athletes, proficient practitioners of high-risk (n = 141) and low-risk sports (n = 132) were compared for scores on sensation seeking and then genotyped at 33 polymorphic loci in 14 candidate genes. As expected, athletes participating in high-risk sports score higher on sensation seeking than did low-risk sport athletes (P sport participation for two genes (stathmin, (P = .004) and brain-derived neurotrophic factor (P = .03)) as well as when demographically matched subsets of the sport cohorts were compared (P < .05); however, in all cases, associations did not survive correction for multiple testing.

  6. The high heritability of educational achievement reflects many genetically influenced traits, not just intelligence.

    Science.gov (United States)

    Krapohl, Eva; Rimfeld, Kaili; Shakeshaft, Nicholas G; Trzaskowski, Maciej; McMillan, Andrew; Pingault, Jean-Baptiste; Asbury, Kathryn; Harlaar, Nicole; Kovas, Yulia; Dale, Philip S; Plomin, Robert

    2014-10-21

    Because educational achievement at the end of compulsory schooling represents a major tipping point in life, understanding its causes and correlates is important for individual children, their families, and society. Here we identify the general ingredients of educational achievement using a multivariate design that goes beyond intelligence to consider a wide range of predictors, such as self-efficacy, personality, and behavior problems, to assess their independent and joint contributions to educational achievement. We use a genetically sensitive design to address the question of why educational achievement is so highly heritable. We focus on the results of a United Kingdom-wide examination, the General Certificate of Secondary Education (GCSE), which is administered at the end of compulsory education at age 16. GCSE scores were obtained for 13,306 twins at age 16, whom we also assessed contemporaneously on 83 scales that were condensed to nine broad psychological domains, including intelligence, self-efficacy, personality, well-being, and behavior problems. The mean of GCSE core subjects (English, mathematics, science) is more heritable (62%) than the nine predictor domains (35-58%). Each of the domains correlates significantly with GCSE results, and these correlations are largely mediated genetically. The main finding is that, although intelligence accounts for more of the heritability of GCSE than any other single domain, the other domains collectively account for about as much GCSE heritability as intelligence. Together with intelligence, these domains account for 75% of the heritability of GCSE. We conclude that the high heritability of educational achievement reflects many genetically influenced traits, not just intelligence.

  7. Optimisation of a high speed rotating composite drive shaft using a genetic algorithm - Hybrid high modulus-high resistance carbon solutions

    CERN Document Server

    Montagnier, Olivier

    2011-01-01

    This study deals with the optimisation of subcritical and supercritical laminated composite drive shafts, based on a genetic algorithm. The first part focuses on the modelling of a composite drive shaft. Flexural vibrations in a simply supported composite drive shaft mounted on viscoelastic supports, including shear effects are studied. In particular, an analytic stability criterion is developed to ensure the integrity of the system. The torsional strength is then computed with the maximum stress criterion, assuming the coupling effects to be null. Torsional buckling of thin walled composite tubes is modelled using a combination between laminate theory and Fl\\"ugge theory. In the second part, the genetic algorithm is developed. The last part presents a comparative study between various composite materials solutions on a helicopter tail rotor driveline. In particular, hybrid tubes consisting of high modulus and high resistance carbon/epoxy plies are studied. These solutions make it possible to replace the conv...

  8. New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius )

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments ( 109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.

  9. Genetic Diversity of High and Low Molecular Weight Glutenin Subunits in Algerian Aegilops geniculata

    Directory of Open Access Journals (Sweden)

    Asma MEDOURI

    2014-12-01

    Full Text Available Aegilops geniculata Roth is an annual grass relative to cultivated wheat and is widely distributed in North Algeria. Endosperm storage proteins of wheat and its relatives, namely glutenins and gliadins, play an important role in dough properties and bread making quality. In the present study, the different alleles encoded at the four glutenin loci (Glu-M1, Glu-U1, Glu-M3 and Glu-U3 were identified from thirty five accessions of the tetraploid wild wheat A. geniculata collected in Algeria using Sodium dodecyl Sulfate - Polyacrylamide Gel Electrophoresis (SDS-PAGE. At Glu-M1 and Glu-U1 loci, encoding high molecular weight glutenin subunits (HMW-GS or A-subunits, 15 and 12 alleles were observed respectively, including one new subunit. B-Low molecular weight glutenin subunits zone (B-LMW-GS displayed a far greater variation, as 28 and 25 alleles were identified at loci Glu-M3 and Glu-U3 respectively. Thirty two subunits patterns were revealed at the C subunits- zone and a total of thirty four patterns resulted from the genetic combination of the two zones (B- and C-zone. The wide range of glutenin subunits variation (high molecular weight glutenin subunits and low molecular weight glutenin subunits in this species has the potential to enhance the genetic variability for improving the quality of wheat./span>

  10. GENETIC ALGORITHMS AND GAME THEORY FOR HIGH LIFT DESIGN PROBLEMS IN AERODYNAMICS

    Institute of Scientific and Technical Information of China (English)

    PériauxJacques; WangJiangfeng; WuYizhao

    2002-01-01

    A multi-objective evolutionary optimization method (combining genetic algorithms(GAs)and game theory(GT))is presented for high lift multi-airfoil systems in aerospace engineering.Due to large dimension global op-timization problems and the increasing importance of low cost distributed parallel environments,it is a natural idea to replace a globar optimization by decentralized local sub-optimizations using GT which introduces the notion of games associated to an optimization problem.The GT/GAs combined optimization method is used for recon-struction and optimization problems by high lift multi-air-foil desing.Numerical results are favorably compared with single global GAs.The method shows teh promising robustness and efficient parallel properties of coupled GAs with different game scenarios for future advanced multi-disciplinary aerospace techmologies.

  11. A high-resolution neutron spectra unfolding method using the Genetic Algorithm technique

    CERN Document Server

    Mukherjee, B

    2002-01-01

    The Bonner sphere spectrometers (BSS) are commonly used to determine the neutron spectra within various nuclear facilities. Sophisticated mathematical tools are used to unfold the neutron energy distribution from the output data of the BSS. This paper highlights a novel high-resolution neutron spectra-unfolding method using the Genetic Algorithm (GA) technique. The GA imitates the biological evolution process prevailing in the nature to solve complex optimisation problems. The GA method was utilised to evaluate the neutron energy distribution, average energy, fluence and equivalent dose rates at important work places of a DIDO class research reactor and a high-energy superconducting heavy ion cyclotron. The spectrometer was calibrated with a sup 2 sup 4 sup 1 Am/Be (alpha,n) neutron standard source. The results of the GA method agreed satisfactorily with the results obtained by using the well-known BUNKI neutron spectra unfolding code.

  12. Genetic variants in EPAS1 contribute to adaptation to high-altitude hypoxia in Sherpas.

    Directory of Open Access Journals (Sweden)

    Masayuki Hanaoka

    Full Text Available Sherpas comprise a population of Tibetan ancestry in the Himalayan region that is renowned for its mountaineering prowess. The very small amount of available genetic information for Sherpas is insufficient to explain their physiological ability to adapt to high-altitude hypoxia. Recent genetic evidence has indicated that natural selection on the endothelial PAS domain protein 1 (EPAS1 gene was occurred in the Tibetan population during their occupation in the Tibetan Plateau for millennia. Tibetan-specific variations in EPAS1 may regulate the physiological responses to high-altitude hypoxia via a hypoxia-inducible transcription factor pathway. We examined three significant tag single-nucleotide polymorphisms (SNPs, rs13419896, rs4953354, and rs4953388 in the EPAS1 gene in Sherpas, and compared these variants with Tibetan highlanders on the Tibetan Plateau as well as with non-Sherpa lowlanders. We found that Sherpas and Tibetans on the Tibetan Plateau exhibit similar patterns in three EPAS1 significant tag SNPs, but these patterns are the reverse of those in non-Sherpa lowlanders. The three SNPs were in strong linkage in Sherpas, but in weak linkage in non-Sherpas. Importantly, the haplotype structured by the Sherpa-dominant alleles was present in Sherpas but rarely present in non-Sherpas. Surprisingly, the average level of serum erythropoietin in Sherpas at 3440 m was equal to that in non-Sherpas at 1300 m, indicating a resistant response of erythropoietin to high-altitude hypoxia in Sherpas. These observations strongly suggest that EPAS1 is under selection for adaptation to the high-altitude life of Tibetan populations, including Sherpas. Understanding of the mechanism of hypoxia tolerance in Tibetans is expected to provide lights to the therapeutic solutions of some hypoxia-related human diseases, such as cardiovascular disease and cancer.

  13. Type 2 diabetes mellitus non-genetic Rhesus monkey model induced by high fat and high sucrose diet.

    Science.gov (United States)

    Lu, Shuai-yao; Qi, Su-dong; Zhao, Yuan; Li, Yan-yan; Yang, Feng-mei; Yu, Wen-hai; Jin, Ma; Chen, Li-Xiong; Wang, Jun-bin; He, Zhan-long; Li, Hong-jun

    2015-01-01

    To build an ideal animal model for studying the mechanism of occurrence, developing and treating of diabetes become a more important issue, facing with the fact that the big threat of diabetes to human health has been worsen. First, we used the normal control diets or the high-fat/high-sucrose diets to feed the adult rhesus monkeys and the macaques induced by the high-fat/high-sucrose diets in the high-fat/high-sucrose group and the type 2 diabetes mellitus (T2DM) group developed the hyperglycemia, hyperinsulinemia at 6 months in accordance with the precious researches that reported that minipigs, rats and mice could develop hyperglycemia, hyperinsulinemia, hyperlipidemia and obesity after being induced with high-fat/high-carbohydrate diets. Second, the rhesus monkeys in T2DM group were injected STZ at a low dosage of 35 mg/kg BW to induce glucose persistent elevation which maintained pretty well after 12 months. Third, we took the assay of glucose tolerance test and insulin resistance index, assessed the changing tendency of serum resistin and analysed the pathological characteristics of the tissues like pancreas and liver by staining in different ways. The results indicate the rhesus monkeys in T2DM group have lots of clinical features of T2DM. The experimental non-genetic T2DM rhesus monkeys model not only contribute to simulating of clinical manifestations and pathological features of human T2DM, but also may be a good kind of model for research on the treatment of T2DM and for new drugs evaluation.

  14. Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird

    Science.gov (United States)

    Wiley, Anne E.; Welch, Andreanna J.; Ostrom, P.H.; James, Helen F.; Stricker, C.A.; Fleischer, R.C.; Gandhi, H.; Adams, J.; Ainley, D.G.; Duvall, F.; Holmes, N.; Hu, D.; Judge, S.; Penniman, J.; Swindle, K.A.

    2012-01-01

    Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?? 13C, ?? 15N and ??D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?? ST = 0. 50 (p < 0. 0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower ?? 13C and ?? 15N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated ?? 15N values at the food web base. ?? 15N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather ??D varied from -69 to 53???. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. ?? 2011 Springer-Verlag (outside the USA).

  15. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei.

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-10-27

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

  16. Design of high performance multilayer microwave absorbers using fast Pareto genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    JIANG LiYong; LI XiangYin; ZHANG Jie

    2009-01-01

    The application of the Non-dominated Sorting Genetic Algorithm Ⅱ (NSGA-Ⅱ) in designing microwave absorbers is described in this paper. To obtain high performance coatings, we put forward three cost functions, which represent three objectives of strong-absorption, broad-bandwidth and thin structure, and study the tradeoffs between each other. Numerical calculations on available materials in 2-18 GHz are implemented to construct the Pareto front and Pareto-optimal surface for two and three objectives respectively. Results indicate that the NSGA-Ⅱ can work more efficiently and effectively than traditional Pareto genetic algorithms. Additionally, we present several particular designs from the above Pareto front (surface) for potential applications in different frequency bands. For example, a four-layer ab-sorber with thickness of 2.8071 mm is obtained to provide average reflection coefficient of -11.95 dB and average reflection bandwidth of 0.5780 in 2-18 GHz, considering arbitrary incident angles (0°-89°) and both TE and TM polarizations.

  17. Hepatic lipase, genetically elevated high-density lipoprotein, and risk of ischemic cardiovascular disease

    DEFF Research Database (Denmark)

    Johannsen, Trine Holm; Kamstrup, Pia R; Andersen, Rolf V;

    2008-01-01

    CONTEXT: Hepatic lipase influences metabolism of high-density lipoprotein (HDL), a risk factor for ischemic cardiovascular disease (ICD: ischemic heart disease and ischemic cerebrovascular disease). OBJECTIVE: We tested the hypothesis that genetic variation in the hepatic lipase genetic variants V...... of whom had incident ICD during 28 yr of follow-up. For the case-control studies, 2110 ischemic heart disease patients vs. 4899 controls and 769 ischemic cerebrovascular disease patients vs. 2836 controls, respectively, were genotyped. Follow-up was 100% complete. RESULTS: HDL cholesterol was higher by 0.......21 mmol/liter in S267F heterozygotes, by 0.06 mmol/liter in -480c>t heterozygotes, and by 0.13 mmol/liter in -480c>t homozygotes, as compared with noncarriers. These HDL increases theoretically predicted hazard ratios for ICD of 0.87 [95% confidence interval (CI) 0.84-0.90], 0.96 (95% CI 0.95-0.97), and 0...

  18. High urban breeding densities do not disrupt genetic monogamy in a bird species.

    Science.gov (United States)

    Rodriguez-Martínez, Sol; Carrete, Martina; Roques, Séverine; Rebolo-Ifrán, Natalia; Tella, José L

    2014-01-01

    Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process.

  19. High urban breeding densities do not disrupt genetic monogamy in a bird species.

    Directory of Open Access Journals (Sweden)

    Sol Rodriguez-Martínez

    Full Text Available Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%, but relatively high levels of intraspecific brood parasitism (8.82%. However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process.

  20. Design of high performance multilayer microwave absorbers using fast Pareto genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The application of the Non-dominated Sorting Genetic Algorithm Ⅱ (NSGA-Ⅱ) in designing microwave absorbers is described in this paper. To obtain high performance coatings,we put forward three cost functions,which represent three objectives of strong-absorption,broad-bandwidth and thin structure,and study the tradeoffs between each other. Numerical calculations on available materials in 2―18 GHz are implemented to construct the Pareto front and Pareto-optimal surface for two and three objectives respectively. Results indicate that the NSGA-Ⅱ can work more efficiently and effectively than traditional Pareto genetic algorithms. Additionally,we present several particular designs from the above Pareto front (surface) for potential applications in different frequency bands. For example,a four-layer absorber with thickness of 2.8071 mm is obtained to provide average reflection coefficient of -11.95 dB and average reflection bandwidth of 0.5780 in 2―18 GHz,considering arbitrary incident angles (0°―89°) and both TE and TM polarizations.

  1. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

    Directory of Open Access Journals (Sweden)

    Mark McMullan

    Full Text Available The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC of guppies (Poecilia reticulata to study the turnover rate of alleles (temporal genetic differentiation, G'(ST. Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1 overdominant selection, (2 fluctuating population size within a metapopulation, and (3 the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST outlier analysis may obscure the signal of selection.

  2. Effects of genetic and non-genetic factors on growth traits of high yielding dairy seed calves and genetic parameter estimates

    Directory of Open Access Journals (Sweden)

    Syed Mohammad Ashiqur Rahman

    2015-12-01

    Full Text Available The study was conducted to know the effects of several genetic and non-genetic factors like season, sex, year of birth, genotype of calves and milk yield of dam associated with growth performance of crossbred calves. Data were collected from registered farmers during the period of May, 2011 to April, 2013. Birth weight, three-month weight, six-month weight, weaning weight and heritability estimates of those growth performances were performed using a total of 82 registered calves which had pedigree information having the genotypes of 25% Local - 75% Friesian and 37.5% Local - 62.5% Friesian. The average birth, three-month, six-month and weaning weight of calves were 29.33, 64.32, 99.06 and 151.77 kg, respectively. The effects of non-genetic factors like sex, season of birth and genotype were non-significant (P>0.05 for the traits birth weight, three-month, six-month, weaning weight and average daily gain of calves. However, year of birth was found significant on birth (P0.05 on weaning weight and average daily gain of calves. The heritability estimates were 0.40±0.09, 0.46±0.08, 0.39±0.12 and 0.50±0.12 for the traits birth weight, three-month weight, six-month weight and weaning weight, respectively. Estimated heritabilities of live weights suggest that individual own performance basis selection would be more effective for increasing growth and therefore, should be paid more emphasis in cattle improvement program.

  3. Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.

    Directory of Open Access Journals (Sweden)

    Qiao Fan

    Full Text Available As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL. Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, β = -0.16 mm per minor allele, P(meta =2.69 × 10(-10. The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR =0.75, 95% CI: 0.68-0.84, P(meta =4.38 × 10(-7 in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia.

  4. Genetic basis of unstable expression of high gamma-tocopherol content in sunflower seeds

    Directory of Open Access Journals (Sweden)

    García-Moreno María J

    2012-05-01

    Full Text Available Abstract Background Tocopherols are natural antioxidants with both in vivo (vitamin E and in vitro activity. Sunflower seeds contain predominantly alpha-tocopherol (>90% of total tocopherols, with maximum vitamin E effect but lower in vitro antioxidant action than other tocopherol forms such as gamma-tocopherol. Sunflower germplasm with stable high levels of gamma-tocopherol (>85% has been developed. The trait is controlled by recessive alleles at a single locus Tph2 underlying a gamma-tocopherol methyltransferase (gamma-TMT. Additionally, unstable expression of increased gamma-tocopherol content in the range from 5 to 85% has been reported. The objective of this research was to determine the genetic basis of unstable expression of high gamma-tocopherol content in sunflower seeds. Results Male sterile plants of nuclear male sterile line nmsT2100, with stable high gamma-tocopherol content, were crossed with plants of line IAST-1, with stable high gamma-tocopherol content but derived from a population that exhibited unstable expression of the trait. F2 seeds showed continuous segregation for gamma-tocopherol content from 1.0 to 99.7%. Gamma-tocopherol content in F2 plants (average of 24 individual F3 seeds segregated from 59.4 to 99.4%. A genetic linkage map comprising 17 linkage groups (LGs was constructed from this population using 109 SSR and 20 INDEL marker loci, including INDEL markers for tocopherol biosynthesis genes. QTL analysis revealed a major QTL on LG 8 that corresponded to the gamma-TMT Tph2 locus, which suggested that high gamma-tocopherol lines nmsT2100 and IAST-1 possess different alleles at this locus. Modifying genes were identified at LGs 1, 9, 14 and 16, corresponding in most cases with gamma-TMT duplicated loci. Conclusions Unstable expression of high gamma-tocopherol content is produced by the effect of modifying genes on tph2a allele at the gamma-TMT Tph2 gene. This allele is present in line IAST-1 and is different to

  5. A likely case of scurvy in a rural Early Classic Maya burial from Actun Uayazba Kab, Belize.

    Science.gov (United States)

    Wrobel, Gabriel

    2014-11-01

    A Maya burial of a late adolescent (Burial 98-3) found in the rockshelter entrance of Actun Uayazba Kab (AUK), Belize, displays a combination of lesions that is consistent with scurvy. Signs include large, active lesions on the posterior surfaces of maxilla; relatively mild porotic hyperostosis along the midline of the skull on the parietals and occipital; cribra orbitalia; potential pinprick lesions on the greater wings of sphenoid and temporal; reactive lesions on the palate, temporal lines of frontal and parietals, and external and internal surfaces of zygomatics; small lesions on the popliteal surfaces of both femora; and periodontal disease. Identification of scurvy at AUK potentially informs the analysis of other primary burials and scattered bone found there and at other nearby sites, which often reveal evidence of nonspecific lesions that are usually attributed to anemia and infection, but that are also consistent with scurvy. The social and ecological context of this Protoclassic (0-AD 300) individual, who lived in a rural agricultural community with no evidence of complex social hierarchy, contrasts with typical discussions of disease among the Maya, which tend to focus on the degrading effects of overcrowding and resource deficiencies. While scurvy has been largely overlooked in the Maya area, this study supports earlier arguments for its presence that were based largely on clinical and ethnographic analogies and suggests the need to incorporate scurvy into broader synergistic models of ancient health.

  6. A "coca-cola" shape: cultural change, body image, and eating disorders in San Andrés, Belize.

    Science.gov (United States)

    Anderson-Fye, Eileen P

    2004-12-01

    Eating disorders have been associated with developing nations undergoing rapid social transition, including participation in a global market economy and heavy media exposure. San Andrés, Belize, a community with many risk factors associated with the cross-cultural development of eating disorders, has shown remarkable resistance to previously documented patterns, despite a local focus on female beauty. Drawing on longitudinal person-centered ethnography with adolescent girls, this article examines why this community appears exceptional in light of the literature. First, community beauty and body image ideals and practices are explicated. Then, a protective ethnopsychology is proposed as a key mediating factor of the rapid socio-cultural change among young women. Finally, possible nascent cases of eating disordered behavior are discussed in light of their unique phenomenology: that is, having to do more with economic opportunity in the tourism industry and less with personal distress or desire for thinness. Close, meaning-centered examination of eating and body image practices may aid understanding and prevention of eating disorders among adolescents undergoing rapid social change in situations of globalization and immigration.

  7. A high-performance genetic algorithm: using traveling salesman problem as a case.

    Science.gov (United States)

    Tsai, Chun-Wei; Tseng, Shih-Pang; Chiang, Ming-Chao; Yang, Chu-Sing; Hong, Tzung-Pei

    2014-01-01

    This paper presents a simple but efficient algorithm for reducing the computation time of genetic algorithm (GA) and its variants. The proposed algorithm is motivated by the observation that genes common to all the individuals of a GA have a high probability of surviving the evolution and ending up being part of the final solution; as such, they can be saved away to eliminate the redundant computations at the later generations of a GA. To evaluate the performance of the proposed algorithm, we use it not only to solve the traveling salesman problem but also to provide an extensive analysis on the impact it may have on the quality of the end result. Our experimental results indicate that the proposed algorithm can significantly reduce the computation time of GA and GA-based algorithms while limiting the degradation of the quality of the end result to a very small percentage compared to traditional GA.

  8. High-Throughput SNP Discovery And Genetic Mapping In Perennial Ryegrass

    DEFF Research Database (Denmark)

    Asp, Torben; Studer, Bruno; Lübberstedt, Thomas

    Gene-associated single nucleotide polymorphisms (SNPs) are of major interest for genome analysis and breeding applications in the key grassland species perennial ryegrass. High-throughput 454 Titanium transcriptome sequencing was performed on two genotypes, which previously have been used to esta...... in the VrnA mapping population. Here we report on large-scale SNP discovery, and the construction of a genetic map enabling QTL fine mapping, map-based cloning, and comparative genomics in perennial ryegrass....... to establish the VrnA F2 mapping population. The sequences were assembled and used for in-silico SNP discovery. SNPs supported by a minimum number of eight reads, within candidate genes for important agronomic traits, were selected for Illumina GoldenGate genotyping and used to map 768 expressed genes...

  9. High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato

    Science.gov (United States)

    Behringer, F. J.; Lomax, T. L.

    1999-01-01

    Mutation of the Lazy-2 (Lz-2) gene in tomato (Lycopersicon esculentum mill.) produces a phytochrome-dependent reversal of shoot gravitropism, providing a unique genetic resource for investigating how signals from light modulate gravitropism. We mapped the Lz-2 gene using RFLPs and a PCR-based technique to assess the feasibility of positional cloning. Analysis of a 1338 plant backcross population between L. esculentum and L. pennellii placed Lz-2 within a 1.2 cM interval on chromosome 5, 0.4 cM from TG504-CT201A interval. The inabililty to resolve these markers indicates that Lz-2 resides in a centromeric region in which recombination is highly suppressed. Lazy-2 is tightly linked to but does not encode the gene for ACC4, an enzyme involved in ethylene biosynthesis. We also observed that Lz-2 is partially dominant under certain conditions and stages of development.

  10. Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts.

    Science.gov (United States)

    Haynes, Benjamin T; Marcus, Alan D; Higgins, Damien P; Gongora, Jaime; Gray, Rachael; Šlapeta, Jan

    2014-12-01

    The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology.

  11. Global Characterization of Genetic Variation by Using High-Throughput Technologies

    DEFF Research Database (Denmark)

    Zhan, Bujie

    Genetic variation, variation in alleles of genomes, occurs bith within and among populations and individuals. Genetic variation is important because it provides the "raw material" for evolution. Discovery of vatiants that determine phenotypes became a fundamental premise of genetic research...... into genetic variation in bovine and swine genomes and relevant methodologies; valuable resources such as novel genome sequences of pathogens, genome annotations and genetic variations were produced for research communities regard to animal health and welfare in animal breeding industriy....... This projekt aimed to characterize large scale of genetic vaiations in complex genomes by applying hig-throughput technologies and bioinformatic approache4s, to help investigate genetic foundation of disease susceptibility and product traits in livestock species. This PhD project provide a comprehensive sight...

  12. Genetic Analysis of High Bone Mass Cases from the BARCOS Cohort of Spanish Postmenopausal Women

    Science.gov (United States)

    Urreizti, Roser; Civit, Sergi; Cols, Neus; García-Giralt, Natàlia; Yoskovitz, Guy; Aranguren, Alvaro; Malouf, Jorge; Di Gregorio, Silvana; Río, Luís Del; Güerri, Roberto; Nogués, Xavier; Díez-Pérez, Adolfo; Grinberg, Daniel; Balcells, Susana

    2014-01-01

    The aims of the study were to establish the prevalence of high bone mass (HBM) in a cohort of Spanish postmenopausal women (BARCOS) and to assess the contribution of LRP5 and DKK1 mutations and of common bone mineral density (BMD) variants to a HBM phenotype. Furthermore, we describe the expression of several osteoblast-specific and Wnt-pathway genes in primary osteoblasts from two HBM cases. A 0.6% of individuals (10/1600) displayed Z-scores in the HBM range (sum Z-score >4). While no mutation in the relevant exons of LRP5 was detected, a rare missense change in DKK1 was found (p.Y74F), which cosegregated with the phenotype in a small pedigree. Fifty-five BMD SNPs from Estrada et al. [NatGenet 44:491-501,2012] were genotyped in the HBM cases to obtain risk scores for each individual. In this small group of samples, Z-scores were found inversely related to risk scores, suggestive of a polygenic etiology. There was a single exception, which may be explained by a rare penetrant genetic variant, counterbalancing the additive effect of the risk alleles. The expression analysis in primary osteoblasts from two HBM cases and five controls suggested that IL6R, DLX3, TWIST1 and PPARG are negatively related to Z-score. One HBM case presented with high levels of RUNX2, while the other displayed very low SOX6. In conclusion, we provide evidence of lack of LRP5 mutations and of a putative HBM-causing mutation in DKK1. Additionally, we present SNP genotyping and expression results that suggest additive effects of several genes for HBM. PMID:24736728

  13. Exploring the Effects of Active Learning on High School Students' Outcomes and Teachers' Perceptions of Biotechnology and Genetics Instruction

    Science.gov (United States)

    Mueller, Ashley L.; Knobloch, Neil A.; Orvis, Kathryn S.

    2015-01-01

    Active learning can engage high school students to learn science, yet there is limited understanding if active learning can help students learn challenging science concepts such as genetics and biotechnology. This quasi-experimental study explored the effects of active learning compared to passive learning regarding high school students'…

  14. Social Engagement with Parents in 11-Month-Old Siblings at High and Low Genetic Risk for Autism Spectrum Disorder

    Science.gov (United States)

    Campbell, Susan B.; Leezenbaum, Nina B.; Mahoney, Amanda S.; Day, Taylor N.; Schmidt, Emily N.

    2015-01-01

    Infant siblings of children with an autism spectrum disorder are at heightened genetic risk to develop autism spectrum disorder. We observed high risk (n?=?35) and low risk (n?=?27) infants at 11?months during free play with a parent. Children were assessed for autism spectrum disorder in toddlerhood. High-risk infants with a later diagnosis…

  15. High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

    Science.gov (United States)

    2010-01-01

    Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees. PMID:21637609

  16. High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae

    Directory of Open Access Journals (Sweden)

    Roberto Tarazi

    2010-01-01

    Full Text Available Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.

  17. Pattern of genetic differentiation of an incipient speciation process: The case of the high Andean killifish Orestias

    Science.gov (United States)

    Guerrero-Jiménez, Claudia Jimena; Peña, Fabiola; Morales, Pamela; Méndez, Marco; Sallaberry, Michel; Vila, Irma; Poulin, Elie

    2017-01-01

    During the Pleistocene and Holocene, the southwest Andean Altiplano (17°-22°S) was affected by repeated fluctuations in water levels, high volcanic activity and major tectonic movements. In the early Holocene the humid Tauca phase shifted to the arid conditions that have lasted until the present, producing endorheic rivers, lakes, lagoons and wetlands. The endemic fish Orestias (Cyprinodontidae) represents a good model to observe the genetic differentiation that characterizes an incipient speciation process in allopatry since the morphospecies described inhabit a restricted geographic area, with present habitat fragmentation. The genetic diversity and population structure of four endemic morphospecies of Orestias (Cyprinodontidae) found in the Lauca National Park (LNP) analyzed with mitochondrial markers (Control Region) and eight microsatellites, revealed the existence of genetic groups that matches the fragmentation of these systems. High values of genetic and phylogeographic differentiation indices were observed between Chungará Lake and Piacota lagoon. The group composed of the Lauca River, Copapujo and Chuviri wetlands sampling sites showed a clear signal of expansion, with a star-like haplotype network. Levels of genetic differentiation were lower than in Chungará and Piacota, suggesting that these localities would have differentiated after the bottlenecks linked to the collapse of Parinacota volcano. The Parinacota sample showed a population signal that differed from the other localities revealing greater genetic diversity and a disperse network, presenting haplotypes shared with other LNP localities. A mixing pattern of the different genetic groups was evident using the microsatellite markers. The chronology of the vicariance events in LNP may indicate that the partition process of the Orestias populations was gradual. Considering this, and in view of the genetic results, we may conclude that the morphospecies from LNP are populations in ongoing

  18. Loss of genetic diversity as a consequence of selection in response to high pCO 2

    OpenAIRE

    Lloyd, Melanie M.; Makukhov, April D.; Pespeni, Melissa H.

    2016-01-01

    Abstract Standing genetic variation may allow for rapid evolutionary response to the geologically unprecedented changes in global conditions. However, there is little known about the consequences of such rapid evolutionary change. Here, we measure genetic responses to experimental low and high pCO 2 levels in purple sea urchin larvae, Strongylocentrotus purpuratus. We found greater loss of nucleotide diversity in high pCO 2 levels (18.61%; 900 μatm) compared to low pCO 2 levels (10.12%; 400 μ...

  19. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    Science.gov (United States)

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  20. Unique Features of High-Density Lipoproteins in the Japanese: In Population and in Genetic Factors

    Directory of Open Access Journals (Sweden)

    Shinji Yokoyama

    2015-04-01

    Full Text Available Despite its gradual increase in the past several decades, the prevalence of atherosclerotic vascular disease is low in Japan. This is largely attributed to difference in lifestyle, especially food and dietary habits, and it may be reflected in certain clinical parameters. Plasma high-density lipoprotein (HDL levels, a strong counter risk for atherosclerosis, are indeed high among the Japanese. Accordingly, lower HDL seems to contribute more to the development of coronary heart disease (CHD than an increase in non-HDL lipoproteins at a population level in Japan. Interestingly, average HDL levels in Japan have increased further in the past two decades, and are markedly higher than in Western populations. The reasons and consequences for public health of this increase are still unknown. Simulation for the efficacy of raising HDL cholesterol predicts a decrease in CHD of 70% in Japan, greater than the extent by reducing low-density lipoprotein cholesterol predicted by simulation or achieved in a statin trial. On the other hand, a substantial portion of hyperalphalipoproteinemic population in Japan is accounted for by genetic deficiency of cholesteryl ester transfer protein (CETP, which is also commonly unique in East Asian populations. It is still controversial whether CETP mutations are antiatherogenic. Hepatic Schistosomiasis is proposed as a potential screening factor for historic accumulation of CETP deficiency in East Asia.

  1. High Genetic Diversity of Measles Virus, World Health Organization European Region, 2005–2006

    Science.gov (United States)

    Brown, Kevin E.; Jin, Li; Santibanez, Sabine; Shulga, Sergey V.; Aboudy, Yair; Demchyshyna, Irina V.; Djemileva, Sultana; Echevarria, Juan E.; Featherstone, David F.; Hukic, Mirsada; Johansen, Kari; Litwinska, Bogumila; Lopareva, Elena; Lupulescu, Emilia; Mentis, Andreas; Mihneva, Zefira; Mosquera, Maria M.; Muscat, Mark; Naumova, M.A.; Nedeljkovic, Jasminka; Nekrasova, Ljubov S.; Magurano, Fabio; Fortuna, Claudia; Rebelo de Andrade, Helena; Richard, Jean-Luc; Robo, Alma; Rota, Paul A.; Samoilovich, Elena O.; Sarv, Inna; Semeiko, Galina V.; Shugayev, Nazim; Utegenova, Elmira S.; van Binnendijk, Rob; Vinner, Lasse; Waku-Kouomou, Diane; Wild, T. Fabian; Brown, David W.G.; Mankertz, Annette; Muller, Claude P.; Mulders, Mick N.

    2008-01-01

    During 2005–2006, nine measles virus (MV) genotypes were identified throughout the World Health Organization European Region. All major epidemics were associated with genotypes D4, D6, and B3. Other genotypes (B2, D5, D8, D9, G2, and H1) were only found in limited numbers of cases after importation from other continents. The genetic diversity of endemic D6 strains was low; genotypes C2 and D7, circulating in Europe until recent years, were no longer identified. The transmission chains of several indigenous MV strains may thus have been interrupted by enhanced vaccination. However, multiple importations from Africa and Asia and virus introduction into highly mobile and unvaccinated communities caused a massive spread of D4 and B3 strains throughout much of the region. Thus, despite the reduction of endemic MV circulation, importation of MV from other continents caused prolonged circulation and large outbreaks after their introduction into unvaccinated and highly mobile communities. PMID:18258089

  2. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    Directory of Open Access Journals (Sweden)

    Wang Nian

    2012-08-01

    Full Text Available Abstract Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

  3. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis.

    Directory of Open Access Journals (Sweden)

    Le Wang

    Full Text Available The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

  4. High prevalence and genetic diversity of HCV among HIV-1 infected people from various high-risk groups in China.

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    Hong Shang

    Full Text Available BACKGROUND: Co-infection with HIV-1 and HCV is a significant global public health problem and a major consideration for anti-HIV-1 treatment. HCV infection among HIV-1 positive people who are eligible for the newly launched nationwide anti-HIV-1 treatment program in China has not been well characterized. METHODOLOGY: A nationwide survey of HIV-1 positive injection drug uses (IDU, former paid blood donors (FBD, and sexually transmitted cases from multiple provinces including the four most affected provinces in China was conducted. HCV prevalence and genetic diversity were determined. We found that IDU and FBD have extremely high rates of HCV infection (97% and 93%, respectively. Surprisingly, people who acquired HIV-1 through sexual contact also had a higher rate of HCV infection (20% than the general population. HIV-1 subtype and HCV genotypes were amazingly similar among FBD from multiple provinces stretching from Central to Northeast China. However, although patterns of overland trafficking of heroin and distinct HIV-1 subtypes could be detected among IDU, HCV genotypes of IDU were more diverse and exhibited significant regional differences. CONCLUSION: Emerging HIV-1 and HCV co-infection and possible sexual transmission of HCV in China require urgent prevention measures and should be taken into consideration in the nationwide antiretroviral treatment program.

  5. Using the Eastern Hellbender Salamander in a High School Genetics & Ecological Conservation Activity

    Science.gov (United States)

    Chudyk, Sarah; McMillan, Amy; Lange, Catherine

    2014-01-01

    This article contains an original 5E lesson plan developed from conservation genetics research on the giant North American hellbender salamander, Cryptobranchus alleganiensis alleganiensis. The lesson plan provides background information on the hellbender, reviews basic genetics, and exposes students to the scientific process that is used during…

  6. High density SNP and SSR-based genetic maps of two independent oil palm hybrids

    NARCIS (Netherlands)

    Ting, N.C.; Jansen, J.; Mayes, S.; Massawe, F.; Sambanthamurthi, R.; Cheng-Li Ooi, L.; Chin, C.W.; Arulandoo, X.; Seng, T.Y.; Alwee, S.S.R.S.; Ithnin, M.; Singh, R.

    2014-01-01

    BACKGROUND: Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers wer

  7. Unexpectedly high genetic variation in large unisexual clumps of the subdioecious plant Honckenya peploides

    DEFF Research Database (Denmark)

    Sánchez-Vilas, Julia; Philipp, Marianne; Retuerto, Rubén

    2010-01-01

    Honckenya peploides is a subdioecious dune plant that reproduces both sexually and by clonal growth. In northwest Spain this species was found to exhibit an extreme spatial segregation of the sexes, and our objective was to investigate genetic variation in unisexual clumps. Genetic variation was ...

  8. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

    Directory of Open Access Journals (Sweden)

    Nagy Ervin D

    2012-09-01

    Full Text Available Abstract Background Cultivated peanut (Arachis hypogaea is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago

  9. High prevalence, genetic diversity and intracellular growth ability of Legionella in hot spring environments.

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    Tian Qin

    Full Text Available BACKGROUND: Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. METHODS: Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE and sequence-based typing (SBT were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. RESULTS: Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (p<0.01. The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01. Legionella pneumophila was the most frequently isolated species (98.9%, and the isolated serogroups included serogroups 3 (25.3%, 6 (23.4%, 5 (19.2%, 1 (18.5%, 2 (10.2%, 8 (0.4%, 10 (0.8%, 9 (1.9% and 12 (0.4%. Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. CONCLUSIONS: Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control

  10. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

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    Jiali Wang

    Full Text Available Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene of the planktonic microbial eukaryotes (nano- and picoeukaryotes in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%, whereas Stramenopiles (26.65% and Alveolates (10.84% are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%, whereas less represented in other hypersaline lakes such as Gahai (0.50% and Xiaochaidan (1.15%. Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  11. Genetic algorithm based optimization of pulse profile for MOPA based high power fiber lasers

    Science.gov (United States)

    Zhang, Jiawei; Tang, Ming; Shi, Jun; Fu, Songnian; Li, Lihua; Liu, Ying; Cheng, Xueping; Liu, Jian; Shum, Ping

    2015-03-01

    Although the Master Oscillator Power-Amplifier (MOPA) based fiber laser has received much attention for laser marking process due to its large tunabilty of pulse duration (from 10ns to 1ms), repetition rate (100Hz to 500kHz), high peak power and extraordinary heat dissipating capability, the output pulse deformation due to the saturation effect of fiber amplifier is detrimental for many applications. We proposed and demonstrated that, by utilizing Genetic algorithm (GA) based optimization technique, the input pulse profile from the master oscillator (current-driven laser diode) could be conveniently optimized to achieve targeted output pulse shape according to real parameters' constraints. In this work, an Yb-doped high power fiber amplifier is considered and a 200ns square shaped pulse profile is the optimization target. Since the input pulse with longer leading edge and shorter trailing edge can compensate the saturation effect, linear, quadratic and cubic polynomial functions are used to describe the input pulse with limited number of unknowns(<5). Coefficients of the polynomial functions are the optimization objects. With reasonable cost and hardware limitations, the cubic input pulse with 4 coefficients is found to be the best as the output amplified pulse can achieve excellent flatness within the square shape. Considering the bandwidth constraint of practical electronics, we examined high-frequency component cut-off effect of input pulses and found that the optimized cubic input pulses with 300MHz bandwidth is still quite acceptable to satisfy the requirement for the amplified output pulse and it is feasible to establish such a pulse generator in real applications.

  12. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

    Science.gov (United States)

    Zhou, Zunchun; Liu, Shikai; Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-01-01

    Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

  13. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

    Directory of Open Access Journals (Sweden)

    Stiassny Melanie LJ

    2010-05-01

    Full Text Available Abstract Background It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood. Results We examined genetic and morphological divergence among populations of two narrowly endemic cichlid species, Teleogramma depressum and Lamprologus tigripictilis, from a 100 km stretch of the lower Congo River using both nDNA microsatellites and mtDNA markers along with coordinate-based morphological techniques. In L. tigripictilis, the strongest genetic break was concordant with measurable phenotypic divergence but no morphological disjunction was detected for T. depressum despite significant differentiation at mtDNA and nDNA microsatellite markers. Conclusions The genetic markers revealed patterns of philopatry and estimates of genetic isolation that are among the highest reported for any African cichlid species over a comparable geographic scale. We hypothesize that the high levels of philopatry observed are generated and maintained by the extreme hydrology of the lower Congo River.

  14. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

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    Xue-Feng Ma

    Full Text Available We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS, identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7, presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

  15. Genetic identification of a small and highly isolated population of fin whales (Balaenoptera physalus) in the Sea of Cortez, Mexico

    NARCIS (Netherlands)

    Berube, M; Urban, J; Dizon, AE; Brownell, RL; Palsboll, PJ

    2002-01-01

    For many years, researchers have speculated that fin whales are year-round residents in the Sea of Cortez (= Gulf of California). Previous work by Berube and co-workers has shown that the degree of genetic diversity among fin whales in the Sea of Cortez at nuclear and mitochondrial loci is highly re

  16. Maximization of induction motor torque in the zone of high speed of rotor using a genetic algorithm

    OpenAIRE

    2013-01-01

    Is studied the problem of quality improving of the vector-controlled induction motor drives. Using genetic algorithm obtained a law forming of the rotor flux linkage that maximizes the torque of an induction motor with constraints voltage and stator current. Numerical studies have shown that the proposed law can significantly increase the motor torque in the area of high speed of rotor.

  17. High abundance of genetic Bacteroidetes markers for total fecal pollution in pristine alpine soils suggests lack in specificity for feces

    Science.gov (United States)

    Vierheilig, Julia; Farnleitner, Andreas H.; Kollanur, Denny; Blöschl, Günter; Reischer, Georg H.

    2012-01-01

    Two frequently applied genetic Bacteroidetes markers for total fecal pollution (AllBac and BacUni) were found in high numbers in pristine soil samples of two alpine catchment areas casting doubt on their value as fecal indicators. This finding underlines the necessity to evaluate assays locally and against non-intestinal samples before application. PMID:22285854

  18. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

    Science.gov (United States)

    In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

  19. A twin study of the genetics of high cognitive ability selected from 11,000 twin pairs in six studies from four countries.

    Science.gov (United States)

    Haworth, Claire M A; Wright, Margaret J; Martin, Nicolas W; Martin, Nicholas G; Boomsma, Dorret I; Bartels, Meike; Posthuma, Danielle; Davis, Oliver S P; Brant, Angela M; Corley, Robin P; Hewitt, John K; Iacono, William G; McGue, Matthew; Thompson, Lee A; Hart, Sara A; Petrill, Stephen A; Lubinski, David; Plomin, Robert

    2009-07-01

    Although much genetic research has addressed normal variation in intelligence, little is known about the etiology of high cognitive abilities. Using data from 11,000 twin pairs (age range = 6-71 years) from the genetics of high cognitive abilities consortium, we investigated the genetic and environmental etiologies of high general cognitive ability (g). Age-appropriate psychometric cognitive tests were administered to the twins and used to create g scores standardized within each study. Liability-threshold model fitting was used to estimate genetic and environmental parameters for the top 15% of the distribution of g. Genetic influence for high g was substantial (0.50, with a 95% confidence interval of 0.41-0.60). Shared environmental influences were moderate (0.28, 0.19-0.37). We conclude that genetic variation contributes substantially to high g in Australia, the Netherlands, the United Kingdom and the United States.

  20. Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin

    Science.gov (United States)

    Nao, Naganori; Yamagishi, Junya; Miyamoto, Hiroko; Igarashi, Manabu; Manzoor, Rashid; Ohnuma, Aiko; Tsuda, Yoshimi; Furuyama, Wakako; Shigeno, Asako; Kajihara, Masahiro; Kishida, Noriko; Yoshida, Reiko

    2017-01-01

    ABSTRACT Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes. PMID:28196963

  1. Diagnosis of genetic predisposition for lactose intolerance by high resolution melting analysis.

    Science.gov (United States)

    Delacour, Hervé; Leduc, Amandine; Louçano-Perdriat, Andréa; Plantamura, Julie; Ceppa, Franck

    2017-02-01

    Lactose, the principle sugar in milk, is a disaccharide hydrolyzed by intestinal lactase into glucose and galactose, which are absorbed directly by diffusion in the intestine. The decline of lactase expression (or hypolactasia) in intestinal microvilli after weaning is a normal phenomenon in mammals known as lactase deficiency. It is observed in nearly 75% of the world population and is an inherited autosomal recessive trait with incomplete penetrance. It is caused by SNPs in a regulatory element for lactase gene. In Indo-European, lactase deficiency is associated with rs4982235 SNP (or -13910C>T). The aim of this study is to describe a method based on high resolution melting for rapidly detecting genetic predisposition to lactose intolerance. Analytical performance of the assay was assessed by evaluating within and betwwen-run precision and by comparing the results (n = 50 patients) obtained with the HRM assay to those obtained with the gold standard (Sanger sequencing of the region of interest). In silico prediction of HRM curves was performed to evaluate the potential impact of the other SNPs described within the PCR product on the HRM analytical performances. The assay has good performance (CV lactose intolerance.

  2. Creating highly amplified enzyme-linked immunosorbent assay signals from genetically engineered bacteriophage.

    Science.gov (United States)

    Brasino, Michael; Lee, Ju Hun; Cha, Jennifer N

    2015-02-01

    For early detection of many diseases, it is critical to be able to diagnose small amounts of biomarkers in blood or serum. One of the most widely used sensing assays is the enzyme-linked immunosorbent assay (ELISA), which typically uses detection monoclonal antibodies conjugated to enzymes to produce colorimetric signals. To increase the overall sensitivities of these sensors, we demonstrate the use of a dually modified version of filamentous bacteriophage Fd that produces significantly higher colorimetric signals in ELISAs than what can be achieved using antibodies alone. Because only a few proteins at the tip of the micron-long bacteriophage are involved in antigen binding, the approximately 4000 other coat proteins can be augmented-by either chemical functionalization or genetic engineering-with hundreds to thousands of functional groups. In this article, we demonstrate the use of bacteriophage that bear a large genomic fusion that allows them to bind specific antibodies on coat protein 3 (p3) and multiple biotin groups on coat protein 8 (p8) to bind to avidin-conjugated enzymes. In direct ELISAs, the anti-rTNFα (recombinant human tumor necrosis factor alpha)-conjugated bacteriophage show approximately 3- to 4-fold gains in signal over that of anti-rTNFα, demonstrating their use as a platform for highly sensitive protein detection.

  3. High genetic differentiation between the M and S molecular forms of Anopheles gambiae in Africa.

    Directory of Open Access Journals (Sweden)

    Caroline Esnault

    Full Text Available BACKGROUND: Anopheles gambiae, a major vector of malaria, is widely distributed throughout sub-Saharan Africa. In an attempt to eliminate infective mosquitoes, researchers are trying to develop transgenic strains that are refractory to the Plasmodium parasite. Before any release of transgenic mosquitoes can be envisaged, we need an accurate picture of the differentiation between the two molecular forms of An. gambiae, termed M and S, which are of uncertain taxonomic status. METHODOLOGY/PRINCIPAL FINDINGS: Insertion patterns of three transposable elements (TEs were determined in populations from Benin, Burkina Faso, Cameroon, Ghana, Ivory Coast, Madagascar, Mali, Mozambique, Niger, and Tanzania, using Transposon Display, a TE-anchored strategy based on Amplified Fragment Length Polymorphism. The results reveal a clear differentiation between the M and S forms, whatever their geographical origin, suggesting an incipient speciation process. CONCLUSIONS/SIGNIFICANCE: Any attempt to control the transmission of malaria by An. gambiae using either conventional or novel technologies must take the M/S genetic differentiation into account. In addition, we localized three TE insertion sites that were present either in every individual or at a high frequency in the M molecular form. These sites were found to be located outside the chromosomal regions that are suspected of involvement in the speciation event between the two forms. This suggests that these chromosomal regions are either larger than previously thought, or there are additional differentiated genomic regions interspersed with undifferentiated regions.

  4. High Genetic Differentiation between the M and S Molecular Forms of Anopheles gambiae in Africa

    Science.gov (United States)

    Esnault, Caroline; Boulesteix, Matthieu; Duchemin, Jean Bernard; Koffi, Alphonsine A.; Chandre, Fabrice; Dabiré, Roch; Robert, Vincent; Simard, Frédéric; Tripet, Frédéric; Donnelly, Martin J.; Fontenille, Didier; Biémont, Christian

    2008-01-01

    Background Anopheles gambiae, a major vector of malaria, is widely distributed throughout sub-Saharan Africa. In an attempt to eliminate infective mosquitoes, researchers are trying to develop transgenic strains that are refractory to the Plasmodium parasite. Before any release of transgenic mosquitoes can be envisaged, we need an accurate picture of the differentiation between the two molecular forms of An. gambiae, termed M and S, which are of uncertain taxonomic status. Methodology/Principal Findings Insertion patterns of three transposable elements (TEs) were determined in populations from Benin, Burkina Faso, Cameroon, Ghana, Ivory Coast, Madagascar, Mali, Mozambique, Niger, and Tanzania, using Transposon Display, a TE-anchored strategy based on Amplified Fragment Length Polymorphism. The results reveal a clear differentiation between the M and S forms, whatever their geographical origin, suggesting an incipient speciation process. Conclusions/Significance Any attempt to control the transmission of malaria by An. gambiae using either conventional or novel technologies must take the M/S genetic differentiation into account. In addition, we localized three TE insertion sites that were present either in every individual or at a high frequency in the M molecular form. These sites were found to be located outside the chromosomal regions that are suspected of involvement in the speciation event between the two forms. This suggests that these chromosomal regions are either larger than previously thought, or there are additional differentiated genomic regions interspersed with undifferentiated regions. PMID:18414665

  5. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

    Science.gov (United States)

    Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A. A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

    2016-12-01

    Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.

  6. Genetic inviability is a major driver of type III survivorship in experimental families of a highly fecund marine bivalve.

    Science.gov (United States)

    Plough, L V; Shin, G; Hedgecock, D

    2016-02-01

    The offspring of most highly fecund marine fish and shellfish suffer substantial mortality early in the life cycle, complicating prediction of recruitment and fisheries management. Early mortality has long been attributed to environmental factors and almost never to genetic sources. Previous work on a variety of marine bivalve species uncovered substantial genetic inviability among the offspring of inbred crosses, suggesting a large load of early-acting deleterious recessive mutations. However, genetic inviability of randomly bred offspring has not been addressed. Here, genome-wide surveys reveal widespread, genotype-dependent mortality in randomly bred, full-sib progenies of wild-caught Pacific oysters (Crassostrea gigas). Using gene-mapping methods, we infer that 11-19 detrimental alleles per family render 97.9-99.8% of progeny inviable. The variable genomic positions of viability loci among families imply a surprisingly large load of partially dominant or additive detrimental mutations in wild adult oysters. Although caution is required in interpreting the relevance of experimental results for natural field environments, we argue that the observed genetic inviability corresponds with type III survivorship, which is characteristic of both hatchery and field environments and that our results, therefore, suggest the need for additional experiments under the near-natural conditions of mesocosms. We explore the population genetic implications of our results, calculating a detrimental mutation rate that is comparable to that estimated for conifers and other highly fecund perennial plants. Genetic inviability ought to be considered as a potential major source of low and variable recruitment in highly fecund marine animals.

  7. Topology of genetic associations between regional gray matter volume and intellectual ability: Evidence for a high capacity network.

    Science.gov (United States)

    Bohlken, Marc M; Brouwer, Rachel M; Mandl, René C W; Hedman, Anna M; van den Heuvel, Martijn P; van Haren, Neeltje E M; Kahn, René S; Pol, Hilleke E Hulshoff

    2016-01-01

    Intelligence is associated with a network of distributed gray matter areas including the frontal and parietal higher association cortices and primary processing areas of the temporal and occipital lobes. Efficient information transfer between gray matter regions implicated in intelligence is thought to be critical for this trait to emerge. Genetic factors implicated in intelligence and gray matter may promote a high capacity for information transfer. Whether these genetic factors act globally or on local gray matter areas separately is not known. Brain maps of phenotypic and genetic associations between gray matter volume and intelligence were made using structural equation modeling of 3T MRI T1-weighted scans acquired in 167 adult twins of the newly acquired U-TWIN cohort. Subsequently, structural connectivity analyses (DTI) were performed to test the hypothesis that gray matter regions associated with intellectual ability form a densely connected core. Gray matter regions associated with intellectual ability were situated in the right prefrontal, bilateral temporal, bilateral parietal, right occipital and subcortical regions. Regions implicated in intelligence had high structural connectivity density compared to 10,000 reference networks (p=0.031). The genetic association with intelligence was for 39% explained by a genetic source unique to these regions (independent of total brain volume), this source specifically implicated the right supramarginal gyrus. Using a twin design, we show that intelligence is genetically represented in a spatially distributed and densely connected network of gray matter regions providing a high capacity infrastructure. Although genes for intelligence have overlap with those for total brain volume, we present evidence that there are genes for intelligence that act specifically on the subset of brain areas that form an efficient brain network.

  8. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Directory of Open Access Journals (Sweden)

    Chiao-Ling Lo

    2016-08-01

    Full Text Available Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP. This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross resulted in small haplotype blocks (HB with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS, were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50% of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284 and intronic regions (169 with the least in exon's (4, suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a, excitatory receptors (Grin2a, Gria3, Grip1, neurotransmitters (Pomc, and synapses (Snap29. This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  9. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  10. Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).

    Science.gov (United States)

    Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W

    2013-10-23

    We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents.

  11. Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea

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    Jingqun Ao

    2015-11-01

    Full Text Available High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs evenly distributed across the large yellow croaker (Larimichthys crocea genome were identified using restriction-site associated DNA sequencing (RAD-seq. Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs. The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04% of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus and medaka (Oryzias latipes. Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

  12. The role of boundary organizations in co-management: examining the politics of knowledge integration in a marine protected area in Belize

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    Noella J. Gray

    2016-08-01

    Full Text Available Marine protected areas (MPAs are an increasingly popular tool for management of the marine commons. Effective governance is essential if MPAs are to achieve their objectives, yet many MPAs face conflicts and governance challenges, including lack of trust and knowledge integration between fishers, scientists, and policy makers. This paper considers the role of a boundary organization in facilitating knowledge integration in a co-managed MPA, the Gladden Spit and Silk Cayes Marine Reserve in Belize. Boundary organizations can play an important role in resource management, by bridging the science-policy divide, facilitating knowledge integration, and enabling communication in conditions of uncertainty. Drawing on ethnographic research conducted in Belize, the paper identifies four challenges for knowledge integration. First, actors have divergent perspectives on whether and how knowledge is being integrated. Second, actors disagree on resource conditions within the MPA and how these should be understood. Third, in order to maintain accountability with multiple actors, including fishers, government, and funders, the boundary organization has promoted the importance of different types of knowledge for different purposes (science and fishers’ knowledge, rather than the integration of these. Finally, a lack of trust and uneven power relations make it difficult to separate knowledge claims from political claims. However, even if knowledge integration proves difficult, boundary organizations may still play an important role by maintaining accountability, providing space for conflicting understandings to co-exist, and ultimately for governance institutions to evolve.

  13. Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

    Science.gov (United States)

    Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

    2014-12-12

    Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P < 0.0001). Sampled demes sites (1- 7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (Rxy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

  14. High-performance genetically targetable optical neural silencing by light-driven proton pumps.

    Science.gov (United States)

    Chow, Brian Y; Han, Xue; Dobry, Allison S; Qian, Xiaofeng; Chuong, Amy S; Li, Mingjie; Henninger, Michael A; Belfort, Gabriel M; Lin, Yingxi; Monahan, Patrick E; Boyden, Edward S

    2010-01-07

    The ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 (Arch) from Halorubrum sodomense enables near-100% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light. Arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 pA at light powers easily achievable in vivo. Furthermore, Arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. These properties of Arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally relevant timescales. Arch function in neurons is well tolerated because pH excursions created by Arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins or natural spike firing. To highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue-green light-drivable proton pump from the fungus Leptosphaeria maculans (Mac) can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue versus red light. Light-driven proton pumps thus represent a high-performance and extremely versatile class of 'optogenetic' voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.

  15. Genetic and morphometric differences between yellowtail snapper (Ocyurus chrysurus, Lutjanidae populations of the tropical West Atlantic

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    Anderson V. Vasconcellos

    2008-01-01

    Full Text Available Populations of Ocyurus chrysurus were compared genetically and morphometrically along the West Atlantic coast to test the null hypothesis of population homogeneity in the area. Brazilian populations were found to be differentiated in shape (canonical variates analysis; F[48,515] = 10.84, p < 0.0001. Analyses of mitochondrial DNA sequences (663 bp of the control region did not show any differences between Brazilian populations but could detect differences between Brazilian and Caribbean (Belize populations. The samples from Pernambuco differed significantly from the other Brazilian populations in allozyme frequencies (11 loci; F ST = 0.167; p < 0.05, but this may have resulted from the small number of samples analysed for that population. Sequence variation of Belize samples departed from neutral expectations (Fu's FS = -8.88; p < 0.001. A mismatch distribution analysis points to an ancient population expansion in that area. We conclude that the genetic data do not allow the rejection of the null hypothesis of panmixia for Brazilian yellowtail snapper populations which should be treated as a single genetic stock, with a latitudinal gradient on their morphology which probably results from phenotypic plasticity. On the other hand, there is a severe restriction to gene flow between O. chrysurus populations from the Caribbean and from the southwestern Atlantic.

  16. Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium.

    Science.gov (United States)

    Walworth, Nathan G; Lee, Michael D; Fu, Fei-Xue; Hutchins, David A; Webb, Eric A

    2016-11-22

    Most investigations of biogeochemically important microbes have focused on plastic (short-term) phenotypic responses in the absence of genetic change, whereas few have investigated adaptive (long-term) responses. However, no studies to date have investigated the molecular progression underlying the transition from plasticity to adaptation under elevated CO2 for a marine nitrogen-fixer. To address this gap, we cultured the globally important cyanobacterium Trichodesmium at both low and high CO2 for 4.5 y, followed by reciprocal transplantation experiments to test for adaptation. Intriguingly, fitness actually increased in all high-CO2 adapted cell lines in the ancestral environment upon reciprocal transplantation. By leveraging coordinated phenotypic and transcriptomic profiles, we identified expression changes and pathway enrichments that rapidly responded to elevated CO2 and were maintained upon adaptation, providing strong evidence for genetic assimilation. These candidate genes and pathways included those involved in photosystems, transcriptional regulation, cell signaling, carbon/nitrogen storage, and energy metabolism. Conversely, significant changes in specific sigma factor expression were only observed upon adaptation. These data reveal genetic assimilation as a potentially adaptive response of Trichodesmium and importantly elucidate underlying metabolic pathways paralleling the fixation of the plastic phenotype upon adaptation, thereby contributing to the few available data demonstrating genetic assimilation in microbial photoautotrophs. These molecular insights are thus critical for identifying pathways under selection as drivers in plasticity and adaptation.

  17. Germplasm Collection from Last Remnants of Rice Landrace Genetic Diversity in High Altitude Areas of Kashmir Himalayas

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    Sheikh Mohd SULTAN

    2013-12-01

    Full Text Available The aim of the present study was to know about past and present cultivation and status of rice landraces in Kashmir province of Indian Himalayan state of Jammu and Kashmir. Tremendous genetic diversity has existed in past in paddy fields throughout Kashmir especially in remote high altitude areas and more than 4 dozen named landraces have been recorded in the literature. Elderly farmers in their sixties and beyond still fondly remember these landraces and often recall quality attributes in many of these genetic resources. Most of the landraces have now disappeared from the local production system and only few are presently being cultivated and that too in a very small area. The reasons as to why farmers lost interest in these genetic resources and why few landraces are still popular in farmer fields have been discussed. Our study has revealed that variability in paddy fields has now been drastically reduced to few high altitude areas where also it is seriously endangered. We argue that collection of well adapted traditional varieties from these ‘last remnants of rice genetic diversity’ in Kashmir is an important task especially under prevailing uncertain social and climatic conditions to ensure a sustainable environment. 32 germplasm accessions of some landraces have been collected during our survey in these areas. These have been deposited in National Seed Gene Bank at NBPGR, New Delhi for conservation and characterization.

  18. High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River.

    Science.gov (United States)

    So, N; Maes, G E; Volckaert, F A M

    2006-02-01

    The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds.

  19. Gene Flow Results in High Genetic Similarity Between Sibiraea (Rosaceae species in the Qinghai-Tibetan Plateau

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    Peng-Cheng Fu

    2016-10-01

    Full Text Available Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of S. laevigata and S. angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45% rather than between species (4.39%. We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of these 2 species resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures between the species occurred.

  20. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

    Science.gov (United States)

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-07-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

  1. High resolution genetic map of the adenomatous polyposis coli gene (APC) region

    Energy Technology Data Exchange (ETDEWEB)

    Olschwang, S.; Laurent-Puig, P.; Melot, T. [Institut Curie, Paris (France)

    1995-05-08

    Familial adenomatous polyposis coli (APC) is a dominantly inherited colorectal cancer susceptibility disease caused by mutation in a gene called APC located on chromosome 5q21. Presymptomatic diagnosis of this condition is recommended because it enables restriction of the efficient but demanding prevention program to those relatives that are genetically affected. The large size of the APC gene makes the direct search for the casual alteration difficult to implement in routine diagnostic laboratories. Because APC appears to be genetically homogeneous with alteration in a single locus causing the disease, cosegregation analysis may represent an alternative efficient method for presymptomatic diagnosis. However, the reliability of the risk estimation by linkage analysis in APC families is hampered by the lack of a short range genetic map of the APC locus. A combined approach including genotyping of 65 APC families, analysis of the CEPH database, and complementary typing of both APC and CEPH families has made it possible to derive the following genetic map: Centromere-[D5S82-D5S49]-0.02-D5S122-0.01-D5S136-0.01-D5S135-0.02-[APC-D5S346-MCC]-0.04-[D5S81-D5S64]-Telomere. This order, which differs from previously proposed genetic maps, is fully compatible with recent physical mapping data. These data should contribute to increase the reliability of the presymptomatic test for APC. 42 refs., 1 fig., 3 tabs.

  2. Optimization of Residual Stress of High Temperature Treatment Using Genetic Algorithm and Neural Network

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    M. Susmikanti

    2015-12-01

    Full Text Available In a nuclear industry area, high temperature treatment of materials is a factor which requires special attention. Assessment needs to be conducted on the properties of the materials used, including the strength of the materials. The measurement of material properties under thermal processes may reflect residual stresses. The use of Genetic Algorithm (GA to determine the optimal residual stress is one way to determine the strength of a material. In residual stress modeling with several parameters, it is sometimes difficult to solve for the optimal value through analytical or numerical calculations. Here, GA is an efficient algorithm which can generate the optimal values, both minima and maxima. The purposes of this research are to obtain the optimization of variable in residual stress models using GA and to predict the center of residual stress distribution, using fuzzy neural network (FNN while the artificial neural network (ANN used for modeling. In this work a single-material 316/316L stainless steel bar is modeled. The minimal residual stresses of the material at high temperatures were obtained with GA and analytical calculations. At a temperature of 6500C, the GA optimal residual stress estimation converged at –711.3689 MPa at adistance of 0.002934 mm from center point, whereas the analytical calculation result at that temperature and position is -975.556 MPa . At a temperature of 8500C, the GA result was -969.868 MPa at 0.002757 mm from the center point, while with analytical result was -1061.13 MPa. The difference in residual stress between GA and analytical results at a temperatureof6500C is about 27 %, while at 8500C it is 8.67 %. The distribution of residual stress showed a grouping concentrated around a coordinate of (-76; 76 MPa. The residuals stress model is a degree-two polynomial with coefficients of 50.33, -76.54, and -55.2, respectively, with a standard deviation of 7.874.

  3. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus.

    Science.gov (United States)

    Tian, Meilin; Li, Yangping; Jing, Jing; Mu, Chuang; Du, Huixia; Dou, Jinzhuang; Mao, Junxia; Li, Xue; Jiao, Wenqian; Wang, Yangfan; Hu, Xiaoli; Wang, Shi; Wang, Ruijia; Bao, Zhenmin

    2015-10-06

    Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.

  4. Molecular genetic studies in black families with sickle cell anemia and unusually high levels of fetal hemoglobin.

    Science.gov (United States)

    Seltzer, W K; Abshire, T C; Lane, P A; Roloff, J S; Githens, J H

    1992-01-01

    Clinical, hematologic, and molecular genetic studies are reported for five families with SS patients having unusually high fetal hemoglobin (Hb F) levels (mean 28.3%, range 19-42%). Some of the individuals were symptom-free and one was not anemic. However, some were symptomatic despite a very high Hb F. Neither the Hb F level nor the F cell distribution entirely explained the variation in clinical severity. Molecular genetic studies identified the Senegal haplotype with the associated -158 G gamma (C----T) mutation in two of the five families. The -202 G gamma (C----G) mutation was not found in any of the individuals studied. Sequencing of the gamma-globin gene promoters to detect genetic high F determinants not detectable by restriction digestion was not performed. All AS parents and AS siblings demonstrated elevated F cells when the Senegal/-158 G gamma (C----T) mutation was present with either the beta S or beta A allele. Double heterozygosity for two different high F determinants in some SS patients is suggested by the studies in at least one family. Discordance among siblings in clinical and hematologic manifestations in two families provides additional evidence for loci regulating Hb F cell production which are not linked to the beta-globin gene clusters.

  5. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

    Science.gov (United States)

    Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

    2016-01-01

    Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

  6. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

    Directory of Open Access Journals (Sweden)

    Yan Holtz

    Full Text Available Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2 and a recent durum elite cultivar (Silur. Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

  7. Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting.

    Science.gov (United States)

    Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna

    2011-09-01

    A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.

  8. Prevalent ciliate symbiosis on copepods: high genetic diversity and wide distribution detected using small subunit ribosomal RNA gene.

    Science.gov (United States)

    Guo, Zhiling; Liu, Sheng; Hu, Simin; Li, Tao; Huang, Yousong; Liu, Guangxing; Zhang, Huan; Lin, Senjie

    2012-01-01

    Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA)-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups), six (containing 99% of all the sequences) belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus), and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally.

  9. Prevalent ciliate symbiosis on copepods: high genetic diversity and wide distribution detected using small subunit ribosomal RNA gene.

    Directory of Open Access Journals (Sweden)

    Zhiling Guo

    Full Text Available Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups, six (containing 99% of all the sequences belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus, and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally.

  10. Chaotic genetic patchiness and high relatedness of a poecilogonous polychaete in a heterogeneous estuarine landscape

    DEFF Research Database (Denmark)

    Hansen, Benni Winding; Banta, Gary Thomas; Kesäniemi, Jenni E;

    2014-01-01

    of individuals with different degrees of relatedness. Relatedness within a site could be increased by limited larval dispersal, collective dispersal of related larvae, sweepstakes reproductive success, or asexual reproduction, but distinguishing between these requires further study. Using a “seascape genetics...

  11. Cultivar based selection and genetic analysis of strawberry fruits with high levels of health promoting compounds.

    Science.gov (United States)

    Padula, Maria Carmela; Lepore, Laura; Milella, Luigi; Ovesna, Jaroslava; Malafronte, Nicola; Martelli, Giuseppe; de Tommasi, Nunziatina

    2013-10-15

    Twenty different strawberry genotypes from phenolic compound content and genetic diversity have been investigated. Twelve phenolic derivatives in the strawberry fruit extracts, their total phenolic content (TPC) and their radical scavenging activity have been quantified. In order to study the influence of the genetic basis of each cultivar (cv) on the chemical composition of fruits, Principal Component Analysis of the obtained data was also used. Significant differences in the content of individual anthocyanins among the 20cvs have been found. Pelargonidin 3-O-glucoside was the predominant anthocyanin in the strawberry extracts with 61.0% of the total anthocyanins in Salva cv, followed by cyanidin 3-O-glucoside. TPC values ranged from 129,96 (Laica cv) to 269,04 (Naiad cv) mg of gallic acid equivalent per 100g of fresh weight and it was congruent previous studies. Moreover RAPD markers have been applied in order to describe their genetic relationships. A total of 32decamer primers were used in RAPD analysis; 19 of them provided at least one polymorphic band, the remaining primers were monomorphic. A total of 124 bands were detected with the mean number of 11.53 accountable fragments per primer and 59.98% were polymorphic. The results of the present study highlighted the health-promoting compound content of strawberry fruits, and provided a good prospect for discriminating strawberries by phenolic content and genetic analysis.

  12. Supporting Learning of High-School Genetics Using Authentic Research Practices: The Teacher's Role

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2011-01-01

    In this study we describe the support provided by a biology teacher during learning using a web-based research simulation that makes use of authentic research practices in genetics, including the use of a heuristic strategy to compare mutated and normal versions of a character at all the organisational levels. Authentic scientific practices…

  13. High genetic variation among Aschersonia placenta (Clavicipitaceae) isolates from citrus orchards in China.

    Science.gov (United States)

    Wang, P P; Song, X H; Zhang, H Y

    2013-12-04

    Aschersonia placenta had been recognized as an important fungal pathogen of whiteflies. In recent years, natural occurrence of Aschersonia in whitefly populations was observed in many citrus orchards in the southern regions of China. We analyzed 60 A. placenta isolates obtained from Chinese citrus orchards, using inter-simple sequence repeats to examine the genetic diversity and to determine whether intraspecific variation is correlated with geographic origin. One hundred and fourteen fragments were generated from these isolates; 97% were polymorphic. The Nei's gene diversity (H) was estimated to be 0.1748 within the populations (range 0.0974-0.2179) and 0.3057 at the species level. Analysis of molecular variance showed that the genetic variation was found mainly within populations (74.9%). The coefficient of gene differentiation (GST = 0.4315) indicated that 56.85% of the genetic diversity resided within populations. The Mantel test revealed no significant correlation between the genetic distance and the corresponding geographical distance (r = 0.142 and P = 0.887); the unweighted pair-group method using arithmetic average clustering gave similar results.

  14. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.

    Directory of Open Access Journals (Sweden)

    Ruth Hershberg

    2008-12-01

    Full Text Available Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC. However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

  15. Investigating the Impact of Video Games on High School Students' Engagement and Learning about Genetics

    Science.gov (United States)

    Annetta, Leonard A.; Minogue, James; Holmes, Shawn Y.; Cheng, Meng-Tzu

    2009-01-01

    The popularity of video games has transcended entertainment crossing into the world of education. While the literature base on educational gaming is growing, there is still a lack of systematic study of this emerging technology's efficacy. This quasi-experimental study evaluated a teacher created video game on genetics in terms of its affective…

  16. USF-1 genetic polymorphisms confer a high risk of nonalcoholic fatty liver disease in Chinese population.

    Science.gov (United States)

    Wang, Ying; Wang, Bai-Fang; Tong, Jing; Chang, Bing; Wang, Bing-Yuan

    2015-01-01

    Genetic polymorphisms in upstream transcription factor 1 (USF1) were investigated for their links to increased risk of nonalcoholic fatty liver disease (NAFLD) in Chinese population. Between January 2013 and April 2014, 174 patients with NAFLD in the First Affiliated Hospital of China Medical University were selected for this study. A group of 100 healthy subjects were identified as the control group. The MALDI-TOF-MS, a mass spectrometry based technique, was used to detect USF-1 genetic polymorphisms using PCR amplified DNA products. Furthermore, Automatic Chemistry Analyzer (ACA) was used to determine the clinical indicators. Genotypes, allele frequencies and clinical indicators were measured to assess NAFLD risk in relation to the SNPs. USF-1 rs6427573 genetic polymorphisms were associated with an increased risk of NAFLD (AA vs. GG: OR = 3.16, 95% CI = 1.56-6.43, P = 0.001; GA + AA vs. GG: OR = 1.87, 95% CI = 1.13-3.09, P = 0.015; GG + AA vs. AA: OR = 2.96, 95% CI = 1.49-5.88, P = 0.001; G vs. A: OR = 2.10, 95% CI = 1.43-3.09, P 0.05). Two USF-1 genetic polymorphisms, rs6427573 and rs2516839, may present an increased risk of NAFLD.

  17. Biophysical connectivity explains population genetic structure in a highly dispersive marine species

    Science.gov (United States)

    Truelove, Nathan K.; Kough, Andrew S.; Behringer, Donald C.; Paris, Claire B.; Box, Stephen J.; Preziosi, Richard F.; Butler, Mark J.

    2017-03-01

    Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster ( Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F ST of 0.0016 ( P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus ( P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation ( P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

  18. High-resolution genetic mapping of maize pan-genome sequence anchors

    Science.gov (United States)

    In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome’, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome’s complexity hinde...

  19. A Study on the Bionomics of Anopheles darlingi Root (Diptera: Culicidae) in Belize, Central America

    Science.gov (United States)

    2004-03-01

    shown). (B) A supervised classification of the image was used to quantify the difference in pixel counts of broadleaf/ palm forest (green), pasture...flow by bulldozed forest debris; contamination of freshwater by agrochemicals; and eutrophication of waterways by discharge from food and sugar...conditions of high populations and/or malaria transmission, the application of oils to potential breeding habitats surrounding homes will be performed

  20. PTEN mutation analysis in two genetic subtypes of high-grade oligodendroglial tumors. PTEN is only occasionally mutated in one of the two genetic subtypes.

    Science.gov (United States)

    Jeuken, J W; Nelen, M R; Vermeer, H; van Staveren, W C; Kremer, H; van Overbeeke, J J; Boerman, R H

    2000-05-01

    We recently identified two genetic subtypes of high-grade oligodendroglial tumors (HG-OT): 1p-/19q- HG-OT are characterized by a loss of chromosome 1p32-36 (del(1)(p32-p36) and/or a del(19)(q13. 3); whereas +7/-10 HG-OT harbor a gain of chromosome 7 (+7) and/or a -10 without a loss of 1p32-36 and 19q13.3. Because a -10 and a +7 are most frequently detected in glioblastomas (GBM), the genotype of +7/-10 HG-OT suggests that these tumors are GBM with a prominent oligodendroglial phenotype rather than anaplastic oligodendrogliomas. PTEN is a tumor suppressor gene, located at 10q23.3, which is involved in tumor progression of GBM and other neoplasms. In this study, we screened for PTEN mutations in six low-grade oligodendroglial tumors (LG-OT), five 1p-/19q- HG-OT, seven +7/-10 HG-OT, and nine xenografted GBM. PTEN mutations were detected in none of the LG-OT and 1p-/19q- HG-OT, once in +7/-10 HG-OT, and frequently in GBM. As one of the +7/-10 HG-OT harbored a PTEN mutation, this demonstrates that PTEN can be involved in the oncogenesis of this genetic subtype of HG-OT. The lower frequency of PTEN mutations in +7/-10 HG-OT compared to GBM suggests that these tumors are of a distinct tumor type rather than GBM. Published by Elsevier Science Inc.

  1. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq.

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    Full Text Available As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive "Yanjiang" variety as the female parent with the salt-tolerant "9901" variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq, leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for "Yanjiang", 47.41-fold for "9901", and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs. The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.

  2. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq).

    Science.gov (United States)

    Zhang, Jian; Yuan, Huwei; Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

    2016-01-01

    As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive "Yanjiang" variety as the female parent with the salt-tolerant "9901" variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for "Yanjiang", 47.41-fold for "9901", and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.

  3. The Effects of Coping Therapy on General Health of Pregnant Women with High Risk of Genetics Abnormalities in their Fetus

    Directory of Open Access Journals (Sweden)

    F Nazmiye

    2016-11-01

    Full Text Available Introduction: The physiological changes in pregnancy lead to the psychological pressures. Therefore, there is a need for applying cognitive behavioral and emotional confronting to encounter these problems. The present research investigated the effect of coping therapy on general health of pregnant women with high risk of genetic abnormalities in their fetus. Methods: The present study was a semi experimental research. Pre and post tests were used to investigate coping therapy between 30 pregnant women who were referred to Khatomolanbia Genetic Clinic, Yazd, Iran. All the women had pregnancy screening test with high risk of genetics abnormalities in their fetus. They were divided randomly into two groups of case and controls. The test of GHQ was performed in both groups, then the case groups went under 8 sessions of teaching coping therapy each lasting 120 min. After finishing the sessions, post test was performed and analyzing the data using descriptive statistical index and covariance analysis test. Results: Teaching coping therapy to case group caused improvement in their GHQ mark, and this change was significantly different from the change in the GHQ mark of control group. In addition, there was a significant decrease in anxiety, depression and physical signs and an improvement of social function in case group compare to the control group. Discussion: Teaching coping therapy can improve the general health of pregnant women with high risk of genetic abnormalities in their fetus. Therefore, presenting educational courses to the women can improve their general health indices in addition to preventing the probable effects of stress on fetus.

  4. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq)

    Science.gov (United States)

    Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

    2016-01-01

    As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree. PMID:27327501

  5. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

    Science.gov (United States)

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A; Catenacci, Daniel V T; Hudson, Richard R; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-11-24

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

  6. Quantifying multi-ethnic representation in genetic studies of high mortality diseases.

    Science.gov (United States)

    Chen, Rong; Dudley, Joel T; Ruau, David; Butte, Atul J

    2012-01-01

    Most GWASs were performed using study populations with Caucasian ethnicity or ancestry, and findings from one ethnic subpopulation might not always translate to another. We curated 4,573 genetic studies on 763 human diseases and identified 3,461 disease-susceptible SNPs with genome-wide significance; only 10% of these had been validated in at least two different ethnic populations. SNPs for autoimmune diseases demonstrated the lowest percentage of cross-ethnicity validation. We used the mortality data from the Center for Disease Control and Prevention and identified 19 diseases killing over 10,000 Americans per year that were still lacking publications of even a single cross-ethnic SNP. Fifteen of these diseases had never been studied in large GWAS in non-Caucasian populations, including chronic liver diseases and cirrhosis, leukemia, and non-Hodgkin's lymphoma. Our results demonstrate that diseases killing most Americans are still lacking genetic studies across ethnicities.

  7. NON-SYNDROMIC HEARING LOSS AND HIGH-THROUGHPUT STRATEGIES TO DECIPHER ITS GENETIC HETEROGENEITY

    Institute of Scientific and Technical Information of China (English)

    Liu Xue Zhong; Shan Kun; Qing Jing; Cheng Jing; YanDenise

    2013-01-01

    Hearing loss (HL) is the most common sensory disorder, affecting all age groups, ethnicities, and gen-ders. According to World Health Organization (WHO) estimates in 2005, 278 million people worldwide have moderate to profound HL in both ears. Results of the 2002 National Health Interview Survey indicate that nearly 31 million of all non-institutionalized adults (aged 18 and over) in the United States have trouble hearing. Epidemiological studies have estimated that approximately 50%of profound HL can be attributed to genetic causes. With over 60 genes implicated in nonsyndromic hearing loss, it is also an extremely het-erogeneous trait. Recent progress in identifying genes responsible for hearing loss enables otolaryngologists and other clinicians to apply molecular diagnosis by genetic testing. The advent of the $1000 genome has the potential to revolutionize the identification of genes and their mutations underlying genetic disorders. This is especially true for extremely heterogeneous Mendelian conditions such as deafness, where the muta-tion, and indeed the gene, may be private. The recent technological advances in target-enrichment methods and next generation sequencing offer a unique opportunity to break through the barriers of limitations im-posed by gene arrays. These approaches now allow for the complete analysis of all known deafness-causing genes and will result in a new wave of discoveries of the remaining genes for Mendelian disorders. This re-view focuses on describing genotype-phenotype correlations of the most frequent genes including GJB2, which is responsible for more than half of cases, followed by other common genes and on discussing the im-pact of genomic advances for comprehensive genetic testing and gene discovery in hereditary hearing loss.

  8. Genetically designed biosensing systems for high-throughput screening of pharmaceuticals, clinical diagnostics, and environmental monitoring

    Science.gov (United States)

    Wenner, Brett R.; Douglass, Phillip; Shrestha, Suresh; Sharma, Bethel V.; Lai, Siyi; Madou, Marc J.; Daunert, Sylvia

    2001-05-01

    The genetically-modified binding proteins calmodulin, the phosphate binding protein, the sulfate binding protein, and the galactose/glucose binding protein have been successfully employed as biosensing elements for the detection of phenothiazines, phosphate, sulfate, and glucose, respectively. Mutant proteins containing unique cysteine residues were utilized in the site-specific labeling of environment-sensitive fluorescent probes. Changes in the environment of the probes upon ligand-induced conformational changes of the proteins result in changes in fluorescence intensity.

  9. Genetic mapping identifies novel highly protective antigens for an apicomplexan parasite.

    Directory of Open Access Journals (Sweden)

    Damer P Blake

    Full Text Available Apicomplexan parasites are responsible for a myriad of diseases in humans and livestock; yet despite intensive effort, development of effective sub-unit vaccines remains a long-term goal. Antigenic complexity and our inability to identify protective antigens from the pool that induce response are serious challenges in the development of new vaccines. Using a combination of parasite genetics and selective barriers with population-based genetic fingerprinting, we have identified that immunity against the most important apicomplexan parasite of livestock (Eimeria spp. was targeted against a few discrete regions of the genome. Herein we report the identification of six genomic regions and, within two of those loci, the identification of true protective antigens that confer immunity as sub-unit vaccines. The first of these is an Eimeria maxima homologue of apical membrane antigen-1 (AMA-1 and the second is a previously uncharacterised gene that we have termed 'immune mapped protein-1' (IMP-1. Significantly, homologues of the AMA-1 antigen are protective with a range of apicomplexan parasites including Plasmodium spp., which suggest that there may be some characteristic(s of protective antigens shared across this diverse group of parasites. Interestingly, homologues of the IMP-1 antigen, which is protective against E. maxima infection, can be identified in Toxoplasma gondii and Neospora caninum. Overall, this study documents the discovery of novel protective antigens using a population-based genetic mapping approach allied with a protection-based screen of candidate genes. The identification of AMA-1 and IMP-1 represents a substantial step towards development of an effective anti-eimerian sub-unit vaccine and raises the possibility of identification of novel antigens for other apicomplexan parasites. Moreover, validation of the parasite genetics approach to identify effective antigens supports its adoption in other parasite systems where legitimate

  10. High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia.

    Science.gov (United States)

    Casas-Vargas, Andrea; Gómez, Alberto; Briceño, Ignacio; Díaz-Matallana, Marcela; Bernal, Jaime E; Rodríguez, José Vicente

    2011-12-01

    Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.

  11. An analysis of modern pollen rain from the Maya lowlands of northern Belize

    Science.gov (United States)

    Bhattacharya, T.; Beach, T.; Wahl, D.

    2011-01-01

    In the lowland Maya area, pollen records provide important insights into the impact of past human populations and climate change on tropical ecosystems. Despite a long history of regional paleoecological research, few studies have characterized the palynological signatures of lowland ecosystems, a fact which lowers confidence in ecological inferences made from palynological data. We sought to verify whether we could use pollen spectra to reliably distinguish modern ecosystem types in the Maya lowlands of Central America. We collected 23 soil and sediment samples from eight ecosystem types, including upland, riparian, secondary, and swamp (bajo) forests; pine savanna; and three distinct wetland communities. We analyzed pollen spectra with non-metric multidimensional scaling (NMDS), and found significant compositional differences in ecosystem types' pollen spectra. Forested sites had spectra dominated by Moraceae/Urticaceae pollen, while non-forested sites had significant portions of Poaceae, Asteraceae, and Amaranthaceae pollen. Upland, bajo, and riparian forest differed in representation of Cyperaceae, Bactris-type, and Combretaceae/Melastomataceae pollen. High percentages of pine (Pinus), oak (Quercus), and the presence of Byrsonima characterized pine savanna. Despite its limited sample size, this study provides one of the first statistical analyses of modern pollen rain in the Maya lowlands. Our results show that pollen assemblages can accurately reflect differences between ecosystem types, which may help refine interpretations of pollen records from the Maya area. ?? 2010 Elsevier B.V.

  12. Artificial Selection Reveals High Genetic Variation in Phenology at the Trailing Edge of a Species Range.

    Science.gov (United States)

    Sheth, Seema Nayan; Angert, Amy Lauren

    2016-02-01

    Species responses to climate change depend on the interplay of migration and adaptation, yet we know relatively little about the potential for adaptation. Genetic adaptations to climate change often involve shifts in the timing of phenological events, such as flowering. If populations at the edge of a species range have lower genetic variation in phenological traits than central populations, then their persistence under climate change could be threatened. To test this hypothesis, we performed artificial selection experiments using the scarlet monkeyflower (Mimulus cardinalis) and compared genetic variation in flowering time among populations at the latitudinal center, northern edge, and southern edge of the species range. We also assessed whether selection on flowering time yielded correlated responses in functional traits, potentially representing a cost associated with early or late flowering. Contrary to prediction, southern populations exhibited greater responses to selection on flowering time than central or northern populations. Further, selection for early flowering resulted in correlated increases in specific leaf area and leaf nitrogen, whereas selection for late flowering led to decreases in these traits. These results provide critical insights about how spatial variation in the potential for adaptation may affect population persistence under changing climates.

  13. Differences in foraging ecology align with genetically divergent ecotypes of a highly mobile marine top predator.

    Science.gov (United States)

    Jeglinski, Jana W E; Wolf, Jochen B W; Werner, Christiane; Costa, Daniel P; Trillmich, Fritz

    2015-12-01

    Foraging differentiation within a species can contribute to restricted gene flow between ecologically different groups, promoting ecological speciation. Galapagos sea lions (Zalophus wollebaeki) show genetic and morphological divergence between the western and central archipelago, possibly as a result of an ecologically mediated contrast in the marine habitat. We use global positioning system (GPS) data, time-depth recordings (TDR), stable isotope and scat data to compare foraging habitat characteristics, diving behaviour and diet composition of Galapagos sea lions from a western and a central colony. We consider both juvenile and adult life stages to assess the potential role of ontogenetic shifts that can be crucial in shaping foraging behaviour and habitat choice for life. We found differences in foraging habitat use, foraging style and diet composition that aligned with genetic differentiation. These differences were consistent between juvenile and adult sea lions from the same colony, overriding age-specific behavioural differences. Our study contributes to an understanding of the complex interaction of ecological condition, plastic behavioural response and genetic make-up of interconnected populations.

  14. High genetic variability of HIV-1 in female sex workers from Argentina

    Directory of Open Access Journals (Sweden)

    Carr Jean K

    2007-08-01

    Full Text Available Abstract Background A cross-sectional study on 625 Female Sex Workers (FSWs was conducted between 2000 and 2002 in 6 cities in Argentina. This study describes the genetic diversity and the resistance profile of the HIV-infected subjects. Results Seventeen samples from HIV positive FSWs were genotyped by env HMA, showing the presence of 9 subtype F, 6 subtype B and 2 subtype C. Sequence analysis of the protease/RT region on 16 of these showed that 10 were BF recombinants, three were subtype B, two were subtype C, and one sample presented a dual infection with subtype B and a BF recombinant. Full-length genomes of five of the protease/RT BF recombinants were also sequenced, showing that three of them were CRF12_BF. One FSW had a dual HIV-1 infection with subtype B and a BF recombinant. The B sections of the BF recombinant clustered closely with the pure B sequence isolated from the same patient. Major resistance mutations to antiretroviral drugs were found in 3 of 16 (18.8% strains. Conclusion The genetic diversity of HIV strains among FSWs in Argentina was extensive; about three-quarters of the samples were infected with diverse BF recombinants, near twenty percent had primary ART resistance and one sample presented a dual infection. Heterosexual transmission of genetically diverse, drug resistant strains among FSWs and their clients represents an important and underestimated threat, in Argentina.

  15. Genetic Algorithm for Innovative Device Designs in High-Efficiency III-V Nitride Light-Emitting Diodes

    Science.gov (United States)

    Zhu, Di; Schubert, Martin F.; Cho, Jaehee; Schubert, E. Fred; Crawford, Mary H.; Koleske, Daniel D.; Shim, Hyunwook; Sone, Cheolsoo

    2012-01-01

    Light-emitting diodes are becoming the next-generation light source because of their prominent benefits in energy efficiency, versatility, and benign environmental impact. However, because of the unique polarization effects in III-V nitrides and the high complexity of light-emitting diodes, further breakthroughs towards truly optimized devices are required. Here we introduce the concept of artificial evolution into the device optimization process. Reproduction and selection are accomplished by means of an advanced genetic algorithm and device simulator, respectively. We demonstrate that this approach can lead to new device structures that go beyond conventional approaches. The innovative designs originating from the genetic algorithm and the demonstration of the predicted results by implementing structures suggested by the algorithm establish a new avenue for complex semiconductor device design and optimization.

  16. Genetic inhibition of neurotransmission reveals role of glutamatergic input to dopamine neurons in high-effort behavior.

    Science.gov (United States)

    Hutchison, M A; Gu, X; Adrover, M F; Lee, M R; Hnasko, T S; Alvarez, V A; Lu, W

    2017-02-14

    Midbrain dopamine neurons are crucial for many behavioral and cognitive functions. As the major excitatory input, glutamatergic afferents are important for control of the activity and plasticity of dopamine neurons. However, the role of glutamatergic input as a whole onto dopamine neurons remains unclear. Here we developed a mouse line in which glutamatergic inputs onto dopamine neurons are specifically impaired, and utilized this genetic model to directly test the role of glutamatergic inputs in dopamine-related functions. We found that while motor coordination and reward learning were largely unchanged, these animals showed prominent deficits in effort-related behavioral tasks. These results provide genetic evidence that glutamatergic transmission onto dopaminergic neurons underlies incentive motivation, a willingness to exert high levels of effort to obtain reinforcers, and have important implications for understanding the normal function of the midbrain dopamine system.Molecular Psychiatry advance online publication, 14 February 2017; doi:10.1038/mp.2017.7.

  17. Genome-wide association study of triglyceride response to a high-fat meal among participants of the NHLBI genetics of lipid lowering drugs and diet network (GOLDN)

    Science.gov (United States)

    Objective: The triglyceride (TG) response to a high-fat meal (postprandial lipemia, PPL) affects cardiovascular disease risk and is influenced by genes and environment. Genes involved in lipid metabolism have dominated genetic studies of PPL TG response. We sought to elucidate common genetic variant...

  18. Targeted high-throughput growth hormone 1 gene sequencing reveals high within-breed genetic diversity in South African goats.

    Science.gov (United States)

    Ncube, K T; Mdladla, K; Dzomba, E F; Muchadeyi, F C

    2016-06-01

    This study assessed the genetic diversity in the growth hormone 1 gene (GH1) within and between South African goat breeds. Polymerase chain reaction-targeted gene amplification together with Illumina MiSeq next-generation sequencing (NGS) was used to generate the full length (2.54 kb) of the growth hormone 1 gene and screen for SNPs in the South African Boer (SAB) (n = 17), Tankwa (n = 15) and South African village (n = 35) goat populations. A range of 27-58 SNPs per population were observed. Mutations resulting in amino acid changes were observed at exons 2 and 5. Higher within-breed diversity of 97.37% was observed within the population category consisting of SA village ecotypes and the Tankwa goats. Highest pairwise FST values ranging from 0.148 to 0.356 were observed between the SAB and both the South African village and Tankwa feral goat populations. Phylogenetic analysis indicated nine genetic clusters, which reflected close relationships between the South African populations and the other international breeds with the exception of the Italian Sarda breeds. Results imply greater potential for within-population selection programs, particularly with SA village goats.

  19. Petroleum geology and resources of southeastern Mexico, northern Guatemala, and Belize

    Science.gov (United States)

    Peterson, James A.

    1983-01-01

    sequence that overlies the Mesozoic carbonate complex on the Yucatan platform. During the past 10 years, about 50 large oil fields were discovered in the Reforma and offshore Campeche areas. Oil is produced from intensely microfractured Cretaceous, Paleocene, and Upper Jurassic dolomite reservoirs on blockfaulted salt swells or domes. Most fields are located in the Mesozoic carbonate-bank margin and forebank talus (Tamabra) facies, which passes through the offshore Campeche and onshore Reforma areas. Oil source rocks are believed to be organic-rich shales and shaly carbonate rocks of latest Jurassic and possibly Early Cretaceous age. At least six of the Mesozoic discoveries are giant or supergiant fields. The largest is the Cantarell complex (about 8 billion to 10 billion barrels (BB)) in the offshore Campeche area and the Bermudez complex (about 8 BB) in the Reforma onshore area. Oil columns are unusually large (from 50 m to as much as 1,000 m, or 160 ft to 3,300 ft). Production rates are extremely high, averaging at least 3,000 to 5,000 barrels of oil per day (bo/d); some wells produce more than 20,000 bo/d, particularly in the offshore Campeche area, where 30,000- to 60,000-bo/d wells are reported. Tertiary basin fields produce primarily from Miocene sandstone reservoirs. About 50 of these are oil fields ranging from 1 million barrels (MMB) to 200 MMB in size, located on faulted salt structures in the Isthmus Saline basin. Another 30 are gas or gas-condensate fields of a few billion cubic feet to 3 trillion to 4 trillion cubic feet (Tcf) located on salt structures or probable salt structures in the Macuspana, Comalcalco, Isthmus Saline, and Veracruz basins. Source rocks for the gas are believed to be carbonaceous shales interbedded with the sandstone reservoir bodies. Identified reserves in the southeastern Mexico-Guatemala area, almost all in the Mesozoic fields, are about 53 BB of oil, 3 BB of natural gas liquids, and 65 Tcf of gas. The estimat

  20. High-grade endometrial stromal sarcomas: a clinicopathologic study of a group of tumors with heterogenous morphologic and genetic features.

    Science.gov (United States)

    Sciallis, Andrew P; Bedroske, Patrick P; Schoolmeester, John K; Sukov, William R; Keeney, Gary L; Hodge, Jennelle C; Bell, Debra A

    2014-09-01

    The existence of a "high-grade endometrial stromal sarcoma" category of tumors has been a controversial subject owing to, among other things, the difficulty in establishing consistent diagnostic criteria. Currently, the recommended classification for such tumors is undifferentiated uterine/endometrial sarcoma. Interest in this subject has recently increased markedly with the identification of recurrent molecular genetic abnormalities. At Mayo Clinic, a group of neoplasms has been observed that morphologically resemble, either cytologically or architecturally, classic "low-grade" endometrial stromal sarcoma but feature obvious deviations, specifically, 17 tumors with unequivocally high-grade morphology. These high-grade tumors displayed 3 morphologic themes: (1) tumors with a component that is identical to low-grade ESS that transitions abruptly into an obviously higher-grade component; (2) tumors composed exclusively of high-grade cells with uniform nuclear features but with a permeative pattern of infiltration; (3) tumors similar to the second group but with a different, yet characteristic, cytomorphology featuring enlarged round to ovoid cells (larger than those found in low-grade ESS) with smooth nuclear membranes and distinct chromatin clearing but lacking prominent nucleoli. We collected clinicopathologic data, applied immunohistochemical studies, and also tested tumors by fluorescence in situ hybridization for abnormalities in JAZF1, PHF1, YWHAE, and CCND1. Tumors from these 3 groups were found to be immunohistochemically and genetically distinct from one another. Most notable was the fact that category 3 contained all the cases that tested positive for YWHAE rearrangement, did not show any classic translocations for JAZF1, PHF1, or CCND1, often presented at a high stage, and behaved aggressively. This study demonstrates the morphologic, immunophenotypic, and molecular genetic heterogeneity that exists within "undifferentiated endometrial sarcomas" as

  1. Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms.

    Science.gov (United States)

    Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

    2015-01-05

    The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.

  2. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

    Science.gov (United States)

    Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel

    2016-01-01

    Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens. PMID:26921302

  3. Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal

    Science.gov (United States)

    Gomes, Cidália; Sousa, Ronaldo; Mendes, Tito; Borges, Rui; Vilares, Pedro; Vasconcelos, Vitor; Guilhermino, Lúcia; Antunes, Agostinho

    2016-01-01

    The Asian clam, Corbicula fluminea, is an invasive alien species (IAS) originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers), morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River) and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity. PMID:27391333

  4. High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H.

    Science.gov (United States)

    Shahinnia, Fahimeh; Druka, Arnis; Franckowiak, Jerome; Morgante, Michele; Waugh, Robbie; Stein, Nils

    2012-02-01

    Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC(7)F(3) nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

  5. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

    Directory of Open Access Journals (Sweden)

    Marie Foulongne-Oriol

    2016-05-01

    Full Text Available Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG, and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens.

  6. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.

    Science.gov (United States)

    Zhan, Aibin; Bailey, Sarah A; Heath, Daniel D; Macisaac, Hugh J

    2014-09-01

    Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification.

  7. Genetic Discrimination

    Science.gov (United States)

    ... in Genetics Archive Regulation of Genetic Tests Genetic Discrimination Overview Genetic Information Nondiscrimination Act Genetic Discrimination and ... gov/employees/process.cfm Top of page Genetic Discrimination and Other Laws Bill Clinton's Executive Order Prohibiting ...

  8. Genotype-phenotype correlations in a mountain population community with high prevalence of Wilson's disease: genetic and clinical homogeneity.

    Directory of Open Access Journals (Sweden)

    Relu Cocoş

    Full Text Available Wilson's disease is an autosomal recessive disorder caused by more than 500 mutations in ATP7B gene presenting considerably clinical manifestations heterogeneity even in patients with a particular mutation. Previous findings suggested a potential role of additional genetic modifiers and environment factors on phenotypic expression among the affected patients. We conducted clinical and genetic investigations to perform genotype-phenotype correlation in two large families living in a socio-culturally isolated community with the highest prevalence of Wilson's disease ever reported of 1 ∶ 1130. Sequencing of ATP7B gene in seven affected individuals and 43 family members identified a common compound heterozygous genotype, H1069Q/M769H-fs, in five symptomatic and two asymptomatic patients and detected the presence of two out of seven identified single nucleotide polymorphisms in all affected patients. Symptomatic patients had similar clinical phenotype and age at onset (18 ± 1 years showing dysarthria and dysphagia as common clinical features at the time of diagnosis. Moreover, all symptomatic patients presented Kayser-Fleischer rings and lack of dystonia accompanied by unfavourable clinical outcomes. Our findings add value for understanding of genotype-phenotype correlations in Wilson's disease based on a multifamily study in an isolated population with high extent of genetic and environmental homogeneity as opposed to majority of reports. We observed an equal influence of presumed other genetic modifiers and environmental factors on clinical presentation and age at onset of Wilson's disease in patients with a particular genotype. These data provide valuable inferences that could be applied for predicting clinical management in asymptomatic patients in such communities.

  9. High genetic connectivity among estuarine populations of the riverbream Acanthopagrus vagus along the southern African coast

    Science.gov (United States)

    Oosthuizen, Carel J.; Cowley, Paul D.; Kyle, Scotty R.; Bloomer, Paulette

    2016-12-01

    Physical and/or physiological constraints are assumed to isolate fish populations confined to or dependent on estuarine habitats. Strong isolation by distance is thus expected to affect connectivity. Such structuring has important implications for sustainable utilisation and replenishment of estuarine stocks that are heavily exploited. Here we present a preliminary investigation of the phylogenetic relationships of the riverbream (Acanthopagrus species) along the southern African coast and the geographic genetic structure of what appears to be a locally endemic species or lineage. Mitochondrial DNA (mtDNA) cytochrome b sequences support the notion that the species occurring along the southern African coast is A. vagus and not A. berda as previously thought. Yet, the taxonomy of this widespread Indo-West Pacific species or species-complex requires more in-depth investigation. No genetic differentiation was detected among estuarine populations of A. vagus based on the analyses of mtDNA ND2 gene sequences and 10 polymorphic nuclear microsatellite markers. The star-like genealogy and statistical analyses are consistent with a recent population expansion event. Spatial analyses of microsatellite genotypes fail to reject the null hypothesis of panmixia, indicative of a recent population expansion or ongoing gene flow between different estuaries. The northern localities were identified as containing most of the observed variation. This study not only provides insight into the phylogenetic relationship of A. vagus relative to other Acanthopagrus species but also sheds light on the demographic history and contemporary gene flow of the species.

  10. Harnessing a high cargo-capacity transposon for genetic applications in vertebrates.

    Directory of Open Access Journals (Sweden)

    Darius Balciunas

    2006-11-01

    Full Text Available Viruses and transposons are efficient tools for permanently delivering foreign DNA into vertebrate genomes but exhibit diminished activity when cargo exceeds 8 kilobases (kb. This size restriction limits their molecular genetic and biotechnological utility, such as numerous therapeutically relevant genes that exceed 8 kb in size. Furthermore, a greater payload capacity vector would accommodate more sophisticated cis cargo designs to modulate the expression and mutagenic risk of these molecular therapeutics. We show that the Tol2 transposon can efficiently integrate DNA sequences larger than 10 kb into human cells. We characterize minimal sequences necessary for transposition (miniTol2 in vivo in zebrafish and in vitro in human cells. Both the 8.5-kb Tol2 transposon and 5.8-kb miniTol2 engineered elements readily function to revert the deficiency of fumarylacetoacetate hydrolase in an animal model of hereditary tyrosinemia type 1. Together, Tol2 provides a novel nonviral vector for the delivery of large genetic payloads for gene therapy and other transgenic applications.

  11. Belize Area Study

    Science.gov (United States)

    1983-11-20

    is greater than Costa Rica and Janica, similar to El Salvador and Mexico, but less than Guatemtala and Paraguay. In 1981, one-fourth to one-half of...as well as increased poaching by foreign fishing boats. Poachery is difficult to control but with the addition of two patrol boats and two aircrafts...resettlement program. The U. N. effort is directed by Regina Coballer, whose office is located in Costa Rica . There are at least three resettlement areas in

  12. Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

    Directory of Open Access Journals (Sweden)

    Symula Rebecca E

    2013-02-01

    Full Text Available Abstract Background Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI. This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep. Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina fuscipes fuscipes, but it is not limited to a single host haplotype, suggesting that CI did not impact its population structure. However, host population genetic differentiation could have been generated if multiple Wolbachia strains interacted in some populations. Here, we investigated Wolbachia genetic variation in G. f. fuscipes populations of known host genetic composition in Uganda. We tested for the presence of multiple Wolbachia strains using Multi-Locus Sequence Typing (MLST and for an association between geographic region and host mtDNA haplotype using Wolbachia DNA sequence from a variable locus, groEL (heat shock protein 60. Results MLST demonstrated that some G. f. fuscipes carry Wolbachia strains from two lineages. GroEL revealed high levels of sequence diversity within and between individuals (Haplotype diversity = 0.945. We found Wolbachia associated with 26 host mtDNA haplotypes, an unprecedented result. We observed a geographical association of one Wolbachia lineage with southern host mtDNA haplotypes, but it was non-significant (p = 0.16. Though most Wolbachia-infected host haplotypes were those found in the contact region between host mtDNA groups, this association was non

  13. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538

    Science.gov (United States)

    Fatima, Syeda Akash; Yang, Jiezhi; Chen, Wanquan; Liu, Taiguo; Hu, Yuting; Li, Qing; Guo, Jingwei; Zhang, Min; Lei, Li; Li, Xin; Tang, Shengwen; Luo, Peigao

    2016-01-01

    The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs. PMID:27755575

  14. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538.

    Science.gov (United States)

    Zhong, Shengfu; Ma, Lixia; Fatima, Syeda Akash; Yang, Jiezhi; Chen, Wanquan; Liu, Taiguo; Hu, Yuting; Li, Qing; Guo, Jingwei; Zhang, Min; Lei, Li; Li, Xin; Tang, Shengwen; Luo, Peigao

    2016-01-01

    The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs.

  15. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

  16. Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the Iron Quadrangle, southeastern Brazil.

    Science.gov (United States)

    Leles, Bruno; Chaves, Anderson V; Russo, Philip; Batista, João A N; Lovato, Maria Bernadete

    2015-01-01

    Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.

  17. Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the Iron Quadrangle, southeastern Brazil.

    Directory of Open Access Journals (Sweden)

    Bruno Leles

    Full Text Available Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae. Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03. Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001, reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.

  18. The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

    Energy Technology Data Exchange (ETDEWEB)

    Podsiadlowski, L.; Carapelli, A.; Nardi, F.; Dallai, R.; Koch,M.; Boore, J.L.; Frati, F.

    2005-12-01

    Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

  19. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.

    Directory of Open Access Journals (Sweden)

    Sung-Chur Sim

    Full Text Available The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88% passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals, EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals, and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals. The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins, respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates

  20. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population.

    Directory of Open Access Journals (Sweden)

    Adam L Bailey

    Full Text Available Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 10(6-10(7 RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF 5 (SHFV-krc2 only and 7 (SHFV-krc1 and SHFV-krc2. Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses.

  1. NON-LINEAR DYNAMIC MODEL RETRIEVAL OF SUBTROPICAL HIGH BASED ON EMPIRICAL ORTHOGONAL FUNCTION AND GENETIC ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ren; HONG Mei; SUN Zhao-bo; NIU Sheng-jie; ZHU Wei-jun; MIN Jin-zhong; WAN Qi-lin

    2006-01-01

    Aiming at the difficulty of accurately constructing the dynamic model of subtropical high, based on the potential height field time series over 500 hPa layer of T106 numerical forecast products, by using EOF(empirical orthogonal function) temporal-spatial separation technique, the disassembled EOF time coefficients series were regarded as dynamical model variables, and dynamic system retrieval idea as well as genetic algorithm were introduced to make dynamical model parameters optimization search, then, a reasonable non-linear dynamic model of EOF time-coefficients was established. By dynamic model integral and EOF temporal-spatial components assembly, a mid-/long-term forecast of subtropical high was carried out. The experimental results show that the forecast results of dynamic model are superior to that of general numerical model forecast results.A new modeling idea and forecast technique is presented for diagnosing and forecasting such complicated weathers as subtropical high.

  2. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1.

    Science.gov (United States)

    LaFave, Matthew C; Varshney, Gaurav K; Vemulapalli, Meghana; Mullikin, James C; Burgess, Shawn M

    2014-09-01

    Substantial intrastrain variation at the nucleotide level complicates molecular and genetic studies in zebrafish, such as the use of CRISPRs or morpholinos to inactivate genes. In the absence of robust inbred zebrafish lines, we generated NHGRI-1, a healthy and fecund strain derived from founder parents we sequenced to a depth of ∼50×. Within this strain, we have identified the majority of the genome that matches the reference sequence and documented most of the variants. This strain has utility for many reasons, but in particular it will be useful for any researcher who needs to know the exact sequence (with all variants) of a particular genomic region or who wants to be able to robustly map sequences back to a genome with all possible variants defined.

  3. High Prevalence and Genetic Diversity of Campylobacter jejuni in Wild Crows and Pigeons.

    Science.gov (United States)

    Ramonaitė, Sigita; Novoslavskij, Aleksandr; Zakarienė, Gintarė; Aksomaitienė, Jurgita; Malakauskas, Mindaugas

    2015-11-01

    The occurrence, seasonal variation and genetic diversity of Campylobacter spp. in pigeons and crows over a 1-year period were evaluated. Campylobacter spp. were isolated from 166 (34.6 %) out of 480 wild bird faecal samples. The occurrence of Campylobacter spp. in faecal samples was higher among crows (39.2 %) than pigeons (30.0 %), (P Campylobacter jejuni was the most common species detected among wild bird faecal samples (98.2 %). Meanwhile, Campylobacter coli prevalence in wild bird faecal samples was low-6 %. The Simpson's diversity index of C. jejuni flaA RFLP types was lower in pigeons (D = 0.88) compared with C. jejuni isolates detected in crows (D = 0.97). Obtained results revealed that C. jejuni are widely prevalent among crows and pigeons, indicating these wild birds as potential infection sources to humans. Further studies are required to determine crows and pigeons role in zoonotic transmission of Campylobacter.

  4. HIGH DENSITY CULTIVATION OF GENETICALLY-ENGINEERED CHO CELL LINES WITH MICROCARRIER CULTURE SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    肖成祖; 黄子才; 刘凤云; 郭志霞; 高丽华

    1994-01-01

    Genetically-enginecred CHO cell lines,rβ-13and CLF-8B2,were cultivated with the MC-1 microcarrier cul-ture system.The cell density could be enhanced by increasing the concentration of microcarrier.At a microcarrier concentration of 10 mg/ml.the cell density could reach 4 to 5×106 cells/ml.It was shown that these cell itnes would spontaneously release from the microcarrier to attach to and proliferate on fresh microcatriera.We were thus able to scale up cultivation using a simple methcd,i.e.by adding fresh mlcrocarriers and medium directiy in-to the culture system to about 2,4 or 8 times the original volume.Using a 2 L bioreactor for several weeks at medium perfusion rates of 0.5 to 3working volumes.Prourokinase was stably secreted.

  5. Movement patterns of Antillean manatees in Chetumal Bay (Mexico) and coastal Belize: A challenge for regional conservation

    Science.gov (United States)

    Castelblanco-Martínez, Delma Nataly; Padilla-Saldivar, J.; Hernández-Arana, Héctor Abuid; Slone, D.H.; Reid, J.P.; Morales-Vela, B.

    2013-01-01

    Information from 15 satellite-tracked Antillean manatees (Trichechus manatus manatus) was analyzed in order to assess individual movements, home ranges, and high-use areas for conservation decisions. Manatees were captured in Chetumal Bay, Mexico, and tagged with Argos-monitored satellite transmitters. Location of the manatees and physical characteristics were assessed to describe habitat properties. Most manatees traveled to freshwater sources. The Maximum Area Size (MAS) for each manatee was determined using the observation-area method. Additional kernel densities of 95% home range and 50% Center of Activity (COA) were also calculated, with manatees having 1–3 COAs. Manatees exhibited two different movement patterns: remaining in Chetumal Bay, and long-distance (up to 240 km in 89 d). The residence time in Chetumal Bay was higher for females (89.6% of time) than for males (72.0%), but the daily travel rate (0.4–0.5 km/d) was similar for both sexes. Most of the COAs fell within Natural Protected Areas (NPA). However, manatees also travel for long distances into unprotected areas, where they face uncontrolled boat traffic, fishing activities, and habitat loss. Conservation of movement corridors may promote long-distance movements and facilitate genetic exchange.

  6. A High-Throughput Regeneration and Transformation Platform for Production of Genetically Modified Banana.

    Science.gov (United States)

    Tripathi, Jaindra N; Oduor, Richard O; Tripathi, Leena

    2015-01-01

    Banana (Musa spp.) is an important staple food as well as cash crop in tropical and subtropical countries. Various bacterial, fungal, and viral diseases and pests such as nematodes are major constraints in its production and are currently destabilizing the banana production in sub-Saharan Africa. Genetic engineering is a complementary option used for incorporating useful traits in banana to bypass the long generation time, polyploidy, and sterility of most of the cultivated varieties. A robust transformation protocol for farmer preferred varieties is crucial for banana genomics and improvement. A robust and reproducible system for genetic transformation of banana using embryogenic cell suspensions (ECS) has been developed in this study. Two different types of explants (immature male flowers and multiple buds) were tested for their ability to develop ECS in several varieties of banana locally grown in Africa. ECS of banana varieties "Cavendish Williams" and "Gros Michel" were developed using multiple buds, whereas ECS of "Sukali Ndiizi" was developed using immature male flowers. Regeneration efficiency of ECS was about 20,000-50,000 plantlets per ml of settled cell volume (SCV) depending on variety. ECS of three different varieties were transformed through Agrobacterium-mediated transformation using gusA reporter gene and 20-70 independent transgenic events per ml SCV of ECS were regenerated on selective medium. The presence and integration of gusA gene in transgenic plants was confirmed by PCR, dot blot, and Southern blot analysis and expression by histochemical GUS assays. The robust transformation platform was successfully used to generate hundreds of transgenic lines with disease resistance. Such a platform will facilitate the transfer of technologies to national agricultural research systems (NARS) in Africa.

  7. Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.

    Directory of Open Access Journals (Sweden)

    Gang Li

    2013-05-01

    Full Text Available Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA, there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10(-9. Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10(-9, a finding corroborated by expression quantitative trait loci (eQTL analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2 and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65, a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L and conduct an HTS of 1,982 chemical compounds and FDA-approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel

  8. Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

    Science.gov (United States)

    Li, Gang; Diogo, Dorothée; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J.; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L.; Siminovitch, Katherine A.; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K.; Worthington, Jane; Gupta, Namrata; Clemons, Paul A.; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M.

    2013-01-01

    Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10−9). Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10−9), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA–approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in

  9. Genetics Home Reference: leukoencephalopathy with thalamus and brainstem involvement and high lactate

    Science.gov (United States)

    ... Health Conditions LTBL leukoencephalopathy with thalamus and brainstem involvement and high lactate Enable Javascript to view the expand/collapse ... Close All Description Leukoencephalopathy with thalamus and brainstem involvement and high lactate ( LTBL ) is a disorder that affects the ...

  10. Centennial and Extreme Climate Variability in the Last 1500 Year from the Belize Central Shelf Lagoon (Central America): Successive Droughts and Floods Linked to the Demise of the Mayan Civilization

    Science.gov (United States)

    Droxler, A. W.; Agar Cetin, A.; Bentley, S. J.

    2014-12-01

    This study focuses on the last 1500 yr precipitation record archived in the mixed carbonate/siliciclastic sediments accumulated in the Belize Central Shelf Lagoon, part of the Yucatan Peninsula eastern continental margin, proximal to the land areas where the Mayan Civilization thrived and then abruptly collapsed. This study is mainly based upon the detailed analyses of cores, BZE-RH-SVC-58 and 68, retrieved in 30 and 19 m of water depth from Elbow Caye Lagoon and English Caye Channel, respectively. The core timeframe is well-constrained by AMS radiocarbon dating of benthic foraminifera, Quinqueloculina. Carbonate content was determined by carbonate bomb, particle size fractions with a Malvern Master Sizer 2000 particle size analyzer, and element (Ti, Si, K, Fe, Al, Ca, and Sr) counts via X-Ray Fluorescence (XRF). The variations of elements such as Ti and K counts, and Ti/Al in these two cores have recorded, in the past past 1500 years, the weathering rate variations of the adjacent Maya Mountain, defining alternating periods of high precipitation and droughts, linked to large climate fluctuations and extreme events, highly influenced by the ITCZ latitudinal migration. The CE 800-900 century just preceding the Medieval Climate Anomaly (MCA), characterized by unusually low Ti counts and Ti/Al, is interpreted to represent a time of low precipitation and resulting severe droughts in the Yucatan Peninsula, contemporaneous with the Mayan Terminal Classic Collapse. High Ti counts and Ti/Al, although highly variable, during the MCA (CE 900-1350) are interpreted as an unusually warm period characterized by two 100-to-250 years-long intervals of higher precipitation when the number of tropical cyclones peaked. These two intervals of high precipitation during the MCA are separated by a century (CE 1000 -1100) of severe droughts and low tropical storm frequency coinciding with the collapse of Chichen Itza (CE 1040-1100). The Little Ice Age (CE 1350-1850), several centuries

  11. Rapid genetic diagnosis and prenatal diagnosis of spinal muscular atrophy by denaturing high-performance liquid chromatography

    Institute of Scientific and Technical Information of China (English)

    ZHU Hai-yan; WU Ling-qian; PAN Qian; TANG Bei-sha; LIANG De-sheng; LONG Zhi-gao; DAI He-ping; XIA Kun; XIA Jia-hui

    2006-01-01

    @@ Spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disorder1 (1in 6000 to 10 000 births) caused by mutations in the SMN1 gene at 5q13. More than 90%-98% of SMA patients show homozygous deletion of SMN1,2which has proved to be useful in the diagnosis of SMA. But it is hampered because of the existence of a highly homologous gene, SMN2.3 Based on nucleotide mismatches between SMN1 and SMN2,the following two DNA tests are usually performed:single-strand conformational polymorphism (SSCP)3and polymerase chain reaction (PCR) followed by a restriction enzyme digestion.4,5 In this study we developed a new method for rapid genetic diagnosis of SMA by denaturing high-performance liquid chromatography (DHPLC), which is based on different retention of homoduplexes and heteroduplexes in detecting the homozygous deletion of SMN1. Both genetic and prenatal diagnoses were performed successfully for a SMA family by DHPLC, which was confirmed as a rapid and effective technique for detecting the deletion of SMN1.

  12. Genetic engineering of Pseudomonas putida KT2440 for rapid and high-yield production of vanillin from ferulic acid.

    Science.gov (United States)

    Graf, Nadja; Altenbuchner, Josef

    2014-01-01

    Vanillin is one of the most important flavoring agents used today. That is why many efforts have been made on biotechnological production from natural abundant substrates. In this work, the nonpathogenic Pseudomonas putida strain KT2440 was genetically optimized to convert ferulic acid to vanillin. Deletion of the vanillin dehydrogenase gene (vdh) was not sufficient to prevent vanillin degradation. Additional inactivation of a molybdate transporter, identified by transposon mutagenesis, led to a strain incapable to grow on vanillin as sole carbon source. The bioconversion was optimized by enhanced chromosomal expression of the structural genes for feruloyl-CoA synthetase (fcs) and enoyl-CoA hydratase/aldolase (ech) by introduction of the strong tac promoter system. Further genetic engineering led to high initial conversion rates and molar vanillin yields up to 86% within just 3 h accompanied with very low by-product levels. To our knowledge, this represents the highest productivity and molar vanillin yield gained with a Pseudomonas strain so far. Together with its high tolerance for ferulic acid, the developed, plasmid-free P. putida strain represents a promising candidate for the biotechnological production of vanillin.

  13. Phase-specific brain change of spatial working memory processing in genetic and ultra-high risk groups of schizophrenia.

    Science.gov (United States)

    Choi, Jung-Seok; Park, Ji-Young; Jung, Myung Hun; Jang, Joon Hwan; Kang, Do-Hyung; Jung, Wi Hoon; Han, Ji Yeon; Choi, Chi-Hoon; Hong, Kyung Sue; Kwon, Jun Soo

    2012-11-01

    Spatial working memory (WM) processing has 3 distinct phases: encoding, maintenance, and retrieval and its dysfunction is a core feature in schizophrenia. We examined phase-specific brain activations associated with spatial WM in first-degree relatives of schizophrenia (genetic high risk, GHR), ultra-high risk (UHR) subjects, patients with schizophrenia, and healthy controls. We used an event-related functional magnetic resonance imaging in 17 GHR subjects, 21 UHR subjects, 15 clinically stable patients with schizophrenia and 16 healthy controls, while subjects were performing a spatial delayed-response task. During the encoding phase, the GHR group showed increased activation in the fronto-parietal regions, whereas the UHR and schizophrenia groups showed significantly less activation in these regions than did the healthy control group. Especially, frontal activation was strongest in GHR subjects, followed by healthy controls, and occurred to a lesser degree in the UHR group, with the least activation occurring in the schizophrenia group. During the maintenance phase, the thalamus showed a differential activation, similar to frontal activation pattern during the encoding phase. During the retrieval phase, no prominent differential activations were found. Increased activations were observed in the superior temporal gyrus during the encoding and maintenance phases in the GHR, UHR, and schizophrenia groups relative to healthy controls. Our findings suggest that functional deficits associated with spatial WM processing emerge in the UHR before the onset of schizophrenia and compensatory neural processes exist in the GHR with genetic liability to schizophrenia.

  14. Optimization of High-Speed Train Control Strategy for Traction Energy Saving Using an Improved Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Ruidan Su

    2014-01-01

    Full Text Available A parallel multipopulation genetic algorithm (PMPGA is proposed to optimize the train control strategy, which reduces the energy consumption at a specified running time. The paper considered not only energy consumption, but also running time, security, and riding comfort. Also an actual railway line (Beijing-Shanghai High-Speed Railway parameter including the slop, tunnel, and curve was applied for simulation. Train traction property and braking property was explored detailed to ensure the accuracy of running. The PMPGA was also compared with the standard genetic algorithm (SGA; the influence of the fitness function representation on the search results was also explored. By running a series of simulations, energy savings were found, both qualitatively and quantitatively, which were affected by applying cursing and coasting running status. The paper compared the PMPGA with the multiobjective fuzzy optimization algorithm and differential evolution based algorithm and showed that PMPGA has achieved better result. The method can be widely applied to related high-speed train.

  15. Delineating genetic relationships among the Maya.

    Science.gov (United States)

    Ibarra-Rivera, Lisa; Mirabal, Sheyla; Regueiro, Manuela M; Herrera, Rene J

    2008-03-01

    By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire.

  16. A High-Density Genetic Map for Cucumber (Cucumis Sativus L. Based on Specific Length Amplified Fragment (SLAF Sequencing and QTL Analysis of Fruit Traits in Cucumber

    Directory of Open Access Journals (Sweden)

    Wenying eZhu

    2016-04-01

    Full Text Available High-density genetic linkage map plays an important role in genome assembly and QTL fine mapping. Since the coming of next-generation sequencing (NGS, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000×S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on 7 chromosomes, and spanned 1061.19cM. The average genetic distance is 0.35cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.

  17. Exploratory study of the feasibility and utility of the colored eco-genetic relationship map (CEGRM) in women at high genetic risk of developing breast cancer.

    Science.gov (United States)

    Peters, June A; Kenen, Regina; Giusti, Ruthann; Loud, Jennifer; Weissman, Nancy; Greene, Mark H

    2004-10-15

    We report here the results of an exploratory feasibility study of the colored eco-genetic relationship map (CEGRM), a novel, recently-developed psychosocial assessment tool, which incorporates features of the genetic pedigree, family systems genogram, and ecomap. The CEGRM presents a simple, concise, visual representation of the social interaction domains of information, services, and emotional support through the application of color-coded symbols to the genetic pedigree. The interactive process of completing the CEGRM was designed to facilitate contemporary genetic counseling goals of: (a) understanding the client in the context of her/his social milieu; (b) bolstering client self-awareness and insight; (c) fostering active client participation and mutuality in the counseling interaction; (d) eliciting illuminating social narratives; and (e) addressing outstanding emotional issues. Twenty women participating in a breast imaging study of women from families with BRCA1/2 mutations completed and evaluated various aspects of the CEGRM. We found that efficient construction of the CEGRM was feasible, and that compliance was excellent. Participants developed insights into their social milieu through observing the visual pattern of relationships illustrated by the CEGRM. The process of co-constructing the CEGRM fostered the participant's active involvement in the session, marked by mutuality and increased empathy. In this clinical research context, the participants felt free to share poignant stories about their friends and families. Further studies are planned to refine the CEGRM and to examine its utility in cancer genetics research.

  18. Measles virus genetic evolution throughout an imported epidemic outbreak in a highly vaccinated population.

    Science.gov (United States)

    Muñoz-Alía, Miguel Ángel; Fernández-Muñoz, Rafael; Casasnovas, José María; Porras-Mansilla, Rebeca; Serrano-Pardo, Ángela; Pagán, Israel; Ordobás, María; Ramírez, Rosa; Celma, María Luisa

    2015-01-22

    Measles virus circulates endemically in African and Asian large urban populations, causing outbreaks worldwide in populations with up-to-95% immune protection. We studied the natural genetic variability of genotype B3.1 in a population with 95% vaccine coverage throughout an imported six month measles outbreak. From first pass viral isolates of 47 patients we performed direct sequencing of genomic cDNA. Whilst no variation from index case sequence occurred in the Nucleocapsid gene hyper-variable carboxy end, in the Hemagglutinin gene, main target for neutralizing antibodies, we observed gradual nucleotide divergence from index case along the outbreak (0% to 0.380%, average 0.138%) with the emergence of transient and persistent non-synonymous and synonymous mutations. Little or no variation was observed between the index and last outbreak cases in Phosphoprotein, Nucleocapsid, Matrix and Fusion genes. Most of the H non-synonymous mutations were mapped on the protein surface near antigenic and receptors binding sites. We estimated a MV-Hemagglutinin nucleotide substitution rate of 7.28 × 10-6 substitutions/site/day by a Bayesian phylogenetic analysis. The dN/dS analysis did not suggest significant immune or other selective pressures on the H gene during the outbreak. These results emphasize the usefulness of MV-H sequence analysis in measles epidemiological surveillance and elimination programs, and in detection of potentially emergence of measles virus neutralization-resistant mutants.

  19. High Genetic Diversity of Microbial Cellulase and Hemicellulase Genes in the Hindgut of Holotrichia parallela Larvae

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    Ping Sheng

    2015-07-01

    Full Text Available In this study, we used a culture-independent method based on library construction and sequencing to analyze the genetic diversity of the cellulase and hemicellulase genes of the bacterial community resident in the hindgut of Holotrichia parallela larvae. The results indicate that there is a large, diverse set of bacterial genes encoding lignocellulose hydrolysis enzymes in the hindgut of H. parallela. The total of 101 distinct gene fragments (similarity <95% of glycosyl hydrolase families including GH2 (24 genes, GH8 (27 genes, GH10 (19 genes, GH11 (14 genes and GH36 (17 genes families was retrieved, and certain sequences of GH2 (10.61%, GH8 (3.33%, and GH11 (18.42% families had <60% identities with known sequences in GenBank, indicating their novelty. Based on phylogenetic analysis, sequences from hemicellulase families were related to enzymes from Bacteroidetes and Firmicutes. Fragments from cellulase family were most associated with the phylum of Proteobacteria. Furthermore, a full-length endo-xylanase gene was obtained, and the enzyme exhibited activity over a broad range of pH levels. Our results indicate that there are large number of cellulolytic and xylanolytic bacteria in the hindgut of H. parallela larvae, and these symbiotic bacteria play an important role in the degradation of roots and other organic matter for the host insect.

  20. Analysis of genetic interaction networks shows that alternatively spliced genes are highly versatile.

    Science.gov (United States)

    Talavera, David; Sheoran, Ritika; Lovell, Simon C

    2013-01-01

    Alternative splicing has the potential to increase the diversity of the transcriptome and proteome. Where more than one transcript arises from a gene they are often so different that they are quite unlikely to have the same function. However, it remains unclear if alternative splicing generally leads to a gene being involved in multiple biological processes or whether it alters the function within a single process. Knowing that genetic interactions occur between functionally related genes, we have used them as a proxy for functional versatility, and have analysed the sets of genes of two well-characterised model organisms: Caenorhabditis elegans and Drosophila melanogaster. Using network analyses we find that few genes are functionally homogenous (only involved in a few functionally-related biological processes). Moreover, there are differences between alternatively spliced genes and genes with a single transcript; specifically, genes with alternatively splicing are, on average, involved in more biological processes. Finally, we suggest that factors other than specific functional classes determine whether a gene is alternatively spliced.

  1. Unexpected high genetic diversity at the extreme northern geographic limit of Taurulus bubalis (Euphrasen, 1786.

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    Vítor C Almada

    Full Text Available The longspined bullhead (Taurulus bubalis, Euphrasen 1786 belongs to the family Cottidae and is a rocky shore species that inhabits the intertidal zones of the Eastern Atlantic since Iceland, southward to Portugal and also the North Sea and Baltic, northward to the Gulf of Finland, with some occurrences in the northern Mediterranean coasts eastward to the Gulf of Genoa. We analysed the phylogeographic patterns of this species using mitochondrial and nuclear markers in populations throughout most of its distributional range in west Europe. We found that T. bubalis has a relatively shallow genealogy with some differentiation between Atlantic and North Sea. Genetic diversity was homogeneous across all populations studied. The possibility of a glacial refugium near the North Sea is discussed. In many, but not all, marine temperate organisms, patterns of diversity are similar across the species range. If this phenomenon proves to be most common in cold adapted species, it may reflect the availability of glacial refugia not far from their present-day northern limits.

  2. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

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    Sergio Alvarez-Pérez

    Full Text Available The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA of four core housekeeping genes (rrs, gyrB, rpoB and rpoD. A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1; P. fluorescens, P. lutea and P. syringae (NG 2; and P. rhizosphaerae (NG 3. Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  3. Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.

    Science.gov (United States)

    Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

    2009-12-01

    A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles.

  4. Structural dysconnectivity of key cognitive and emotional hubs in young people at high genetic risk for bipolar disorder.

    Science.gov (United States)

    Roberts, G; Perry, A; Lord, A; Frankland, A; Leung, V; Holmes-Preston, E; Levy, F; Lenroot, R K; Mitchell, P B; Breakspear, M

    2016-12-20

    Emerging evidence suggests that psychiatric disorders are associated with disturbances in structural brain networks. Little is known, however, about brain networks in those at high risk (HR) of bipolar disorder (BD), with such disturbances carrying substantial predictive and etiological value. Whole-brain tractography was performed on diffusion-weighted images acquired from 84 unaffected HR individuals with at least one first-degree relative with BD, 38 young patients with BD and 96 matched controls (CNs) with no family history of mental illness. We studied structural connectivity differences between these groups, with a focus on highly connected hubs and networks involving emotional centres. HR participants showed lower structural connectivity in two lateralised sub-networks centred on bilateral inferior frontal gyri and left insular cortex, as well as increased connectivity in a right lateralised limbic sub-network compared with CN subjects. BD was associated with weaker connectivity in a small right-sided sub-network involving connections between fronto-temporal and temporal areas. Although these sub-networks preferentially involved structural hubs, the integrity of the highly connected structural backbone was preserved in both groups. Weaker structural brain networks involving key emotional centres occur in young people at genetic risk of BD and those with established BD. In contrast to other psychiatric disorders such as schizophrenia, the structural core of the brain remains intact, despite the local involvement of network hubs. These results add to our understanding of the neurobiological correlates of BD and provide predictions for outcomes in young people at high genetic risk for BD.Molecular Psychiatry advance online publication, 20 December 2016; doi:10.1038/mp.2016.216.

  5. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range

    KAUST Repository

    Vignaud, Thomas M.

    2014-10-13

    For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ∼0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.

  6. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    Institute of Scientific and Technical Information of China (English)

    SHAN Tifeng; PANG Shaojun; LIU Feng; XU Na; ZHAO Xiaobo; GAO Suqin

    2012-01-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation.To better understand the genetic relationships of different gametophyte cultures isolated from different sources,20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U.pinnatifida isolated from wild sporophytes in Vladivostok,Russia and from cultivated sporophytes from Dalian and Qingdao,China.One locus was abandoned because of poor amplification.At the sex-linked locus of Up-AC-2A8,3 alleles were detected in 25 female gametophyte clones,with sizes ranging from 307 to 316 bp.At other loci,3 to 7 alleles were detected with an average of 4.5 alleles per locus.The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones,respectively.The average gene diversity for Russian,Chinese,and for the combined total of gametophyte clones was 0.1,0.4,and 0.5,respectively.Russian gametophyte clones had unique alleles at 7 out of the 19 loci.In cluster analysis,Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance.Overall,high genetic diversity was detected in gametophyte clones isolated from the two countries.These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  7. Altered expression of MGMT in high-grade gliomas results from the combined effect of epigenetic and genetic aberrations.

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    João Ramalho-Carvalho

    Full Text Available MGMT downregulation in high-grade gliomas (HGG has been mostly attributed to aberrant promoter methylation and is associated with increased sensitivity to alkylating agent-based chemotherapy. However, HGG harboring 10q deletions also benefit from treatment with alkylating agents. Because the MGMT gene is mapped at 10q26, we hypothesized that both epigenetic and genetic alterations might affect its expression and predict response to chemotherapy. To test this hypothesis, promoter methylation and mRNA levels of MGMT were determined by quantitative methylation-specific PCR (qMSP or methylation-specific multiplex ligation dependent probe amplification (MS-MLPA and quantitative RT-PCR, respectively, in a retrospective series of 61 HGG. MGMT/chromosome 10 copy number variations were determined by FISH or MS-MLPA analysis. Molecular findings were correlated with clinical parameters to assess their predictive value. Overall, MGMT methylation ratios assessed by qMSP and MS-MLPA were inversely correlated with mRNA expression levels (best coefficient value obtained with MS-MLPA. By FISH analysis in 68.3% of the cases there was loss of 10q26.1 and in 15% of the cases polysomy was demonstrated; the latter displayed the highest levels of transcript. When genetic and epigenetic data were combined, cases with MGMT promoter methylation and MGMT loss depicted the lowest transcript levels, although an impact in response to alkylating agent chemotherapy was not apparent. Cooperation between epigenetic (promoter methylation and genetic (monosomy, locus deletion changes affecting MGMT in HGG is required for effective MGMT silencing. Hence, evaluation of copy number alterations might add relevant prognostic and predictive information concerning response to alkylating agent-based chemotherapy.

  8. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.

    Science.gov (United States)

    Vignaud, Thomas M; Mourier, Johann; Maynard, Jeffrey A; Leblois, Raphael; Spaet, Julia; Clua, Eric; Neglia, Valentina; Planes, Serge

    2014-11-01

    For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.

  9. Genetic Analysis and Preliminary Mapping of a Highly Male-Sterile Gene in Foxtail Millet (Setaria italica L. Beauv.) Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; DIAO Xian-min; GUO Ping-yi; WANG Zhi-lan; YANG Hui-qing; YUAN Feng; GUO Er-hu; TIAN Gang; AN Yuan-huai; LI Hui-xia; WANG Yu-wen

    2013-01-01

    Breeding of male-sterile lines has become the mainstream for the heterosis utilization in foxtail millet, but the genetic basis of most male-sterile lines used for the hybrid is still an area to be elucidated. In this study, a highly male-sterile line Gao146A was investigated. Genetic analysis indicated that the highly male-sterile phenotype was controlled by a single recessive gene a single recessive gene. Using F2 population derived from cross Gao146A/K103, one gene controlling the highly male-sterility, tentatively named asms1, which linked to SSR marker b234 with genetic distance of 16.7 cM, was mapped on the chromosome VI. These results not only laid the foundation for ifne mapping of this highly male-sterile gene, but also helped to accelerate the improvement of highly male-sterile lines by using molecular marker assisted breeding method.

  10. High Genetic Differentiation among European White Oak Species (Quercus spp. at a Dehydrin Gene

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    Iacob CRĂCIUNESC

    2015-12-01

    Full Text Available Dehydryn genes are involved in plant response to environmental stress and may be useful to examine functional diversity in relation to adaptive variation. Recently, a dehydrin gene (DHN3 was isolated in Quercus petraea and showed little differentiation between populations of the same species in an altitudinal transect. In the present study, inter- and intraspecific differentiation patterns in closely related and interfertile oaks were investigated for the first time at the DHN3 locus. A four-oak-species stand (Quercus frainetto Ten., Q. petraea (Matt. Liebl., Q. pubescens Willd., Q. robur L. and two populations for each of five white oak species (Q. frainetto Ten., Q. petraea (Matt. Liebl., Q. pubescens Willd., Q. robur L. and Q. pedunculiflora K. Koch were analyzed. Three alleles shared by all five oak species were observed. However, only two alleles were present in each population, but with different frequencies according to the species. At population level, all interspecific pairs of populations showed significant differentiation, except for pure Q. robur and Q. pedunculiflora populations. In contrast, no significant differentiation (p > 0.05 was found among conspecific populations. The DHN3 locus proved to be very useful to differentiate Q. frainetto and Q. pubescens from Q. pedunculiflora (FST = 0.914 and 0.660, respectively and Q. robur (FST = 0.858 and 0.633, respectively. As expected, the lowest level of differentiation was detected between the most closely related species, Q. robur and Q. pedunculiflora (FST = 0.020. Our results suggest that DHN3 can be an important genetic marker for differentiating among European white oak species.

  11. Applications of Genetically Modified Immunobiotics with High Immunoregulatory Capacity for Treatment of Inflammatory Bowel Diseases

    Science.gov (United States)

    Shigemori, Suguru; Shimosato, Takeshi

    2017-01-01

    Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn’s disease, are chronic inflammatory diseases characterized by dysregulated immune responses of the gastrointestinal tract. In recent years, the incidence of IBDs has increased in developed nations, but their prophylaxis/treatment is not yet established. Site-directed delivery of molecules showing anti-inflammatory properties using genetically modified (gm)-probiotics shows promise as a new strategy for the prevention and treatment of IBD. Advantages of gm-probiotics include (1) the ability to use bacteria as a delivery vehicle, enabling safe and long-term use by humans, (2) decreased risks of side effects, and (3) reduced costs. The intestinal delivery of anti-inflammatory proteins such as cytokines and enzymes using Lactococcus lactis has been shown to regulate host intestinal homeostasis depending on the delivered protein-specific machinery. Additionally, clinical experience using interleukin 10-secreting Lc. lactis has been shown to be safe and to facilitate biological containment in IBD therapy. On the other hand, some preclinical studies have demonstrated that gm-strains of immunobiotics (probiotic strains able to beneficially regulate the mucosal immunity) provide beneficial effects on intestinal inflammation as a result of the synergy between the immunoregulatory effects of the bacterium itself and the anti-inflammatory effects of the delivered recombinant proteins. In this review, we discuss the rapid progression in the development of strategies for the prophylaxis and treatment of IBD using gm-probiotics that exhibit immune regulation effects (gm-immunobiotics). In particular, we discuss the type of strains used as delivery agents. PMID:28179904

  12. Systemic administration of high-molecular weight hyaluronan stimulates wound healing in genetically diabetic mice.

    Science.gov (United States)

    Galeano, Mariarosaria; Polito, Francesca; Bitto, Alessandra; Irrera, Natasha; Campo, Giuseppe M; Avenoso, Angela; Calò, Margherita; Lo Cascio, Patrizia; Minutoli, Letteria; Barone, Mauro; Squadrito, Francesco; Altavilla, Domenica

    2011-07-01

    Hyaluronic acid (HA), an essential component of the extracellular matrix, is an efficient space filler that maintains hydration, serves as a substrate for assembly of proteoglycans and is involved in wound healing. Although numerous pieces of evidence demonstrate beneficial effects in promoting wound healing in diabetes, a systemic approach has never been tested. We used an incisional wound healing model in genetically diabetic mice to test the effects of systemic injection of HA. Diabetic (n=56) and normoglycemic (n=56) mice were subjected to incision and randomized (8 groups of 7 animals each) to receive HA at different doses, 7.5, 15 and 30mg/kg/i.p., or vehicle (0.9% NaCl solution) for 12days. At the end of the experiment animals were sacrificed and skin wounds were excised for histological, biochemical and molecular analysis. Histology revealed that the most effective dose to improve wound repair and angiogenesis in diabetic mice was 30mg/kg. Furthermore HA injection (30mg/kg) improved the altered healing pattern in diabetic animals, increased skin remodeling proteins TGF-β and transglutaminase-II and restored the altered expression of cyclin B1/Cdc2 complex. Evaluation of skin from diabetic animals injected with HA revealed also an increase in HA content, suggesting that systemic injection may be able to restore the reduced intracellular HA pool of diabetic mice. Finally HA markedly improved skin mechanical properties. These promising results, if confirmed in a clinical setting, may improve the care and management of diabetic patients.

  13. Expression of genes controlling fat deposition in two genetically diverse beef cattle breeds fed high or low silage diets

    Science.gov (United States)

    2013-01-01

    Background Both genetic background and finishing system can alter fat deposition, thus indicating their influence on adipogenic and lipogenic factors. However, the molecular mechanisms underlying fat deposition and fatty acid composition in beef cattle are not fully understood. This study aimed to assess the effect of breed and dietary silage level on the expression patterns of key genes controlling lipid metabolism in subcutaneous adipose tissue (SAT) and longissimus lumborum (LL) muscle of cattle. To that purpose, forty bulls from two genetically diverse Portuguese bovine breeds with distinct maturity rates, Alentejana and Barrosã, were selected and fed either low (30% maize silage/70% concentrate) or high silage (70% maize silage/30% concentrate) diets. Results The results suggested that enhanced deposition of fatty acids in the SAT from Barrosã bulls, when compared to Alentejana, could be due to higher expression levels of lipogenesis (SCD and LPL) and β-oxidation (CRAT) related genes. Our results also indicated that SREBF1 expression in the SAT is increased by feeding the low silage diet. Together, these results point out to a higher lipid turnover in the SAT of Barrosã bulls when compared to Alentejana. In turn, lipid deposition in the LL muscle is related to the expression of adipogenic (PPARG and FABP4) and lipogenic (ACACA and SCD) genes. The positive correlation between ACACA expression levels and total lipids, as well trans fatty acids, points to ACACA as a major player in intramuscular deposition in ruminants. Moreover, results reinforce the role of FABP4 in intramuscular fat development and the SAT as the major site for lipid metabolism in ruminants. Conclusions Overall, the results showed that SAT and LL muscle fatty acid composition are mostly dependent on the genetic background. In addition, dietary silage level impacted on muscle lipid metabolism to a greater extent than on that of SAT, as evaluated by gene expression levels of adipogenic and

  14. Taxonomic analysis of cryptococcus species complex strain S8012 revealed Cryptococcus gattii with high heterogeneity on the genetics

    Institute of Scientific and Technical Information of China (English)

    CHEN Min; LIAO Wan-qing; WU Shao-xi; YAO Zhi-rong; PAN Wei-hua; LIAO Yong

    2011-01-01

    Background Initially, Cryptococcus (C.) neoformans was previously divided into two varieties comprising C. neoformans var. neoformans and C. neoformans var. gattii. Currently, taxonomic studies defined C. neoformans as C. species complex, which contains C. neoformans var. neoformans (serotype D), the hybrid isolates (serotype AD), C. neoformans var. grubii (serotype A) and C. gattii (serotypes B and C). However, Liao and his team once isolated a unique C. gattii isolate, namely strain S8012 with unique phenotype from cerebrospinal fluid (CSF) of a 43-year-old male patient in the Shanghai Changzheng Hospital and described as C. neoformans var. shanghaiensis in 1980s. The aim of this study was to explore the genetic background and polymorphism of Chinese clinical C. gattii isolates.Methods S8012 was analyzed as representative strain using the M13-polymerase chain reaction (PCR) fingerprinting pattern and multilocus sequence analysis including internal transcribed spacers of rDNA (ITS region), the intergenic spacer 1 regions (IGS1), RPB1, RPB2, CNLAC1, and TEF1 genes.Results The PCR fingerprinting pattern results showed strain S8012 belonged to molecular types VGI, and phylogenetic analysis suggested strain S8012 was grouped into the cluster of C. gattii environmental isolates originated from Eucalyptus camaldulensis trees in Australia.Conclusion C. gattii isolates from Chinese patients expresses high polymorphism on the phenotype, and molecular type VQI isolates from China have a close genetic relationship with the C. gattii isolates from Australia.

  15. Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications.

    Science.gov (United States)

    Armstrong, E; Leizagoyen, C; Martínez, A M; González, S; Delgado, J V; Postiglioni, A

    2011-01-01

    The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2-4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F(IS) index was -0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species.

  16. High-density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family.

    Science.gov (United States)

    Brelsford, A; Rodrigues, N; Perrin, N

    2016-01-01

    Sex chromosome differentiation in Rana temporaria varies strikingly among populations or families: whereas some males display well-differentiated Y haplotypes at microsatellite markers on linkage group 2 (LG2), others are genetically undistinguishable from females. We analysed with RADseq markers one family from a Swiss lowland population with no differentiated sex chromosomes, and where sibship analyses had failed to detect any association between the phenotypic sex of progeny and parental haplotypes. Offspring were reared in a common tank in outdoor conditions and sexed at the froglet stage. We could map a total of 2177 SNPs (1123 in the mother, 1054 in the father), recovering in both adults 13 linkage groups (= chromosome pairs) that were strongly syntenic to Xenopus tropicalis despite > 200 My divergence. Sexes differed strikingly in the localization of crossovers, which were uniformly distributed in the female but limited to chromosome ends in the male. None of the 2177 markers showed significant association with offspring sex. Considering the very high power of our analysis, we conclude that sex determination was not genetic in this family; which factors determined sex remain to be investigated.

  17. Label-free and high-sensitive detection for genetic point mutation based on hyperspectral interferometry

    Science.gov (United States)

    Fu, Rongxin; Li, Qi; Zhang, Junqi; Wang, Ruliang; Lin, Xue; Xue, Ning; Su, Ya; Jiang, Kai; Huang, Guoliang

    2016-10-01

    Label free point mutation detection is particularly momentous in the area of biomedical research and clinical diagnosis since gene mutations naturally occur and bring about highly fatal diseases. In this paper, a label free and high sensitive approach is proposed for point mutation detection based on hyperspectral interferometry. A hybridization strategy is designed to discriminate a single-base substitution with sequence-specific DNA ligase. Double-strand structures will take place only if added oligonucleotides are perfectly paired to the probe sequence. The proposed approach takes full use of the inherent conformation of double-strand DNA molecules on the substrate and a spectrum analysis method is established to point out the sub-nanoscale thickness variation, which benefits to high sensitive mutation detection. The limit of detection reach 4pg/mm2 according to the experimental result. A lung cancer gene point mutation was demonstrated, proving the high selectivity and multiplex analysis capability of the proposed biosensor.

  18. High Genetic Diversity and Insignificant Interspecific Differentiation in Opisthopappus Shih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China

    Directory of Open Access Journals (Sweden)

    Rongmin Guo

    2013-01-01

    Full Text Available Opisthopappus Shih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely, O. taihangensis (Ling Shih and O. longilobus Shih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR to analyze the genetic diversity and genetic structure from different levels (genus, species, and population in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB of up to 90.91% at genus level. At species level, both O. taihangensis (PPB=90.12%, H=0.1842, and I=0.289 and O. longilobus (PPB=95.21%, H=0.2226, and I=0.3542 have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation in O. longilobus (84.95% was higher than that in O. taihangensis (80.45%. A certain genetic differentiation among populations in O. taihangensis was found (Gst=0.2740, Φst=0.196 and genetic differentiation in O. longilobus was very small (Gst=0.1034, Φst=0.151. Gene flow in different degrees (Nm=1.325 and 4.336, resp. and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst=0.0453 between species and the clustering result based on the genetic distance showed that interspecific differentiation between O. taihangensis and O. longilobus was not significant and could occur lately.

  19. [High-priority research directions in genetics, and the breeding of the sugar beet (Beta vulgaris L.) in the 21st century].

    Science.gov (United States)

    Kornienko, A V; Podvigina, O A; Zhuzhzhalova, T P; Fedulova, T P; Bogomolov, M A; Oshevnev, V P; Butorina, A K

    2014-11-01

    High-priority research directions for the genetics and breeding of the sugar beet in the 21st century were developed with consideration of the available scientific achievements of domestic and foreign scholars. These directions unite the classical and molecular approaches to solving the problems of increasing the effectiveness of sugar beet breeding carried out on a genetic basis, and they correspond to the contemporary level of scientific research. Seven such directions are proposed.

  20. Comparative Vector Bionomics and Morphometrics of Two Genetically Distinct Field Populations of Anopheles darlingi Root from Belize, Central America and Zungarococha, Peru, South America

    Science.gov (United States)

    2014-01-31

    Sociedade Brasileira de Medicina Tropical 46: 172-7 64. Garrett-Jones C. 1964. The Human Blood Index of Malaria Vectors in Relation to...Revista da Sociedade Brasileira de Medicina Tropical 24: 13-20 94. Klingenberg CP. 2002. Morphometrics and the role of the phenotype in studies of the...Anopheles species from Porto Velho, Rondonia state, western Amazon, Brazil. Revista do Instituto de Medicina Tropical de Sao Paulo 54:331-5 125. Morales

  1. Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles.

    Science.gov (United States)

    Zhang, Yu; Li, Xuegong; Bartlett, Douglas H; Xiao, Xiang

    2015-06-01

    A key aspect of marine environments is elevated pressure; for example, ∼70% of the ocean is at a pressure of at least 38MPa. Many types of Bacteria and Archaea reside under these high pressures, which drive oceanic biogeochemical cycles and catalyze reactions among rocks, sediments and fluids. Most marine prokaryotes are classified as piezotolerant or as (obligate)-piezophiles with few cultivated relatives. The biochemistry and physiology of these organisms are largely unknown. Recently, high-pressure cultivation technology has been combined with omics and DNA recombination methodologies to examine the physiology of piezophilic marine microorganisms. We are now beginning to understand the adaptive mechanisms of these organisms, along with their ecological functions and evolutionary processes. This knowledge is leading to the further development of high-pressure-based biotechnology.

  2. Genetic covariation between theAuthor Recognition Test and reading and verbal abilities: what can we learn from the analysis of high performance?

    Science.gov (United States)

    Martin, Nicolas W; Hansell, Narelle K; Wainwright, Mark A; Shekar, Sri N; Medland, Sarah E; Bates, Timothy C; Burt, Jennifer S; Martin, Nicholas G; Wright, Margaret J

    2009-07-01

    The Author Recognition Test (ART) measures print exposure and is a unique predictor of phonological and orthographic processes in reading. In a sample of adolescent and young adult twins and siblings (216 MZ/430 DZ pairs, 307 singletons; aged 11-29 years) ART scores were moderately heritable (67%) and correlated with reading and verbal abilities, with genes largely accounting for the covariance. We also examine whether high (and low) (i.e. 1SD above the mean) represents a quantitative extreme of the normal distribution. Heritability for high ART was of similar magnitude to the full sample, but, a specific genetic factor, independent from both low ART performance and high reading ability, accounted for 53-58% of the variance. This suggests a distinct genetic etiology for high ART ability and we speculate that the specific genetic influence is on orthographical processing, a critical factor in developing word recognition skills.

  3. Flora and fauna of the Himalayan Region. High altitude plant genetics; Flora e fauna della regione Himalayana. Risorse genetiche vegetali

    Energy Technology Data Exchange (ETDEWEB)

    Lovari, Sandro; Fanciulli, Paolo [Siena, Univ. (Italy). Dipt. di Biologia Evolutiva; Buffa, Giorgio [Turin, Univ. (Italy). Dipt. di Biologia Vegetale; Ferrari, Carlo [Bologna, Univ. (Italy). Dipt. di Biologia Evoluzionistica Sperimentale; Parrini, Paolo [Legnaro, Univ. (Italy). Dipt. di Agronomia Ambientale e Produzione Vegetali; Mongini, Emanuele; Baldaccini, Emilio [Pisa, Univ. (Italy). Dipt. di Scienze del Comportamento Animale e dell`Uomo

    1997-05-01

    Research has been carried out (1992-1994) on high altitude plant genetics, particularly of cultivated species, to evaluate their potentialities as food resources and for conservation aspects. Observations have also carried out (1994) on plant communities of the Upper Khumbu, Sagarmatha National Park (Nepal), with emphasis on their use bu musk deer Moschus chrysogaster, Himalayan tahr, Hemitragurs jemiahicus, and domestic yak Bos grunniens. Since 1989 aspects of social behaviour of the Himalayan goral, Nemorhaedus goral and tahr have also been studied respectively in India, Himachal Pradesj, and Nepal, Khumbu Himal. Ornithologic surveys have been carried out (1992-1993) in Pakistan (Upper Hunza, Kunjerab and neighbour areas) and in Nepal (Khumbu Himal). In 1994 a short survey on the Collembolans of Sagarmatha National Park (Nepal) was made.

  4. Structural optimisation of a high speed Organic Rankine Cycle generator using a genetic algorithm and a finite element method

    Energy Technology Data Exchange (ETDEWEB)

    Palko, S. [Machines Division, ABB industry Oy, Helsinki (Finland)

    1997-12-31

    The aim in this work is to design a 250 kW high speed asynchronous generator using a genetic algorithm and a finite element method for Organic Rankine Cycle. The characteristics of the induction motors are evaluated using two-dimensional finite element method (FEM) The movement of the rotor and the non-linearity of the iron is included. In numerical field problems it is possible to find several local extreme for an optimisation problem, and therefore the algorithm has to be capable of determining relevant changes, and to avoid trapping to a local minimum. In this work the electromagnetic (EM) losses at the rated point are minimised. The optimisation includes the air gap region. Parallel computing is applied to speed up optimisation. (orig.) 2 refs.

  5. Relationship between gyrification and functional connectivity of the prefrontal cortex in subjects at high genetic risk of schizophrenia.

    Science.gov (United States)

    Dauvermann, Maria R; Mukherjee, Prerona; Moorhead, William T; Stanfield, Andrew C; Fusar-Poli, Paolo; Lawrie, Stephen M; Whalley, Heather C

    2012-01-01

    Measures of cortical folding ('gyrification') and connectivity are both reported to be disrupted in schizophrenia. There are also reports that increases in prefrontal gyrification may be predictive of subsequent illness in individuals at familial risk of the disorder. Such measures therefore have important potential clinical relevance. The nature of the relationship between cortical morphology and underlying connectivity is however unclear. In the current study we sought to explore the relationship between measures of gyrification and functional connectivity in a cohort of individuals at high genetic risk for the disorder. The theoretical background is based on the hypothesis that increased gyrification index (GI) in the prefrontal cortex may reflect increased short range regional connectivity. The cohort comprised 68 young unaffected relatives of schizophrenia patients and 21 healthy controls. Cortical folding was assessed using an automated Gyrification Index method (A-GI). Participants performed the Hayling sentence completion paradigm in the scanner and measures of functional connectivity were assessed using a correlation based approach. In the high risk subjects significant positive associations were found between prefrontal GI and prefrontal lateral-medial connectivity, while a negative correlation was found between prefrontal GI and prefrontal-thalamic connectivity. These associations indicate that measures describing morphological features of the brain surface relate to measures of underlying functional connectivity in the high risk subjects. Correlations in high risk people were more pronounced than in control subjects. We suggest our previous finding of increased prefrontal gyrification may therefore relate to increased local short range prefrontal connectivity and reduced long range connectivity.

  6. Unraveling the genetic expression of the highly variable immune receptors of a killer

    NARCIS (Netherlands)

    Vendelbosch, S.

    2015-01-01

    The Killer Immunoglobulin-like Receptors (KIRs) are a family of highly variable receptors which regulate cytotoxicity of Natural Killer (NK) cells and a subset of T-cells. The KIR genes, clustered on the genome in the KIR locus, are distributed unequally across the population due to variation in gen

  7. High-Dimensional Cox Regression Analysis in Genetic Studies with Censored Survival Outcomes

    Directory of Open Access Journals (Sweden)

    Jinfeng Xu

    2012-01-01

    Full Text Available With the advancement of high-throughput technologies, nowadays high-dimensional genomic and proteomic data are easy to obtain and have become ever increasingly important in unveiling the complex etiology of many diseases. While relating a large number of factors to a survival outcome through the Cox relative risk model, various techniques have been proposed in the literature. We review some recently developed methods for such analysis. For high-dimensional variable selection in the Cox model with parametric relative risk, we consider the univariate shrinkage method (US using the lasso penalty and the penalized partial likelihood method using the folded penalties (PPL. The penalization methods are not restricted to the finite-dimensional case. For the high-dimensional (p→∞, p≪n or ultrahigh-dimensional case (n→∞, n≪p, both the sure independence screening (SIS method and the extended Bayesian information criterion (EBIC can be further incorporated into the penalization methods for variable selection. We also consider the penalization method for the Cox model with semiparametric relative risk, and the modified partial least squares method for the Cox model. The comparison of different methods is discussed and numerical examples are provided for the illustration. Finally, areas of further research are presented.

  8. Genetic analysis of long-lived families reveals novel variants influencing high density-lipoprotein cholesterol

    DEFF Research Database (Denmark)

    Feitosa, Mary F; Wojczynski, Mary K; Straka, Robert

    2014-01-01

    The plasma levels of high-density lipoprotein cholesterol (HDL) have an inverse relationship to the risks of atherosclerosis and cardiovascular disease (CVD), and have also been associated with longevity. We sought to identify novel loci for HDL that could potentially provide new insights...

  9. High-throughput open source computational methods for genetics and genomics

    NARCIS (Netherlands)

    Prins, J.C.P.

    2015-01-01

    Biology is increasingly data driven by virtue of the development of high-throughput technologies, such as DNA and RNA sequencing. Computational biology and bioinformatics are scientific disciplines that cross-over between the disciplines of biology, informatics and statistics; which is clearly refle

  10. Heritability of high sugar consumption through drinks and the genetic correlation with substance use

    NARCIS (Netherlands)

    Treur, J.L.; Boomsma, D.I.; Ligthart, R.S.L.; Willemsen, G.; Vink, J.M.

    2016-01-01

    Background: High sugar consumption contributes to the rising prevalence of obesity. Sugar can have rewarding effects that are similar to, but less strong than, the effects of addictive substances. People who consume large amounts of sugar also tend to use more addictive substances, but it is unclear

  11. Comments on “High Altitude Pulmonary Edema in an Experienced Mountaineer. Possible Genetic Predisposition”

    Directory of Open Access Journals (Sweden)

    Gaurav Sikri

    2015-10-01

    Full Text Available We appreciate the letter to the editor and are pleased to respond regarding our recent case study regarding high altitude pulmonary edema in an experienced mountaineer. The letter raises some valid questions regarding our treatment decisions. With this, as with most emergency department (ED patients, it must be understood that the initial treatment reflected the breadth of our differential diagnosis.

  12. SNP interaction detection with Random Forests in high-dimensional genetic data

    Directory of Open Access Journals (Sweden)

    Winham Stacey J

    2012-07-01

    Full Text Available Abstract Background Identifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF are a popular data-mining technique that can accommodate a large number of predictor variables and allow for complex models with interactions. RF analysis produces measures of variable importance that can be used to rank the predictor variables. Thus, single nucleotide polymorphism (SNP analysis using RFs is gaining popularity as a potential filter approach that considers interactions in high-dimensional data. However, the impact of data dimensionality on the power of RF to identify interactions has not been thoroughly explored. We investigate the ability of rankings from variable importance measures to detect gene-gene interaction effects and their potential effectiveness as filters compared to p-values from univariate logistic regression, particularly as the data becomes increasingly high-dimensional. Results RF effectively identifies interactions in low dimensional data. As the total number of predictor variables increases, probability of detection declines more rapidly for interacting SNPs than for non-interacting SNPs, indicating that in high-dimensional data the RF variable importance measures are capturing marginal effects rather than capturing the effects of interactions. Conclusions While RF remains a promising data-mining technique that extends univariate methods to condition on multiple variables simultaneously, RF variable importance measures fail to detect interaction effects in high-dimensional data in the absence of a strong marginal component, and therefore may not be useful as a filter technique that allows for interaction effects in genome-wide data.

  13. Genetic testing and first presymptomatic diagnosis in Moroccan families at high risk for breast/ovarian cancer.

    Science.gov (United States)

    Laarabi, Fatima Zahra; Jaouad, Imane Cherkaoui; Ouldim, Karim; Aboussair, Nisrine; Jalil, Abdelouahed; Gueddari, Brahim El Khalil El; Benjaafar, Noureddine; Sefiani, Abdelaziz

    2011-03-01

    Germline mutations in the BRCA1 and BRCA2 genes highly predispose to breast and ovarian cancers and are responsible for a substantial proportion of familial breast and ovarian cancers. No female individuals from families from Morocco affected by breast cancer with mutations of these genes have previously been reported, and clinicians in Morocco are unaccustomed to dealing with healthy female individuals carrying mutations in the BRCA genes. This study aimed to report the initial experience of a group of Moroccan investigators carrying out predictive genetic testing to detect a known familial mutation in healthy Moroccan females with a high risk of developing breast cancer and to introduce supervision of these asymptomatic female carriers as a new approach in the prevention and early diagnosis of breast and ovarian cancers in Morocco. Presymptomatic diagnosis was carried out using DNA genetic testing in 5 healthy Moroccan female individuals from three families with an elevated risk of developing breast cancer. These are the first Moroccan families reported to be affected by breast cancers associated with BRCA mutations. Presymptomatic diagnosis was carried out for breast cancer in 5 female individuals from three Moroccan families with BRCA mutations. Two of the families are the first reported incidence of the founder mutation Ashkenazi BRCA1-185_186delAG in Moroccan patients. The third family carried the known BRCA2 mutation c.5073dupA/p.trp1692metfsX3. We tested the presence of these mutations in 5 asymptomatic healthy females from the three families. Two sisters from family 1 carried the BRCA1-185_186delAG mutation, whereas the third female individual from family 2 carried the c.5073dupA/p.trp1692metfsX3 mutation. However, one healthy female individual and her mother from family 3 did not carry the familial mutation of the BRCA1 gene. This study found BRCA mutations in three asymptomatic subjects, suggesting that this is the first step towards the development of

  14. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans

    Directory of Open Access Journals (Sweden)

    Ben Dhiab Mohamed

    2008-02-01

    Full Text Available Abstract Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1 a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2 the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.

  15. High Frequency of Hb E-Saskatoon (HBB: c.67G > A) in Brazilians: A New Genetic Origin?

    Science.gov (United States)

    Wagner, Sandrine C; Lindenau, Juliana D; Castro, Simone M de; Santin, Ana Paula; Zaleski, Carina F; Azevedo, Laura A; Ribeiro Dos Santos, Ândrea K C; Dos Santos, Sidney E B; Hutz, Mara H

    2016-08-01

    Hb E-Saskatoon [β22(B4)Glu→Lys, HBB: c.67G > A] is a rare, nonpathological β-globin variant that was first described in a Canadian woman of Scottish and Dutch ancestry and has since then been detected in several populations. The aim of the present study was to identify the origin of Hb E-Saskatoon in Brazil using β-globin haplotypes and genetic ancestry in carriers of this hemoglobin (Hb) variant. Blood samples were investigated by isoelectric focusing (IEF) and high performance liquid chromatography (HPLC) using commercial kits. Hb E-Saskatoon was confirmed by amplification of the HBB gene, followed by sequence analysis. Haplotypes of the β-globin gene were determined by polymerase chain reaction (PCR), followed by digestion with specific restriction enzymes. Individual ancestry was estimated with 48 biallelic insertion/deletions using three 16-plex PCR amplifications. The IEF pattern was similar to Hbs C (HBB: c.19G > A) and Hb E (HBB: c.79G > A) [isoelectric point (pI): 7.59-7.65], and HPLC results showed an elution in the Hb S (HBB: c.20A > T) window [retention time (RT): 4.26-4.38]. DNA sequencing of the amplified β-globin gene showed a mutation at codon 22 (GAA>AAA) corresponding to Hb E-Saskatoon. A total of 11 cases of this variant were identified. In nine unrelated individuals, Hb E-Saskatoon was in linkage disequilibrium with haplotype 2 [+ - - - -]. All subjects showed a high degree of European contribution (mean = 0.85). Hb E-Saskatoon occurred on the β-globin gene of haplotype 2 in all Brazilian carriers. These findings suggest a different genetic origin for this Hb variant from that previously described.

  16. A pilot pharmacotherapy trial for depressed youths at high genetic risk for bipolarity.

    Science.gov (United States)

    Findling, Robert L; Lingler, Jacqui; Rowles, Brieana M; McNamara, Nora K; Calabrese, Joseph R

    2008-12-01

    Children and adolescents who are the offspring of a bipolar parent and who first present with major depressive disorder (MDD) are at high risk for eventually developing bipolar disorder. In this report, the authors describe a group of 9 such high-risk children and adolescents with MDD, aged 7-16 years, who were randomized to receive treatment with either paroxetine monotherapy or combination paroxetine-divalproex sodium therapy. In the long-term management of depressive symptomatology in these patients, neither treatment appeared to be particularly effective. As a result, future treatment studies in this population appear to be warranted, not only due to the putative impending risk of developing bipolar disorder, but also the manifest risk of current depressive episodes.

  17. The genetic landscape of high-risk neuroblastoma | Office of Cancer Genomics

    Science.gov (United States)

    Abstract: Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 affected individuals (cases) using a combination of whole-exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative.

  18. High-density lipoproteincholesterol, reverse cholesterol transport, and cardiovascular risk: a tale of genetics?

    Directory of Open Access Journals (Sweden)

    Giovanni Cimmino

    2013-10-01

    Full Text Available Cholesterol deposition plays a central role in atherogenesis. The accumulation of lipid material is the result of an imbalance between the influx and efflux of cholesterol within the arterial wall. High levels of plasma low-density lipoprotein-cholesterol are considered the major mechanism responsible for the influx and accumulation of cholesterol in the arterial wall, while high-density lipoprotein (HDL- cholesterol seems responsible for its efflux. The mechanism by which cholesterol is removed from extra-hepatic organs and delivered to the liver for its catabolism and excretion is called reverse cholesterol transport (RCT. Epidemiological evidence has associated high levels of HDL-cholesterol/ApoA-I with protection against atherosclerotic disease, but the ultimate mechanism(s responsible for the beneficial effect is not well established. HDLs are synthesized by the liver and small intestine and released to the circulation as a lipid-poor HDL (nascent HDL, mostly formed by ApoA-I and phospholipids. Through their metabolic maturation, HDLs interact with the ABCA1 receptor in the macrophage surface increasing their lipid content by taking phospholipids and cholesterol from macrophages becoming mature HDL. The cholesterol of the HDLs is transported to the liver, via the scavenger receptor class B, type I, for further metabolization and excretion to the intestines in the form of bile acids and cholesterol, completing the process of RCT. It is clear that an inherited mutation or acquired abnormality in any of the key players in RCT mat affect the atherosclerotic process.

  19. Characterization of a genetically reconstituted high-affinity system for serotonin transport

    Energy Technology Data Exchange (ETDEWEB)

    Chang, A.S.S.; Lam, D.M.K. (Baylor College of Medicine, Woodlands, TX (USA) Baylor College of Medicine, Houston, TX (USA)); Frnka, J.V.; Chen, D. (Baylor College of Medicine, Woodlands, TX (USA))

    1989-12-01

    By transfecting mouse fibroblast L-M cells with human genomic DNA, the authors have established and identified several clonal cell lines that stably express a high-affinity serotonin (5-HT)-uptake mechanism absent in untransfected host cells. One such cell line, L-S1, possesses features of 5-({sup 3}H)HT uptake similar to those previously characterized in the central nervous system and blood platelets: (i) specificity for 5-HT; (ii) antagonism by imipramine, a known inhibitor of high-affinity 5-HT uptake; (iii) both Na{sup +} and temperature dependence; (iv) kinetic saturability; and (v) high affinity for 5-HT. This cell line can be used to compare the relative efficacies of known blockers of 5-HT uptake and thereby offers a rapid and reliable assay system for testing novel inhibitors of this system. Since L-S1 contains stably integrated human DNA in its genome, they postulate that the observed 5-HT-uptake system resulted from the expression of human gene(s) coding for the 5-HT transporter. Thus, cell lines such as L-S1 may represent novel means for screening and developing therapeutic agents specific for neutrotransmitter-uptake systems as well as substrate for the cloning and elucidation of the genes encoding the various neurotransmitter transporters.

  20. The population genetics of Pseudomonas aeruginosa isolates from different patient populations exhibits high-level host specificity.

    Directory of Open Access Journals (Sweden)

    Rosa van Mansfeld

    Full Text Available OBJECTIVE: To determine whether highly prevalent P. aeruginosa sequence types (ST in Dutch cystic fibrosis (CF patients are specifically linked to CF patients we investigated the population structure of P. aeruginosa from different clinical backgrounds. We first selected the optimal genotyping method by comparing pulsed-field gel electrophoresis (PFGE, multilocus sequence typing (MLST and multilocus variable number tandem-repeat analysis (MLVA. METHODS: Selected P. aeruginosa isolates (n = 60 were genotyped with PFGE, MLST and MLVA to determine the diversity index (DI and congruence (adjusted Rand and Wallace coefficients. Subsequently, isolates from patients admitted to two different ICUs (n = 205, from CF patients (n = 100 and from non-ICU, non-CF patients (n = 58, of which 19 were community acquired were genotyped with MLVA to determine distribution of genotypes and genetic diversity. RESULTS: Congruence between the typing methods was >79% and DIs were similar and all >0.963. Based on costs, ease, speed and possibilities to compare results between labs an adapted MLVA scheme called MLVA9-Utrecht was selected as the preferred typing method. In 363 clinical isolates 252 different MLVA types (MTs were identified, indicating a highly diverse population (DI  = 0.995; CI  = 0.993-0.997. DI levels were similarly high in the diverse clinical sources (all >0.981 and only eight genotypes were shared. MTs were highly specific (>80% for the different patient populations, even for similar patient groups (ICU patients in two distinct geographic regions, with only three of 142 ICU genotypes detected in both ICUs. The two major CF clones were unique to CF patients. CONCLUSION: The population structure of P. aeruginosa isolates is highly diverse and population specific without evidence for a core lineage in which major CF, hospital or community clones co-cluster. The two genotypes highly prevalent among Dutch CF patients appeared unique to CF patients

  1. High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus;

    2016-01-01

    with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates......Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards...

  2. An automatic scanning method for high throughput microscopic system to facilitate medical genetic diagnosis: an initial study

    Science.gov (United States)

    Qiu, Yuchen; Chen, Xiaodong; Li, Zheng; Li, Yuhua; Chen, Wei R.; Zheng, Bin; Li, Shibo; Liu, Hong

    2012-03-01

    The purpose of this paper is to report a new automatic scanning scheme for high throughput microscopic systems aiming to facilitate disease diagnosis in genetic laboratories. To minimize the impact of the random vibration and mechanical drifting of the scanning stage in microscopic image acquisition, auto-focusing operations are usually applied repeatedly during the scanning process. Such methods ensure the acquisition of well focused images for clinical diagnosis, but are time consuming. The technique investigated in this preliminary study applies the auto-focusing operations at a limited number of locations on the slide. For the rest of the imaging field, the focusing position is quickly adjusted through linear interpolation. In this initial validation study, blood pathological slides containing both metaphase and interphase cells are scanned. For a selected area of 6.9mm×6.9mm, a number of 2×2, 3×2, 3×3, and 4×4 positions are evenly sampled for auto-focusing operations. Respectively, 25, 29, 40, and 41 clinically meaningful cells are identified for each sampling scheme. For the specific case investigated, the results demonstrate that the 4 position auto-focusing scheme could obtain the adequate number of clinically meaningful cells for the diagnosis. The schemes with more auto-focusing operations provide an option for high reliability diagnosis when clinically necessary. More comprehensive research is planned, and that may lead to optimal design of trade-off for developing the scanning scheme of the high throughput microscopic systems.

  3. The Influence of Self-Efficacy Beliefs and Metacognitive Prompting on Genetics Problem Solving Ability among High School Students in Kenya

    Science.gov (United States)

    Aurah, Catherine Muhonja

    Within the framework of social cognitive theory, the influence of self-efficacy beliefs and metacognitive prompting on genetics problem solving ability among high school students in Kenya was examined through a mixed methods research design. A quasi-experimental study, supplemented by focus group interviews, was conducted to investigate both the outcomes and the processes of students' genetics problem-solving ability. Focus group interviews substantiated and supported findings from the quantitative instruments. The study was conducted in 17 high schools in Western Province, Kenya. A total of 2,138 high school students were purposively sampled. A sub-sample of 48 students participated in focus group interviews to understand their perspectives and experiences during the study so as to corroborate the quantitative data. Quantitative data were analyzed through descriptive statistics, zero-order correlations, 2 x 2 factorial ANOVA,, and sequential hierarchical multiple regressions. Qualitative data were transcribed, coded, and reported thematically. Results revealed metacognitive prompts had significant positive effects on student problem-solving ability independent of gender. Self-efficacy and metacognitive prompting significantly predicted genetics problem-solving ability. Gender differences were revealed, with girls outperforming boys on the genetics problem-solving test. Furthermore, self-efficacy moderated the relationship between metacognitive prompting and genetics problem-solving ability. This study established a foundation for instructional methods for biology teachers and recommendations are made for implementing metacognitive prompting in a problem-based learning environment in high schools and science teacher education programs in Kenya.

  4. Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

    Science.gov (United States)

    Pandey, Manish K.; Agarwal, Gaurav; Kale, Sandip M.; Clevenger, Josh; Nayak, Spurthi N.; Sriswathi, Manda; Chitikineni, Annapurna; Chavarro, Carolina; Chen, Xiaoping; Upadhyaya, Hari D.; Vishwakarma, Manish K.; Leal-Bertioli, Soraya; Liang, Xuanqiang; Bertioli, David J.; Guo, Baozhu; Jackson, Scott A.; Ozias-Akins, Peggy; Varshney, Rajeev K.

    2017-01-01

    Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut. PMID:28091575

  5. MassCode liquid arrays as a tool for multiplexed high-throughput genetic profiling.

    Directory of Open Access Journals (Sweden)

    Gregory S Richmond

    Full Text Available Multiplexed detection assays that analyze a modest number of nucleic acid targets over large sample sets are emerging as the preferred testing approach in such applications as routine pathogen typing, outbreak monitoring, and diagnostics. However, very few DNA testing platforms have proven to offer a solution for mid-plexed analysis that is high-throughput, sensitive, and with a low cost per test. In this work, an enhanced genotyping method based on MassCode technology was devised and integrated as part of a high-throughput mid-plexing analytical system that facilitates robust qualitative differential detection of DNA targets. Samples are first analyzed using MassCode PCR (MC-PCR performed with an array of primer sets encoded with unique mass tags. Lambda exonuclease and an array of MassCode probes are then contacted with MC-PCR products for further interrogation and target sequences are specifically identified. Primer and probe hybridizations occur in homogeneous solution, a clear advantage over micro- or nanoparticle suspension arrays. The two cognate tags coupled to resultant MassCode hybrids are detected in an automated process using a benchtop single quadrupole mass spectrometer. The prospective value of using MassCode probe arrays for multiplexed bioanalysis was demonstrated after developing a 14plex proof of concept assay designed to subtype a select panel of Salmonella enterica serogroups and serovars. This MassCode system is very flexible and test panels can be customized to include more, less, or different markers.

  6. Genetic diversity of HCV among various high risk populations (IDAs, thalassemia, hemophilia, HD patients) in Iran

    Institute of Scientific and Technical Information of China (English)

    Rafiei A; Darzyani Azizi M; Taheri S; Haghshenas MR; Hosseinian A; Makhlough A

    2013-01-01

    Objective: To determine the patterns of distribution of HCV genotypes among high risk population in north of Iran. Methods: A cross-sectional study was conducted on 135 HCV RNA-positive high risk individuals including thalassemia, hemophilia, patients under hemodialysis and intravenous drug addicts. HCV genotypes were determined based on amplification with type-specific primers methods. Results: Among the 187 anti-HCV positive samples, only 135 (72.2%) gave HCV-RNA positvity. Over all, the most identified HCV type was genotype 3a (51.1%) followed by 1a (27.4%), 1b (8.2%). Sixteen (11.9%) out of 135 HCV RNA-positive participants have infected with more than one genotype or subtypes as follow; 1a/1b in 11 (8.2%), 2/3a in 3 (2.2%), and 1a/1b/3a in 2 (1.5%). Stratification of participants revealed that HCV subtype 3a was more prominent in thalassemia, hemophilia and HD patients but 1a and 1b were frequent in intravenous drug addicts. Conclusions: This study is the first report on HCV genotypes among Iranian subjects with different exposure categories resided in Mazandaran, where genotype 3a was found to be the most frequent genotype in thalassemia, hemophilia, and hemodialysis patients but not in IDAs. Since the addiction age is decreasing in Iran and a lot of addicts are IDAs, it might change the subtype pattern of HCV in general population.

  7. Genetic evidence of a high-affinity cyanuric acid transport system in Pseudomonas sp. ADP.

    Science.gov (United States)

    Platero, Ana I; Santero, Eduardo; Govantes, Fernando

    2014-03-01

    The Pseudomonas sp. ADP plasmid pADP-1 encodes the activities involved in the hydrolytic degradation of the s-triazine herbicide atrazine. Here, we explore the presence of a specific transport system for the central intermediate of the atrazine utilization pathway, cyanuric acid, in Pseudomonas sp. ADP. Growth in fed-batch cultures containing limiting cyanuric acid concentrations is consistent with high-affinity transport of this substrate. Acquisition of the ability to grow at low cyanuric acid concentrations upon conjugal transfer of pADP1 to the nondegrading host Pseudomonas putida KT2442 suggests that all activities required for this phenotype are encoded in this plasmid. Co-expression of the pADP1-borne atzDEF and atzTUVW genes, encoding the cyanuric acid utilization pathway and the subunits of an ABC-type solute transport system, in P. putida KT2442 was sufficient to promote growth at cyanuric acid concentrations as low as 50 μM in batch culture. Taken together, our results strongly suggest that the atzTUVW gene products are involved in high-affinity transport of cyanuric acid.

  8. A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements.

    Directory of Open Access Journals (Sweden)

    Jason E Chan

    2011-05-01

    Full Text Available Ty elements are high copy number, dispersed repeated sequences in the Saccharomyces cerevisiae genome known to mediate gross chromosomal rearrangements (GCRs. Here we found that introduction of Ty912, a previously identified Ty1 element, onto the non-essential terminal region of the left arm of chromosome V led to a 380-fold increase in the rate of accumulating GCRs in a wild-type strain. A survey of 48 different mutations identified those that either increased or decreased the rate of Ty-mediated GCRs and demonstrated that suppression of Ty-mediated GCRs differs from that of both low copy repeat sequence- and single copy sequence-mediated GCRs. The majority of the Ty912-mediated GCRs observed were monocentric nonreciprocal translocations mediated by RAD52-dependent homologous recombination (HR between Ty912 and a Ty element on another chromosome arm. The remaining Ty912-mediated GCRs appeared to involve Ty912-mediated formation of unstable dicentric translocation chromosomes that were resolved by one or more Ty-mediated breakage-fusion-bridge cycles. Overall, the results demonstrate that the Ty912-mediated GCR assay is an excellent model for understanding mechanisms and pathways that suppress genome rearrangements mediated by high copy number repeat sequences, as well as the mechanisms by which such rearrangements occur.

  9. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology.

    Directory of Open Access Journals (Sweden)

    María Laura Gutiérrez

    Full Text Available The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP-arrays to define those chromosomal regions which most commonly harbour copy number (CN alterations and loss of heterozygozity (LOH in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70% extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9 versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11. From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterozygozity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.

  10. Pattern matching in high energy physics by using neural network and genetic algorithm

    CERN Document Server

    Castellano, M G; Bevilacqua, V; Nappi, E

    2000-01-01

    In this paper two different approaches to provide information from events by high energy physics experiments are shown. Usually the representations produced in such experiments are spot-composed and the classical algorithms to be needed for data analysis are time consuming. For this reason the possibility to speed up pattern recognition tasks by soft computing approach with parallel algorithms has been investigated. The first scheme shown in the following is a two-layer neural network with forward connections, the second one consists of an evolutionary algorithm with elitistic strategy and mutation and cross-over adaptive probability. Test results of these approaches have been carried out analysing a set of images produced by an optical ring imaging Cherenkov (RICH) detector at CERN. (10 refs).

  11. High-Throughput Genetic Analysis and Combinatorial Chiral Separations Based on Capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Wenwan Zhong

    2003-08-05

    Capillary electrophoresis (CE) offers many advantages over conventional analytical methods, such as speed, simplicity, high resolution, low cost, and small sample consumption, especially for the separation of enantiomers. However, chiral method developments still can be time consuming and tedious. They designed a comprehensive enantioseparation protocol employing neutral and sulfated cyclodextrins as chiral selectors for common basic, neutral, and acidic compounds with a 96-capillary array system. By using only four judiciously chosen separation buffers, successful enantioseparations were achieved for 49 out of 54 test compounds spanning a large variety of pKs and structures. Therefore, unknown compounds can be screened in this manner to identify optimal enantioselective conditions in just one rn. In addition to superior separation efficiency for small molecules, CE is also the most powerful technique for DNA separations. Using the same multiplexed capillary system with UV absorption detection, the sequence of a short DNA template can be acquired without any dye-labels. Two internal standards were utilized to adjust the migration time variations among capillaries, so that the four electropherograms for the A, T, C, G Sanger reactions can be aligned and base calling can be completed with a high level of confidence. the CE separation of DNA can be applied to study differential gene expression as well. Combined with pattern recognition techniques, small variations among electropherograms obtained by the separation of cDNA fragments produced from the total RNA samples of different human tissues can be revealed. These variations reflect the differences in total RNA expression among tissues. Thus, this Ce-based approach can serve as an alternative to the DNA array techniques in gene expression analysis.

  12. Development and genetic characterization of high-functional Rubus coreanus mutants

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Byung Yeoup; Kim, Jae Sung; Kim, Jin Hong

    2008-07-15

    The gamma irradiation as a 100 Gy lead to mutate Bokbunja seed as well as induction of germination, in addition, the optimum condition for inducing mutation is that H2SO4 should be treated after gamma irradiation in vivo. In order to breed the useful mutants in black raspberry, cultivated in Gochanggun, 2-year-old nursery stocks were irradiated with 70 (264 lines) and 120 Gy (360 lines) of gamma-ray. The LD50 dose was identified as 70 Gy. Morphological characteristics of the variants were observed such as stem variation, no. of thorn and no. of sucker compared with donor cultivar. The comparison of morphological and chemical characteristics between Rubus coreanus and Rubus occidentalis was carried out and these two species are quite different that is, number of cortex cells in Rubus occidentalis are much higher than Rubus coreanus. Rubus occidentalis highly contained glucose, xylose, and arabinose, and well developed secondary cell wall compared with Rubus coreanus. We carried out to obtain phylogenetic information on Korean cultivated bramble (KCB) by comparing its specific and random genomic and chloroplast sequences. The characteristics of nuclear and chloroplast genomes of KCB accessions are significantly different from those of other Rubus species. Phylogentic relationship inferred from these molecular features suggest that KCB accessions are relatively more closely related to black raspberry than to R. coreanus. Rubus are classified into 4 developing fruit stages such as green, yellow, red, and black color. The anthocyanin content was increased together with maturation, that is black color fruit is the highest anthocyanin content and highly correlated the expression of anthocyanin biosynthesis genes sunch as C4H, F3H. In addition, the expression of genes involved in the anthocynin biosynthesis is modulated by chitosan resulting in enhanced anthocyanin content in ripen fruit

  13. Neurocognitive functioning in a group of offspring genetically at high-risk for schizophrenia in Eastern Turkey.

    Science.gov (United States)

    Ozan, Erol; Deveci, Erdem; Oral, Meltem; Karahan, Utku; Oral, Elif; Aydin, Nazan; Kirpinar, Ismet

    2010-05-31

    We assessed major cognitive domains in symptom-free children of patients with schizophrenia compared to the healthy children of parents with no psychopathology using neurocognitive tests. We hypothesized that, offspring at high-risk for schizophrenia would have significant impairment in major domains: attention, memory, verbal-linguistic ability and executive functions. Thirty symptom-free children (17-males, 13-females; intelligence quotient=99.6+/-13.6; age=12.69+/-2.32 and education=5.8+/-2.3 years) having a parent diagnosed with schizophrenia and 37 healthy children matched for gender (19-males, 18-females), IQ (106.05+/-14.70), age (12.48+/-2.58) and years of education (6.0+/-2.5) were evaluated. The study group showed significant poor performance in cognitive domains, such as working memory (assessed with Auditory consonant trigram test), focused attention (Stroop test), attention speed (Trail making test), divided attention (Auditory consonant trigram test), executive functions (Wisconsin card sorting test), verbal fluency (Controlled word association test) and declarative memory (Rey verbal learning and Short-term memory test). However, no group differences were detected either on verbal attention (Digit span forward test) or sustained attention (TOVA, a continuous performance task); the latter as consistently reported to be a predictor of schizophrenia. In order to determine the cognitive endophenotype of schizophrenia, it seems more rational to conduct comprehensive evaluation of neurocognitive domains in well-matched groups via using sufficiently challenging tests to detect slight deficits. In addition, longitudinal studies with a larger sample size evaluating neurocognitive functions combined with genetic analysis may provide clues about explaining the genetic background of the disorder within the endophenocognitype concept and serve as new targets for early interventions.

  14. Characterization of polymorphisms and isoforms of the Clostridium perfringens phospholipase C gene (plc) reveals high genetic diversity.

    Science.gov (United States)

    Siqueira, Flávia F; Almeida, Marcelle O; Barroca, Tatiana M; Horta, Carolina C R; Carmo, Anderson O; Silva, Rodrigo O S; Pires, Prhiscylla S; Lobato, Francisco C F; Kalapothakis, Evanguedes

    2012-10-12

    Clostridium perfringens phospholipase C (Cp-PLC), also called alpha-toxin, is encoded by the plc gene and has been implicated in several diseases; however, only a few studies have described polymorphisms in this gene. The aim of this study was to analyze polymorphisms in the Cp-PLC nucleotide and amino acid sequences obtained from isolates from different regions and to compare them to Clostridium phospholipase C sequences deposited in the NCBI database. Environmental samples (sediment, poultry feed, sawdust) and stool samples (from poultry, bovine, swine, horse, caprine, bird, dog, rabbit, toucan) were collected from healthy and sick animals. A total of 73 isolates were analyzed with the majority of samples belonging to the toxin type A subtype and possessing the gene encoding for the beta-2 toxin. Comparison of plc gene sequences from respective isolates revealed a high genetic diversity in the nucleotide sequences of mature Cp-PLC. Sequence comparisons identified 30 amino acid substitutions and 34 isoforms including some isoforms with substitutions in amino acids critical to toxin function. Comparison of sequences obtained in this study to Cp-PLC sequences obtained from the NCBI database resulted in the identification of 11 common haplotypes and 22 new isoforms. Phylogenetic analysis of phospholipase C sequences obtained from other Clostridium species identified relationships previously described. This report describes a broad characterization of the genetic diversity in the C. perfringens plc gene resulting in the identification of various isoforms. A better understanding of sequences encoding phospholipase C isoforms may reveal changes associated with protein function and C. perfringens virulence.

  15. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish.

    Science.gov (United States)

    Liu, S; Li, Y; Qin, Z; Geng, X; Bao, L; Kaltenboeck, L; Kucuktas, H; Dunham, R; Liu, Z

    2016-02-01

    Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform both of their parent species in a number of traits. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence in the face of gene flow, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array. A total of 26,238 SNPs were mapped to 29 linkage groups, with 12,776 unique marker positions. The linkage map spans approximately 3240 cM with an average intermarker distance of 0.25 cM. A fraction of markers (986 of 12,776) exhibited significant deviation from the expected Mendelian ratio of segregation, and they were clustered in major genomic blocks across 15 LGs, most notably LG9 and LG15. The distorted markers exhibited significant bias for maternal alleles among the backcross progenies, suggesting strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks should lend insights into speciation as marked by incompatibilities between the two species. Such findings should also have profound implications for understanding the genomic evolution of closely related species as well as the introgression of hybrid production programs in aquaculture.

  16. High-density SNP genotyping of tomato (Solanum lycopersicum L. reveals patterns of genetic variation due to breeding.

    Directory of Open Access Journals (Sweden)

    Sung-Chur Sim

    Full Text Available The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA and pairwise estimates of F(st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage, particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  17. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  18. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data

    DEFF Research Database (Denmark)

    Risgaard, B; Jabbari, R; Refsgaard, L;

    2013-01-01

    , when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were...... genotyped in a second Danish control population (n = 536) with available electrocardiograms. In ESP, we identified 38 of 355 (10%) variants, distributed on 272 heterozygote carriers and two homozygote carriers. The genes investigated were on average screened in 6258 individuals. This corresponds...... to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research...

  19. High genetic diversity detected in olives beyond the boundaries of the Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Mehdi Hosseini-Mazinani

    Full Text Available BACKGROUND: Olive trees (Olea europaea subsp. europaea var. europaea naturally grow in areas spanning the Mediterranean basin and towards the East, including the Middle East. In the Iranian plateau, the presence of olives has been documented since very ancient times, though the early history of the crop in this area is shrouded in uncertainty. METHODS: The varieties presently cultivated in Iran and trees of an unknown cultivation status, surviving under extreme climate and soil conditions, were sampled from different provinces and compared with a set of Mediterranean cultivars. All samples were analyzed using SSR and chloroplast markers to establish the relationships between Iranian olives and Mediterranean varieties, to shed light on the origins of Iranian olives and to verify their contribution to the development of the current global olive variation. RESULTS: Iranian cultivars and ecotypes, when analyzed using SSR markers, clustered separately from Mediterranean cultivars and showed a high number of private alleles, on the contrary, they shared the same single chlorotype with the most widespread varieties cultivated in the Mediterranean. CONCLUSION: We hypothesized that Iranian and Mediterranean olive trees may have had a common origin from a unique center in the Near East region, possibly including the western Iranian area. The present pattern of variation may have derived from different environmental conditions, distinct levels and selection criteria, and divergent breeding opportunities found by Mediterranean and Iranian olives.These unexpected findings emphasize the importance of studying the Iranian olive germplasm as a promising but endangered source of variation.

  20. Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.

    Science.gov (United States)

    Beesley, Nicola J; Williams, Diana J L; Paterson, Steve; Hodgkinson, Jane

    2017-01-01

    Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.

  1. Framing recommendations to promote prevention behaviors among people at high risk: A simulation study of responses to melanoma genetic test reporting.

    Science.gov (United States)

    Taber, Jennifer M; Aspinwall, Lisa G

    2015-10-01

    A CDKN2A/p16 mutation confers 76 % lifetime risk of developing melanoma to US residents, and high-risk individuals are counseled to use sunscreen. Generally, for patients at population risk, gain framing more effectively promotes prevention behaviors; however, it is unknown whether loss frames might more effectively promote behavioral intentions and perceived control over disease risk among high-risk patients. Undergraduates (N = 146) underwent a simulated genetic counseling and test reporting session for hereditary melanoma. Participants watched a video of a genetic counselor providing information in which genetic risk of melanoma (Low: 15 %; High: 76 %) and framed recommendations to use sunscreen (Loss: Risk may increase by 15 % if don't use sunscreen; Gain: Risk may decrease by 15 % if use sunscreen) were manipulated. Controlling for baseline sunscreen use, high-risk participants given loss frames reported greater beliefs that sunscreen would reduce risk than high-risk participants given gain frames. Further, high-risk participants with fair skin tended to report greater intentions to use sunscreen when given loss frames versus gain frames. Perceived control over risk mediated the effect of message frame and disease risk on intentions to use sunscreen. When counseling patients with elevated cancer risk, genetic counselors may consider framing prevention behavioral recommendations in terms of potential losses.

  2. Melanoma genetics

    DEFF Research Database (Denmark)

    Read, Jazlyn; Wadt, Karin A W; Hayward, Nicholas K

    2016-01-01

    Approximately 10% of melanoma cases report a relative affected with melanoma, and a positive family history is associated with an increased risk of developing melanoma. Although the majority of genetic alterations associated with melanoma development are somatic, the underlying presence...... of heritable melanoma risk genes is an important component of disease occurrence. Susceptibility for some families is due to mutation in one of the known high penetrance melanoma predisposition genes: CDKN2A, CDK4, BAP1, POT1, ACD, TERF2IP and TERT. However, despite such mutations being implicated...... in a combined total of approximately 50% of familial melanoma cases, the underlying genetic basis is unexplained for the remainder of high-density melanoma families. Aside from the possibility of extremely rare mutations in a few additional high penetrance genes yet to be discovered, this suggests a likely...

  3. Genetic drift. The ancient Egyptian dwarfs of the pyramids: the high official and the female worker.

    Science.gov (United States)

    Kozma, Chahira; Sarry El Din, Azza Mohamed; El Shafy El Banna, Rokia Abd; El Samie Kandeel, Wafaa Abd; Lachman, Ralph

    2011-08-01

    The existence of dwarfism is amply documented in ancient Egypt due to the rich biological and artistic legacies. In previous articles published in this journal, I discussed the roles of people with skeletal dysplasia in ancient Egyptian civilization. In this article I, along with my Egyptian and American colleagues, describe two skeletons of dwarfs that date to 2700-2184 BCE and were unearthed from a funerary complex near the Great Pyramids in Giza. The first skeleton belongs to a high official, Per-ni-ankh-w, who died between 45 and 50 years of age. His statue is on display in the Egyptian Museum of Cairo. The second skeleton belongs to a pregnant female worker found with a fetus in situ. Her estimated age at death was 25-30 years. She most likely died during childbirth due to a small pelvic outlet as supported by her narrow sacrum. The fetal bones appear normal. Radiological examination of both skeletons confirmed the clinical diagnosis of achondroplasia. Ancient Egyptians concerned themselves with the search for spiritual fulfillment through the tradition of moral teachings. Amenemope, a wise man who lived during the reign of Amenhotep III (1391-1354 BCE), advocated respect toward individuals with disabilities: Do not jeer at a blind man nor tease a dwarf, Neither interfere with the condition of a cripple. Do not taunt a man who is in the hand of God, Nor scowl at him if he errs. In summary, artistic, biological, and written resources indicate that dwarfs were well integrated in ancient Egyptian society.

  4. A high throughput genetic screen identifies new early meiotic recombination functions in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Arnaud De Muyt

    2009-09-01

    Full Text Available Meiotic recombination is initiated by the formation of numerous DNA double-strand breaks (DSBs catalysed by the widely conserved Spo11 protein. In Saccharomyces cerevisiae, Spo11 requires nine other proteins for meiotic DSB formation; however, unlike Spo11, few of these are conserved across kingdoms. In order to investigate this recombination step in higher eukaryotes, we took advantage of a high-throughput meiotic mutant screen carried out in the model plant Arabidopsis thaliana. A collection of 55,000 mutant lines was screened, and spo11-like mutations, characterised by a drastic decrease in chiasma formation at metaphase I associated with an absence of synapsis at prophase, were selected. This screen led to the identification of two populations of mutants classified according to their recombination defects: mutants that repair meiotic DSBs using the sister chromatid such as Atdmc1 or mutants that are unable to make DSBs like Atspo11-1. We found that in Arabidopsis thaliana at least four proteins are necessary for driving meiotic DSB repair via the homologous chromosomes. These include the previously characterised DMC1 and the Hop1-related ASY1 proteins, but also the meiotic specific cyclin SDS as well as the Hop2 Arabidopsis homologue AHP2. Analysing the mutants defective in DSB formation, we identified the previously characterised AtSPO11-1, AtSPO11-2, and AtPRD1 as well as two new genes, AtPRD2 and AtPRD3. Our data thus increase the number of proteins necessary for DSB formation in Arabidopsis thaliana to five. Unlike SPO11 and (to a minor extent PRD1, these two new proteins are poorly conserved among species, suggesting that the DSB formation mechanism, but not its regulation, is conserved among eukaryotes.

  5. High-throughput, luciferase-based reverse genetics systems for identifying inhibitors of Marburg and Ebola viruses.

    Science.gov (United States)

    Uebelhoer, Luke S; Albariño, César G; McMullan, Laura K; Chakrabarti, Ayan K; Vincent, Joel P; Nichol, Stuart T; Towner, Jonathan S

    2014-06-01

    Marburg virus (MARV) and Ebola virus (EBOV), members of the family Filoviridae, represent a significant challenge to global public health. Currently, no licensed therapies exist to treat filovirus infections, which cause up to 90% mortality in human cases. To facilitate development of antivirals against these viruses, we established two distinct screening platforms based on MARV and EBOV reverse genetics systems that express secreted Gaussia luciferase (gLuc). The first platform is a mini-genome replicon to screen viral replication inhibitors using gLuc quantification in a BSL-2 setting. The second platform is complementary to the first and expresses gLuc as a reporter gene product encoded in recombinant infectious MARV and EBOV, thereby allowing for rapid quantification of viral growth during treatment with antiviral compounds. We characterized these viruses by comparing luciferase activity to virus production, and validated luciferase activity as an authentic real-time measure of viral growth. As proof of concept, we adapt both mini-genome and infectious virus platforms to high-throughput formats, and demonstrate efficacy of several antiviral compounds. We anticipate that both approaches will prove highly useful in the development of anti-filovirus therapies, as well as in basic research on the filovirus life cycle.

  6. Sports genetics: the PPARA gene and athletes’ high ability in endurance sports. A systematic review and meta-analysis

    Science.gov (United States)

    Tuvblad, C; Forero, DA

    2015-01-01

    A meta-analysis was performed with the aim of re-evaluating the role of the peroxisome proliferator activated receptor alpha (PPARA) gene intron 7 G/C polymorphism (rs4253778) in athletes’ high ability in endurance sports. Design: A meta-analysis of case control studies assessing the association between the G/C polymorphisms of the PPARA gene and endurance sports was conducted. The Cochrane Review Manager software was used to compare the genotype and allele frequencies between endurance athletes and controls to determine whether a genetic variant is more common in athletes than in the general population. Five studies, encompassing 760 endurance athletes and 1792 controls, fulfilled our inclusion criteria. The pooled odds ratio (and confidence intervals, CIs) for the G allele compared to the C allele was 1.65 (95% CI 1.39-1.96). The pooled OR for the GG genotype compared to the GC genotype was 1.79 (95% CI 1.44-2.22), and for the GG genotype compared to the CC genotype 2.37 (95% CI 1.40-3.99). There was no evidence of heterogeneity (I2 =0%) or of publication bias. Athletes with high ability in endurance sports had a higher frequency of the GG genotype and G allele. PMID:26985127

  7. Attitudes toward direct-to-consumer advertisements and online genetic testing among high-risk women participating in a hereditary cancer clinic.

    Science.gov (United States)

    Perez, Giselle K; Cruess, Dean G; Cruess, Stacy; Brewer, Molly; Stroop, Jennifer; Schwartz, Robin; Greenstein, Robert

    2011-07-01

    Genetic testing for the breast cancer genes 1/2 (BRCA 1/2) has helped women determine their risk of developing breast and ovarian cancer. As interest in genetic testing has grown, companies have created strategies to disseminate information about testing, including direct-to-consumer advertising (DTCA) and online genetic testing. This study examined attitudes toward DTCA and online testing for BRCA among 84 women at a high-risk clinic as well as additional factors that may be associated with these attitudes, such as personal and familial cancer history, cancer worry and risk perception, and history with genetic testing/counseling. Results showed that the majority of the women held favorable attitudes toward DTCA for BRCA testing but did not support online testing. Factors such as familial ovarian cancer, cancer worry, and satisfaction with genetic counseling/testing were associated with positive attitudes toward DTCA, whereas personal breast cancer history was related to negative attitudes. The findings suggest that women may view DTCA as informational but rely on physicians for help in their decision to undergo testing, and also suggest that cancer history may affect women's acceptance of DTCA and genetic testing.

  8. Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

    Directory of Open Access Journals (Sweden)

    Pilar Suárez-Montes

    2016-12-01

    Full Text Available Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate, indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4, medium (3, and small (5 forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61, weak genetic structure (Rst = 0.037, and slight inbreeding in small fragments. Effective population sizes (Ne were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events

  9. Study of genetic effects of high energy radiations with different ionizing capacities on extracellular phages.

    Science.gov (United States)

    Bresler, S E; Kalinin, V L; Kopylova, Y U; Krivisky, A S; Rybchin, V N; Shelegedin, V N

    1975-07-01

    The inactivating and mutagenic action of high-energy radiations with different ionizing capacities (gamma-rays, protons, alpha-particles and accelerated ions of 12C and 20Ne) was studied by using coliphages lambda11 and SD as subjects. In particular the role of irradiation conditions (broth suspension, pure buffer, dry samples) and of the host functions recA, exrA and polA was investigated. The dose-response curve of induced mutagenesis was studied by measuring the yield of vir mutants in lambda11 and plaque mutants in SD. The following results were obtained. (1) The inactivation kinetics of phages under the action of gamma-rays and protons was first order to a survival of 10(-7). Heavy ions also showed exponential inactivation kinetics to a survival of 10(-4). At higher doses of 20Ne ion bombardment some deviation from one-hit kinetics was observed. For dry samples of phages the dimensions of targets for all types of radiation were approximately proportional to the molecular weights of phage DNA's. For densely ionizing radiation (heavy ions) the inactivating action was 3-5 times weaker than for gamma-rays and protons. (2) Mutagenesis was observed for all types of radiation, but heavy ions were 1-5-2 times less efficient than gamma-rays. For both phages studied the dose-response curve of mutagenesis was non-linear. The dependence on the dose was near to parabolic for lambda11. For SD a plateau or maximum of mutagenesis was observed for the relative number of mutants at a survival of about 10(-4). (3) Host-cell functions recA and exrA were practically indifferent for survival of gamma-irradiated phage lambda11, but indispensable for mutagenesis. Mutation recAI3 abolished induced vir mutations totally and exrA- reduced them significantly. The absence of the function polA had a considerable influence on phage survival, but no effect on vir mutation yield (if compared at the same survival level). (4) In conditions of indirect action of gamma-rays no vir mutations were

  10. Genetic Analysis of long-lived families reveals novel variants influencing high density-lipoprotein cholesterol

    Directory of Open Access Journals (Sweden)

    Mary F Feitosa

    2014-06-01

    Full Text Available The plasma levels of high-density lipoprotein cholesterol (HDL have an inverse relationship to the risks of atherosclerosis and cardiovascular disease, and have also been associated with longevity. We sought to identify novel loci for HDL that could potentially provide new insights into biological regulation of HDL metabolism in healthy-longevous subjects. We performed a genome-wide association scan on HDL using a mixed model approach to account for family structure using kinship coefficients. A total of 4,114 subjects of European descent (480 families were genotyped at ~2.3 million SNPs and ~38 million SNPs were imputed using the 1000 Genome Cosmopolitan reference panel in MACH. We identified novel variants near-NLRP1 (17p13 associated with an increase of HDL levels at genome-wide significant level (p< 5.0E-08. Additionally, several CETP (16q21 and ZNF259-APOA5-A4-C3-A1 (11q23.3 variants associated with HDL were found, replicating those previously reported in the literature. A possible regulatory variant upstream of NLRP1 that is associated with HDL in these elderly LLFS subjects may also contribute to their longevity and health. Our NLRP1 intergenic SNPs show a potential regulatory function in ENCODE; however, it is not clear whether they regulate NLRP1 or other more remote gene. NLRP1 plays an important role in the induction of apoptosis, and its inflammasome is critical for mediating innate immune responses. Nlrp1a (a mouse ortholog of human NLRP1 interacts with SREBP-1a (17p11 which has a fundamental role in lipid concentration and composition, and is involved in innate immune response in macrophages. The NLRP1 region is conserved in mammals, but also has evolved adaptively showing signals of positive selection in European populations that might confer an advantage. NLRP1 intergenic SNPs have also been associated with immunity/inflammasome disorders which highlights the biological importance of this chromosomal region.

  11. Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

    NARCIS (Netherlands)

    Li, Gang; Diogo, Dorothee; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J.; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L.; Siminovitch, Katherine A.; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K.; Worthington, Jane; Gupta, Namrata; Clemons, Paul A.; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M.

    2013-01-01

    Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant

  12. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1 pandemic.

    Directory of Open Access Journals (Sweden)

    Juan Téllez-Sosa

    Full Text Available BACKGROUND: Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The "deep sequencing" approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. METHODOLOGY AND PRINCIPAL FINDINGS: We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1 pandemic (A(H1N1pdm virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n  =  299 taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July to second wave (September-November of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. CONCLUSIONS: NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that

  13. Generating information-rich high-throughput experimental materials genomes using functional clustering via multitree genetic programming and information theory.

    Science.gov (United States)

    Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M

    2015-04-13

    High-throughput experimental methodologies are capable of synthesizing, screening and characterizing vast arrays of combinatorial material libraries at a very rapid rate. These methodologies strategically employ tiered screening wherein the number of compositions screened decreases as the complexity, and very often the scientific information obtained from a screening experiment, increases. The algorithm used for down-selection of samples from higher throughput screening experiment to a lower throughput screening experiment is vital in achieving information-rich experimental materials genomes. The fundamental science of material discovery lies in the establishment of composition-structure-property relationships, motivating the development of advanced down-selection algorithms which consider the information value of the selected compositions, as opposed to simply selecting the best performing compositions from a high throughput experiment. Identification of property fields (composition regions with distinct composition-property relationships) in high throughput data enables down-selection algorithms to employ advanced selection strategies, such as the selection of representative compositions from each field or selection of compositions that span the composition space of the highest performing field. Such strategies would greatly enhance the generation of data-driven discoveries. We introduce an informatics-based clustering of composition-property functional relationships using a combination of information theory and multitree genetic programming concepts for identification of property fields in a composition library. We demonstrate our approach using a complex synthetic composition-property map for a 5 at. % step ternary library consisting of four distinct property fields and finally explore the application of this methodology for capturing relationships between composition and catalytic activity for the oxygen evolution reaction for 5429 catalyst compositions in a

  14. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    Directory of Open Access Journals (Sweden)

    Yash Paul Khajuria

    Full Text Available The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777 of an inter-specific reference mapping population. High amplification efficiency (87%, experimental validation success rate (81% and polymorphic potential (55% of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48% detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%. An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777 having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped

  15. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    Science.gov (United States)

    Khajuria, Yash Paul; Saxena, Maneesha S; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest

  16. Genetic characterization of Neotropical Jabiru Storks: Insights for conservation

    Science.gov (United States)

    Lopes, I.F.; Haig, S.M.; Lama, S.N.D.

    2010-01-01

    Jabiru Stork (Jabiru mycteria is listed under Appendix I of CITES and considered threatened in Central America. The first population genetic analysis of Jabiru Storks was carried out using mitochondrial DNA (mtDNA) control region sequences (520 bp) and five heterologous microsatellite loci. Samples were collected from the field (N = 49) and museum skins (N = 22) in Central (mainly Belize, Nicaragua and Costa Rica) and South America (Colombia, Venezuela, Peru and Brazil). A decline of mtDNA diversity was observed in comparisons between past (N = 20) and present (N = 40) samples collected in Central America and northern South America. Similar levels of microsatellite loci diversity were observed among contemporary samples. Lower levels of mtDNA variability were observed in samples from Central America and northern South America when compared to the Brazilian Pantanal region. Significant levels of genetic differentiation were found between contemporary locations sampled, whereas non-significant results were observed for historic samples. The non-geographic association of haplotypes observed at the cladograms and the recent divergence times estimated between locations are indicative of an evolutionary history of a large population size with limited population structure. Reconnection of populations via increased gene flow, particularly in Central America, is recommended if genetic structure and status are to be restored.

  17. Serotonin release in the caudal nidopallium of adult laying hens genetically selected for high and low feather pecking behavior: An in vivo microdialysis study

    NARCIS (Netherlands)

    Kops, M.S.; Kjaer, J.B.; Güntürkün, O.; Westphal, K.C.G.; Korte-Bouws, G.A.H.; Olivier, B.; Bolhuis, J.E.; Korte, S.M.

    2014-01-01

    Severe feather pecking (FP) is a detrimental behavior causing welfare problems in laying hens. Divergent genetic selection for FP in White Leghorns resulted in strong differences in FP incidences between lines. More recently, it was shown that the high FP (HFP) birds have increased locomotor activit

  18. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, Anna;

    2008-01-01

    and Cosenza. CONCLUSION: Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean...

  19. Genetic factors associated with intestinal metaplasia in a high risk Singapore-Chinese population: a cohort study

    Directory of Open Access Journals (Sweden)

    Salto-Tellez Manuel

    2009-10-01

    Full Text Available Abstract Background Intestinal metaplasia (IM is an important precursor lesion in the development of gastric cancer (GC. The aim of this study was to investigate genetic factors previously linked to GC risk for their possible association with IM. A total of 18 polymorphisms in 14 candidate genes were evaluated in a Singapore-Chinese population at high risk of developing GC. Methods Genotype frequencies were compared between individuals presenting with (n = 128 or without (n = 246 IM by both univariate and multivariate analysis. Results Carriers of the NQO1 609 T allele showed an association with IM in individuals who were seropositive for Helicobacter pylori (HP+; OR = 2.61, 95%CI: 1.18-5.80, P = .018. The IL-10 819 C allele was also associated with IM in HP+ individuals (OR = 2.32, 95%CI: 1.21-4.43, P = 0.011, while the PTPN11 A allele was associated with IM in HP- individuals (OR = 2.51, 95%CI: 1.16-5.40, P = 0.019, but showed an inverse association in HP+ subjects (OR = 0.46, 95%CI: 0.21-0.99, P = 0.048. Conclusion Polymorphisms in NQO1, IL-10 and PTPN11, in combination with HP status, could be used to identify individuals who are more likely to develop IM and therefore GC.

  20. Optimization of total harmonic current distortion and torque pulsation reduction in high-power induction motors using genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    Arash SAYYAH; Mitra AFLAK; Alireza REZAZADEH

    2008-01-01

    This paper presents a powerful application of genetic algorithm (GA) for the minimization of the total harmonic current distortion (THCD) in high-power induction motors fed by voltage source inverters,based on an approximate harmonic model. That is,having defined a desired fundamental output voltage,optimal pulse patterns (switching angles) are determined to produce the fundamental output voltage while minimizing the THCD. The complete results for the two cases of three and five switching instants in the first quarter period of pulse width modulation (PWM) waveform are presented. Presence of harmonics in the stator excitation leads to a pulsing-torque component. Considering the fact that if the pulsing-torques are at low frequencies,they can cause troublesome speed fluctuations,shaft fatigue,and unsatisfactory performance in the feedback control system,the 5th,7th,11 th,and 13th current harmonics (in the case of five switching angles) are con strained at some pre-specified values,to mitigate the detrimental effects of low-frequency harmonics. At the same time,the THCD is optimized while the required fun-damental output voltage is maintained.

  1. MACRO: a combined microchip-PCR and microarray system for high-throughput monitoring of genetically modified organisms.

    Science.gov (United States)

    Shao, Ning; Jiang, Shi-Meng; Zhang, Miao; Wang, Jing; Guo, Shu-Juan; Li, Yang; Jiang, He-Wei; Liu, Cheng-Xi; Zhang, Da-Bing; Yang, Li-Tao; Tao, Sheng-Ce

    2014-01-21

    The monitoring of genetically modified organisms (GMOs) is a primary step of GMO regulation. However, there is presently a lack of effective and high-throughput methodologies for specifically and sensitively monitoring most of the commercialized GMOs. Herein, we developed a multiplex amplification on a chip with readout on an oligo microarray (MACRO) system specifically for convenient GMO monitoring. This system is composed of a microchip for multiplex amplification and an oligo microarray for the readout of multiple amplicons, containing a total of 91 targets (18 universal elements, 20 exogenous genes, 45 events, and 8 endogenous reference genes) that covers 97.1% of all GM events that have been commercialized up to 2012. We demonstrate that the specificity of MACRO is ~100%, with a limit of detection (LOD) that is suitable for real-world applications. Moreover, the results obtained of simulated complex samples and blind samples with MACRO were 100% consistent with expectations and the results of independently performed real-time PCRs, respectively. Thus, we believe MACRO is the first system that can be applied for effectively monitoring the majority of the commercialized GMOs in a single test.

  2. Genetic Particle Swarm Optimization-Based Feature Selection for Very-High-Resolution Remotely Sensed Imagery Object Change Detection.

    Science.gov (United States)

    Chen, Qiang; Chen, Yunhao; Jiang, Weiguo

    2016-07-30

    In the field of multiple features Object-Based Change Detection (OBCD) for very-high-resolution remotely sensed images, image objects have abundant features and feature selection affects the precision and efficiency of OBCD. Through object-based image analysis, this paper proposes a Genetic Particle Swarm Optimization (GPSO)-based feature selection algorithm to solve the optimization problem of feature selection in multiple features OBCD. We select the Ratio of Mean to Variance (RMV) as the fitness function of GPSO, and apply the proposed algorithm to the object-based hybrid multivariate alternative detection model. Two experiment cases on Worldview-2/3 images confirm that GPSO can significantly improve the speed of convergence, and effectively avoid the problem of premature convergence, relative to other feature selection algorithms. According to the accuracy evaluation of OBCD, GPSO is superior at overall accuracy (84.17% and 83.59%) and Kappa coefficient (0.6771 and 0.6314) than other algorithms. Moreover, the sensitivity analysis results show that the proposed algorithm is not easily influenced by the initial parameters, but the number of features to be selected and the size of the particle swarm would affect the algorithm. The comparison experiment results reveal that RMV is more suitable than other functions as the fitness function of GPSO-based feature selection algorithm.

  3. Highly Sensitive Detection of Organophosphate Insecticides Using Biosensors Based on Genetically Engineered Acetylcholinesterase and Poly(3,4-Ethylenedioxythiophene

    Directory of Open Access Journals (Sweden)

    Tomasz Sikora

    2011-01-01

    Full Text Available A poly(3,4-ethylenedioxythiophene (PEDOT conducting ink is presented as a new electroactive material to be incorporated in acetylcholinesterase-(AChE- based screen printed biosensors, acting not only as a conducting template but also as an electrochemical mediator for thiocholine oxidation. Two different strategies have been studied for the chemical synthesis of PEDOT: (a a classical oxidative polymerisation and (b a more innovative enzymatic polymerisation, giving a water-soluble PEDOT. The use of this water-soluble conducting polymer as mediator in screen-printed biosensors enables its deposition by printing like the rest of the layers. Highly sensitive acetylcholinesterase-(AChE- based screen-printed biosensors have been constructed using both classical and enzymatic PEDOT, in combination with genetically modified AChE. These electrodes allow the measurement of thiocholine oxidation at potentials of 100 mV versus Ag/AgCl reference electrode through the mediation of PEDOT. Inhibition of thiocholine production in presence of CPO allow for detection of this pesticide in concentrations as low as 1·10−10 M.

  4. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii

    Science.gov (United States)

    Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le

    2016-01-01

    A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection. PMID:27587236

  5. Genetic Convergence in the Adaptation of Dogs and Humans to the High-Altitude Environment of the Tibetan Plateau

    Science.gov (United States)

    Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

    2014-01-01

    The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. PMID:25091388

  6. High Prevalence and Genetic Polymorphisms of Legionella in Natural and Man-Made Aquatic Environments in Wenzhou, China.

    Science.gov (United States)

    Zhang, Leyi; Li, Yi; Wang, Xin; Shangguan, Zhihui; Zhou, Haijian; Wu, Yuejin; Wang, Lianghuai; Ren, Hongyu; Hu, Yun; Lin, Meifen; Qin, Tian

    2017-02-24

    demonstrate a high prevalence and genetic polymorphism of Legionella in Wenzhou's environmental water system. The investigated environmental water sources pose a potential threat to the public where intervention could help to prevent the occurrence of Legionnaires' disease.

  7. A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

    Science.gov (United States)

    Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

    2016-01-01

    Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major

  8. Effects of genetic mutations and chemical exposures on Caenorhabditis elegans feeding: evaluation of a novel, high-throughput screening assay.

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    Windy A Boyd

    Full Text Available BACKGROUND: Government agencies have defined a need to reduce, refine or replace current mammalian-based bioassays with testing methods that use alternative species. Invertebrate species, such as Caenorhabditis elegans, provide an attractive option because of their short life cycles, inexpensive maintenance, and high degree of evolutionary conservation with higher eukaryotes. The C. elegans pharynx is a favorable model for studying neuromuscular function, and the effects of chemicals on neuromuscular activity, i.e., feeding. Current feeding methodologies, however, are labor intensive and only semi-quantitative. METHODOLOGY/PRINCIPAL FINDINGS: Here a high-throughput assay is described that uses flow cytometry to measure C. elegans feeding by determining the size and intestinal fluorescence of hundreds of nematodes after exposure to fluorescent-labeled microspheres. This assay was validated by quantifying fluorescence in feeding-defective C. elegans (eat mutants, and by exposing wild-type nematodes to the neuroactive compounds, serotonin and arecoline. The eat mutations previously determined to cause slow pumping rates exhibited the lowest feeding levels with our assay. Concentration-dependent increases in feeding levels after serotonin exposures were dependent on food availability, while feeding levels decreased in arecoline-exposed nematodes regardless of the presence of food. The effects of the environmental contaminants, cadmium chloride and chlorpyrifos, on wild-type C. elegans feeding were then used to demonstrate an application of the feeding assay. Cadmium exposures above 200 microM led to a sharp drop in feeding levels. Feeding of chlorpyrifos-exposed nematodes decreased in a concentration-dependent fashion with an EC(50 of 2 microM. CONCLUSIONS/SIGNIFICANCE: The C. elegans fluorescence microsphere feeding assay is a rapid, reliable method for the assessment of neurotoxic effects of pharmaceutical drugs, industrial chemicals or

  9. Hunting, swimming, and worshiping: human cultural practices illuminate the blood meal sources of cave dwelling Chagas vectors (Triatoma dimidiata in Guatemala and Belize.

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    Lori Stevens

    2014-09-01

    Full Text Available Triatoma dimidiata, currently the major Central American vector of Trypanosoma cruzi, the parasite that causes Chagas disease, inhabits caves throughout the region. This research investigates the possibility that cave dwelling T. dimidiata might transmit the parasite to humans and links the blood meal sources of cave vectors to cultural practices that differ among locations.We determined the blood meal sources of twenty-four T. dimidiata collected from two locations in Guatemala and one in Belize where human interactions with the caves differ. Blood meal sources were determined by cloning and sequencing PCR products amplified from DNA extracted from the vector abdomen using primers specific for the vertebrate 12S mitochondrial gene. The blood meal sources were inferred by ≥ 99% identity with published sequences. We found 70% of cave-collected T. dimidiata positive for human DNA. The vectors had fed on 10 additional vertebrates with a variety of relationships to humans, including companion animal (dog, food animals (pig, sheep/goat, wild animals (duck, two bat, two opossum species and commensal animals (mouse, rat. Vectors from all locations fed on humans and commensal animals. The blood meal sources differ among locations, as well as the likelihood of feeding on dog and food animals. Vectors from one location were tested for T. cruzi infection, and 30% (3/10 tested positive, including two positive for human blood meals.Cave dwelling Chagas disease vectors feed on humans and commensal animals as well as dog, food animals and wild animals. Blood meal sources were related to human uses of the caves. We caution that just as T. dimidiata in caves may pose an epidemiological risk, there may be other situations where risk is thought to be minimal, but is not.

  10. Genetic diversity and phylogeography of highly zoonotic Echinococcus granulosus genotype G1 in the Americas (Argentina, Brazil, Chile and Mexico) based on 8279bp of mtDNA.

    Science.gov (United States)

    Laurimäe, Teivi; Kinkar, Liina; Andresiuk, Vanessa; Haag, Karen Luisa; Ponce-Gordo, Francisco; Acosta-Jamett, Gerardo; Garate, Teresa; Gonzàlez, Luis Miguel; Saarma, Urmas

    2016-11-01

    Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific genetic variability and is divided into multiple genotypes (G1-G8, G10) with differences in their biology and etiology. Of these, genotype G1 is responsible for the majority of human and livestock infections and has the broadest host spectrum. However, despite the high significance to the public and livestock health, the data on genetic variability and regional genetic differences of genotype G1 in America are scarce. The aim of this study was to evaluate the genetic variability and phylogeography of G1 in several countries in America by sequencing a large portion of the mitochondrial genome. We analysed 8279bp of mtDNA for 52 E. granulosus G1 samples from sheep, cattle and pigs collected in Argentina, Brazil, Chile and Mexico, covering majority of countries in the Americas where G1 has been reported. The phylogenetic network revealed 29 haplotypes and a high haplotype diversity (Hd=0.903). The absence of phylogeographic segregation between different regions in America suggests the importance of animal transportation in shaping the genetic structure of E. granulosus G1. In addition, our study revealed many highly divergent haplotypes, indicating a long and complex evolutionary history of E. granulosus G1 in the Americas.

  11. High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae-Perciformes), in the western South Atlantic revealed through multilocus analysis.

    Science.gov (United States)

    da Silva, Raimundo; Veneza, Ivana; Sampaio, Iracilda; Araripe, Juliana; Schneider, Horacio; Gomes, Grazielle

    2015-01-01

    In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans.

  12. High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae-Perciformes, in the western South Atlantic revealed through multilocus analysis.

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    Raimundo da Silva

    Full Text Available In the present study, five loci (mitochondrial and nuclear were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA, as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans.

  13. Mutation Scanning in a Single and a Stacked Genetically Modified (GM Event by Real-Time PCR and High Resolution Melting (HRM Analysis

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    Sina-Elisabeth Ben Ali

    2014-10-01

    Full Text Available Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU, Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs. In this study, genetic stability of two GMOs was examined using high resolution melting (HRM analysis and real-time polymerase chain reaction (PCR employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73 and a stacked maize (MON88017 × MON810 was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found.

  14. Morfología y representatividad de la vivienda histórica en la frontera México-Belice: algunas notas. Morphology and representativeness of historical housing in the border of Mexico-Belize: some notes. Morfologia e representatividade da moradia histórica na fronteira México-Belize: algumas anotações.

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    Martín Manuel Checa Artasu

    2011-08-01

    Full Text Available Este trabajo analiza la vivienda histórica de la frontera de México con Belice. Este es fruto de un proceso de simbiosis arquitectónica entre la casa maya, modelo vernáculo de esta área, y el modelo de bungaló, propio de la colonización británica. Esta arquitectura se desarrolla por los conflictos políticos y cambios económicos y sociales acontecidos en la zona en la segunda mitad del siglo XX, que obligan al traslado de poblaciones a ambos lados de esta frontera. Se trata de una arquitectura habitacional que deviene elemento protagónico en el paisaje para explicar el proceso de ocupación humana dado en este espacio geográfico y su evolución socioeconómica, y que mantiene, hoy en día, numerosos ejemplos. This paper analyzes the historic housing of Mexico’s border with Belize. This is the result of a process of symbiosis between Mayan home architecture, vernacular model of this area, and the model bungalow, typical of British colonization. This architecture is developed by political conflicts and socio economical changes that occurred in the area during the second half of the twentieth century, which force the transfer of populations on both sides of the border. This is a residential architecture that becomes key feature in the landscape to explain the process of human occupation in this area given its geographical space and its socio-economic evolution that maintains a variety of examples nowadays. Este trabalho analisa a moradia histórica na fronteira entre México e Belize. Ele é fruto der um processo de simbiose arquitetônica entre a moradia maia, modelo vernáculo de esta região, e o modelo do bangalô, próprio da colonização britânica. Esta arquitetura é desenvolvida pelos conflitos políticos e as mudanças econômicas e sociais acontecidas na zona na segunda metade do século que obrigam ao traslado de povoados a ambos os lados da fronteira. Trata-se de uma arquitetura habitacional que devém um elemento

  15. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  16. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing.

    Science.gov (United States)

    Lasho, Terra; Johnson, Sarah H; Smith, David I; Crispino, John D; Pardanani, Animesh; Vasmatzis, George; Tefferi, Ayalew

    2013-09-01

    We used high resolution mate-pair sequencing (HRMPS) in 15 patients with primary myelofibrosis (PMF): eight with normal karyotype and seven with PMF-characteristic cytogenetic abnormalities, including der(6)t(1;6)(q21-23;p21.3) (n = 4), der(7)t(1;7)(q10;p10) (n = 2), del(20)(q11.2q13.3) (n = 3), and complex karyotype (n = 1). We describe seven novel deletions/translocations in five patients (including two with normal karyotype) whose breakpoints were PCR-validated and involved MACROD2, CACNA2D4, TET2, SGMS2, LRBA, SH3D19, INTS3, FOP (CHTOP), SCLT1, and PHF17. Deletions with breakpoints involving MACROD2 (lysine deacetylase; 20p12.1) were recurrent and found in two of the 15 study patients. A novel fusion transcript was found in one of the study patients (INTS3-CHTOP), and also in an additional non-study patient with PMF. In two patients with der(6)t(1;6)(q21-23;p21.3), we were able to map the precise translocation breakpoints, which involved KCNN3 and GUSBP2 in one case and HYDIN2 in another. This study demonstrates the utility of HRMPS in uncovering submicroscopic deletions/translocations/fusions, and precise mapping of breakpoints in those with overt cytogenetic abnormalities. The overall results confirm the genetic heterogeneity of PMF, given the low frequency of recurrent specific abnormalities, identified by this screening strategy. Currently, we are pursuing the pathogenetic relevance of some of the aforementioned findings.

  17. Genetic differences and aberrant methylation in the apelin system predict the risk of high-altitude pulmonary edema

    Science.gov (United States)

    Mishra, Aastha; Kohli, Samantha; Dua, Sanchi; Thinlas, Tashi; Mohammad, Ghulam; Pasha, M. A. Qadar

    2015-01-01

    Hypoxia-inducible factor stimulates the expression of apelin, a potent vasodilator, in response to reduced blood arterial oxygen saturation. However, aberrations in the apelin system impair pulmonary vascular function, potentially resulting in the development of high-altitude (HA)-related disorders. This study aimed to elucidate the genetic and epigenetic regulation of apelin, apelin receptor (APLNR), and endothelial nitric oxide synthase (NOS3) in HA adaptation and HA pulmonary edema (HAPE). A genome-wide association study and sequencing identified variants of apelin, APLNR, and NOS3 that were validated in a larger sample size of HAPE-patients (HAPE-p), HAPE-free controls (HAPE-f), and healthy highland natives (HLs). Apelin-13 and nitrite levels and apelin and NOS3 expression were down-regulated in HAPE-p (P < 0.001). Among the several studied polymorphisms, apelin rs3761581, rs2235312, and rs3115757; APLNR rs11544374 and rs2282623; and NOS3 4b/4a, rs1799983, and rs7830 were associated with HAPE (P < 0.03). The risk allele rs3761581G was associated with a 58.6% reduction in gene expression (P = 0.017), and the risk alleles rs3761581G and rs2235312T were associated with low levels of apelin-13 and nitrite (P < 0.05). The latter two levels decreased further when both of these risk alleles were present in the patients (P < 0.05). Methylation of the apelin CpG island was significantly higher in HAPE-p at 11.92% than in HAPE-f and HLs at ≤7.1% (P < 0.05). Moreover, the methylation effect was 9% stronger in the 5′ UTR and was associated with decreased apelin expression and apelin-13 levels. The rs3761581 and rs2235312 polymorphisms and methylation of the CpG island influence the expression of apelin in HAPE. PMID:25918383

  18. ANDI-03: a genetic algorithm tool for the analysis of activation detector data to unfold high-energy neutron spectra.

    Science.gov (United States)

    Mukherjee, Bhaskar

    2004-01-01

    The thresholds of (n,xn) reactions in various activation detectors are commonly used to unfold the neutron spectra covering a broad energy span, i.e. from thermal to several hundreds of MeV. The saturation activities of the daughter nuclides (i.e. reaction products) serve as the input data of specific spectra unfolding codes, such as SAND-II and LOUHI-83. However, most spectra unfolding codes, including the above, require an a priori (guess) spectrum to starting up the unfolding procedure of an unknown spectrum. The accuracy and exactness of the resulting spectrum primarily depends on the subjectively chosen guess spectrum. On the other hand, the Genetic Algorithm (GA)-based spectra unfolding technique ANDI-03 (Activation-detector Neutron DIfferentiation) presented in this report does not require a specific starting parameter. The GA is a robust problem-solving tool, which emulates the Darwinian Theory of Evolution prevailing in the realm of biological world and is ideally suited to optimise complex objective functions globally in a large multidimensional solution space. The activation data of the 27Al(n,alpha)24Na, 116In(n,gamma)116mIn, 12C(n,2n)11C and 209Bi(n,xn)(210-x)Bi reactions recorded at the high-energy neutron field of the ISIS Spallation source (Rutherford Appleton Laboratory, UK) was obtained from literature and by applying the ANDI-03 GA tool, these data were used to unfold the neutron spectra. The total neutron fluence derived from the neutron spectrum unfolded using GA technique (ANDI-03) agreed within +/-6.9% (at shield top level) and +/-27.2% (behind a 60 cm thick concrete shield) with the same unfolded with the SAND-II code.

  19. Genetic Counseling

    Science.gov (United States)

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  20. Sustaining Rainforest Plants, People and Global Health: A Model for Learning from Traditions in Holistic Health Promotion and Community Based Conservation as Implemented by Q’eqchi’ Maya Healers, Maya Mountains, Belize

    Directory of Open Access Journals (Sweden)

    Pablo Sanchez-Vindas

    2010-10-01

    Full Text Available The present work showcases a model for holistic, sustainable healthcare in indigenous communities worldwide through the implementation of traditional healing practices. The implementation of this model promotes public health and community wellness while addressing crucially important themes such as in situ and ex situ conservation of medicinal plant resources and associated biodiversity, generational transmission of knowledge, and the preservation of biological and cultural diversity for future generations. Being envisaged and implemented by Q’eqchi’ Maya traditional healers of the southern Maya Mountains, Belize, this model can be replicated in other communities worldwide. A ethnobotany study in collaboration with these healers led to collection of 102 medicinal species from Itzama, their traditional healing cultural center and medicinal garden. Of these 102 species, 40 of prior reported 106 consensus study plants were present in the garden. There were 62 plants not previously reported growing in the garden as well. A general comparison of these plants was also made in relation to species reported in TRAMIL network, Caribbean Herbal Pharmacopoeia (CHP, the largest regional medicinal pharmacopoeia. A relative few species reported here were found in the CHP. However, the majority of the CHP plants are common in Belize and many are used by the nearby Mopan and Yucatec Maya. Since these 102 species are relied upon heavily in local primary healthcare, this Q’eqchi’ Maya medicinal garden represents possibilities toward novel sustainable, culturally relative holistic health promotion and community based conservation practices.

  1. Impact of virtual learning environment (VLE): A technological approach to genetics teaching on high school students' content knowledge, self-efficacy and career goal aspirations

    Science.gov (United States)

    Kandi, Kamala M.

    This study examines the effect of a technology-based instructional tool 'Geniverse' on the content knowledge gains, Science Self-Efficacy, Technology Self-Efficacy, and Career Goal Aspirations among 283 high school learners. The study was conducted in four urban high schools, two of which have achieved Adequate Yearly Progress (AYP) and two have not. Students in both types of schools were taught genetics either through Geniverse, a virtual learning environment or Dragon genetics, a paper-pencil activity embedded in traditional instructional method. Results indicated that students in all schools increased their knowledge of genetics using either type of instructional approach. Students who were taught using Geniverse demonstrated an advantage for genetics knowledge although the effect was small. These increases were more pronounced in the schools that had been meeting the AYP goal. The other significant effect for Geniverse was that students in the technology-enhanced classrooms increased in science Self-Efficacy while students in the non-technology enhanced classrooms decreased. In addition, students from Non-AYP schools showed an improvement in Science and Technology Self-Efficacy; however the effects were small. The implications of these results for the future use of technology-enriched classrooms were discussed. Keywords: Technology-based instruction, Self-Efficacy, career goals and Adequate Yearly Progress (AYP).

  2. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms

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    Deal Karin R

    2009-01-01

    Full Text Available Abstract Background Current techniques of screening bacterial artificial chromosome (BAC libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illumina GoldenGate™ assay. Results To test the efficacy of the Golden Gate assay in BAC library screening, multidimensional pools involving 302976 Aegilops tauschii BAC clones were genotyped for the presence/absence of specific gene sequences with multiplexed Illumina GoldenGate oligonucleotide assays previously used to place single nucleotide polymorphisms on an Ae. tauschii genetic map. Of 1384 allele-informative oligonucleotide assays, 87.6% successfully clustered BAC pools into those positive for a BAC clone harboring a specific gene locus and those negative for it. The location of the positive BAC clones within contigs assembled from 199190 fingerprinted Ae. tauschii BAC clones was used to evaluate the precision of anchoring of BAC clones and contigs on the Ae. tauschii genetic map. For 41 (95% assays, positive BAC clones were neighbors in single contigs. Those contigs could be unequivocally assigned to loci on the genetic map. For two (5% assays, positive clones were in two different contigs and the relationships of these contigs to loci on the Ae. tauschii genetic map were equivocal. Screening of BAC libraries with a simple five-dimensional BAC pooling strategy was evaluated and shown to allow direct detection of positive BAC clones without the need for manual deconvolution of BAC clone pools. Conclusion The highly parallel Illumina oligonucleotide assay is shown here to be an efficient tool for screening BAC libraries and a strategy for high

  3. Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper).

    Science.gov (United States)

    Farrell, Edward D; Carlsson, Jeanette E L; Carlsson, Jens

    2016-12-01

    The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (Capros aper) across the species' range. Microsatellite loci were developed de novo and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies-a crucial element for assessment, sustainable management and conservation of valuable biological resources.

  4. Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip.

    Science.gov (United States)

    Cañas-Álvarez, J J; González-Rodríguez, A; Munilla, S; Varona, L; Díaz, C; Baro, J A; Altarriba, J; Molina, A; Piedrafita, J

    2015-11-01

    The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

  5. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists.

    Science.gov (United States)

    Sengupta, Sanghamitra; Zhivotovsky, Lev A; King, Roy; Mehdi, S Q; Edmonds, Christopher A; Chow, Cheryl-Emiliane T; Lin, Alice A; Mitra, Mitashree; Sil, Samir K; Ramesh, A; Usha Rani, M V; Thakur, Chitra M; Cavalli-Sforza, L Luca; Majumder, Partha P; Underhill, Peter A

    2006-02-01

    Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000-15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era--not Indo-European--expansions have shaped the distinctive South Asian Y-chromosome landscape.

  6. Genetic Risk Can Be Decreased: Quitting Smoking Decreases and Delays Lung Cancer for Smokers With High and Low CHRNA5 Risk Genotypes — A Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Li-Shiun Chen

    2016-09-01

    Conclusion: We demonstrate that quitting smoking is highly beneficial in reducing lung cancer risks for smokers regardless of their CHRNA5 rs16969968 genetic risk status. Smokers with high-risk CHRNA5 genotypes, on average, can largely eliminate their elevated genetic risk for lung cancer by quitting smoking- cutting their risk of lung cancer in half and delaying its onset by 7 years for those who develop it. These results: 1 underscore the potential value of smoking cessation for all smokers, 2 suggest that CHRNA5 rs16969968 genotype affects lung cancer diagnosis through its effects on smoking, and 3 have potential value for framing preventive interventions for those who smoke.

  7. Genetic parameters and responses of performance and body composition traits in pigs selected for high and low growth rate on a fixed ration over a set time

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    Nguyen Nguyen

    2005-03-01

    Full Text Available Abstract Two lines of Large White pigs of common genetic origin were divergently selected over four years for high and low growth rate during a 6 week post-weaning test period in which all pigs were fed the same total amount of food (80% of estimated ad libitum intake. Genetic parameters and direct and correlated responses in performance and carcass traits were estimated on 2884 pigs with pedigrees comprising a total of 5324 animals, with restricted maximum likelihood and best linear unbiased prediction methods applied to a multi-trait animal model. Estimates of heritability (± SE were 0.19 ± 0.04 for lifetime daily gain (LDG, 0.16 ± 0.03 for test daily gain (TDG, 0.25 ± 0.04 for ultrasound P2 backfat (UBF and 0.16 ± 0.03 for food conversion ratio during test (TFC, and 0.15 ± 0.04 for daily carcass weight gain (CDG, 0.43 ± 0.06 for carcass backfat (CFT and 0.40 ± 0.06 for carcass lean percentage (LEAN. Common litter effects for TDG, UBF and TFC were less than 5% and for LDG, 17% of total phenotypic variance. Genetic correlations between performance and carcass traits were moderately to highly favourable. After four years of divergent selection for growth rate, the selection responses in estimated breeding value (EBV for TDG were 40.14 and -41.11 g (SED 2.95 for the high and low growth lines, respectively. The regressions of EBV on year of birth, indicate that the annual genetic trend for TDG, was 8.73 g/yr in the high and -8.48 g/yr in the low lines (P

  8. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes

    Science.gov (United States)

    A genetic map of melon enriched for fruit traits was constructed, using a recombinant inbred (RI) population developed from a cross between representatives of the two subspecies of Cucumis melo L.: PI 414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Phenotyping of 99 RI lines was conducte...

  9. A multi-factorial genetic model for prognostic assessment of high risk melanoma patients receiving adjuvant interferon.

    Directory of Open Access Journals (Sweden)

    Ena Wang

    Full Text Available PURPOSE: IFNa was the first cytokine to demonstrate anti-tumor activity in advanced melanoma. Despite the ability of high-dose IFNa reducing relapse and mortality by up to 33%, large majority of patients experience side effects and toxicity which outweigh the benefits. The current study attempts to identify genetic markers likely to be associated with benefit from IFN-a2b treatment and predictive for survival. EXPERIMENTAL DESIGN: We tested the association of variants in FOXP3 microsatellites, CTLA4 SNPs and HLA genotype in 284 melanoma patients and their association with prognosis and survival of melanoma patients who received IFNa adjuvant therapy. RESULTS: Univariate survival analysis suggested that patients bearing either the DRB1*15 or HLA-Cw7 allele suffered worse OS while patients bearing either HLA-Cw6 or HLA-B44 enjoyed better OS. DRB1*15 positive patients suffered also worse RFS and conversely HLA-Cw6 positive patients had better RFS. Multivariate analysis revealed that a five-marker genotyping signature was prognostic of OS independent of disease stage. In the multivariate Cox regression model, HLA-B38 (p = 0.021, HLA-C15 (p = 0.025, HLA-C3 (p = 0.014, DRB1*15 (p = 0.005 and CT60*G/G (0.081 were significantly associated with OS with risk ratio of 0.097 (95% CI, 0.013-0.709, 0.387 (95% CI, 0.169-0.889, 0.449 (95% CI, 0.237-0.851, 1.948 (95% CI, 1.221-3.109 and 1.484 (95% IC, 0.953-2.312 respectively. CONCLUSION: These results suggest that gene polymorphisms relevant to a biological occurrence are more likely to be informative when studied in concert to address potential redundant or conflicting functions that may limit each gene individual contribution. The five markers identified here exemplify this concept though prospective validation in independent cohorts is needed.

  10. A Record of Environmental Change in Caribbean Coral Reefs: Sclerochronology and Geochemistry of O. faveolata as a Paleoclimate Proxy at Coral Gardens and Rocky Point, Belize

    Science.gov (United States)

    DeCorte, I. A.; Greer, L.; Wirth, K. R.; Flowers Falls, E.; Lescinsky, H.; Doss, W. C.

    2015-12-01

    Over the last several decades, Acropora cervicornis has seen a massive die-off in the Caribbean. (Aronson and Precht 2001; Gardner et al., 2003; Greer et al., 2009). The potential causes of decline in A. cervicornis in the Caribbean include: extremes in sea surface temperatures (SST), ocean acidification, eutrophication, white-band disease, storm disturbances, and other anthropogenic disturbances. Contrary to the regional decline in A. cervicornis, Coral Gardens on the Belize Barrier Reef has an Acropora sp. population that appears to be thriving. Through a combination of sclerochronology, stable isotope analysis, and in situ sensor data, this work capitilizes on the opportunity to study reef conditions in a site where micro-environmental conditions appear to be favorable for healthy A. cervicornis coral growth. We use cores from two Orbicella faveolata colonies located within Acropora stands, as A. cervicornis does not reveal annual banding. We compare two cores from one O. faveolata colony at Coral Gardens, first cored in 2011 and again in 2014, to one O. faveolata core at near-by Rocky Point, where A. cervicornis is much less abundant. These cores were x-radiographed in order to expose the annual banding and sampled for stable oxygen and carbon isotope analysis (10-15 samples/cm). We show that, although there are no significant differences in the range of the δ18O and δ13C signature between Rocky Point and Coral Gardens, there is a clear difference in the stress histories at these locations as inferred from linear extension rates (LER's) and annual banding patterns. Rocky Point averages a LER of 10.5±1.4 mm/year (n = 29) over a 30 year record and Coral Gardens averages 9.1±1.2 mm/year (n = 70) from ~1953 - 2001, and averages 6.2±1.6 mm/year (n = 36) from coral years 2001-2014 after an inferred stress-banding event. This is in contrast to the observed overall health of A. cervicornis at the two locations. The inferred stress-banding event is currently

  11. Metamorphic evolution and U-Pb zircon SHRIMP geochronology of the Belizário ultramafic amphibolite, Encantadas Complex, southernmost Brazil

    Directory of Open Access Journals (Sweden)

    Léo A. Hartmann

    2003-09-01

    Full Text Available The integrated investigation of metamorphism and zircon U-Pb SHRIMP geochronology of the Belizário ultramafic amphibolite from southernmost Brazil leads to a better understanding of the processes involved in the generation of the Encantadas Complex. Magmatic evidence of the magnesian basalt or pyroxenite protolith is only preserved in cores of zircon crystals, which are dated at 2257 ± 12 Ma. Amphibolite facies metamorphism M1 formed voluminous hornblende in the investigated rock possibly at 1989 ± 21 Ma. This ultramafic rock was re-metamorphosed at 702±21 Ma during a greenschist facies eventM2; the assemblage actinolite + oligoclase + microcline + epidote + titanite + monazite formed by alteration of hornblende. The metamorphic events are probably related to the Encantadas Orogeny (2257±12 Ma and Camboriú Orogeny (~ 1989 Ma of the Trans-Amazonian Cycle, followed by an orogenic event (702±21 Ma of the Brasiliano Cycle. The intervening cratonic period (2000-700 Ma corresponds to the existence of the Supercontinent Atlantica, known regionally as the Rio de la Plata Craton.O entendimento dos processos evolutivos do Complexo Encantadas no sul do Brasil foi aperfeiçoado através do estudo integrado do metamorfismo de um anfibolito ultramáfico e da geocronologia U-Pb SHRIMP de zircão. Os núcleos herdados de alguns cristais de zircão tem idades em torno de 2257 ±12 Ma e constituem a única evidência preservada do protólito ígneo, que pode ter sido um basalto magnesiano ou um piroxenito. O metamorfismo M de fácies anfibolito formou abundante hornblenda na amostra investigada, possivelmente há 1989 ±21 Ma. Esta rocha ultramáfica foi re-metamorfizada talvez há cerca de 702 ±21 Ma durante um evento M de fácies xistos verdes do metamorfismo regional. Durante o evento M, a hornblenda foi recristalizada e formou a assembléia actinolita + oligoclásio + microclínio + epidoto + titanita + monazita. Estes eventos foram a manifesta

  12. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation.

    Science.gov (United States)

    Nourisson, Coralie; Morales-Vela, Benjamín; Padilla-Saldívar, Janneth; Tucker, Kimberly Pause; Clark, Annmarie; Olivera-Gómez, Leon David; Bonde, Robert; McGuire, Peter

    2011-07-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N(A) = 2.69; H(E) = 0.41 and ChB: N(A) = 3.0; H(E) = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.

  13. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation

    Science.gov (United States)

    Nourisson, Coralie; Morales-Vela, Benjamin; Padilla-Saldivar, Janneth; Tucker, Kimberly Pause; Clark, Ann Marie; Olivera-Gomez, Leon David; Bonde, Robert; McGuire, Peter

    2011-01-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: NA = 2.69; HE = 0.41 and ChB: NA = 3.0; HE = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.

  14. Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    Full Text Available MicroRNAs (miRNAs are key regulators in miRNA-mediated gene regulatory networks and play important roles in many biological processes, such as growth and development of mammals. In this study, we used microarrays to detect 261 miRNAs that are expressed in sheep skeletal muscle. We found 22 miRNAs that showed high levels of expression and equated to 89% of the total miRNA. Genetic variations in these 22 pri-miRNAs were further investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP and sequencing. A total of 49 genetic variations, which included 41 single nucleotide polymorphisms (SNPs and 8 deletions/insertions, were identified in four sheep breeds. Three variations were further researched in a larger sample set, including five sheep breeds with different meat production performances. We found that the genotype and allele frequencies of the CCC deletion/insertion in pri-miR-133a were significantly related to the sheep meat production trait. Finally, cell assays and quantitative reverse transcription PCR (qRT-PCR were employed to investigate the effect of pri-miRNA genetic variation on the miRNA biogenesis process. The results confirmed that genetic variations can influence miRNA biogenesis and increase or decrease the levels of mature miRNAs, in accordance with the energy and stability change of hair-pin secondary structures. Our findings will help to further the understanding of the functions of genetic variations in sheep pri-miRNAs in skeletal muscle growth and development.

  15. From Africa to Europe and back: refugia and range shifts cause high genetic differentiation in the Marbled White butterfly Melanargia galathea

    Directory of Open Access Journals (Sweden)

    Rödder Dennis

    2011-07-01

    Full Text Available Abstract Background The glacial-interglacial oscillations caused severe range modifications of biota. Thermophilic species became extinct in the North and survived in southern retreats, e.g. the Mediterranean Basin. These repeated extinction and (recolonisation events led to long-term isolation and intermixing of populations and thus resulted in strong genetic imprints in many European species therefore being composed of several genetic lineages. To better understand these cycles of repeated expansion and retraction, we selected the Marbled White butterfly Melanargia galathea. Fourty-one populations scattered over Europe and the Maghreb and one population of the sibling taxon M. lachesis were analysed using allozyme electrophoresis. Results We obtained seven distinct lineages applying neighbour joining and STRUCTURE analyses: (i Morocco, (ii Tunisia, (iii Sicily, (iv Italy and southern France, (v eastern Balkans extending to Central Europe, (vi western Balkans with western Carpathian Basin as well as (vii south-western Alps. The hierarchy of these splits is well matching the chronology of glacial and interglacial cycles since the Günz ice age starting with an initial split between the galathea group in North Africa and the lachesis group in Iberia. These genetic structures were compared with past distribution patterns during the last glacial stage calculated with distribution models. Conclusions Both methods suggest climatically suitable areas in the Maghreb and the southern European peninsulas with distinct refugia during the last glacial period and underpin strong range expansions to the North during the Postglacial. However, the allozyme patterns reveal biogeographical structures not detected by distribution modelling as two distinct refugia in the Maghreb, two or more distinct refugia at the Balkans and a close link between the eastern Maghreb and Sicily. Furthermore, the genetically highly diverse western Maghreb might have acted as source

  16. Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

    Science.gov (United States)

    Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.

    2014-01-01

    Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (Ne). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated Ne of mottled ducks to 33 % of the equilibrium Ne and yielded an estimated Ne consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

  17. Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle.

    Science.gov (United States)

    Zhang, Wei; Wang, Limin; Zhou, Ping; Song, Guangchao; Shen, Min; Gan, Shangquan; Shi, Guoqing

    2015-01-01

    MicroRNAs (miRNAs) are key regulators in miRNA-mediated gene regulatory networks and play important roles in many biological processes, such as growth and development of mammals. In this study, we used microarrays to detect 261 miRNAs that are expressed in sheep skeletal muscle. We found 22 miRNAs that showed high levels of expression and equated to 89% of the total miRNA. Genetic variations in these 22 pri-miRNAs were further investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing. A total of 49 genetic variations, which included 41 single nucleotide polymorphisms (SNPs) and 8 deletions/insertions, were identified in four sheep breeds. Three variations were further researched in a larger sample set, including five sheep breeds with different meat production performances. We found that the genotype and allele frequencies of the CCC deletion/insertion in pri-miR-133a were significantly related to the sheep meat production trait. Finally, cell assays and quantitative reverse transcription PCR (qRT-PCR) were employed to investigate the effect of pri-miRNA genetic variation on the miRNA biogenesis process. The results confirmed that genetic variations can influence miRNA biogenesis and increase or decrease the levels of mature miRNAs, in accordance with the energy and stability change of hair-pin secondary structures. Our findings will help to further the understanding of the functions of genetic variations in sheep pri-miRNAs in skeletal muscle growth and development.

  18. [Sickle cell anemia causes varied symptoms and high morbidity. Serious prognosis in the most common genetic disease in the world].

    Science.gov (United States)

    Kjellander, Christian; Sennström, Maria K B; Stiller, Viveka; Ågren, Anna

    2015-03-03

    Sickle cell anemia is a life-threatening disease, and the most common genetic disease in the world. The prevalence of sickle cell anemia in Sweden is unknown. Sickle cell anemia is an important disease, because of its variable complications, in many medical and surgical specialties. The overview highlights common medical problems encountered in sickle cell anemia presented through a case report of a pregnant woman.

  19. High risk genetic factor in Chinese patients with idiopathic male infertility:deletion of DAZ gene copy on Y chromosome

    Institute of Scientific and Technical Information of China (English)

    杨元; 肖翠英; 张思仲; 张思孝; 黄明孔; 林立

    2004-01-01

    @@ Idiopathic azoospermia or oligozoospermia affects approximately 2%-4% of all married males. Recently studies have confirmed that the deletion of DAZ in AZFc region of Y chromosome may be one of the important genetic aetiologies of Caucasian male infertility. To determine the relationship between DAZ gene deletion and idiopathic male infertility in Chinese population, we analysed the DAZ gene copy number of AZFc region in patients with idiopathic azoospermia or oligozoospermia, as well as fertile Chinese men.

  20. Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

    Science.gov (United States)

    Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

    2015-01-01

    Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

  1. Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish.

    Science.gov (United States)

    Wang, Xiaozhu; Liu, Shikai; Jiang, Chen; Geng, Xin; Zhou, Tao; Li, Ning; Bao, Lisui; Li, Yun; Yao, Jun; Yang, Yujia; Zhong, Xiaoxiao; Jin, Yulin; Dunham, Rex; Liu, Zhanjiang

    2017-02-01

    The ability to survive hypoxic conditions is important for various organisms, especially for aquatic animals. Teleost fish, representing more than 50 % of vertebrate species, are extremely efficient in utilizing low levels of dissolved oxygen in water. However, huge variations exist among various taxa of fish in their ability to tolerate hypoxia. In aquaculture, hypoxia tolerance is among the most important traits because hypoxia can cause major economic losses. Genetic enhancement for hypoxia tolerance in catfish is of great interest, but little was done with analysis of the genetic architecture of hypoxia tolerance. The objective of this study was to conduct a genome-wide association study to identify QTLs for hypoxia tolerance using the catfish 250K SNP array with channel catfish families from six strains. Multiple significant and suggestive QTLs were identified across and within strains. One significant QTL and four suggestive QTLs were identified across strains. Six significant QTLs and many suggestive QTLs were identified within strains. There were rare overlaps among the QTLs identified within the six strains, suggesting a complex genetic architecture of hypoxia tolerance. Overall, within-strain QTLs explained larger proportion of phenotypic variation than across-strain QTLs. Many of genes within these identified QTLs have known functions for regulation of oxygen metabolism and involvement in hypoxia responses. Pathway analysis indicated that most of these genes were involved in MAPK or PI3K/AKT/mTOR signaling pathways that were known to be important for hypoxia-mediated angiogenesis, cell proliferation, apoptosis and survival.

  2. Game Bozo – genetics: a didactic proposal as an alternative to DNA replication of teaching in high school

    Directory of Open Access Journals (Sweden)

    Letícia de Oliveira Rosa

    2016-12-01

    Full Text Available Today, despite hearing much talking about the DNA molecule in newspapers, magazines, news and TV programs, it is still perceived many difficulties for the students to assimilate the concepts and understand the gene processes. Faced with this reality is that the idea of creating a playful activity arose, as a methodological tool, in order to arouse the interest of students to study scientific concepts addressed in genetics education, including those involved in the DNA replication process. The game was developed by students of Biological Sciences Degree, the IFAM (Federal Institute of Science and Technology Amazon in Molecular Genetics discipline. Which, inspired by the traditional game Bozó, created the Bozó-genetic game, which consists of playing the dice, adding the numbers present on the faces of the dice and score according to the rules of the game. A simple, low cost and efficient alternative in transmission of scientific knowledge easily and interactively, with the possibility of aid student and teacher in the teaching-learning process.

  3. High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions.

    Directory of Open Access Journals (Sweden)

    Erika Garay

    2014-02-01

    Full Text Available Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways. Here, we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions (epistasis among these factors. Specifically, we developed an automated competition-based assay for chronological lifespan, defined as stationary-phase survival of yeast populations, and used it to phenotype over 5,600 single- or double-gene knockouts at unprecedented quantitative resolution. We found that 14% of the viable yeast mutant strains were affected in their stationary-phase survival; the extent of true-positive chronological lifespan factors was estimated by accounting for the effects of culture aeration and adaptive regrowth. We show that lifespan extension by dietary restriction depends on the Swr1 histone-exchange complex and that a functional link between autophagy and the lipid-homeostasis factor Arv1 has an impact on cellular lifespan. Importantly, we describe the first genetic interaction network based on aging phenotypes, which successfully recapitulated the core-autophagy machinery and confirmed a role of the human tumor suppressor PTEN homologue in yeast lifespan and phosphatidylinositol phosphate metabolism. Our quantitative analysis of longevity factors and their genetic interactions provides insights into the gene-network interactions of aging cells.

  4. High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions.

    Science.gov (United States)

    Garay, Erika; Campos, Sergio E; González de la Cruz, Jorge; Gaspar, Ana P; Jinich, Adrian; Deluna, Alexander

    2014-02-01

    Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways. Here, we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions (epistasis) among these factors. Specifically, we developed an automated competition-based assay for chronological lifespan, defined as stationary-phase survival of yeast populations, and used it to phenotype over 5,600 single- or double-gene knockouts at unprecedented quantitative resolution. We found that 14% of the viable yeast mutant strains were affected in their stationary-phase survival; the extent of true-positive chronological lifespan factors was estimated by accounting for the effects of culture aeration and adaptive regrowth. We show that lifespan extension by dietary restriction depends on the Swr1 histone-exchange complex and that a functional link between autophagy and the lipid-homeostasis factor Arv1 has an impact on cellular lifespan. Importantly, we describe the first genetic interaction network based on aging phenotypes, which successfully recapitulated the core-autophagy machinery and confirmed a role of the human tumor suppressor PTEN homologue in yeast lifespan and phosphatidylinositol phosphate metabolism. Our quantitative analysis of longevity factors and their genetic interactions provides insights into the gene-network interactions of aging cells.

  5. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef.

    Science.gov (United States)

    van Oppen, Madeleine J H; Lukoschek, Vimoksalehi; Berkelmans, Ray; Peplow, Lesa M; Jones, Alison M

    2015-01-01

    Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes

  6. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef

    Directory of Open Access Journals (Sweden)

    Madeleine J.H. van Oppen

    2015-07-01

    Full Text Available Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative

  7. High genetic diversity in the coat protein and 3' untranslated regions among geographical isolates of Cardamom mosaic virus from south India

    Indian Academy of Sciences (India)

    T Jacob; T Jebasingh; M N Venugopal; R Usha

    2003-09-01

    A survey was conducted to study the biological and genetic diversity of Cardamom mosaic virus (CdMV) that causes the most widespread disease in the cardamom growing area in the Western Ghats of south India. Six distinct subgroups were derived based on their symptomatology and host range from the sixty isolates collected. The serological variability between the virus isolates was analysed by ELISA and Western blotting. The 3′ terminal region consisting of the coat protein (CP) coding sequence and 3′ untranslated region (3′UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3′UTR, making CdMV one of the highly variable members of Potyviridae. The possible occurrence of recombination between the isolates and the movement of the virus in the cardamom tract of south India are discussed.

  8. Population genetic structure and diversity of high value vulnerable medicinal plant Acorus calamus in India using RAPD and chloroplast microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    H. S. Ginwal; Neha Mittal; Arvind Tomar; V. K. Varshney

    2011-01-01

    Acorus calamus is a highly valued medicinal plant with globaldistribution used in several drugs of health care systems. We evaluatedthe genetic diversity and population structure of 50 populations of A.calamus from different geographical regions in India through RAPD andchloroplast microsatellite markers. From the total screened 82 RAPDprimers and 18 cpSSR primers, 10 RAPD and nine cpSSRs were foundpolymorphic. The selected 10 RAPD primers produced a total of 96reproducible bands, out of which 65 were polymorphic (67.70%).Whereas, the selected nine cpSSR markers produced 26 alleles and all ofthem were polymorphic. The mean genetic diversity (H) among popula-tions using RAPD (H= 0.263) and cpSSR (H=0.530) markers washigher in comparison to the mean genetic diversity within populations.Mean coefficient of gene differentiation (G) between the populationswas also high for both RAPD (G=0.830) and cpSSR markers (G=0.735), whereas the estimated gene flow was very low for RAPD (Nm =0.102) and for cpSSR (Nm = 0.179). AMOVA analysis revealed thatmore genetic variation resided among the populations than within popu-lations. Significant differences (p < 0.001) were observed between thepopulations and individuals within the populations. Cluster analysis ofRAPD and cpSSR data using UPGMA algorithm based on Nei's geneticsimilarity matrix placed the 50 populations into two main clusters. Theimplication of the results of this study in devising strategy for conserva-tion of A. Calamus is discussed.

  9. Genetic evaluation of seeds of highly endangered Pinus uliginosa Neumann from Węgliniec reserve for ex-situ conservation program

    Directory of Open Access Journals (Sweden)

    Andrzej Lewandowski

    2011-01-01

    Full Text Available Peat-bog pine Pinus uliginosa Neumann has become extinct or rare in many parts of Europe. We have investigated the levels of genetic variation and inbreeding in seeds collected from a highly endangered reserve of this species in Poland, using allozymes as genetic markers. Generally, a high level of genetic variation was observed. The mean expected heterozygosity was 0.376, while average (Na and effective (Ne numbers of alleles per locus were 2.45 and 1.67, respectively. Nevertheless, we have detected relatively low levels of outcrossing, and potential biparental inbreeding. The population-wide multilocus outcrossing rate was estimated to be 0.706 (±0.091, while the minimum variance mean of single-locus estimates was distinctly lower (ts=0.611. The estimates of outcrossing calculated for individual trees ranged widely from 0.051 to 1.017, indicating the complexity of outcrossing patterns. The investigated population of P. uliginasa from Węgliniec is small and surrounded by extensive forest stands of P. sylvestris. Our three-year records of phenological observations demonstrated that flowering periods for P. uliginosa and P. sylvestris overlap, allowing for cross-pollination. The possibility of P. uliginosa pollination by P. sylvestris creates a potential danger of genetic erosion of the P. uliginosa gene pool. Nonetheless, based on a species specific cpDNA marker we have found that among 533 seedlings of P. uliginosa there were only six seedlings carrying cpDNA marker specific for P. sylvestris, indicating that such hybridization seems to be rare.

  10. Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

    Science.gov (United States)

    Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P

    1999-12-01

    Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical t