Thomas Meredith M
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
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.
Hunter, M.E.; Auil-Gomez, N. E.; Tucker, K.P.; Bonde, R.K.; Powell, J.; McGuire, P.M.
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.
Rina Girard Kaminsky; Steven K Ault; Phillip Castillo; Kenton Serrano; Guillermo Troya
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.
Lechleitner, Franziska A.; Breitenbach, Sebastian F. M.; McIntyre, Cameron; Asmerom, Yemane; Prufer, Keith M.; Polyak, Victor; Culleton, Brendan J.; Kennett, Douglas J.; Eglinton, Timothy I.; Baldini, James U. L.
Speleothem 14C has recently emerged as a potentially powerful proxy for climate reconstruction. Several studies have highlighted the link between karst hydrology and speleothem 14C content, and a number of possible causes for this relationship have been proposed, such as dripwater flow dynamics in the karst and changes in soil organic matter (SOM) turnover time (e.g. Griffiths et al., 2012). Here we present a high resolution 14C record for a stalagmite (YOK-I) from Yok Balum cave in southern Belize, Central America. YOK-I grew continuously over the last 2000 years, and has been dated very precisely with the U-Th method (40 dates, mean uncertainty ventilation and hydrologic resilience to seismic activity, Journal of Cave and Karst Studies
Vajda, Vivi; Ocampo, Adriana; Ferrow, Embaie;
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...
Traci Kuratomi; Dougal Martin; Jorge Ducci; Alfredo Rihm; María del Rosario Navia Díaz; Javier Grau
In the last decade, Belize has seen major improvements in access to water, but it is behind in achieving universal access to improved sanitation facilities. Belize has also made progress in terms of the disposal of solid waste in the central and western regions, including in the largest urban area, Belize City. Despite these developments, there is a need to further improve the performance of these sectors, especially in terms of wastewater collection and treatment in urban areas throughout th...
Parham, Leda; de Rivera, Ivette Lorenzana; Murillo, Wendy; Naver, Lars; Largaespada, Natalia; Albert, Jan; Karlsson, Annika C
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.
The ancient Maya site of Lamanai in northern Belize is unusual because it was not abandoned like many sites in the ninth century and flourished in the subsequent Postclassic period (AD 900–1450). Lamanai was the centre for an elaborate ceramic style and more than three decades of research at the site have produced an outstanding collection of highly decorated vessels. What do the Postclassic ceramics of Lamanai tell us about life at the site in the Postclassic, and about the Postclassic Maya ...
Full Text Available The ancient Maya site of Lamanai in northern Belize is unusual because it was not abandoned like many sites in the ninth century and flourished in the subsequent Postclassic period (AD 900–1450. Lamanai was the centre for an elaborate ceramic style and more than three decades of research at the site have produced an outstanding collection of highly decorated vessels. What do the Postclassic ceramics of Lamanai tell us about life at the site in the Postclassic, and about the Postclassic Maya world?
Belize is a well-forested area of 22,960 square kilometers. Its capital is Belmopan. The country is generally flat north of the capital city. The flat, swampy Caribbean Coast of Belize gradually ascends to the low peaks of the Maya and Cockscomb Mountains (elevation to 1,120 meters). The area south of the Maya Mountains is much more rugged than the area to the north. The country is drained by seventeen rivers, the chief ones being the Belize, Hondo, New, Sibun, Monkey and Moho. There is 'hurricane danger in the July-October period. Belize has reportedly been surveyed by Gamma Ray Spectrometer for phosphates which probably would have contained sufficient uranium to be detectable. The survey traversed about 1,000 line kms along major north-south and east-west roads as well as many secondary roads and trails. The uranium readings ranged from 0. to 9.9 ppm with a uranium content of 1-2 ppm in the limestone areas and 2-7 ppm in the alluvium-covered areas. The U/Th ratio varied from 0.11 to 1.65. A recent traverse across the Mountain Pine Ridge batholith gave one reading as high as 36 ppm but the average was about 9-10 ppm. The upper 1000-3000 feet of core and cuttings from nine deep oil wells were checked for phosphates and uranium. Most of the core and cuttings were almost pure limestones. The P203 content was less than 0.05 percent and no uranium was detected. It is very doubtful that any significant uranium occurrences will be found in the sediments surrounding the Maya Mountain uplift. However, there is a slight chance that uranium might occur in the granites and pegmatites in the Maya Mountains. The potential of Belize is estimated to be in the less than 1.000 tonnes uranium range, considering the restricted range, of geologic environments encountered there
Kangas, Patrick; Shave, Mary; Shave, Paul
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.
Gischler, Eberhard; Hudson, J. Harold
Previously, knowledge of the Holocene development of the Belize Barrier Reef (BBR)—the largest reef system in the Atlantic Ocean—was limited to one location (Carrie Bow Cay). We present new data from 11 rotary drill cores taken at 9 locations and 36 radiometric ages that indicate that the BBR was established from >8.26 to 6.68 ky BP on Pleistocene reef limestones, presumably deposited during oxygen isotope stage 5. The nonsynchronous start of Holocene reef growth was a consequence of variation in elevation of antecedent topography, largely controlled by underlying NNE-trending structures. From north to south, Pleistocene elevation decreases along these structural trends, probably reflecting differential subsidence and variations in karst topography. Reef anatomy is characterized by three facies. In order of decreasing abundance, these facies are represented by corals (mainly Acropora palmata and members of the Montastraea annularis group), by unconsolidated sand and rubble, and by well-cemented coral grainstones-rudstones. Holocene reef accumulation rates average 3.25 m/ky. The degree of reef consolidation is negatively correlated with Holocene thicknesses, indicating that slowly growing reefs are better cemented than fast growing ones. We present a Holocene sea-level curve for Belize based on 36 dates from this study and 33 dates from our previous studies in the area.
Cathro, Helen P; Loya, Theresa; Dominguez, Frederick; Howe, Susan L; Howell, Renee; Orndorff, Kyle; Moreno, Jessica; Mendez, Elena; Fung, Po Chu; Beer, Natalie L; Allen, Peter; Sosa, Alba M; Gurka, Kelly K; Stoler, Mark H; Frierson, Henry F
Cervical carcinoma is the most common cancer among Belizean women; however, data regarding the frequency of human papillomavirus (HPV) genotypes and their association with cervical cancer are nonexistent. We therefore included HPV genotyping as part of a week-long cervical cancer screening campaign conducted in Belize City in 2007. Conventional Papanicolaou smears with Hybrid Capture (HC) 2 HPV testing were performed on 463 women. All HC2-positive samples were genotyped using a developmental GP5+/GP6+ polymerase chain reaction-coupled Luminex assay for 2 low-risk and 18 high-risk HPV types. The prevalence of high-risk HPV was 15.6% in the total population, 10.1% in those with normal cytologic findings, and 93.3% in women with a high-grade squamous intraepithelial lesion. Of patients with HPV infections, 35% had multiple types (5.4% of the total group). Of all women and of women with normal cytologic findings, 5.2% and 2.8%, respectively, had HPV16 or 18. For all women, HPV16, 18, 56, and 52 were present in decreasing order of frequency. HPV11 was present in only one patient, and none had HPV6. HPV16 was found in 47% of high-grade squamous epithelial lesions; however, no case of HSIL had HPV18 or 45. HPV35 and HPV58 were the next most common types in high-grade squamous intraepithelial lesion, each occurring in 20% of cases of high-grade squamous intraepithelial lesion, followed by HPV31 in 13.3%. Although women younger than 25 years old were underrepresented, these data suggest that the HPV profile of this cohort of Belizean women differs somewhat from that in the region. In addition, these data are of importance with regard to the development of HPV vaccines that will be used in less developed countries, where care should be taken not to implement vaccination at the cost of basic screening and diagnostic services. PMID:19299000
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
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.
Lowland savannas occupy almost 10% of the total land area of Belize, comprising landscapes with high ecological and economical value. The most distinctive tree of the Belizean savanna, the Caribbean pine (Pinus caribaea var. hondurensis), is valuable not only as a timber resource, but also in forming natural habitats for the local endangered species. However, degradation by frequent fires, anthropogenic pressures and climate change often convert gallery pine forests and dense tree savannas (s...
Rainwater, T R; Platt, S G; Robbins, R G; McMurry, S T
Parasitism of crocodilians by ticks has rarely been reported, and to our knowledge only seven published accounts exist. On 3 July 1999, we collected four ticks from a subadult Morelet's crocodile (Crocodylus moreletii) captured in northern Belize. These were identified as Amblyomma dissimile (one female), and Amblyomma sp. (two nymphs, one larva). The crocodile was captured on land approximately 100 m from water, and all four ticks were attached to loose skin on the lateral surface of the tail. Crocodilians are most susceptible to terrestrial ectoparasites, including ticks, during overland movements. However, most such movements occur in response to drought, when tick questing activity is suppressed, which likely accounts for the small numbers of tick specimens recorded from crocodilians and the absence of any noticeable impact of parasitism on host fitness. PMID:11763751
Rainwater, T R; McMurry, S T; Platt, S G
Two Morelet's crocodiles (Crocodylus moreletii) captured on 21 March 1997 and 20 April 1998 in the New River system, Belize exhibited ectromelia of one forelimb. External and radiograph examination appears to indicate limb agenesis of unknown etiology, as there is no apparent scarring or skeletal trauma. These two individuals represent the only cases of missing limbs from 642 individuals captured in this study and to our knowledge, the first reported cases in Morelet's crocodile. Several factors including age and diet of the reproducing female, extremes in nest conditions (egg incubation temperature and humidity), and exposure to environmental contaminants can cause developmental abnormalities in crocodilians and may have contributed to the condition observed in these animals. Survival rates for hatchling crocodilians are generally low, and embryonic malformations such as ectromelia may constitute an added disadvantage to survival. However, both individuals examined in this study were vigorous and appeared in good condition. PMID:10073362
Chicas, S. D.; Omine, K.; Arevalo, B.; Ford, J. B.; Sugimura, K.
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.
Schnedl, Jakob; Auer, Herbert; Fischer, Marcellus; Tomaso, Herbert; Pustelnik, Tom; Mooseder, Gerhard
Cutaneous leishmaniasis of the New World, in particular when caused by Leishmania (L.) braziliensis, harbours the risk of lymphogenic as well as hematogenic dissemination. This may result in mucocutaneous leishmaniasis causing severe destruction of orofacial structures. Dissemination may occur years after the disappearance of the skin lesions. In contrast, cutaneous leishmaniasis of the old world, is typically restricted to the site of inoculation. Therefore, a conservative diagnostic and therapeutic approach is usually sufficient. Infections acquired in the new world should be treated systemically, if infection with Leishmania (Viannia) braziliensis complex cannot be excluded. Here we report on three Austrian soldiers, who, weeks after having participated in an international jungle patrol course in Belize, presented themselves with multiple ulcers on the upper limbs. Diagnosis of cutaneous leishmaniasis was made based upon histological evaluation of biopsies taken from several ulcers revealing the presence of leishmanial bodies, and detection of amastigote leishmania in smears of material obtained from the ulcers. As species phenotyping could not be performed, infection with L. brasiliensis as well as progression into a mucocutaneous form were possible, demanding systemic therapy. Several treatment options including local cryotherapy with liquid nitrogen, paromomycin (Humatis Pulvis, Parke-Davis) 15% topically or oral fluconazole (Diflucan, Pfizer) 200 mg/d were applied, but showed no effect. Hence, a systemic therapy with intravenous pentamidine (Pentacarinat, Gerot), three times in total, 3-4 mg/kg body weight each, led to a complete regression of the lesions within four weeks. PMID:17987367
Wu, T H; Rainwater, T R; Platt, S G; McMurry, S T; Anderson, T A
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. PMID:10705543
Emma Näslund-Hadley; Haydée Alonzo; Dougal Martin
Belize is paying a lot for education but getting little. More youth are outside the school system than in it and many fail to make the transition to the workforce. More and more youth drop out of school and become involved in gang activities. Action is needed if Belize is not to lose a whole generation of youth. This document discusses the current situation of the Belizean education sector and its progress over the last 10 years, its relative performance compared with other countries in the r...
Sachs, Paige; Diaz Rodriguez, Gloria Alicia; Briceno, Ireneo; King, Russell; Achee, Nicole L; Grieco, John P
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.
Wu, T H; Rainwater, T R; Platt, S G; McMurry, S T; Anderson, T A
Organochlorine (OC) residues were recently detected in nonviable Morelet's crocodile (Crocodylus moreletii) eggs from northern Belize. To further the assessment of contaminant exposure in Belizean crocodiles, nonviable Morelet's crocodile eggs (n = 11) from southern Belize and American crocodile (Crocodylus acutus) eggs (n = 12) from the coastal zones of Belize were screened for 20 OCs. Results indicated p,p-DDE to be the most prevalent OC (96% occurrence) in eggs examined, with concentrations ranging from 5 to 372 ng/g. These concentrations are similar to those observed in crocodile eggs (10-180 ng/g) from northern Belize. A general trend toward higher DDE concentrations in Morelet's crocodile eggs (mean = 103 ppb) compared with American crocodile eggs (mean = 31 ppb) was observed. However, this trend may be due to site-specific contamination rather than differences in interspecific susceptibility to chemical exposure. Other OCs detected in crocodile eggs included the parent compound, p,p-DDT, and its metabolite, p, p-DDD. PMID:11141295
Integrated coastal and ocean management requires transparent and accessible approaches for understanding the influence of human activities on marine environments. Here we introduce a model for assessing the combined risk to habitats from multiple ocean uses. We apply the model to coral reefs, mangrove forests and seagrass beds in Belize to inform the design of the country’s first Integrated Coastal Zone Management (ICZM) Plan. Based on extensive stakeholder engagement, review of existing legislation and data collected from diverse sources, we map the current distribution of coastal and ocean activities and develop three scenarios for zoning these activities in the future. We then estimate ecosystem risk under the current and three future scenarios. Current levels of risk vary spatially among the nine coastal planning regions in Belize. Empirical tests of the model are strong—three-quarters of the measured data for coral reef health lie within the 95% confidence interval of interpolated model data and 79% of the predicted mangrove occurrences are associated with observed responses. The future scenario that harmonizes conservation and development goals results in a 20% reduction in the area of high-risk habitat compared to the current scenario, while increasing the extent of several ocean uses. Our results are a component of the ICZM Plan for Belize that will undergo review by the national legislature in 2015. This application of our model to marine spatial planning in Belize illustrates an approach that can be used broadly by coastal and ocean planners to assess risk to habitats under current and future management scenarios. (letter)
A total of 1316 individuals were studied in seven villages in Belize, Central America. This represented 92% of the area population aged over 18. Generally, they were members of three ethnic groups--Maya, Spanish, and Creole. The systolic and diastolic IV and V blood pressures were recorded using standardised procedure. Significant differences in blood pressure, weight, and obesity were found between ethnic groups in both sexes, Creoles having higher means than the other groups. Significant re...
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.
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.
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.
Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J
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. PMID:26974968
Michael K Steinberg
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.
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
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. PMID:17182086
Rainwater, Thomas R. [Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 (United States)]. E-mail: email@example.com; 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)
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.
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
Nunez, Elvis Enrique; Pringle, Rose M.; Showalter, Kevin Tyler
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.
Describes set of specific steps (procedural knowledge) used when solving monohybrid/dihybrid cross problems and extent to which students could justify execution of each step in terms of their conceptual knowledge of genetics and meiosis. Implications for genetics instruction are discussed. (JN)
Rural tropical ecosystems are subject to many traditional land uses that employ the indigenous karst resources: rock, water, soil, vegetation, and wildlife. Individual resource pressures often are subtle, but their combined impact can precipitate instability in the tropical karst environment, potentially resulting in disruption of food, water, and fuel supplies. The karst of central Belize was used intensively for some six centuries by Maya farmers, but between the 10th and 19th centuries AD most of it reverted to secondary forest. Commercial logging dominated the 19th and early 20th centuries, followed by the expansion of subsistence and commercial agriculture after 1945. In the 1980s resource use has accelerated as population and other pressures increase. Much karst remains forested, but there is increasing clearance for agricultural uses, particularly for citrus cultivation and small-scale mixed agriculture. Soil depletion has begun to occur, water resources are increasingly taxed, and some wildlife is threatened by habitat destruction and increased hunting. Lime production for the citrus industry has promoted quarrying, water extraction, and fuelwood use. Environmental stresses currently do not exceed the threshold of instability, but the rapidly developing rural economy warrants careful monitoring of resource pressures.
Rainwater, T R; Adair, B M; Platt, S G; Anderson, T A; Cobb, G P; McMurry, S T
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. PMID:11910460
... 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...
Frappier, A.; Sahagian, D.
The high winds, storm surge, and extreme precipitation produced by landfalling tropical cyclones (hurricanes and tropical storms) generate some of the most deadly and destructive natural disasters faced by coastal populations. Stakeholders such as coastal planners and developers, property owners, emergency planners, and (re)insurers are concerned about future risk from the most devastating events, particularly because significant changes in climatic boundary conditions have been projected for this century. However, historical tropical cyclone records are not sufficient to address the sensitivity of hurricane intensity to projected changes, and modeling exercises have as yet been unable to settle the debate. Consequently, paleotempestologists have turned to the geologic record for more information about past hurricane activity that could be used to improve forward models. Toward that end, we have developed a new proxy for individual tropical cyclone rainfall events using very high-resolution δ 18O analyses of speleothem calcite. This proxy is based on the depleted isotopic signature of tropical cyclone rainfall compared to other summer season meteoric waters. We applied recent developments in microsampling techniques to a rapidly growing speleothem from Belize, Central America. The resulting record (20 micron sampling interval, yielding ~weekly temporal resolution) allowed us to detect individual, historical tropical cyclone events over the last three decades. The speleothem δ 18O paleotempestology proxy facilitates very accurate estimates of the time between tropical cyclone events: the proxy was able to resolve two hurricanes that struck Belize in the same year. The recurrence interval (RI) we estimated using the speleothem hurricane record agrees closely with the RI published for the same period by the Belize Meteorological Service. Preliminary work indicates that the δ 18O storm signal preserved in speleothem calcite carries some information about the local
Weller, Errin Teresa
This dissertation presents the results of the remote sensing and artifact re-analysis of the archaeological site of Barton Ramie, Belize. The site was the focus of Dr. Gordon R. Willey's innovative archaeological program in the Belize River Valley to study ancient Maya settlement, environment, and population in 1954-1956. Through the use of artifact analysis combined with the examination of high-resolution Worldview-1 imagery and a Geographic Information System (GIS)-based spatial analysis, I consider how the inhabitants of Barton Ramie forged community functioning and identity. I focus on the range of intra-site diversity including differential access to labor, goods, land, and the activities evidenced in households and non-domestic structures. Using a community theory framework, emphasizing the many practices that tied the community together, I underscore the variability expressed in architectural elaboration, sumptuary goods, ritual, and specialization. That variability has profound implications for understanding community diversity and economic, social, and ritual functioning. High-resolution panchromatic Worldview-1 satellite imagery successfully detected the remains of Barton Ramie settlement. Surface archaeology has been largely destroyed due to extensive agricultural activities in recent decades. GIS analysis and ground-truthing determined that mound size is the primary factor enabling detection of ancient features. The confirmation of features in an intensively plowed environment has implications including settlement, survey, and population for other disturbed environments. I argue that the Barton Ramie community developed from a complex interaction of networks and practices. These include activities at the household level, articulation between households to form sub-communities (or neighborhoods), and a larger imagined community of the Barton Ramie polity. Individual households articulated to form seven discrete sub-communities, bounded by landscape
Pepper, Christopher B; Rainwater, Thomas R; Platt, Steven G; Dever, Jennifer A; Anderson, Todd A; McMurry, Scott T
Recent studies examined the utility of the chorioallantoic membrane (CAM) as a nonlethal, noninvasive indicator of environmental contaminant exposure in oviparous wildlife. The CAM is a highly vascularized extraembryonic membrane that functions as a site for respiration, nutrient transport, and waste storage during embryonic development. After hatching, the CAM is usually discarded with the eggshell and can be used for chemical residue analysis. Chorioallantoic membranes have been used successfully to examine contaminant exposure and predict chemical concentrations in multiple species of birds and reptiles. In this study, we examined organochlorine (OC) pesticide concentrations in CAMs from eggs of Morelet's crocodiles (Crocodylus moreletii) from northern Belize. Multiple OCs were detected in crocodile CAMs, including aldrin, dieldrin, endrin, dichlorodiphenyltrichloroethane, dichlorodiphenyldichloroethane, dichlorodiphenyldichloroethylene (DDE), heptachlor, lindane, and methoxychlor. Number and concentrations of OC compounds in CAMs were variable. The most prevalent contaminant detected was DDE, which occurred in 69% of CAMs, with concentrations ranging from 0.3 parts per billion (ppb) to 17.0 ppb. The OC burdens in crocodile CAMs confirm contamination of eggs and suggest exposure in embryos and maternal females. These results further support the use of CAMs as qualitative indicators of OC exposure in oviparous wildlife. The efficacy of this sampling technique in the field will depend on the logistics and cost associated with CAM collection and the specific life history traits of the wildlife species. PMID:15465717
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.
Souza-Firmino, T S; Alevi, K C C; Pereira, L L V; Souza, E R S; Júnior, F C S; Banho, C A; Carmo, G O; Itoyama, M M
The stink bug Pachycoris torridus is listed among the most polyphagous insects in the world and it is a major pest of diverse crops, in particular the physic nut Jatropha curcas, which is used as a raw material for biodiesel production. A peculiar characteristic of this species is its high phenotypic variability, a characteristic that makes identification difficult: P. torridus has been described as a new species eight times. Thus, to aid in identification, genetic characterization of this insect was performed. We verified that, due to the high genetic variability of P. torridus, several genetic patterns exist that result in the same phenotype. PMID:26600488
Müntz, K; Christov, V; Saalbach, G; Saalbach, I; Waddell, D; Pickardt, T; Schieder, O; Wüstenhagen, T
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.
International Monetary Fund
Belizeâ€™s economy is projected to decelerate in 2009 owing to the global downturn. Real GDP growth is projected at 1 percent, reflecting the impact of declining tourism, remittances, and foreign direct investment inflows. Executive Directors have welcomed the broadly favorable economic performance in 2008, and have commended the authoritiesâ€™ commitment to pursue sound macroeconomic and financial sector policies to manage near-term risks. Directors have also emphasized that strong macroecon...
Schmidt, Sabrina; Saxenhofer, Moritz; Drewes, Stephan; Schlegel, Mathias; Wanka, Konrad M; Frank, Raphael; Klimpel, Sven; von Blanckenhagen, Felix; Maaz, Denny; Herden, Christiane; Freise, Jona; Wolf, Ronny; Stubbe, Michael; Borkenhagen, Peter; Ansorge, Hermann; Eccard, Jana A; Lang, Johannes; Jourdain, Elsa; Jacob, Jens; Marianneau, Philippe; Heckel, Gerald; Ulrich, Rainer G
Tula virus (TULV) is a vole-associated hantavirus with low or no pathogenicity to humans. In the present study, 686 common voles (Microtus arvalis), 249 field voles (Microtus agrestis) and 30 water voles (Arvicola spec.) were collected at 79 sites in Germany, Luxembourg and France and screened by RT-PCR and TULV-IgG ELISA. TULV-specific RNA and/or antibodies were detected at 43 of the sites, demonstrating a geographically widespread distribution of the virus in the studied area. The TULV prevalence in common voles (16.7 %) was higher than that in field voles (9.2 %) and water voles (10.0 %). Time series data at ten trapping sites showed evidence of a lasting presence of TULV RNA within common vole populations for up to 34 months, although usually at low prevalence. Phylogenetic analysis demonstrated a strong genetic structuring of TULV sequences according to geography and independent of the rodent species, confirming the common vole as the preferential host, with spillover infections to co-occurring field and water voles. TULV phylogenetic clades showed a general association with evolutionary lineages in the common vole as assessed by mitochondrial DNA sequences on a large geographical scale, but with local-scale discrepancies in the contact areas. PMID:26831932
Petersen, H.I.; Holland, B.; Nytoft, H.P.;
This study reviews the stratigraphy and the poorly documented petroleum geology of the Belize-Guatemala area in northern Central America. Guatemala is divided by the east-west trending La Libertad arch into the North and South Petén Basins. The arch is the westward continuation of the Maya...
P.P.A.M. van Thiel; J.E. Zeegelaar; T. van Gool; W.R. Faber; P.A. Kager
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
James M. Conlon
This paper provides an example of the use of corporate group analysis at the major ceremonial centre of Baking Pot, and uses comparative data from the site core of Baking Pot, other major centres in the upper Belize Valley, and various other sources throughout the Maya lowlands.
James M. Conlon
Full Text Available This paper provides an example of the use of corporate group analysis at the major ceremonial centre of Baking Pot, and uses comparative data from the site core of Baking Pot, other major centres in the upper Belize Valley, and various other sources throughout the Maya lowlands.
García-Morales, Alma Estrella; Elías-Gutiérrez, Manuel
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. PMID:19069767
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.
Link, J M; Anjos, J C; Bediaga, I; Castromonte, C; Göbel, C; Machado, A A; Magnin, J; Massafferri, A; De Miranda, J M; Pepe, I M; Polycarpo, E; Dos Reis, A C; Carrillo, S; Casimiro, E; Cuautle, E; Sánchez-Hernández, A; Uribe, C; Vázquez, F; Agostino, L; Cinquini, L; Cumalat, J P; O'Reilly, B; Segoni, I; Stenson, K; Butler, J N; Cheung, H W K; Chiodini, G; Gaines, I; Garbincius, P H; Garren, L A; Gottschalk, E; Kasper, P H; Kreymer, A E; Kutschke, R; Wang, M; Benussi, L; Bertani, M; Bianco, S; Fabbri, Franco Luigi; Pacetti, S; Zallo, A; Reyes, M; Cawlfield, C; Kim, D Y; Rahimi, A; Wiss, J; Gardner, R; Kryemadhi, A; Chung, Y S; Kang, J S; Ko, B R; Kwak, J W; Lee, K B; Cho, K; Park, H; Alimonti, G; Barberis, S; Boschini, M; Cerutti, A; D'Angelo, P; Di Corato, M; Dini, P; Edera, L; Erba, S; Inzani, P; Leveraro, F; Malvezzi, S; Menasce, D; Mezzadri, M; Moroni, L; Pedrini, D; Pontoglio, C; Prelz, F; Rovere, M; Sala, S; Davenport, T F; Arena, V; Boca, G; Bonomi, G; Gianini, G; Liguori, G; Lopes-Pegna, D; Merlo, M M; Pantea, D; Ratti, S P; Riccardi, C; Vitulo, P; Hernández, H; López, A M; Méndez, H; Paris, A; Quinones, J; Ramírez, J E; Zhang, Y; Wilson, J R; Handler, T; Mitchell, R; Engh, D; Hosack, M; Johns, W E; Luiggi, E; Moore, J E; Nehring, M; Sheldon, P D; Vaandering, E W; Webster, M; Sheaff, M
We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.
Kenrick W. Williams
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.
Moss, N; Stone, M C; Smith, J B
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)
Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU
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].
Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong;
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...
Lee, R.Y.; Porubsky, W.P.; Feller, Ilka C.; McKee, K.L.; Joye, S.B.
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
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.
Vahidi, S M F; Faruque, M O; Falahati Anbaran, M; Afraz, F; Mousavi, S M; Boettcher, P; Joost, S; Han, J L; Colli, L; Periasamy, K; Negrini, R; Ajmone-Marsan, P
Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7-22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72-0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed. PMID:26953226
Townsend, Joseph E.; Courtney, Travis A.; Aichelman, Hannah E.; Davies, Sarah W.; Lima, Fernando P.; Castillo, Karl D.
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
Baumann, Justin H; Townsend, Joseph E; Courtney, Travis A; Aichelman, Hannah E; Davies, Sarah W; Lima, Fernando P; Castillo, Karl D
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
Pope, Kevin; Masuoka, Penny; Rejmankova, Eliska; Grieco, John; Johnson, Sarah; Roberts, Donald
The distribution of Anopheles mosquito habitats and land use in northern Belize is examined with satellite data. -A land cover classification based on multispectral SPOT and multitemporal Radarsat images identified eleven land cover classes, including agricultural, forest, and marsh types. Two of the land cover types, Typha domingensis marsh and flooded forest, are Anopheles vestitipennis larval habitats. Eleocharis spp. marsh is the larval habitat for Anopheles albimanus. Geographic Information Systems (GIS) analyses of land cover demonstrate that the amount of T-ha domingensis in a marsh is positively correlated with the amount of agricultural land in the adjacent upland, and negatively correlated with the amount of adjacent forest. This finding is consistent with the hypothesis that nutrient (phosphorus) runoff from agricultural lands is causing an expansion of Typha domingensis in northern Belize. This expansion of Anopheles vestitipennis larval habitat may in turn cause an increase in malaria risk in the region.
Healy, Paul F.; Helmke, Christophe G.B.; Awe, Jaime J.;
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....
Inter-American Development Bank (IDB)
This documents contains Disaster Risk and Disaster Management indicators for Belize calculated according to the methodology developed by the Bank. This System of Indicators had three specific objectives: i) improvement in the use and presentation of information on risk. This assists policymakers in identifying investment priorities to reduce risk (such as prevention and mitigation measures), and directs the post disaster recovery process; ii) to provide a way to measure key elements of vulner...
Dillon, A.; Kelly, M J
We used remote cameras to obtain information on an elusive species and to examine the effects of different camera trapping methodologies on abundance estimates. We determined activity pattern, trail use, trap success, and density of ocelot Leopardus pardalis in seven camera-trap surveys across two habitat types in western Belize: tropical broad-leaf rainforest and tropical pine forest. Ocelots in the rainforest were active mostly at night, in particular immediately after sunset, and they trav...
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 ...
Christine White; Jay Maxwell; Alexis Dolphin; Jocelyn Williams; Fred Longstaffe
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 deg...
Pope, Kevin; Masuoka, Penny; Rejmankova, Eliska; Grieco, John; Johnson, Sarah; Roberts, Donald
Satellite imagery of northern Belize is used to examine the distribution of land use and breeding habitats of the malaria vector the Anopheles mosquito. A land cover classification based on multispectral SPOT and multitemporal Radarsat images identified eleven land cover classes, including agricultural, forest, and marsh types. Two of the land cover types, Typha domingensis marsh and flooded forest, are Anopheles vestitipennis larval habitats, and one, Eleocharis spp. marsh, is the larval habitat for Anopheles albimanus. Geographic Information Systems (GIS) analyses of land cover demonstrate that the amount of Typha domingensis in a marsh is positively correlated with the amount of agricultural land in the adjacent upland, and negatively correlated with the amount of adjacent forest. This finding is consistent with the hypothesis that nutrient (phosphorus) runoff from agricultural lands is causing an expansion of Typha domingensis in northern Belize. Thus, land use induced expansion of Anopheles vestitipennis larval habitat is potentially increasing malaria risk in Belize, and in other regions where Anopheles vestitipennis is a major malaria vector.
Background. Studies of individuals at high genetic risk (HR) of schizophrenia have shown subtle deficits in the domains of executive functions. However, executive abilities also depend on working memory, which is one of the most prominent impairments associated with vulnerability to schizophrenia. The present study examines whether working memory deficits could account for impairments usually attributed to executive dysfunctions. Methods. A total of 100 HR and 27 control participants were ...
Yuan HUANG; Chang-Qin ZHANG; De-Zhu LI
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.
... 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 ...
Beach, T.; Luzzadder-Beach, S.; Krause, S.; Doyle, C.
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.
Blum K et al
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
Ivo D Dinov
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.
Kareem M. Usher
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.
Analysis of stable isotopes and major ions in groundwater and surface waters in Belize, Central America was carried out to identify processes that may affect drinking water quality. Belize has a subtropical rainforest/savannah climate with a varied landscape composed predominantly of carbonate rocks and clastic sediments. Stable oxygen (δ18O) and hydrogen (δD) isotope ratios for surface and groundwater have a similar range and show high d-excess (10-40.8%o). The high d-excess in water samples suggest secondary continental vapor flux mixing with incoming vapor from the Caribbean Sea. Model calculations indicate that moisture derived from continental evaporation contributes 13% to overhead vapor load. In surface and groundwater, concentrations of dissolved inorganic carbon (DIC) ranged from 5.4 to 112.9 mg C/l and δ13CDIC ranged from -7.4 to -17.4%o. SO42, Ca2+ and Mg2+ in the water samples ranged from 2-163, 2-6593 and 2-90 mg/l, respectively. The DIC and δ13CDIC indicate both open and closed system carbonate evolution. Combined δ13CDIC and Ca2+, Mg2+, and SO42- suggest additional groundwater evolution by gypsum dissolution and calcite precipitation. The high SO42-content of some water samples indicates regional geologic control on water quality. Similarity in the range of δ18O, δD and δ13CDIC for surface waters and groundwater used for drinking water supply is probably due to high hydraulic conductivities of the karstic aquifers. The results of this study indicate rapid recharge of groundwater aquifers, groundwater influence on surface water chemistry and the potential of surface water to impact groundwater quality and vise versa
Full Text Available The last decade has seen considerable advances in our understanding of the genetic basis of skin disease, as a consequence of high throughput sequencing technologies including next generation sequencing and whole exome sequencing. We have now determined the genes underlying several monogenic diseases, such as harlequin ichthyosis, Olmsted syndrome, and exfoliative ichthyosis, which have provided unique insights into the structure and function of the skin. In addition, through genome wide association studies we now have an understanding of how low penetrance variants contribute to inflammatory skin diseases such as psoriasis vulgaris and atopic dermatitis, and how they contribute to underlying pathophysiological disease processes. In this review we discuss strategies used to unravel the genes underlying both monogenic and complex trait skin diseases in the last 10 years and the implications on mechanistic studies, diagnostics, and therapeutics.
Alkorta-Aranburu, Gorka; Beall, Cynthia M; Witonsky, David B; Gebremedhin, Amha; Pritchard, Jonathan K; Di Rienzo, Anna
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.
Buenfil-Rojas, A M; Álvarez-Legorreta, T; Cedeño-Vázquez, J R
The aim of this study was to determine concentrations of heavy metals (cadmium [Cd] and mercury [Hg]) and metallothioneins (MTs) in blood plasma and caudal scutes of Morelet's crocodile (Crocodylus moreletii) from Rio Hondo, a river and natural border between Mexico and Belize. Three transects of the river (approximately 20 km each) were surveyed in September 2012 and April 2013, and samples were collected from 24 crocodiles from these areas. In blood plasma, Cd (7.6 ± 9.6 ng/ml) was detected in 69 % of samples (n = 9); Hg (12.2 ± 9.2 ng/ml) was detected in 46 % of samples (n = 6); and MTs (10,900 ± 9,400 ng/ml) were detected in 92 % of samples (n = 12). In caudal scutes samples, Cd (31.7 ± 39.4 ng/g) was detected in 84 % of samples (n = 12) and Hg (374.1 ± 429.4 ng/g) in 83 % of samples (n = 20). No MTs were detected in caudal scutes. Hg concentrations in scutes from the Rio Hondo were 2- to 5-fold greater than those previously reported in scutes from other localities in northern Belize. In blood plasma, a significant positive relationship between Hg and body size was observed. Mean concentrations of Cd and MTs in size classes suggest that MTs may be related to Cd exposure. This is the first report of MT presence in crocodile blood. PMID:25355289
Jesse Guite Hastings
Full Text Available Motivated by biogeography and a desire for alignment with the funding priorities of donors, the twenty-first century has seen big international NGOs shifting towards a large-scale conservation approach. This shift has meant that even before stakeholders at the national and local scale are involved, conservation programmes often have their objectives defined and funding allocated. This paper uses the experiences of Conservation International′s Marine Management Area Science (MMAS programme in Belize and Panama to explore how to build participation at the national and local scale while working within the bounds of the current conservation paradigm. Qualitative data about MMAS was gathered through a multi-sited ethnographic research process, utilising document review, direct observation, and semi-structured interviews with 82 informants in Belize, Panama, and the United States of America. Results indicate that while a large-scale approach to conservation disadvantages early national and local stakeholder participation, this effect can be mediated through focusing engagement efforts, paying attention to context, building horizontal and vertical partnerships, and using deliberative processes that promote learning. While explicit consideration of geopolitics and local complexity alongside biogeography in the planning phase of a large-scale conservation programme is ideal, actions taken by programme managers during implementation can still have a substantial impact on conservation outcomes.
Jacobson, Susan K.
Evaluation of conservation education programs can: (1) provide accountability in demonstrating a program's worth, (2) offer an opportunity for receiving feedback and improving programs, (3) further our understanding of the process of program development, and (4) promote conservation education by substantiating claims about its benefits. The Planning-Process-Product systems evaluation model provides feedback needed for making decisions about the development, implementation, and outcome of a program. Planning evaluation was useful in assessing the needs, goals, opportunities, and constraints of a number of programs in Costa Rica and Belize, such as a forestry education project and a zoo outreach program. It provided a basis for making planning decisions incorporating specific objectives, such as the reforestation of a region or a change in knowledge and attitudes in program participants. Process evaluation provided a Costa Rican sustainable development program with feedback during its implementation and enabled it to modify and improve its newsletter for local farmers and its ecology classes for school children. Product evaluation assessed project accomplishments, such as the 700,000 raised by the Children's Rainforest group and the 20 miles of riparian land under conservation management as part of the Belize Community Baboon Sanctuary project. Outcomes are compared with the programs original monetary or land management objectives to determine the success of the programs and to provide feedback for improvement.
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.
Full Text Available This paper explores processes of islanding, de-islanding, and re-islanding in the context of island cities. Although today popularly associated with rural, peripheral, and isolated landscapes, concepts of the ideal city coincided in Medieval and Renaissance Europe with emergent notions of the ideal island. Major European cities such as Amsterdam, Paris, and Copenhagen were established on densely urbanized small islands. In accordance with dominant political and military philosophies, they were subsequently developed through comprehensive urban design into vast yet coherent urban archipelagos. In contrast, the contemporary development of Belize City as an island city took place through piecemeal land reclamation, absent comprehensive urban design, resulting in a very different kind of urban archipelago. Neither the coherent European island cities nor Belize City are generally regarded as islands today, yet their histories of urban development evidence the impact of spatial attributes of islandness on urban form. Comprehensive urban design efforts are currently directed at land reclamation and waterfront revitalization in Belize City, aiming to restore Belize City’s island city status. We argue that cities can be islanded, de-islanded, and re-islanded in the minds of their inhabitants and that it is necessary to recognize the connection between ideal islands and ideal cities in order to understand the islanding process in full.
Anderson-Fye, Eileen P.
As in other Latin American and Caribbean nations, young women in Belize have made remarkable strides in enrollment in and completion of secondary schooling. In fact, adolescent girls did so well during the 1990s that the usual explanations of increased access to schooling and governmental policy aimed at increasing girls' education did not appear…
Erika Sendra Tavares
Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent
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.
Lazarowitz, Reuven; Bloch, Ilit
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…
Wynne, Cynthia F.; Stewart, Jim; Passmore, Cindy
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.…
McVay, John D; Rodriguez, David; Rainwater, Thomas R; Dever, Jennifer A; Platt, Steven G; McMurry, Scott T; Forstner, Michael R J; Densmore, Llewellyn D
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. PMID:18831002
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
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. PMID:17826876
Camporese, A; Balick, M J; Arvigo, R; Esposito, R G; Morsellino, N; De Simone, F; Tubaro, A
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).
Farrell, T.A.; Marion, J.L.
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.
/ 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
Full Text Available BACKGROUND: Polyandry is widespread throughout the animal kingdom. In the absence of direct benefits of mating with different males, the underlying basis for polyandry is enigmatic because it can carry considerable costs such as elevated exposure to sexual diseases, physical injury or other direct fitness costs. Such costs may be balanced by indirect genetic benefits to the offspring of polyandrous females. We investigated polyandry and patterns of parentage in the spider Stegodyphus lineatus. This species experiences relatively high levels of inbreeding as a result of its spatial population structure, philopatry and limited male mating dispersal. Polyandry may provide an opportunity for post mating inbreeding avoidance that reduces the risk of genetic incompatibilities arising from incestuous matings. However, multiple mating carries direct fitness costs to females suggesting that genetic benefits must be substantial to counter direct costs. METHODOLOGY/PRINCIPAL FINDINGS: Genetic parentage analyses in two populations from Israel and a Greek island, showed mixed-brood parentage in approximately 50% of the broods. The number of fathers ranged from 1-2 indicating low levels of multiple parentage and there was no evidence for paternity bias in mixed-broods from both populations. Microsatellite loci variation suggested limited genetic variation within populations, especially in the Greek island population. Relatedness estimates among females in the maternal generation and potentially interacting individuals were substantial indicating full-sib and half-sib relationships. CONCLUSIONS/SIGNIFICANCE: Three lines of evidence indicate limited potential to obtain substantial genetic benefits in the form of reduced inbreeding. The relatively low frequency of multiple parentage together with low genetic variation among potential mates and the elevated risk of mating among related individuals as corroborated by our genetic data suggest that there are limited
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.
Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J
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. PMID:24751217
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.
The load of mutations disclosed by inbreeding, according to the ethnic group of the parents, has been analyzed in our data. Besides the total of the population, a sample with no alien ancestrals has also been analyzed. Genetic load has been studied for absortions, still births, pos-natal mortality, total mortality, anomalies, total mortality + anomalies, and abnormalities in general
SHENG Jinyu; TANG Liqun; WANG Liang
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.
Two methods to estimate the inbreeding load, employed in our analysis, are reviewed. Besides the total population, a sample constituted of individuals with no alien ancestral is also analysed. The measurements by genetic load models show any clear effect of natural radioactivity (especially for abortions, pre-natal mortality, anomalies, and abnormalities in general). The results on stillbirths and post-natal and total mortalities are discussed and it is concluded that uncontrolled concomitant variables (if not chance alone) cause the differences
Hoseini Alinodehi, Seyed Pourya; Moshfe, Sajjad; Saber Zaeimian, Masoumeh; Khoei, Abdollah; Hadidi, Khairollah
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. PMID:26241984
Hoseini Alinodehi, Seyed Pourya; Moshfe, Sajjad; Saber Zaeimian, Masoumeh; Khoei, Abdollah; Hadidi, Khairollah
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.
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
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
Noreen, Annika M E; Webb, Edward L
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 (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 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. PMID:24367531
Erika C Küchler; Deeley, Kathleen; Ho, Bao; Linkowski, Samantha; Meyer, Chelsea; Noel, Jacqueline; Kouzbari, M Zahir; Bezamat, Mariana; José M Granjeiro; Antunes, Leonardo S; Antunes, Livia Azeredo; de Abreu, Fernanda Volpe; Marcelo C. Costa; Tannure, Patricia N; SEYMEN, Figen
Background Our previous genome-wide linkage scan mapped five loci for caries experience. The purpose of this study was to fine map one of these loci, the locus 13q31.1, in order to identify genetic contributors to caries. Methods Seventy-two pedigrees from the Philippines were studied. Caries experience was recorded and DNA was extracted from blood samples obtained from all subjects. Sixty-one single nucleotide polymorphisms (SNPs) in 13q31.1 were genotyped. Association between caries experie...
Wu, Ted H; Cañas, Jaclyn E; Rainwater, Thomas R; Platt, Steven G; McMurry, Scott T; Anderson, Todd A
Seven complete clutches of Morelet's crocodile (Crocodylus moreletii) eggs were collected in northern Belize and examined for organochlorine (OC) pesticide residues. The primary OC detected, p,p-DDE, was found in every egg analyzed (n=175). Other OCs detected included p,p-DDT, p,p-DDD, methoxychlor, aldrin, and endosulfan I. Concentrations of individual OCs ranged from 4 ppb (ng chemical/g egg wet weight) to greater than 500 ppb. A statistical evaluation of p,p-DDE levels in three complete clutches was used to derive the minimum number of eggs needed from a clutch to precisely determine the mean p,p-DDE concentration representative of that clutch. Sample sizes of 8 (80% confidence level) and 11 (90% confidence level) were determined to yield an accurate estimate of contaminant levels in a full clutch of eggs. The statistically recommended sample size of 11 eggs (at 90% confidence level) was successfully tested on the four additional clutches. PMID:16504356
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
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.
Wu, Ted H. [Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK 99775-6160 (United States); Canas, Jaclyn E. [Institute of Environmental and Human Health, Texas Tech University, Box 41163, Lubbock, TX 79409 (United States); Rainwater, Thomas R. [Institute of Environmental and Human Health, PO Box 764, Jefferson, TX 75657 (United States); Platt, Steven G. [Department of Math and Science, Oglala Lakota College, 490 Piya Wiconi Road, Kyle, SD, 57752 (United States); McMurry, Scott T. [Institute of Environmental and Human Health, Texas Tech University, Box 41163, Lubbock, TX 79409 (United States); Anderson, Todd A. [Institute of Environmental and Human Health, Texas Tech University, Box 41163, Lubbock, TX 79409 (United States)]. E-mail: firstname.lastname@example.org
Seven complete clutches of Morelet's crocodile (Crocodylus moreletii) eggs were collected in northern Belize and examined for organochlorine (OC) pesticide residues. The primary OC detected, p,p-DDE, was found in every egg analyzed (n = 175). Other OCs detected included p,p-DDT, p,p-DDD, methoxychlor, aldrin, and endosulfan I. Concentrations of individual OCs ranged from 4 ppb (ng chemical/g egg wet weight) to greater than 500 ppb. A statistical evaluation of p,p-DDE levels in three complete clutches was used to derive the minimum number of eggs needed from a clutch to precisely determine the mean p,p-DDE concentration representative of that clutch. Sample sizes of 8 (80% confidence level) and 11 (90% confidence level) were determined to yield an accurate estimate of contaminant levels in a full clutch of eggs. The statistically recommended sample size of 11 eggs (at 90% confidence level) was successfully tested on the four additional clutches. -- Sampling the non-viable eggs of a clutch can provide a statistically reasonable estimation of both the organochlorine contaminant distribution and concentrations in that clutch.
Seven complete clutches of Morelet's crocodile (Crocodylus moreletii) eggs were collected in northern Belize and examined for organochlorine (OC) pesticide residues. The primary OC detected, p,p-DDE, was found in every egg analyzed (n = 175). Other OCs detected included p,p-DDT, p,p-DDD, methoxychlor, aldrin, and endosulfan I. Concentrations of individual OCs ranged from 4 ppb (ng chemical/g egg wet weight) to greater than 500 ppb. A statistical evaluation of p,p-DDE levels in three complete clutches was used to derive the minimum number of eggs needed from a clutch to precisely determine the mean p,p-DDE concentration representative of that clutch. Sample sizes of 8 (80% confidence level) and 11 (90% confidence level) were determined to yield an accurate estimate of contaminant levels in a full clutch of eggs. The statistically recommended sample size of 11 eggs (at 90% confidence level) was successfully tested on the four additional clutches. -- Sampling the non-viable eggs of a clutch can provide a statistically reasonable estimation of both the organochlorine contaminant distribution and concentrations in that clutch
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: email@example.com; Selcer, Kyle W. [Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA 15282 (United States)], E-mail: firstname.lastname@example.org; Nespoli, Lisa M. [Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA 15282 (United States)], E-mail: email@example.com; 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: firstname.lastname@example.org; Ray, David A. [Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 (United States)], E-mail: email@example.com; Platt, Steven G. [Department of Biology, P.O. Box C-64, Sul Ross State University, Alpine, TX 79832 (United States)], E-mail: firstname.lastname@example.org; 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: email@example.com; Densmore, Llewellyn D. [Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 (United States)], E-mail: firstname.lastname@example.org; 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: email@example.com; 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: firstname.lastname@example.org
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.
Hekkala, Evon R; Platt, Steven G; Thorbjarnarson, John B; Rainwater, Thomas R; Tessler, Michael; Cunningham, Seth W; Twomey, Christopher; Amato, George
The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062
McKee, K.L.; Faulkner, P.L.
The substrate beneath mangrove forests in the Pelican Cays complex is predominately peat composed mainly of mangrove roots. Leaves and wood account for less than 20% of the peat mass. At Cat Cay, the depth of the peat ranges from 0.2 m along the shoreline to 1.65 m in the island center, indicating that the island has expanded horizontally as well as vertically through below-ground, biogenic processes. Mangrove roots thus play a critical role in the soil formation, vertical accretion, and stability of these mangrove cays. The species composition of fossil roots changes markedly with depth: Rhizophora mangle (red mangrove) was the initial colonizer on a coral base, followed by Avicennia germinans (black mangrove), which increased in abundance and expanded radially from the center of the island. The center of the Avicennia stand ultimately died, leaving an unvegetated, shallow pond. The peat thus retains a record of mangrove development, succession, and deterioration in response to sea-level change and concomitant hydroedaphic conditions controlling dispersal, establishment, growth, and mortality of mangroves on oceanic islands in Belize.
References to obeah pregnancy are widespread in southern Belize, where the belief in supernatural forces combines with Catholic teaching to create a conservative reproductive climate in which illegitimate pregnancy, reproductive misfortunes and maternal death are located in a discourse of shame. Obeah pregnancy is said to result when spiritual forces are unleashed through malicious human intent, causing bodily changes that resemble pregnancy. Death of the woman, however, usually occurs before prenatal confirmation; thus it is often unclear if an obeah pregnancy is a viable pregnancy or some other biomedical - or metaphysical - condition. This paper provides a case study of Petrona, whose story is unique in that she does not die from her purported obeah pregnancy; rather, she lives to bear the consequences of her reproductive behaviours that resulted in the stillbirth of a full-term foetus. Petrona was a traditional birth attendant who is trained to uphold biomedical antenatal protocols. Arguing that Petrona was not adequately educated to fulfill her own prenatal obligations, health care personnel sanctioned Petrona's midwifery practice and left her to process her 'shameful' situation. Ultimately, Petrona's story complicates the culturally disengaged narratives of maternal health and highlights the schism between medical knowledge and socioculturally influenced embodied experience. PMID:22085315
Meloni, Marilena; Reid, Andrea; Caujapé-Castells, Juli; Soto, Moisés; Fernández-Palacios, José María; Conti, Elena
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.
Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan
Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation. PMID:27047511
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
Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J.
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. ...
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.
Onda, Yoshihiko; Mochida, Keiichi
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. PMID:27499684
Walsh, Megan K.; Prufer, Keith M.; Culleton, Brendan J.; Kennett, Douglas J.
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.
Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao
Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149
Full Text Available Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat and DarT (diversity arrays technology. These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species.
Helmke, Christophe G.B.
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...
Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.
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.
Ugelvig, Line V.; Kronauer, Daniel J. C.; Schrempf, Alexandra; Heinze, Jürgen; Cremer, Sylvia
Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the ind...
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.
Wanek, Wolfgang; Hofmann, Julia; Feller, Ilka C.
SummaryBulk precipitation, throughfall and stemflow were collected to study anthropogenic effects on above-ground nutrient cycling in an off-shore mangrove forest ( Rhizophora mangle L.) on Twin Cays, Belize. Samples were collected in a nitrogen limited fringe and phosphorus limited dwarf zone, and from an adjacent nitrogen fertilized fringe and a phosphorus fertilized dwarf zone. Inorganic cations and anions, dissolved organic carbon (DOC) and nitrogen (DON) were analysed. Throughfall represented 84% of precipitation volume. Sea salt ions (Cl -, Na +, SO42- and Mg 2+) and DOC accounted for the highest proportion of solutes in rainwater, throughfall and stemflow in R. mangle stands. Non-marine sources dominated the flux of DON, DOC, NO3-, NH4+, and inorganic P (P i) in bulk precipitation and throughfall and partially contributed to Ca 2+ and K +. Deposition ratios (throughfall deposition:bulk deposition) showed that inorganic NH4+, and less so P i were retained in the canopy of R. mangle from throughfall while all other solutes increased. Canopy leaching contributed in increasing order to net throughfall of Ca 2+, Cl -, SO42-/K, Mg 2+ and Na + but dry deposition dominated the net throughfall flux during the investigated period. Fertilizer treatment and zone did only slightly affect solute concentrations of hot-water extracts of leaves, of throughfall and stemflow in stands of similar stature. While litterfall and primary production have previously been shown to increase substantially upon nutrient enrichment of mangroves we therefore conclude that fertilization, as a surrogate of anthropogenic eutrophication, may not increase nutrient leaching from mangrove canopies, and thus may only have a minor effect on soluble organic matter cycling and inputs into mangrove food webs.
Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa
A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597
XUEDa-Wei; GEXue-Jun; HAOGang; ZHANGChang-Qin
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.
Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline
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 importance of
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
Kohler, Christian G; Richard, Jan A; Brensinger, Colleen M; Borgmann-Winter, Karin E; Conroy, Catherine G; Moberg, Paul J; Gur, Ruben C; Gur, Raquel E; Calkins, Monica E
A large body of literature has documented facial emotion perception impairments in schizophrenia. More recently, emotion perception has been investigated in persons at genetic and clinical high-risk for psychosis. This study compared emotion perception abilities in groups of young persons with schizophrenia, clinical high-risk, genetic risk and healthy controls. Groups, ages 13-25, included 24 persons at clinical high-risk, 52 first-degree relatives at genetic risk, 91 persons with schizophrenia and 90 low risk persons who completed computerized testing of emotion recognition and differentiation. Groups differed by overall emotion recognition abilities and recognition of happy, sad, anger and fear expressions. Pairwise comparisons revealed comparable impairments in recognition of happy, angry, and fearful expressions for persons at clinical high-risk and schizophrenia, while genetic risk participants were less impaired, showing reduced recognition of fearful expressions. Groups also differed for differentiation of happy and sad expressions, but differences were mainly between schizophrenia and control groups. Emotion perception impairments are observable in young persons at-risk for psychosis. Preliminary results with clinical high-risk participants, when considered along findings in genetic risk relatives, suggest social cognition abilities to reflect pathophysiological processes involved in risk of schizophrenia. PMID:24582775
Full Text Available Abstract Background Ants typically distinguish nestmates from non-nestmates based on the perception of colony-specific chemicals, particularly cuticular hydrocarbons present on the surface of the ants' exoskeleton. These recognition cues are believed to play an important role in the formation of vast so-called supercolonies that have been described for some invasive ant species, but general conclusions about the role of these cues are hampered by only few species being studied. Here we use data on cuticular hydrocarbons, aggression and microsatellite genetic markers to investigate the interdependence of chemical recognition cues, genetic distance and nestmate discrimination in the pharaoh ant (Monomorium pharaonis, a widespread pest species, and ask whether introduced populations of this species are genetically differentiated and exhibit intraspecific aggression. Results Microsatellite analyses of a total of 35 colonies from four continents revealed extremely high levels of genetic differentiation between almost all colonies (FST = 0.751 ± 0.006 SE and very low within-colony diversity. This implies that at least 34 and likely hundreds more independent lineages of this ant have spread worldwide. Aggression tests involving workers from 14 different colonies showed only low levels of aggression, even between colonies that were geographically and/or genetically very distant. Chemical analyses of groups of worker ants showed that all colonies had the same cuticular compounds, which varied only quantitatively among colonies. There was a positive correlation between geographical and genetic distance, but no other significant relationships were detected between aggression, chemical profile, genetic distance and geographical distance. Conclusions The pharaoh ant has a global invasion history of numerous independent introductions resulting in genetically highly differentiated colonies typically displaying surprisingly low levels of intraspecific
Meilin Tian; Yangping Li; Jing Jing; Chuang Mu; Huixia Du; Jinzhuang Dou; Junxia Mao; Xue Li; Wenqian Jiao; Yangfan Wang; Xiaoli Hu; Shi Wang; Ruijia Wang; Zhenmin Bao
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 sit...
Baden, Maria; Särkinen, Tiina; Conde, Dalia Amor;
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...
ZHOU Wei; LI ShaoLin; MA Gang; CHANG XiaoLin; MA Xing; ZHANG Chao
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.
Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon
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.
Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon
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. PMID:26949947
Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel
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.
Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Serrão, Ester Alvares
The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038
Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.
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
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.
Bennett-Martin, Paulita; Visaggi, Christy C; Hawthorne, Timothy L
Monitoring of marine debris (also known as marine litter) is an essential step in the process to eradicate ecological dangers in marine ecosystems caused by humans. This study examines marine debris in the Caribbean country of Belize using geographic information systems (GIS) to develop (1) a detailed data library for use on handheld Global Positioning System (GPS) units and tablets with mobile mapping applications for deployment in the field and (2) a freely available, online mapping portal to share data with Belizeans to encourage future citizen science efforts. Four diverse communities were targeted ranging from larger more populated towns, to smaller villages across central and southern Belize: San Pedro, Caye Caulker, Punta Gorda, and Monkey River. Fieldwork was conducted over 1 month, during which data points were collected in 50-m surveys followed by debris cleanup and removal. Features in our database included material, quantity, item, brand, and condition. Over 6000 pieces of debris were recorded in GIS for further analysis, and 299 gal of debris were removed from the shores of Belize. The most abundant form of debris observed was plastic (commonly bottles) across all locations; plastic comprised 77.6 % of all debris items observed. Through GIS, a detailed snapshot understanding of debris patterns across multiple settings in Belize was documented. Ongoing collaborations with local organizations in Belize have demonstrated significant interest and utility for such GIS approaches in analyzing and managing marine debris. The data, methodology, visual representations, and online mapping platform resulting from this research are a first step in directly supporting local Belizean community advocacy and policy, while contributing to larger institutional strategies for addressing marine debris issues in the Caribbean. PMID:27614957
Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...
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
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.
Wah Ching Lee
Full Text Available A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day.
Hwang, Liang-Dar; Zhu, Gu; Breslin, Paul A S; Reed, Danielle R; Martin, Nicholas G; Wright, Margaret J
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. PMID:26181574
Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha
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.
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.
Winer, Rachel A; Bennett, Eleanor; Murillo, Illouise; Schuetz-Mueller, Jan; Katz, Craig L
Belize trained psychiatric nurse practitioners (PNPs) in the early 1990s to provide mental health services throughout the country. Despite overwhelming success, the program is limited by lack of monitoring, evaluation, and surveillance. To promote quality assurance, we developed a chart audit tool to monitor mental healthcare delivery compliance for initial psychiatric assessment notes completed by PNPs. After reviewing the Belize Health Information System electronic medical record system, we developed a clinical audit tool to capture 20 essential components for initial assessment clinical notes. The audit tool was then piloted for initial assessment notes completed during July through September of 2013. One hundred and thirty-four initial psychiatric interviews were audited. The average chart score among all PNPs was 9.57, ranging from 3 to 15. Twenty-three charts-or 17.2%-had a score of 14 or higher and met a 70% compliance benchmark goal. Among indicators most frequently omitted included labs ordered and named (15.7%) and psychiatric diagnosis (21.6%). Explicit statement of medications initiated with dose and frequency occurred in 47.0% of charts. Our findings provide direction for training and improvement, such as emphasizing the importance of naming labs ordered, medications and doses prescribed, and psychiatric diagnoses in initial assessment clinical notes. We hope this initial assessment helps enhance mental health delivery compliance by prompting creation of BHIS templates, development of audits tools for revisit follow-up visits, and establishment of corrective actions for low-scoring practitioners. These efforts may serve as a model for implementing quality assurance programming in other low resource settings. PMID:25829167
Alves-Stanley, Christy D.; Worthy, Graham A.J.; Bonde, Robert K.
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.
Macedo Selma E
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.
Santamaria, Carlos A; Mateos, Mariana; DeWitt, Thomas J; Hurtado, Luis A
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
Wittrup, Hans H; Andersen, Rolf V; Tybjaerg-Hansen, Anne;
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)....
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.
Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury
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. PMID:25347541
Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou
Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016
Yoshikawa, Masaya; Terai, Hidekazu
This paper discusses the architecture for high speed learning of Neural Network (NN) using Genetic Algorithm (GA). The proposed architecture prevents local minimum by using the GA characteristic of holding several individual populations for a population-based search and achieves high speed processing adopting dedicated hardware. To keep general purpose equal software processing, the proposed architecture can be flexible genetic operations on GA and is introduced both Sigmoid function and Heaviside function on NN. Furthermore, the proposed architecture is not optimized only the pipeline at evaluation phase on NN, but also optimized hierarchic pipelines on the whole at evolutionary phase. We have done the simulation, verification and logic synthesis using library of 0.35μm CMOS standard cell. Simulation results evaluating the proposed architecture show to achieve 22 times speed on average compared with software processing.
Wilcke, Arndt; Müller, Bent; Schaadt, Gesa; Kirsten, Holger; Boltze, Johannes
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. PMID:26036858
Wilcke, Arndt; Müller, Bent; Schaadt, Gesa; Kirsten, Holger; Boltze, Johannes
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.
Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth
Our main goal in this study was to explore whether the use of models in molecular genetics instruction in high school can contribute to students' understanding of concepts and processes in genetics. Three comparable groups of 11th and 12th graders participated: The control group (116 students) was taught in the traditional lecture format, while the others received instructions which integrated a bead model (71 students), or an illustration model (71 students). Similar instructions and the same guiding questions accompanied the two models. We used three instruments: a multiple-choice and an open-ended written questionnaire, as well as personal interviews. Five of the multiple-choice questions were also given to students before receiving their genetics instruction (pretest). We found that students who used one of the two types of models improved their knowledge in molecular genetics compared to the control group. However, the open-ended questions revealed that bead model activity was significantly more effective than illustration activity. On the basis of these findings we conclude that, though it is advisable to use a three-dimensional model, such as the bead model, engaging students in activities with illustrations can still improve their achievement in comparison to traditional instruction.
Louis, Marie; Fontaine, Michael C; Spitz, Jérôme; Schlund, Erika; Dabin, Willy; Deaville, Rob; Caurant, Florence; Cherel, Yves; Guinet, Christophe; Simon-Bouhet, Benoit
Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species. PMID:25297864
Ugelvig, Line V; Kronauer, Daniel J C; Schrempf, Alexandra; Heinze, Jürgen; Cremer, Sylvia
Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony. PMID:20444720
Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline
International audience 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...
Khare, Siddharth M.; Awasthi, Anjali; V. Venkataraman; Sandhya P Koushika
Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color...
Thompson, Hayley S; Sussner, Katarina; Schwartz, Marc D; Edwards, Tiffany; Forman, Andrea; Jandorf, Lina; Brown, Karen; Bovbjerg, Dana H; Valdimarsdottir, Heiddis B
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.
Bálint, Miklós; Bartha, László; O'Hara, Robert B; Olson, Matthew S; Otte, Jürgen; Pfenninger, Markus; Robertson, Amanda L; Tiffin, Peter; Schmitt, Imke
Micro-organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host-associated micro-organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common-garden experiment and rDNA metabarcoding to examine the effect of host relocation and high-latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High-latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude and high-latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host-microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts. PMID:25443313
Gómez Díaz, Elena; González-Solís, Jacob; Peinado Morales, Miguel Á. (Miguel Ángel)
Increasing evidence suggests oceanic traits may play a key role in the genetic structuring of marine organisms. Whereas genetic breaks in the open ocean are well known in fishes and marine invertebrates, the importance of marine habitat characteristics in seabirds remains less certain. We investigated the role of oceanic transitions versus population genetic processes in driving population differentiation in a highly vagile seabird, the Cory"s shearwater, combining molecular, morphological an...
Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213
Martins, S M; Melo, P G S; Faria, L C; Souza, T L P O; Melo, L C; Pereira, H S
One of the current focus of common bean breeding programs in Brazil is to increase iron (FeC) and zinc content (ZnC) in grains. The objectives of this study were to estimate genetic parameters for FeC and ZnC in common bean, verify the need for conducting multi-site evaluation tests, identify elite lines that combine high FeC and ZnC with good adaptability, stability, and agronomic potential, and examine the genetic association between FeC and ZnC. Elite lines (140) were evaluated for important agronomic traits in multiple environments. In one trial, FeC and ZnC were evaluated and genetic parameters were estimated. Based on the high heritability estimates and significant selection gains obtained, the conditions for a successful selection was favorable. Of the 140 evaluated lines, 17 had higher FeC and ZnC, and were included in the validation test (2013, five environments), specifically for the evaluation of FeC and ZnC. The line by environment interaction for FeC and ZnC was detected, but it was predominantly simple. The environmental effect strongly influenced FeC and ZnC . The environment Brasília/rainy season was selected as the best evaluation site for preliminary tests for FeC and ZnC, because it resulted in similar conclusions as the mean of the five environments. The lines CNFP 15701 and CNFC 15865 had higher FeC and ZnC and were highly adaptable and stable, and are recommended for utilization in breeding programs. The lines CNFC 15833, CNFC 15703, and CNFP 15676 showed excellent combined agronomic and nutritional traits, and were selected for the development of biofortified cultivars. Additionally, the genetic association between FeC and ZnC was detected. PMID:27323172
LÉO A. HARTMANN; João O. S Santos; Jayme A.D. Leite; Carla C. Porcher; McNaughton, Neal J.
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 ...
Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.
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.
Slack, Susie Johnston; Stewart, Jim
Problem solving is recognized as a valuable educational experience in science. Thus genetics, essentially a problem-solving science included in almost all high school biology courses, offers a fruitful area for studying student problem-solving performance. The research reported in this article describes the performance of 30 high school students solving 119 problems generated by the computer program GENETICS CONSTRUCTION KIT (Jungck & Calley, 1985). Solving GCK problems requires students to plan experiments, generate and interpret data, and reason from effects (phenotypic data) to causes (genotypic data). Research data consisted of transcribed audiotapes of students thinking aloud as they solved problems and computer printouts of initial data and sequence of crosses. Transcripts were analyzed for common actions and comments made during the problem-solving process in terms of initial data redescription and interpretation, hypothesis generation, cross data redescription and interpretation, solution synthesis, and solution confirmation. This study was done in an effort to add to the understanding of student problem-solving strategies and to develop a model of student performance - a model that when combined with a model of expert performance may serve as a basis for improving genetics instruction.
Arlen F. Chase
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.
Johannsen, Trine Holm; Kamstrup, Pia R; Andersen, Rolf V;
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......73M, N193S, S267F, L334F, T383M, and -480c>t influence levels of lipids, lipoproteins, and apolipoproteins and risk of ICD. DESIGN: For the cross-sectional study, we genotyped 9003 individuals from the Copenhagen City Heart Study; hereof were 8971 individuals included in the prospective study, 1747...
Ellis Nathan A
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.
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...
Veerkamp, R.F.; Calus, M.P.L.
Genetic association between traits, and correlated responses resulting from those associations, are generally predicted using genetic correlations. However, depending on the composition and magnitude of the genetic covariance, asymmetry of correlated responses might occur and predictions may last fo
Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua
The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692
Full Text Available The oriental fruit moth Grapholita ( = Cydia molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.
Harrison, Elizabeth; Trexler, Joel C; Collins, Timothy M; Vazquez-Domínguez, Ella; Razo-Mendivil, Ulises; Matamoros, Wilfredo A; Barrientos, Christian
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.
Miller, Jeff F.; Dower, William J.; Tompkins, Lucy S.
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.
Shao, Yong; Li, Jin-Xiu; Ge, Ri-Li; Zhong, Li; Irwin, David M; Murphy, Robert W; Zhang, Ya-Ping
The plateau zokor (Myospalax baileyi) spends its entire life underground in sealed burrows. Confronting limited oxygen and high carbon dioxide concentrations, and complete darkness, they epitomize a successful physiological adaptation. Here, we employ transcriptome sequencing to explore the genetic underpinnings of their adaptations to this unique habitat. Compared to Rattus norvegicus, genes belonging to GO categories related to energy metabolism (e.g. mitochondrion and fatty acid beta-oxidation) underwent accelerated evolution in the plateau zokor. Furthermore, the numbers of positively selected genes were significantly enriched in the gene categories involved in ATPase activity, blood vessel development and respiratory gaseous exchange, functional categories that are relevant to adaptation to high altitudes. Among the 787 genes with evidence of parallel evolution, and thus identified as candidate genes, several GO categories (e.g. response to hypoxia, oxygen homeostasis and erythrocyte homeostasis) are significantly enriched, are two genes, EPAS1 and AJUBA, involved in the response to hypoxia, where the parallel evolved sites are at positions that are highly conserved in sequence alignments from multiple species. Thus, accelerated evolution of GO categories, positive selection and parallel evolution at the molecular level provide evidences to parse the genetic adaptations of the plateau zokor for living in high-elevation burrows. PMID:26602147
ZHOU Yuliang; LU Guihua; JIN Juliang; TONG Fang; ZHOU Ping
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.
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.
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.
Ugelvig, Line V; Kronauer, Daniel Jan Christoph; Schrempf, Alexandra;
group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic...... fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest...
Athanasiadis, Georgios; Jørgensen, Frank G; Cheng, Jade Y; Kjærgaard, Peter C; Schierup, Mikkel H; Mailund, Thomas
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
Athanasiadis, Georgios; Jørgensen, Frank G.; Cheng, Jade Y.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas
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
Knight, Christopher Harold; Alamer, Mohammed A; Sorensen, Annette;
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....
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
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.
Full Text Available BACKGROUND: Several studies have addressed the epidemiology of community-associated Staphylococcus aureus (CA-SA in Europe; nonetheless, a comprehensive perspective remains unclear. In this study, we aimed to describe the population structure of CA-SA and to shed light on the origin of methicillin-resistant S. aureus (MRSA in this continent. METHODS AND FINDINGS: A total of 568 colonization and infection isolates, comprising both MRSA and methicillin-susceptible S. aureus (MSSA, were recovered in 16 European countries, from community and community-onset infections. The genetic background of isolates was characterized by molecular typing techniques (spa typing, pulsed-field gel electrophoresis and multilocus sequence typing and the presence of PVL and ACME was tested by PCR. MRSA were further characterized by SCCmec typing. We found that 59% of all isolates were associated with community-associated clones. Most MRSA were related with USA300 (ST8-IVa and variants (40%, followed by the European clone (ST80-IVc and derivatives (28% and the Taiwan clone (ST59-IVa and related clonal types (15%. A total of 83% of MRSA carried Panton-Valentine leukocidin (PVL and 14% carried the arginine catabolic mobile element (ACME. Surprisingly, we found a high genetic diversity among MRSA clonal types (ST-SCCmec, Simpson's index of diversity = 0.852 (0.788-0.916. Specifically, about half of the isolates carried novel associations between genetic background and SCCmec. Analysis by BURP showed that some CA-MSSA and CA-MRSA isolates were highly related, suggesting a probable local acquisition/loss of SCCmec. CONCLUSIONS: Our results imply that CA-MRSA origin, epidemiology and population structure in Europe is very dissimilar from that of USA.
McIlwrick, Silja; Rechenberg, Alexandra; Matthes, Mariana; Burgstaller, Jessica; Schwarzbauer, Thomas; Chen, Alon; Touma, Chadi
A dysregulation of the hypothalamus-pituitary-adrenocortical (HPA) axis and the experience of early-life adversity are both well-established risk factors for the development of affective disorders, such as major depression. However, little is known about the interaction of these two factors in shaping endophenotypes of the disease. Here, we studied the gene-environment interaction of a genetic predisposition for HPA axis dysregulation with early-life stress (ELS), assessing the short-, as well as the long-lasting consequences on emotional behavior, neuroendocrine functions and gene expression profiles. Three mouse lines, selectively bred for either high (HR), intermediate (IR), or low (LR) HPA axis reactivity, were exposed to one week of ELS using the limited nesting and bedding material paradigm. Measurements collected during or shortly after the ELS period showed that, regardless of genetic background, ELS exposure led to impaired weight gain and altered the animals' coping behavior under stressful conditions. However, only HR mice additionally showed significant changes in neuroendocrine stress responsiveness at a young age. Accordingly, adult HR mice also showed lasting consequences of ELS, including hyperactive stress-coping, HPA axis hyperreactivity, and gene expression changes in the Crh system, as well as downregulation of Fkbp5 in relevant brain regions. We suggest that the genetic predisposition for high stress reactivity interacts with ELS exposure by disturbing the suppression of corticosterone release during a critical period of brain development, thus exerting lasting programming effects on the HPA axis, presumably via epigenetic mechanisms. In concert, these changes lead to the emergence of important endophenotypes associated with affective disorders. PMID:27179233
Full Text Available Species diagnosis in Trogolaphysa has been based, until now, almost exclusively on number of eyes and shape of claws and mucro. Chaetotaxy, a character system important to diagnose species in other genera of scaled Entomobryoidea, has been described only for a few Trogolaphysa species. Here the complete dorsal chaetotaxy of six species of Trogolaphysa is described using the AMS and Szeptycki’s systems for head and body, respectively. A morphology-based parsimony analysis was performed to evaluate whether chaetotaxic characters overcome the influence of putatively cave adaptive convergent characters to resolve species level relationships, and to evaluate the evolution of the dorsal macrochaetae of the head. Phylogenetic analysis using only putative cave-adaptive characters support clades of unrelated taxa, but the addition of chaetotaxy overcomes the influence of convergent characters. A phylogeny based on all characters supports a trend towards reduced head macrochaetae number. Head macrochaetae are lost beginning with A3 and followed, in order, by S5, S3 and M3. In addition, a checklist of New World Trogolaphysa is provided and two new species, Trogolaphysa giordanoae sp. n. and Trogolaphysa jacobyi sp. n., are described on the basis of material collected in six caves in southern Belize.
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.
Anderson-Fye, Eileen P
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.
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. PMID:25105478
Taylor, D.S.; Reyier, E.A.; Davis, W.P.; McIvor, C.C.
We investigated the effects of mangrove cutting on fish assemblages in Twin Cays, Belize, in two habitat types. We conducted visual censuses at two sites in adjoining undisturbed/disturbed (30%–70% of shoreline fringe removed) sub-tidal fringing Rhizophora mangle Linnaeus, 1753. Observers recorded significantly more species and individuals in undisturbed sites, especially among smaller, schooling species (e.g., atherinids, clupeids), where densities were up to 200 times greater in undisturbed habitat. Multivariate analyses showed distinct species assemblages between habitats at both sites. In addition, extensive trapping with wire minnow traps within the intertidal zone in both undisturbed and disturbed fringing and transition (landward) mangrove forests was conducted. Catch rates were low: 638 individuals from 24 species over 563 trap-nights. Trap data, however, indicated that mangrove disturbance had minimal effect on species composition in either forest type (fringe/transition). Different results from the two methods (and habitat types) may be explained by two factors: (1) a larger and more detectable species pool in the subtidal habitat, with visual "access" to all species, and (2) the selective nature of trapping. Our data indicate that even partial clearing of shoreline and more landward mangroves can have a significant impact on local fish assemblages.
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.
Pashaei, Kaveh; Taghiyareh, Fattaneh; Badie, Kambiz
Communication and coordination are the main cores for reaching a constructive agreement among multi-agent systems (MASs). Dividing the overall performance of MAS to individual agents may lead to group learning as opposed to individual learning, which is one of the weak points of MASs. This paper proposes a recursive genetic framework for solving problems with high dynamism. In this framework, a combination of genetic algorithm and multi-agent capabilities is utilised to accelerate team learning and accurate credit assignment. The argumentation feature is used to accomplish agent learning and the negotiation features of MASs are used to achieve a credit assignment. The proposed framework is quite general and its recursive hierarchical structure could be extended. We have dedicated one special controlling module for increasing convergence time. Due to the complexity of blackjack, we have applied it as a possible test bed to evaluate the system's performance. The learning rate of agents is measured as well as their credit assignment. The analysis of the obtained results led us to believe that our robust framework with the proposed negotiation operator is a promising methodology to solve similar problems in other areas with high dynamism.
Deng, J Q; Liu, B Q; Wang, Y; Liu, W; Cai, J F; Long, R; Li, W H
Currently, the widely used automated capillary electrophoresis-based short tandem repeat (STR) genotyping method for genetic screening in forensic practice is laborious, time-consuming, expensive, and technically challenging in some cases. Thus, new molecular-based strategies for conclusively identifying forensically relevant biological evidence are required. Here, we used high-resolution melting analysis (HRM) for Y-chromosome STR genotyping for forensic genetic screening. The reproducibility of the melting profile over dilution, sensitivity, discrimination power, and other factors was preliminarily studied in 10 Y-STR loci. The results showed that HRM-based approaches revealed more genotypes (compared to capillary electrophoresis), showed higher uniformity in replicate tests and diluted samples, and enabled successful detection of DNA at concentrations as low as 0.25 ng. For mixed samples, the melting curve profiles discriminated between mixed samples based on reference samples with high efficiency. The triplex Y-chromosome STR HRM assay was performed and provided a foundation for further studies such as a multiplex HRM assay. The HRM approach is a one-step application and the entire procedure can be completed within 2 h at a low cost. In conclusion, our findings demonstrate that the HRM-based Y-STR assay is a useful screening tool that can be used in forensic practice. PMID:26909950
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>
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...
Tang, Shihua; Li, Feida; Liu, Yintao; Lan, Lan; Zhou, Conglin; Huang, Qing
With the advantage of high speed, big transport capacity, low energy consumption, good economic benefits and so on, high-speed railway is becoming more and more popular all over the world. It can reach 350 kilometers per hour, which requires high security performances. So research on the prediction of high-speed railway settlement that as one of the important factors affecting the safety of high-speed railway becomes particularly important. This paper takes advantage of genetic algorithms to seek all the data in order to calculate the best result and combines the advantage of strong learning ability and high accuracy of wavelet neural network, then build the model of genetic wavelet neural network for the prediction of high-speed railway settlement. By the experiment of back propagation neural network, wavelet neural network and genetic wavelet neural network, it shows that the absolute value of residual errors in the prediction of high-speed railway settlement based on genetic algorithm is the smallest, which proves that genetic wavelet neural network is better than the other two methods. The correlation coefficient of predicted and observed value is 99.9%. Furthermore, the maximum absolute value of residual error, minimum absolute value of residual error-mean value of relative error and value of root mean squared error(RMSE) that predicted by genetic wavelet neural network are all smaller than the other two methods'. The genetic wavelet neural network in the prediction of high-speed railway settlement is more stable in terms of stability and more accurate in the perspective of accuracy.
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.
PériauxJacques; WangJiangfeng; WuYizhao
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.
Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai
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.
Lazarowitz, Reuven; Bloch, Ilit
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 scientists from all the above-mentioned disciplines had been involved in trying to support and develop the eugenics theories. It investigates pre- and postwar theories of the eugenics movement in the United States which were implemented successfully in Germany and a literature survey of the studies of societal issues related to these subjects. The sample consisted of 30 male and female biology teachers. Enclosed are teachers' answers in favor or against including debates about societal issues in their classrooms while teaching the disciplines mentioned above. Teachers' answers were analyzed in relation to three variables: years of teaching experience, gender, and religion faith. Data were collected from questionnaires and personal interviews and analyzed according to qualitative and quantitative methods. The results show that amongst the teachers there is a medium to low level of awareness of societal issues, while mainly emphasizing scientific subjects in preparation of matriculation examinations. The majority of the teachers do not include societal issues in their teaching, but if students raise these issues, teachers claimed to address them. No differences in teachers' opinions to societal issues were found in relation to gender or religious faith. Teachers with more years of teaching experience tend to teach with a more Science, Technology, and Society (STS) approach than novice teachers. The results are discussed in relation to teachers' professional development and teaching strategies are suggested to be used in their classrooms based on a STS approach, which includes the societal issues as a main goal.
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
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.
Poulsen, Tim S; Espersen, Maiken Lise Marcker; Kofoed, Vibeke;
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....... interest was identified from a serial H&E stained slide following tissue cores were transferred to a tissue microarrays (TMA). When using TMA in a routine flow, all patients will be tested for HER2 status with IHC followed by CISH or FISH, thereby providing individual HER2 results. In conclusion, our...
Syed Mohammad Ashiqur Rahman
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.
JIANG LiYong; LI XiangYin; ZHANG Jie
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.
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.
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.
Peacock, E.; Titus, K.; Garshelis, D.L.; Peacock, M.M.; Kuc, M.
We used tetracycline biomarking, augmented with genetic methods to estimate the size of an American black bear (Ursus americanus) population on an island in Southeast Alaska. We marked 132 and 189 bears that consumed remote, tetracycline-laced baits in 2 different years, respectively, and observed 39 marks in 692 bone samples subsequently collected from hunters. We genetically analyzed hair samples from bait sites to determine the sex of marked bears, facilitating derivation of sex-specific population estimates. We obtained harvest samples from beyond the study area to correct for emigration. We estimated a density of 155 independent bears/100 km2, which is equivalent to the highest recorded for this species. This high density appears to be maintained by abundant, accessible natural food. Our population estimate (approx. 1,000 bears) could be used as a baseline and to set hunting quotas. The refined biomarking method for abundance estimation is a useful alternative where physical captures or DNA-based estimates are precluded by cost or logistics. Copyright ?? 2011 The Wildlife Society.
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.
García-Moreno María J
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
Long, Tang; Hu, Wang; Yong, Cai; Lichen, Mao; Guangyao, Li
Springback is related to multi-factors in the process of metal forming. In order to construct an accurate metamodel between technical parameters and springback, a general set of quantitative model assessment and analysis tool, termed high dimension model representations (HDMR), is applied to building metamodel. Genetic algorithm is also integrated for optimization based on metamodel. Compared with widely used metamodeling techniques, the most remarkable advantage of this method is its capacity to dramatically reduce sampling effort for learning the input-output behavior from exponential growth to polynomial level. In this work, the blank holding forces (BHFs) and corresponding key time are design variables. The final springback is well controlled by the HDMR-based metamodeling technique.
Lustig, Yaniv; Hindiyeh, Musa; Orshan, Laor; Weiss, Leah; Koren, Ravit; Katz-Likvornik, Shiri; Zadka, Hila; Glatman-Freedman, Aharona; Mendelson, Ella; Shulman, Lester M
West Nile Virus (WNV) is endemic in Israel and has been the cause of several outbreaks in recent years. In 2000, a countrywide mosquito survey was established to monitor WNV activity and characterize viral genotypes in Israel. We analyzed data from 7135 pools containing 277 186 mosquitoes collected over the past 15 years and, here, report partial sequences of WNV genomes obtained from 102 of the 336 positive mosquito pools. Phylogenetic analysis demonstrated that cluster 4 and the Mediterranean and Eastern European subtypes of cluster 2 within WNV lineage 1 circulated in Israel, as did WNV lineage 2, highlighting a high genetic diversity of WNV genotypes in our region. As a major crossroads for bird migration between Africa and Eurasia and with a long history of human infection, Israel serves as a resource hub for WNV in Africa and Eurasia and provides valuable information on WNV circulation in these regions. PMID:26597260
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 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...... 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....
In order to establish high-frequency regeneration and high-efficiency genetic transformation system in maize, the significance of the 11 factors influencing maize embryonic callus induction and 9 factors affecting embryonic callus differentiation was researched by orthogonal experiment. The results showed that genotype had highly significant impact on induction of embryonic callus. The concentration of 6-BA, AgNO3, 2,4-D, ABA, and medium are the significant factors. The Multi-comparison showed that ABA 2 mg/L has a significant influence. Among the callus differentiation factors, the genotype and 6-BA concentration showed a strong main effect, the concentrations of NAA, medium, KT and 2,4-D had significant impacts on callus differentiation. Southern blotting analysis demonstrated that the resistant callus rate under the selection pressure of 25 mg/L hygromycin was a reliable indicator for system optimization in resistance screening. The concentration of acetosyringone (AS) showed sensitive differences among genotypes. The highest transformation rate was found with the optimized combination of 24-25 degrees C for co-culture temperature, 0.7 ODx15 min for Agrobacterium tumefa-ciens concentration and incubation-time, and pH 5.5-6.2. By this optimized combination, the survival rate of resistant calli as an index for the stable transformation rates of inbred lines Huangzao 4 and Zong 31 by introducing GUS gene into maize inbred lines was as high as 48.6% and 46.2%, respectively. PMID:19933098
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
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
Wang, Haiming; Zhang, Zhenjie; Chen, Zhanqiang; Zhang, Yanru; Lv, Qiang; An, Xiaoping; Tong, Yigang; Carr, Michael J; Sun, Shuhong; Shi, Weifeng
To understand the molecular epidemiology and evolution of avian influenza viruses (AIV) along the East Asian-Australian migration flyway, we collected faecal samples (n=2859) between November 2014 and March 2015 from poultry, environmental sources and wild birds in Dongying, Shandong province and Yancheng, Jiangsu province in eastern China. The presence of AIV RNA was evaluated by real-time PCR and the positivity rate ranged from 0 to 29.3%. In both Dongying and Yancheng, samples collected from live poultry markets had the highest positivity rate for AIV RNA. AIV whole genomes were generated and phylogenetically analysed. Our results demonstrate that most of the viruses belonged to the H9N2 subtype, and could be classified into nine novel genotypes based on the phylogenetic analysis of the eight gene segments of the AIV genomes. This revealed a high genetic diversity of H9N2 in this region and suggested that they might have undergone frequent genetic reassortment. In addition, the internal genes (PB2, etc.) of two viruses from wild birds and several viruses from poultry belonged to the same gene constellation, suggesting a potential inter-host transmission of AIV between wild birds and poultry in live markets along routes of migratory flyways. Our results highlight the high genetic diversity of AIV along the East Asian-Australian migration flyway and the need for more extensive AIV surveillance in eastern China. PMID:26876220
Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. PMID:26626574
Munday, Philip L.; Jones, Geoffrey P.; Hobbs, Jean-Paul A.; Lynne van Herwerden; Jerry, Dean R.
In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic divers...
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.
Dörr, Tobias; Delgado, Fernanda; Umans, Benjamin D; Gerding, Matthew A; Davis, Brigid M; Waldor, Matthew K
Gram-negative bacteria are notoriously resistant to a variety of high-molecular-weight antibiotics due to the limited permeability of their outer membrane (OM). The basis of OM barrier function and the genetic factors required for its maintenance remain incompletely understood. Here, we employed transposon insertion sequencing to identify genes required for Vibrio cholerae resistance to vancomycin and bacitracin, antibiotics that are thought to be too large to efficiently penetrate the OM. The screen yielded several genes whose protein products are predicted to participate in processes important for OM barrier functions and for biofilm formation. In addition, we identified a novel factor, designated vigA (for vancomycin inhibits growth), that has not previously been characterized or linked to outer membrane function. The vigA open reading frame (ORF) codes for an inner membrane protein, and in its absence, cells became highly sensitive to glycopeptide antibiotics (vancomycin and ramoplanin) and bacitracin but not to other large antibiotics or detergents. In contrast to wild-type (WT) cells, the vigA mutant was stained with fluorescent vancomycin. These observations suggest that VigA specifically prevents the periplasmic accumulation of certain large antibiotics without exerting a general role in the maintenance of OM integrity. We also observed marked interspecies variability in the susceptibilities of Gram-negative pathogens to glycopeptides and bacitracin. Collectively, our findings suggest that the OM barrier is not absolute but rather depends on specific OM-antibiotic interactions. PMID:27216069
Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong
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.
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.
Noella J. Gray
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.
Lu, Lin; Chang, Yunlong; Li, Yingmin; Lu, Ming
An orthogonal experiment was conducted by the means of multivariate nonlinear regression equation to adjust the influence of external transverse magnetic field and Ar flow rate on welding quality in the process of welding condenser pipe by high-speed argon tungsten-arc welding (TIG for short). The magnetic induction and flow rate of Ar gas were used as optimum variables, and tensile strength of weld was set to objective function on the base of genetic algorithm theory, and then an optimal design was conducted. According to the request of physical production, the optimum variables were restrained. The genetic algorithm in the MATLAB was used for computing. A comparison between optimum results and experiment parameters was made. The results showed that the optimum technologic parameters could be chosen by the means of genetic algorithm with the conditions of excessive optimum variables in the process of high-speed welding. And optimum technologic parameters of welding coincided with experiment results.
Chudyk, Sarah; McMillan, Amy; Lange, Catherine
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…
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.
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
Sánchez-Vilas, Julia; Philipp, Marianne; Retuerto, Rubén
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 ...
Nagy Ervin D
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
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
Stiassny Melanie LJ
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.
Zhou, Zunchun; Liu, Shikai; Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai
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.
The document reproduces the text of an agreement by exchange of letters with Belize in connection with the Treaty for the Prohibition of Nuclear Weapons in Latin America and the Caribbean. The agreement was approved by the Board of Governors on 18 March 1997 and entered into force on that date
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.
Zhang, Jiawei; Tang, Ming; Shi, Jun; Fu, Songnian; Li, Lihua; Liu, Ying; Cheng, Xueping; Liu, Jian; Shum, Ping
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(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.
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.
Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan
Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He =...
Berube, M; Urban, J; Dizon, AE; Brownell, RL; Palsboll, PJ
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
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:...
Brasino, Michael; Lee, Ju Hun; Cha, Jennifer N
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.
Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani
Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington's Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular. PMID:23863947
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
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.
Plough, L V; Shin, G; Hedgecock, D
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.
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.
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 focus of conservation strategies. ?? 2011 Springer-Verlag (outside the USA).
Hansen, Benni Winding; Banta, Gary Thomas; Kesäniemi, Jenni E;
The genetic structure of benthic marine invertebrates is often described as “chaotic” when genetic structure cannot be explained and barriers to dispersal and gene flow cannot be identified. Here, chaotic patterns of genetic structure for the polychaete Pygospio elegans (Claparède) sampled at 16...... 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...
Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M
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. PMID:27490364
Full Text Available BACKGROUND: The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. METHODOLOGY/PRINCIPAL FINDINGS: To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50% and latency of the optimized engineered gene networks. CONCLUSIONS/SIGNIFICANCE: Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.
Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W
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.
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.
Knight, Julian C.
The EMBO/EMBL symposium ‘Human Variation: Cause and Consequence' highlighted advances in understanding the molecular basis of human genetic variation and its myriad implications for biology, human origins and disease.
Ella Vázquez-Domínguez; Angélica Hernández-Valdés; Aliet Rojas-Santoyo; Luis Zambrano
Given the seasonal nature of ecosystems such as permanent sinkholes ('cenotes') and temporary wetlands, their fi sh fauna experience yearly local extinction and colonization processes, with strong fl uctuations in population size. We evaluated the genetic diversity, population genetic structure and degree of isolation of populations of Poecilia orri and Gambusia yucatana among and within wetlands and cenotes. We also assessed some abiotic characteristics of the water bodies and their potentia...
Cancer treatment is facing major evolution since the advent of targeted therapies. Building genetic profiles could predict sensitivity or resistance to these therapies and highlight disease-specific abnormalities, supporting personalized patient care. In the context of biomedical research and clinical diagnosis, our laboratory has developed an oncogenic panel comprised of 226 genes and a dedicated bioinformatic pipeline to explore somatic mutations in cervical carcinomas, using high-throughput sequencing. Twenty-nine tumors were sequenced for exons within 226 genes. The automated pipeline used includes a database and a filtration system dedicated to identifying mutations of interest and excluding false positive and germline mutations. One-hundred and seventy-six total mutational events were found among the 29 tumors. Our cervical tumor mutational landscape shows that most mutations are found in PIK3CA (E545K, E542K) and KRAS (G12D, G13D) and others in FBXW7 (R465C, R505G, R479Q). Mutations have also been found in ALK (V1149L, A1266T) and EGFR (T259M). These results showed that 48% of patients display at least one deleterious mutation in genes that have been already targeted by the Food and Drug Administration approved therapies. Considering deleterious mutations, 59% of patients could be eligible for clinical trials. Sequencing hundreds of genes in a clinical context has become feasible, in terms of time and cost. In the near future, such an analysis could be a part of a battery of examinations along the diagnosis and treatment of cancer, helping to detect sensitivity or resistance to targeted therapies and allow advancements towards personalized oncology
Anderson V. Vasconcellos
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.
Bhattacharya, T.; Beach, T.; Wahl, D.
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.
Olschwang, S.; Laurent-Puig, P.; Melot, T. [Institut Curie, Paris (France)
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.
Marina S Ascunce
Full Text Available Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus. This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer, and the clothing (body louse (Pediculus humanus humanus Linnaeus. Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long
Wójkiewicz, Błażej; Litkowiec, Monika; Wachowiak, Witold
Gene flow tends to have a homogenising effect on a species' background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine-a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species' putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs
Ascunce, Marina S; Toups, Melissa A; Kassu, Gebreyes; Fane, Jackie; Scholl, Katlyn; Reed, David L
Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary
McCoy, Roger Wesley
Statement of the problem. Few studies in biology education have examined the underlying presuppositions which guide thinking and concept learning in adolescents. The purpose of this study was to describe and understand the biological world views of a variety of high school students before they take biology courses. Specifically, the study examined student world views in the domains of Classification, Relationship and Causation related to the concepts of heredity, evolution and biotechnology. The following served as guiding questions: (1) What are the personal world views of high school students entering biology classes, related to the domain of Classification, Relationship and Causality? (2) How do these student world views confound or enhance the learning of basic concepts in genetics and evolution? Methods. An interpretive method was chosen for this study. The six student participants were ninth graders and represented a wide range of world view backgrounds. A series of three interviews was conducted with each participant, with a focus group used for triangulation of data. The constant comparative method was used to categorize the data and facilitate the search for meaningful patterns. The analysis included a thick description of each student's personal views of classification, evolution and the appropriate use of biotechnology. Results. The study demonstrates that world view is the basis upon which students build knowledge in biology. The logic of their everyday thinking may not match that of scientists. The words they use are sometimes inconsistent with scientific terminology. This study provides evidence that students voice different opinions depending on the social situation, since they are strongly influenced by peers. Students classify animals based on behaviors. They largely believe that the natural world is unpredictable, and that humans are not really part of that world. Half are unlikely to accept the evolution of humans, but may accept it in other
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.
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
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. PMID:26439740
Peterson, James A.
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
Full Text Available Foraging habitats of juveniles of the Mayan cichlid, Cichlasoma urophthalmus (Günther, 1862, were investigated in two mangrove ponds located in Twin Cays offshore islet in Belize: Sink Hole pond (SH and Hidden Lake pond (HL. Sink Hole pond is a semiclosed body of water, whereas Hidden Lake pond is connected by a channel to adjacent seagrass beds that surround the islet. Gut contents of 21 juvenile C. urophthalmus (9.8-13.2 cm total length were analyzed, and five prey taxa were identified. In both mangrove ponds, C. urophthalmus were opportunistic carnivores and consumed primarily crustaceans. Plant material and detritus present in gut contents were most likely ingested incidentally when the fish foraged on small invertebrates. Carbon isotopic values of fish specimens from the two ponds were similar (mean ± SD of -19.2 ± 0.4‰ in SH and -19.4 ± 0.4‰ in HL, and were close to those of mangrove prey (mean ± SD = -20.2 ± 1.5‰, suggesting that this fish species forages in this habitat. Mixing models showed a higher contribution of mangrove food sources to the fish diet than seagrass food sources. This study reveals that young Mayan cichlids, inhabiting two Belize mangrove ponds, are generalists and opportunistic carnivores that forage on mangrove food sources and do not appear to move to adjacent seagrass beds to complement their diets. Understanding trophic linkages between aquatic consumers and food resources may contribute to better management of threatened coastal ecosystems.Habitats de alimentação de juvenis do ciclídeo-maia, Cichlasoma urophthalmus (Günther, 1862, foram investigados em duas lagoas de mangue localizadas nas ilhas Twin Cays em alto mar em Belize: Sink Hole Lake (SH e Hidden Lake (HL. Sink Hole é um corpo d'água parcialmente isolado, enquanto Hidden Lake é ligada por um canal com bancos de sargaços que cercam a ilhota. O conteúdo estomacal de 21 juvenil de C. urophthalmus (9,8-13,2 cm de comprimento total foram
Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna
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.
Schierenbeck, Lisa; Ries, David; Rogge, Kristin; Grewe, Sabrina; Weisshaar, Bernd; Kruse, Olaf
Background: High light tolerance of microalgae is a desired phenotype for efficient cultivation in large scale production systems under fluctuating outdoor conditions. Outdoor cultivation requires the use of either wild-type or non-GMO derived mutant strains due to safety concerns. The identification and molecular characterization of such mutants derived from untagged forward genetics approaches was limited previously by the tedious and time-consuming methods involving techniques such as ...
Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.
We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutati...
Padula, Maria Carmela; Lepore, Laura; Milella, Luigi; Ovesna, Jaroslava; Malafronte, Nicola; Martelli, Giuseppe; de Tommasi, Nunziatina
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.
Gelbart, Hadas; Yarden, Anat
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…
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.
Annetta, Leonard A.; Minogue, James; Holmes, Shawn Y.; Cheng, Meng-Tzu
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…
Risgaard, B; Jabbari, R; Refsgaard, L;
More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved...
Khare, Siddharth M; Awasthi, Anjali; Venkataraman, V; Koushika, Sandhya P
Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semi-automated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of ∼1 μN on an individual pillar and a total average force of ∼7.68 μN. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4 Hz applying an average force of ∼1.58 μN on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces
Seyyed Abed Hosseini
Full Text Available This paper describes an optimal design for multivariable PI controller with a high gain structure for an irregular system by genetic algorithm. PI controllers with a high gain structure leads to the asymptotic decomposition of the fast and slow modes in the closed loop system that have unique characteristics. The slow modes are asymptotically uncontrollable and unobservable; therefore, they have not role in input and output behavior. The closed-loop response is affected only from rapid poles; therefore, the system response will have quick behavior. An essential requirement of this design is that the first Markov parameter of multivariable system (the matrix product CB must have full rank. If the CB matrix is not full rank, the measurement matrix (M is used with internal feedback. In this structure, the measurement matrix is chosen using genetic algorithm in order to reach the stable closed-loop system and minimize interference between outputs. The research is implemented on the two kind of different systems. The results show that the response time of PI controller with a high gain structure by genetic algorithms has good behavior in comparison with other methods.
Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling
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
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.
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
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.
Chen, Rong; Dudley, Joel T; Ruau, David; Butte, Atul J
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.
Casas-Vargas, Andrea; Gómez, Alberto; Briceño, Ignacio; Díaz-Matallana, Marcela; Bernal, Jaime E; Rodríguez, José Vicente
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.
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
Liu Xue Zhong; Shan Kun; Qing Jing; Cheng Jing; YanDenise
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.
Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Christian C Figueroa
It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whale...
Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A.; Davey, Richard T.; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A.; Rehm, Catherine; Greer, Sarah E.; Lucey, Daniel L.; Danley, Kristen
HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence a...
Ranjan Kumar Shaw; Laxmikanta Acharya; Arup Kumar Mukherjee
Genetic diversity was evaluated among 14 cultivars of Catharanthus roseus using RAPD and ISSR markers.The RAPD primers resulted in the amplification of 56 bands, among which 46 (82%) bands were polymorphic Four ISSRprimers amplified 31 loci out of which 17 were polymorphic and 14 are monomorphic. The Jaccard's similarity derived fromthe combined marker system showed that the varieties First Kiss Coral and Cooler Orchid were the most closely relatedcultivars, with 98% similarity. In the dendro...
Castelblanco-Martínez, Delma Nataly; Padilla-Saldivar, J.; Hernández-Arana, Héctor Abuid; Slone, D.H.; Reid, J.P.; Morales-Vela, B.
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.
Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni
The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782
Jeglinski, Jana W E; Wolf, Jochen B W; Werner, Christiane; Costa, Daniel P; Trillmich, Fritz
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.
Jeglinski, Jana W E; Wolf, Jochen B W; Werner, Christiane; Costa, Daniel P; Trillmich, Fritz
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. PMID:26307593
Zhu, Di; Schubert, Martin F.; Cho, Jaehee; Schubert, E. Fred; Crawford, Mary H.; Koleske, Daniel D.; Shim, Hyunwook; Sone, Cheolsoo
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.
Hjortshøj, Rasmus Lund; Ravnshøj, A.R.; Nyman, M.;
and of these 84 showed a unique genotype pattern. The genetic structure of populations in Scotland and Denmark is highly similar and we find no evidence of population sub-division. An analysis of molecular variance was used to show that 86 % of the variance is attributable to within field genetic...
Tomas Mas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, Anna;
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...
Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Figueroa, Christian C
It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a
The Agreement between the Government of Belize and the IAEA for the application of safeguards in connection with the Treaty on the Non-Proliferation of Nuclear Weapons was approved by the Agency's Board of Governors on 19 February 1986 and signed in Vienna on 8 July 1991 and in New York on 13 August 1992; the Protocol hereto was signed in New York on 13 August 1992 and in Vienna on 2 September 1992. The Agreement entered into, force on 21 January 1997. The present documents contains two parts: Part I stipulates the agreement of Belize to accept safeguards on all source or special fissionable material in all peaceful nuclear activities within its territory, under its jurisdiction or carried out under its control anywhere, for the exclusive purpose of verifying that such material is not diverted to nuclear weapons or other nuclear explosive devices. Part II specifies the procedures to be applied in the implementation of the safeguards provisions of part one
Ncube, K T; Mdladla, K; Dzomba, E F; Muchadeyi, F C
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. PMID:26919178
Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang
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.
Zhan, Aibin; Bailey, Sarah A; Heath, Daniel D; Macisaac, Hugh J
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.
Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel
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
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.
Gomes, Cidália; Sousa, Ronaldo; Mendes, Tito; Borges, Rui; Vilares, Pedro; Vasconcelos, Vitor; Guilhermino, Lúcia; Antunes, Agostinho
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
Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin
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.
Bartholomei-Santos, M L; Roratto, P A; Santos, S
Species with a broad distribution rarely have the same genetic make-up throughout their entire range. In some cases, they may constitute a cryptic complex consisting of a few species, each with a narrow distribution, instead of a single-, widely distributed species. These differences can have profound impacts for biodiversity conservation planning. The genetic differentiation of four populations of Aegla longirostri, a freshwater crab found in two geographically isolated basins in Rio Grande do Sul State, Brazil, was investigated by analyzing pentanucleotide multi-loci microsatellites in a heteroduplex assay. Although no morphological differences were evident, we found significant genetic differentiation among the four populations, based on F(ST) values and clustering analysis. This high level of differentiation may be indicative of cryptic species in these populations. If this hypothesis is correct, then the species occurring in the Ibicuí-Mirim River, at the southern limit of the Atlantic Rain Forest, would be under threat, considering its very restricted distribution. PMID:22179994
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.
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.
Na, Rong; Ye, Dingwei; Qi, Jun; Liu, Fang; Lin, Xiaoling; Helfand, Brian T; Brendler, Charles B; Conran, Carly; Gong, Jian; Wu, Yishuo; Gao, Xu; Chen, Yaqing; Zheng, S Lilly; Mo, Zengnan; Ding, Qiang; Sun, Yinghao; Xu, Jianfeng
Genetic risk score (GRS) based on disease risk-associated single nucleotide polymorphisms (SNPs) is an informative tool that can be used to provide inherited information for specific diseases in addition to family history. However, it is still unknown whether only SNPs that are implicated in a specific racial group should be used when calculating GRSs. The objective of this study is to compare the performance of race-specific GRS and nonrace-specific GRS for predicting prostate cancer (PCa) among 1338 patients underwent prostate biopsy in Shanghai, China. A race-specific GRS was calculated with seven PCa risk-associated SNPs implicated in East Asians (GRS7), and a nonrace-specific GRS was calculated based on 76 PCa risk-associated SNPs implicated in at least one racial group (GRS76). The means of GRS7 and GRS76 were 1.19 and 1.85, respectively, in the study population. Higher GRS7 and GRS76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRS7 had a better area under the receiver-operating curve (AUC) than GRS76 for discriminating PCa (0.602 vs 0.573) and high-grade PCa (0.603 vs 0.575) but did not reach statistical significance. GRS7 had a better (up to 13% at different cutoffs) positive predictive value (PPV) than GRS76. In conclusion, a race-specific GRS is more robust and has a better performance when predicting PCa in East Asian men than a GRS calculated using SNPs that are not shown to be associated with East Asians. PMID:27140652
Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie
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.
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
Podsiadlowski, L.; Carapelli, A.; Nardi, F.; Dallai, R.; Koch,M.; Boore, J.L.; Frati, F.
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.
In 1983, two different varieties were treated with five doses of fast neutrons and two concentrations of ethyl methane-sulphonate (EMS) in order to study the effects of different mutagens on the production of mutations with high protein and oil content. The experiment seems to show that EMS had a better effect in inducing such mutations. It showed not only a large variation in extent, but also a higher frequency of mutations. Fast neutrons could also induce mutations with high protein and oil content, but the rate was lower than for EMS. For high protein and oil content mutations induced by fast neutrons, the correlation between the M2 and M3 generations was unstable; it is difficult to forecast the protein and oil content of subsequent generations from seeds of the M2 generation. The high protein and oil content mutations induced by EMS showed a high hereditary value in the M2 and M3 lines. The values of such parameters as hereditary variation, the hereditary variance coefficient, the hereditary capacity and the genetic advance of high protein content mutations were higher than those for high oil content mutations. Thus, it seems easier to induce mutations with high protein rather than high oil content. (author). 8 refs, 2 figs, 4 tabs
Liu, Tian; Guo, Linlin; Pan, Yuling; Zhao, Qi; Wang, Jianhua; Song, Zhenqiao
Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies. PMID:27040179
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.
Jie ZHANG; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Pan, Huitang; Zhong, Junjun; Huang, Long; Liu, Enze
High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landsc...
Ranjan Kumar Shaw
Full Text Available Genetic diversity was evaluated among 14 cultivars of Catharanthus roseus using RAPD and ISSR markers.The RAPD primers resulted in the amplification of 56 bands, among which 46 (82% bands were polymorphic Four ISSRprimers amplified 31 loci out of which 17 were polymorphic and 14 are monomorphic. The Jaccard's similarity derived fromthe combined marker system showed that the varieties First Kiss Coral and Cooler Orchid were the most closely relatedcultivars, with 98% similarity. In the dendrogram constructed on the basis of both RAPD and ISSR data two clear clusterswere obtained. The smaller cluster included C. roseus Cv Blue Pearl and C. roseus Cv. Patricia White and the larger clusterwas subdivided into two sub clusters with C. roseus Cv. First Kiss Polka Dot isolated from the rest of the cultivars. This maybe useful for breeding for improved quality.
Tripathi, Jaindra N; Oduor, Richard O; Tripathi, Leena
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.
Hilmo, Olga; Lundemo, Sverre; Holien, Håkon; Stengrundet, Kirsti; Stenøien, Hans K
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances structures within populations were absent or appeared on small scales (5-10m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity. PMID:22571538
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
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.
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
Mitrovski, P; Heinze, D A; Broome, L; Hoffmann, A A; Weeks, A R
In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F(ST) values between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations. PMID:17181722
Graf, Nadja; Altenbuchner, Josef
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. PMID:24136472
Graf, Nadja; Altenbuchner, Josef
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.
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
@@ 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.
Peters, June A; Kenen, Regina; Giusti, Ruthann; Loud, Jennifer; Weissman, Nancy; Greene, Mark H
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. PMID:15378540
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.
Dawson, Vaille Maree; Venville, Grady
An outcome of science education is that young people have the understandings and skills to participate in public debate and make informed decisions about science issues that influence their lives. Toulmin’s argumentation skills are emerging as an effective strategy to enhance the quality of evidence based decision making in science classrooms. In this case study, an Australian science teacher participated in a one-on-one professional learning session on argumentation before explicitly teaching argumentation skills to two year 10 classes studying genetics. Over two lessons, the teacher used whole class discussion and writing frames of two socioscientific issues to teach students about argumentation. An analysis of classroom observation field notes, audiotaped lesson transcripts, writing frames and student interviews indicate that four factors promoted student argumentation. The factors are: the role of the teacher in facilitating whole class discussion; the use of writing frames; the context of the socioscientific issue; and the role of the students. It is recommended that professional learning to promote student argumentation may need to be tailored to individual teachers and that extensive classroom based research is required to determine the impact of classroom factors on students’ argumentation.
Bertola, L D; Jongbloed, H; van der Gaag, K J; de Knijff, P; Yamaguchi, N; Hooghiemstra, H; Bauer, H; Henschel, P; White, P A; Driscoll, C A; Tende, T; Ottosson, U; Saidu, Y; Vrieling, K; de Iongh, H H
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M
HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.
The use of cassava for the production of single cell protein includes two basic approaches: the selection of strains to utilize cassava carbohydrate for their growth and the improvement of these strains using classic mutagenesis and/or gene engineering techniques and tools. This paper describes molecular genetic procedures applied to increase the amylolytic abilities of the strains of Streptomyces and Thermomonospora genera which are efficient producers of a number of enzymes and to utilize cassava as a carbon source. The specific genes coding the production of alpha-amylase were isolated from Streptomyces limosus and Thermomonospora curvata and inserted into wide spectrum, multicopy plasmid vectors of streptomycetes. The increased dosage of these genes led to over production of alpha-amylases in a series of streptomycete recipients. It is intended that another representative of the order Actinomycetales, Corynebacterium manihot isolated from the cassava root, should be used as a recipient of the prepared wide-spectrum recombined plasmids bearing thermosensitive and thermostable genes (for improvement of utilizing the cassava starch). After verification of the suitability of C. manihot, the strain should be mutagenized to obtain mutants producing increased amounts of an essential amino acid which then would increase the nutritional value of the used microorganism. (author). 7 refs
Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan
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.
SHAN Tifeng; PANG Shaojun; LIU Feng; XU Na; ZHAO Xiaobo; GAO Suqin
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.
Vignaud, Thomas M.
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.
Vignaud, Thomas M; Mourier, Johann; Maynard, Jeffrey A; Leblois, Raphael; Spaet, Julia; Clua, Eric; Neglia, Valentina; Planes, Serge
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. PMID:25251515
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.
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
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.
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.
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
The genus Nairovirus (family Bunyaviridae) contains seven serogroups consisting of 34 predominantly tick-borne viruses, including several associated with severe human and livestock diseases [e.g., Crimean Congo hemorrhagic fever (CCHF) and Nairobi sheep disease (NSD), respectively]. Before this report, no comparative genetic studies or molecular detection assays had been developed for this virus genus. To characterize at least one representative from each of the seven serogroups, reverse transcriptase-polymerase chain reaction (RT-PCR) primers targeting the L polymerase-encoding region of the RNA genome of these viruses were successfully designed based on conserved amino acid motifs present in the predicted catalytic core region. Sequence analysis showed the nairoviruses to be a highly diverse group, exhibiting up to 39.4% and 46.0% nucleotide and amino acid identity differences, respectively. Virus genetic relationships correlated well with serologic groupings and with tick host associations. Hosts of these viruses include both the hard (family Ixodidae) and soft (family Argasidae) ticks. Virus phylogenetic analysis reveals two major monophyletic groups: hard tick and soft tick-vectored viruses. In addition, viruses vectored by Ornithodoros, Carios, and Argas genera ticks also form three separate monophyletic lineages. The striking similarities between tick and nairovirus phylogenies are consistent with possible coevolution of the viruses and their tick hosts. Fossil and phylogenetic data placing the hard tick-soft tick divergence between 120 and 92 million years ago suggest an ancient origin for viruses of the genus Nairovirus
CHEN Min; LIAO Wan-qing; WU Shao-xi; YAO Zhi-rong; PAN Wei-hua; LIAO Yong
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.
Kärst, Stefan; Cheng, Riyan; Schmitt, Armin O; Yang, Hyuna; de Villena, Fernando Pardo Manuel; Palmer, Abraham A; Brockmann, Gudrun A
Intramuscular fat content and water-holding capacity are important traits in livestock as they influence meat quality, nutritive value of the muscle, and animal health. As a model for livestock, two inbred lines of the Berlin Muscle Mouse population, which had been long-term selected for high muscle mass, were used to identify genomic regions affecting intramuscular fat content and water-holding capacity. The intramuscular fat content of the Musculus longissimus was on average 1.4 times higher in BMMI806 than in BMMI816 mice. This was accompanied by a 1.5 times lower water-holding capacity of the Musculus quadriceps in BMMI816 mice. Linkage analyses with 332 G(3) animals of reciprocal crosses between these two lines revealed quantitative trait loci for intramuscular fat content on chromosome 7 and for water-holding capacity on chromosome 2. In part, the identified loci coincide with syntenic regions in pigs in which genetic effects for the same traits were found. Therefore, these muscle-weight-selected mouse lines and the produced intercross populations are valuable genetic resources to identify genes that could also contribute to meat quality in other species. PMID:21732194
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.
Shah, Niraj; Hirakawa, Hideki; Kusakabe, Shohei;
Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping and can aid contig and scaffold anchoring in the final stages of genome assembly. In thi...
Pampoulie, C.; Gysels, E.S.; Maes, G.E.; Hellemans, B.; Leentjes, V.; A. G. Jones; Volckaert, F.A.M.J.
Marine fish seem to experience evolutionary processes that are expected to produce genetically homogeneous populations. We have assessed genetic diversity and differentiation in 15 samples of the sand goby Pomatoschistus minutus (Pallas, 1770) (Gobiidae, Teleostei) from four major habitats within the Southern Bight of the North Sea, using seven microsatellite and 13 allozyme loci. Despite its high dispersal potential, microsatellite loci revealed a moderate level of differentiation (overall F...
Carlos M Restrepo
Full Text Available American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP, a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at
Zhang, Yu; Li, Xuegong; Bartlett, Douglas H; Xiao, Xiang
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.
Palko, S. [Machines Division, ABB industry Oy, Helsinki (Finland)
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.
Magalhaes, Isabel S; Ornelas-Garcıa, Claudia Patricia; Leal-Cardin, Mariana; Ramírez, Tania; Barluenga, Marta
Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The 'desert cichlid' Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages. PMID:26175313
Feitosa, Mary F; Wojczynski, Mary K; Straka, Robert;
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...
Treur, J.L.; Boomsma, D.I.; Ligthart, R.S.L.; Willemsen, G.; Vink, J.M.
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
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
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
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.
Winham Stacey J
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.
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.
Wevers, Diana; Metzger, Sonja; Babweteera, Fred; Bieberbach, Marc; Boesch, Christophe; Cameron, Kenneth; Couacy-Hymann, Emmanuel; Cranfield, Mike; Gray, Maryke; Harris, Laurie A.; Head, Josephine; Jeffery, Kathryn; Knauf, Sascha; Lankester, Felix; Siv Aina J. Leendertz
Adenoviruses (AdVs) broadly infect vertebrate hosts, including a variety of nonhuman primates (NHPs). In the present study, we identified AdVs in NHPs living in their natural habitats, and through the combination of phylogenetic analyses and information on the habitats and epidemiological settings, we detected possible horizontal transmission events between NHPs and humans. Wild NHPs were analyzed with a pan-primate AdV-specific PCR using a degenerate nested primer set that targets the highly...
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.
Acute high altitude disease(AHAD), which can be divided into acute mountain disease (AMS), high altitude pulmonary edema (HAPE) and high altitude cerebral edema (HACE), is one of the special illnesses occurred at high altitude, commonly encountered by travelers to high altitudes (>2 500 m), which affects people's work capacity and health and could be even a life-threatening disease. Despite extensive investigations over the last century, the pathophysiology of AHAD remains elusive. Nevertheless, numerous researches have confirmed the existence of AHAD susceptibility differences. The aim of this paper was to review the epidemiological evidence for a genetic component to the various forms of AHAD so far, as well as to supply helpful reference to its epidemiological studies.%急性高原病(Acute high altitude disease,AHAD)分为急性高原反应、高原肺水肿和高原脑水肿,是高原特发病之一,在高原旅居者中(>2 500 m)具有高发生率,不仅影响人们的工作能力和健康,而且可能危及生命.尽管AHAD 的相关研究已开展百余年,其病理生理机制仍不明确,但大量研究已证实AHAD 存在易感性的差异.文章综述了迄今为止AHAD 的遗传易感性研究进展,以期为AHAD 的流行病学研究提供有益的参考资料.
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.
Qiu, Yuchen; Chen, Xiaodong; Li, Zheng; Li, Yuhua; Chen, Wei R.; Zheng, Bin; Li, Shibo; Liu, Hong
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.
Hesselberg, Marie Louise; Wegener, Gregers; Buchholtz, Poul Erik
Repetitive Magnetic Stimulation (rTMS) has appeared to be a potential non-invasive antidepressant method, which implies non-convulsive focal stimulation of the brain through a time varying magnetic field. The antidepressant potential of rTMS has been supported by animal studies showing a number of interesting similarities between magnetic stimulation and electroconvulsive stimulation (ECS). Despite these positive results, this method still contains many unknown issues. Importantly, there are fundamental uncertainties concerning the optimal combination of stimulus parameters (frequency, intensity, duration, and number of pulses) to obtain an antidepressant effect. Therefore, the present study aimed to qualify the choice of rTMS stimulus frequency in a well-validated genetic animal model of depression, the FSL/FRL rats. We compared the antidepressant effect of low frequency, high frequency rTMS and ECS to sham treatment in FRL and FSL rats using 6 parallel groups. We used the Forced Swim Test and the Open Field Test to screen the depression-like state in rats. We found that both the high frequency and the low frequency rTMS resulted in a significant antidepressant effect. However, this effect was inferior to the effect of ECS. The low frequency and high frequency groups, which received the same total impulse load and stimulus intensity, did not differ with respect to antidepressant efficacy in this study. In conclusion, this study provides robust evidence that both rTMS interventions are efficacious, although not as efficient as ECS. PMID:27473004
Gusev, Oleg; Nakahara, Yuichi; Sakashita, Tetsuya; Kikawada, Takahiro; Okuda, Takashi
Anhydrobiotic larvae of African chironomid Polypedilum vanderplanki are known to show an extremely high tolerance against a range of stresses. The tolerance against various extreme environments exhibited by that insect might be due to being almost completely desiccated replacing water with trehalose, a state where little or no chemical reactions occur. From 2005 dried larvae of this insect are being used in a number of space experiments, both inside and outside of ISS as a model organism for estimation the limits of higher organisms' resistance to space environment stresses and long-term storage of the alive anhydrobiotic organisms during continues spaceflight. We have shown previously that both hydrated and dried larvae of Polypedilum vanderplanki have very higher tolerance against both highand low-linear energy transfer (LET), surviving after 7000Gy irradiation. It was suggested that the larvae would have effective DNA-reparation system in addition to artificial protection provided by glass-stage without water. In the present study we conducted analysis of stress-related gene expression in the larvae after 70-2000 Gy irradiations. Both DNA damage level and activity of DNA-reparation, anti-apoptotic and protein-damage related genes were analyzed. Direct visualization of DNA damage in the larvae fat body cells using Comet Assay showed that fragmented by radiation DNA is re-arranged within 76-98 hours after exposure. We found that massive overexpression of hsp and anti-oxidant genes occur in larvae entering anhydrobiosis , and provides refolding of proteins after rehydration. In the irradiated larvae overexpression of DNA-reparation enzymes anti-apoptotic genes was confirmed, suggesting that survival after high-dose irradiation is a result of combination of highly effective blocking of entering the apoptosis after severe DNA damage and DNA reparation.
Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus;
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...... automation of DNA sequencing....
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.
Rafiei A; Darzyani Azizi M; Taheri S; Haghshenas MR; Hosseinian A; Makhlough A
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.
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.
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populations. All PAP scores (21- 47 mm Hg) fall within the range of low to moderate risks. Differences in means were not significant for any pair of populations. Some of the readings (values <28 mm HG) for the Semien cattle group measured at 3500 m are out of the range of readings of approx. 100,000 cattle that the veterinarian has taken in the Rocky mountains in the course of 20 years. Crosses of the local cattle with Holstein Friesian and Jersey were not more prone to brisket disease than local cattle measured at the same altitudes. In a study comparing PAP readings in yak, cattle and their crosses, the crosses had equally low PAP readings as the yaks. Yaks are known to be resistant to high altitude disease due to an adaptation of vascular system, indicated by thin-walled small pulmonary arteries. The authors speculated about an autosomal dominant gene transmitting genetic attenuation of the hypoxic vasoconstrictor response. We conclude that cattle breeds of North Western Ethiopia are genetically adapted to high altitude. To get an insight on the mechanism of adaptation an in depth histological study on the internal anatomy of cardiovascular and respiratory systems of these genotypes is currently being undertaken. (author)
Full Text Available Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC, the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA and B. oleracea (2n = 18, CC. A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP and simple sequence repeat (SSR markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.
Ozan, Erol; Deveci, Erdem; Oral, Meltem; Karahan, Utku; Oral, Elif; Aydin, Nazan; Kirpinar, Ismet
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. PMID:20435102
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
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.
Liu, S; Li, Y; Qin, Z; Geng, X; Bao, L; Kaltenboeck, L; Kucuktas, H; Dunham, R; Liu, Z
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.
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.
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.
Chung, Byung Yeoup; Kim, Jae Sung; Kim, Jin Hong
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
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
Read, Jazlyn; Wadt, Karin A W; Hayward, Nicholas K
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 herita......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...... 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...... polygenic component to susceptibility, and a unique level of personal melanoma risk influenced by multiple low-risk alleles and genetic modifiers. In addition to conferring a risk of cutaneous melanoma, some 'melanoma' predisposition genes have been linked to other cancers, with cancer clustering observed...
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.
Guldemir, Dilek; Acar, Sumeyra; Otgun, Selin Nar; Unaldi, Ozlem; Gozalan, Aysegul; Ertek, Mustafa; Durmaz, Riza
This study obtained information on the serotypes and molecular typing characteristics of Streptococcus pneumoniae strains causing invasive diseases in Turkey. Sixty-eight S. pneumoniae isolates causing invasive pneumococcal diseases were collected from different regions of Turkey from 2009 to 2011. The isolates were characterized by performing multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and capsular serotyping, and 25 different serotypes were identified. Serotypes 19F, 23F, 1, 14, and 7F were common and accounted for 52.9% of all the serotypes. In addition, 54 different PFGE profiles (pulsotypes) were observed. Twenty-three of the 68 (33.8%) isolates were clustered into 9 pulsotypes. MLST analysis yielded 36 sequence types, of which 12 (33.3%) were novel. A comparison of results with the global pneumococcal MLST database by performing eBURST analysis showed that our strains belonged to 20 different clonal complexes and 5 singletons. In addition, we identified 4 new alleles: 2 gdh, 1 xpt, and 1 ddl. Thus, the results of this study highlighted a high level of diversity among pneumococcal isolates. In addition, the study identified a case of possible capsular switching. PMID:26255730
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.
Tuvblad, C; Forero, DA
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
Kobylecki, Camilla J; Afzal, Shoaib; Davey Smith, George;
BACKGROUND: High intake of fruit and vegetables as well as high plasma vitamin C concentrations have been associated with low risk of ischemic heart disease in prospective studies, but results from randomized clinical trials have been inconsistent. OBJECTIVE: We tested the hypothesis...... that genetically high concentrations of plasma vitamin C, such as with high intake of fruit and vegetables, are associated with low risk of ischemic heart disease and all-cause mortality. DESIGN: We used a Mendelian randomization approach and genotyped for solute carrier family 23 member 1 (SLC23A1) rs33972313...... disease and 0.88 (0.72, 1.08; P = 0.22) for all-cause mortality. CONCLUSIONS: High intake of fruit and vegetables was associated with low risk of ischemic heart disease and all-cause mortality. Although the 95% CI for genetically high plasma vitamin C concentrations overlapped 1.0, which made certain...
Full Text Available Siberian apricot (Prunus sibirica L., an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940. Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species.
Bresler, S E; Kalinin, V L; Kopylova, Y U; Krivisky, A S; Rybchin, V N; Shelegedin, V N
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
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.
Martín Manuel Checa Artasu
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
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.
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
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
Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M
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
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
Lopes, I.F.; Haig, S.M.; Lama, S.N.D.
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.
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.
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
Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le
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
Ježić, Marin; Krstin, Ljiljana; Rigling, Daniel; Curković-Perica, Mirna
The ascomycete fungus Cryphonectria parasitica is an aggressive introduced pathogen of sweet chestnut (Castanea sativa Mill.). It has spread throughout the chestnut-growing areas of Europe, with higher diversity in the regions close to its first introduction and lower diversity in its expanding ranges in Europe. To reconstruct the invasion events that could explain the high diversity of C. parasitica in Croatia and Slovenia, 180 samples were genotyped using 11 sequence-characterized amplified region markers. Eight of 11 loci were found to be polymorphic, and a total of 66 different haplotypes were identified. Bayesian clustering indicated the existence of two clusters, which suggests two separate introductions of C. parasitica in these regions. The first cluster is dominant in western parts of Croatia and Slovenia and the second in eastern and northern regions. The data analysis indicates that northern Italy was the first source of infection, with the subsequent introduction from south-eastern Europe, which contributed significantly to the diversity of the C. parasitica populations tested. Most haplotypes were probably derived through sexual recombination between a few divergent haplotypes, which suggests that multiple introductions and sexual reproduction are important for the formation of genetically diverse C. parasitica populations.
Arash SAYYAH; Mitra AFLAK; Alireza REZAZADEH
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.
Chen, Qiang; Chen, Yunhao; Jiang, Weiguo
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. PMID:27483285
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.
Yang, Rongchang; Palermo, Cindy; Chen, Linda; Edwards, Amanda; Paparini, Andrea; Tong, Kaising; Gibson-Kueh, Susan; Lymbery, Alan; Ryan, Una
Cryptosporidium is an enteric parasite that infects humans and a wide range of animals. Relatively little is known about the epidemiology and taxonomy of Cryptosporidium in fish. In the present study, a total of 775 fish, belonging to 46 species and comprising ornamental fish, marine fish and freshwater fish were screened for the prevalence of Cryptosporidium by PCR. The overall prevalence of Cryptosporidium in fish was 5.3% (41/775), with prevalences ranging from 1.5 to 100% within individual host species. Phylogenetic analysis of these Cryptosporidium isolates as well as 14 isolates from previous studies indicated extensive genetic diversity as well as evidence for mixed infections. At the 18S locus the following species were identified; Cryptosporidium molnari-like genotype (n=14), Cryptosporidium huwi (n=8), piscine genotype 2 (n=4), piscine genotype 3-like (n=1), piscine genotype 4 (n=2), piscine genotype 5 (n=13), piscine genotype 5-like (n=1) and five novel genotypes (n=5). At the actin locus, species identification agreed with the 18S locus for only 52.3% of isolates sequenced, indicating high levels of mixed infections. Future studies will need to employ both morphological characterization and deep sequencing amplicon-based technologies to better understand the epidemiological and phylogenetic relationships of piscine-derived Cryptosporidium species and genotypes, particularly when mixed infections are detected. PMID:26527238
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
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.
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
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
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
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.
Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.
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
Sina-Elisabeth Ben Ali
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.
da Silva, Raimundo; Veneza, Ivana; Sampaio, Iracilda; Araripe, Juliana; Schneider, Horacio; Gomes, Grazielle
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.
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.
Chen, Nanhua; Gao, Qi; Wang, Shanqing; Wang, Guangze; Gatton, Michelle; Cheng, Qin
Chloroquine-resistant Plasmodium falciparum was highly prevalent in Hainan, China, in the 1970s. Twenty-five years after cessation of chloroquine therapy, the prevalence of P. falciparum wild-type Pfcrt alleles has risen to 36% (95% confidence interval, 22.1 to 52.4%). The diverse origins of wild-type alleles indicate that there was no genetic bottleneck caused by high chloroquine resistance.
Lindsay, A.; McCloskey, J.; Nalbant, S. S.; Simao, N.; Murphy, S.; NicBhloscaidh, M.; Steacy, S.
Identifying fault sections where slip deficits have accumulated may provide a means for understanding sequences of large megathrust earthquakes. Stress accumulated during the interseismic period on locked sections of an active fault is stored as potential slip. Where this potential slip remains unreleased during earthquakes, a slip deficit can be said to have accrued. Analysis of the spatial distribution of slip during antecedent events along the fault will show where the locked plate has spent its stored slip and indicate where the potential for large events remains. The location of recent earthquakes and their distribution of slip can be estimated instrumentally. To develop the idea of long-term slip-deficit modelling it is necessary to constrain the size and distribution of slip for pre-instrumental events dating back hundreds of years covering more than one ';seismic cycle'. This requires the exploitation of proxy sources of data. Coral microatolls, growing in the intertidal zone of the outer island arc of the Sunda trench, present the possibility of producing high resolution reconstructions of slip for a number of pre-instrumental earthquakes. Their growth is influenced by tectonic flexing of the continental plate beneath them allows them to act as long term geodetic recorders. However, the sparse distribution of data available using coral geodesy results in a under determined problem with non-unique solutions. Instead of producing one definite model satisfying the observed corals displacements, a Monte Carlo Slip Estimator based on a Genetic Algorithm (MCSE-GA) accelerating the rate of convergence is used to identify a suite of models consistent with the data. Successive iterations of the MCSE-GA sample different displacements at each coral location, from within the spread of associated uncertainties, producing a catalog of models from the full range of possibilities. The suite of best slip distributions are weighted according to their fitness and stacked to
Ascunce, Marina S.; Toups, Melissa A.; Gebreyes Kassu; Jackie Fane; Katlyn Scholl; Reed, David L
Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pedicu...
Fukumura, Tomoe; Kose, Hiroyuki; Takeda, Chiyo; Kurita, Yuko; Ochiai, Kazuhiko; Yamada, Takahisa; Matsumoto, Kozo
The condition of hyperglycemia results from multiple genetic and environmental factors. In recent years much progress has been made with regards to the search for candidate genes involved in the expression of various common diseases including type 2 diabetes. However less is known about the specific genetic and environmental connections that are important for the development of the disease. In the present study, we used hyperglycemic congenic rats to address this issue. When given a normal di...
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. ...
Léo A. Hartmann
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
DeCorte, I. A.; Greer, L.; Wirth, K. R.; Flowers Falls, E.; Lescinsky, H.; Doss, W. C.
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
Minty, C.D. [Natural History Museum, London (United Kingdom); Sutton, D.A.; Rogers, A.D.F.; Bateman, R.M.; Penn, M.; Stafford, P.J.; Sanders, L.M. (eds.)
The Natural Museum of History in London conducted a wildlife impact assessment of the proposed Macal River Upper Storage Facility (MRUSF) in Belize, Central America. The area contains a rare and discrete floral floodplain habitat (riparian shrubland) which acts as a conduit and critical habitat for resident and non-resident fauna and avifauna. In addition, the entire profile of the floodplain habitat of the watershed is important to the sustenance and population viability of a unique Scarlet Macaw subspecies, providing the last remaining habitat for a small population of about 60 to 100 individual birds. Other species have also been identified as regionally, nationally or globally significant. The proposed Chalillo Dam would be constructed on the Macal River Valley, approximately 5 km upstream from Guacamallo Bridge. If the project goes ahead, much of the area will be permanently flooded. The reservoir would flood up to an elevation of 400 m above the mean sea level. This report presented three options. The first option is not to build the Chalillo dam. This would leave the natural riparian habitat biologically rich and ecologically functional. The second option is to choose an alternative site, such as damming one or more of the many tributaries in the Mountain Pine Ridge. The third option is to proceed as planned, but it has been made clear that it will not be possible to mitigate against the long-term impacts on the biodiversity of the catchment, particularly those associated with habitat loss. The MRUSF is likely to cause 80 per cent of the riparian shrubland to be lost and numerous individual animals to die. In addition, it was predicted that the impacts of the project will be much greater in the surrounding areas, reaching much beyond the localized area of the dam and its impoundment. The most obvious option to avoid profound impacts is to not construct the dam. It was emphasized that this option should be seriously considered, particularly if costs outweigh
Qiao, Jiangwei; Cai, Mengxian; Yan, Guixin; Wang, Nian; Li, Feng; Chen, Binyun; Gao, Guizhen; Xu, Kun; Li, Jun; Wu, Xiaoming
Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts. PMID:26031705
Zheng, M; Huang, X; Smith, G K; Yang, X; Gao, X
Recent molecular genetics studies have revealed a correlation between spontaneous, progressive expansion of several DNA trinucleotide repeats and certain hereditary neurodegenerative diseases. Triplet repeat (TR) sequences may be present in structured forms that can mediate the processes interrupting normal cellular replication, transcription, or repair activities, eventually leading to gene mutation. Using high resolution NMR spectroscopy and other biophysical methods, we probed the solution structures and properties of single-stranded TR sequences. These studies have led to the discovery of a new duplex motif (e-motif), present in CCG repeats, and to the elucidation of the structure of the (CTG)3 duplex. In this paper we provide a global picture of the solution behavior of the human disease-related CXG (X = A, C, G, or T) and the comparison GXC (X = A, or T) TR sequences. All six triplet repeats form antiparallel duplexes. The mismatched bases in CAG and CGG repeat duplexes are rather flexible and they do not appear to form stable, paired conformations. By comparison, GAC repeat duplexes and their mismatched A residues are well-structured. Most interestingly, the structures of the disease-related CXG repeats exhibit a propensity for folding at chain lengths as short as 12 residues. Furthermore, the energy barrier for the formation of homo-duplexes from the corresponding complementary hetero-duplexes are much lower for the CXG TR sequences than for the GAC or GTC TR sequences. These results provide insights into the conformation and physiochemical properties of TR sequences. Thus, a basis is provided for further studies of the behavior of long TR sequences in an effort to elucidate the molecular mechanisms of in vivo expansion and function of TR sequences. PMID:8951379
Lasho, Terra; Johnson, Sarah H; Smith, David I; Crispino, John D; Pardanani, Animesh; Vasmatzis, George; Tefferi, Ayalew
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.
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.
The incidence of high myopia is high in population,and is one of the leading causes of vision impairment and blindness. Myopia mostly is regarded as a common complex trait involving multiple interactions between genetic and environmental factors. Genetic factors play a critical role in the development of myopia,especially high myopia. In recent years,a number of genetic loci for high myopia have been identified, including collagen, lumican, growth factors, transcriptional factors, and so on. This article reviews the recent advances in studying the genes related to high myopia.%高度近视在人群当中的患病率较高,是导致低视力及盲的遗传性眼病之一.近视是遗传和环境等多种因素相互作用的结果,高度近视的发生具有明显的遗传倾向,目前已发现了多个高度近视的候选基因位点,包括胶原类基因、基膜类基因、生长因子类基因、转录因子类基因等,本研究就高度近视致病基因研究的新进展做一综述.
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).
Deal Karin R
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
Cañas-Álvarez, J J; González-Rodríguez, A; Munilla, S; Varona, L; Díaz, C; Baro, J A; Altarriba, J; Molina, A; Piedrafita, J
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.
Williams, Dana E.; Miller, M. W.; Baums, I. B.
Elkhorn coral , Acropora palmata, relies heavily on clonal propagation and often displays low genotypic (clonal) diversity. Populations in the Florida Keys experienced rapid declines in tissue cover between 2004 and 2006, largely due to hurricanes and disease, but remained stable from 2006 to 2010. All elkhorn colonies in 150 m2 permanent study plots were genotyped in 2006 ( n = 15 plots) and 2010 ( n = 24 plots), and plots sampled in both years were examined for changes in allelic and genotypic diversity during this period of stable ecological abundance. Overall, genetic diversity of Florida plots was low and declined further over the 4-yr period; seven of the 36 original genets and two of 67 alleles (among five microsatellite loci) were lost completely from the sampled population, and an additional 15 alleles were lost from individual reefs. In 2010, Florida plots (~19 colonies) contained an average of 2.2 ± 1.38 (mean ± SD) genets with a significant negative correlation between colony abundance and genotypic diversity. When scaled to total tissue abundance, genotypic diversity is even lower, with 43 % of genets below the size of sexual maturity. We examined the hypothesized positive relationship of local genotypic diversity with ecological performance measures. In Florida plots ( n = 15), genotypic diversity was not significantly correlated with tissue loss associated with chronic predation, nor with acute disease and storm-fragmentation events, though this relationship may be obscured by the low range of observed diversity and potential confounding with abundance. When more diverse plots in Curaçao ( n = 9) were examined, genotypic diversity was not significantly correlated with resistance during an acute storm disturbance or rate of recovery following disturbance. Cryptic loss of genetic diversity occurred in the apparently stable Florida population and confirms that stable or even increasing abundance does not necessarily indicate genetic stability.
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
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.
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.
Vadaparampil, Susan T; Malo, Teri L.; Nam, Kelli M.; Nelson, Alison; de la Cruz, Cara Z.; Quinn, Gwendolyn P.
We describe the development of a psychoeducational intervention (PEI) to increase uptake of genetic counseling targeted to high-risk breast cancer survivors. Based on previous research, scientific literature, and a review of cancer education websites, we identified potential PEI content. We then assessed the initial acceptability and preference of two booklets of identical content but different layouts, by presenting the booklets to individuals with a personal or family history of breast canc...
Full Text Available Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis, the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS technique to simultaneously discover and genotype single nucleotide polymorphism (SNP markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1,704 and 1,719 markers and encompassed 2,041 cM and 1,874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23 - 1.25 cM. A total of 1,114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2,321 markers and spanned the cumulative length of 2,052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry
Rousseau-Gueutin, Mathieu; Lerceteau-Köhler, Estelle; Barrot, Laure; Sargent, Daniel James; Monfort, Amparo; Simpson, David; Arús, Pere; Guérin, Guy; Denoyes-Rothan, Béatrice
Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. ×ananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny...
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
Cotton genome complexity was investigated with a saturated molecular genetic map that combined several sets of microsatellites or simple sequence repeats (SSR) and the first major public set of single nucleotide polymorphism (SNP) markers in cotton genomes (Gossypium spp.), and that was constructed ...
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.
Kramer, P J
Systems for testing genetic toxicology are components of carcinogenic and genetic risk assessment. Present routine genotoxicity-testing is based on at least 20 years of development during which many different test systems have been introduced and used. Today, it is clear that no single test is capable of detecting all genotoxic agents. Therefore, the usual approach is to perform a standard battery of in-vitro and in-vivo tests for genotoxicity. Work-groups of the European Union (EU), the Organization for Economic Co-operation and Development (OECD), and, very recently, the work-group of the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) have defined such standard battery tests. These and some currently used supplementary or confirmatory tests are briefly discussed here. Additional test systems for the assessment of genotoxic and carcinogenic hazard and risk are seriously needed. These tests must be more relevant to man than are current assays and less demanding in respect of cost, time and number of animals. Another aspect for reassessment derives from the actual situation in the pharmaceutical industry. Companies have to prepare for the world economy of the 21st century. Therefore, pharmaceutical research is speeding up tremendously by use of tools such as genomics, combinatorial chemistry, high throughput screening and proteomics. Toxicology and genotoxicology need to re-evaluate their changing environment and must find ways to respond to these needs. In conclusion, genetic toxicology needs to answer questions coming from two major directions: hazard and risk identification and high throughput testing. PMID:9625484
Nourisson, Coralie; Morales-Vela, Benjamín; Padilla-Saldívar, Janneth; Tucker, Kimberly Pause; Clark, Annmarie; Olivera-Gómez, Leon David; Bonde, Robert; McGuire, Peter
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. PMID:21681472
Nourisson, Coralie; Morales-Vela, Benjamín; Padilla-Saldívar, Janneth; Tucker, Kimberly Pause; Clark, Annmarie; Olivera-Gómez, Leon David; Bonde, Robert; McGuire, Peter
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.
Nourisson, Coralie; Morales-Vela, Benjamin; Padilla-Saldivar, Janneth; Tucker, Kimberly Pause; Clark, Ann Marie; Olivera-Gomez, Leon David; Bonde, Robert; McGuire, Peter
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.
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
Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.
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.
Population generic analyses have been highly successful in deciphering inter- and intraspecific evolutionary relationships, levels of gene flow, genetic divergence and effective population sizes. Parameters estimated by traditional population genetic analyses are evolutionary averages and thus not n
Yang, Weizhao; Qi, Yin; Fu, Jinzhong
High elevation adaptation offers an excellent study system to understand the genetic basis of adaptive evolution. We acquired transcriptome sequences of two closely related lizards, Phrynocephalus przewalskii from low elevations and P. vlangalii from high elevations. Within a phylogenetic framework, we compared their genomic data along with green anole, chicken and Chinese softshell turtle, and identified candidate genes and functional categories that are potentially linked to adaptation to high elevation environments. More than 100 million sequence reads were generated for each species via Illumina sequencing. A de novo assembly produced 70,919 and 62,118 transcripts for P. przewalskii and P. vlangalii, respectively. Based on a well-established reptile phylogeny, we detected 143 positively selected genes (PSGs) along the P. vlangalii lineage from the 7,012 putative orthologs using a branch-site model. Furthermore, ten GO categories and one KEGG pathway that are over-represented by PSGs were recognized. In addition, 58 GO categories were revealed to have elevated evolutionary rates along the P. vlangalii lineage relative to P. przewalskii. These functional analyses further filter out PSGs that are most likely involved in the adaptation process to high elevations. Among them, ADAM17, MD, and HSP90B1 likely contributed to response to hypoxia, and POLK likely contributed to DNA repair. Many other candidate genes involved in gene expression and metabolism were also identified. Genome-wide scan for candidate genes may serve as the first step to explore the genetic basis of high elevation adaptation. Detailed comparative study and functional verification are needed to solidify any conclusions. High elevation adaptation requires coordinated changes in multiple genes that involve various physiological and biochemical pathways; we hope that our genetic studies will provide useful directions for future physiological or molecular studies in reptiles as well as other
Pini, J.; Planes, S.; Rochel, E.; Lecchini, D.; Fauvelot, C.
We investigated the short-term impact of environmental-induced stress on survival and neutral genetic diversity of recently settled juveniles of a damselfish, Dascyllus aruanus, using spatiotemporal caging experiments in various natural environmental conditions in Moorea (French Polynesia). Juveniles' mortality was followed at five study sites and overall four experiments, mortality rates ranged from 0 to 45%. Mortality rate and average daily water temperature were positively correlated ( P = 0.018). Juveniles' mortality rate and allelic richness estimated from ten microsatellite loci were negatively correlated ( P = 0.046). Together, an overdominance of heterozygotes was observed within hostile environments. These results suggest that an allelic richness loss may be expected as a direct consequence of unfavorable environmental conditions. Thus, a worrisome scenario on demographic and genetic consequences may be expected from habitat degradation in the context of global change and human pressure increases.
Mishra, S K; Niranjan, S K; Banerjee, B; Dubey, P K; Gonge, D S; Mishra, B P; Kataria, R S
In this study, genetic diversity analysis of MHC class II-DQA locus helped in identification of 25 new Bubu-DQA nucleotide sequences in swamp buffaloes (Bubalus bubalis carabanesis, Bubu). Phylogenetic analysis revealed the distribution of the buffalo DQA sequences in two major clusters of DQA1 and DQA2 genes, sharing common lineages with corresponding cattle alleles, possibly due to trans-species evolution. However, a highly divergent sequence, Bubu-DQA*2501, homologous to cattle (BoLA) DQA3 allele, was identified, indicating the existence of an additional locus; putative DQA3 in buffalo. PCR-RFLP analysis revealed extensive duplication of DQA locus in swamp buffaloes, sharing DQA1, DQA2, and DQA3 alleles in different combinations in duplicated haplotypes. Higher dN than dS values and Wu-Kabat variability at peptide-binding regions in Bubu-DQA indicated high polymorphism with balancing selection. Levels of genetic diversity within DQA sequences and duplication in a small population of swamp buffalo indicate the genetic richness of the species, important for fitness. PMID:27177904
WANG, X. R.; Szmidt, A E; Savolainen, O.
Pinus densata has been suggested to have originated from hybridization events involving P. tabulaeformis and P. yunnanensis. In this study, allozyme differentiation at 12 loci was studied in 14 populations of P. tabulaeformis, P. densata, and P. yunnanensis from China. The observed genetic composition of P. densata supported the hybrid hypothesis and showed varying degrees of contribution from P. yunnanensis and P. tabulaeformis among its populations. These data, together with previous chloro...
Marie Foulongne-Oriol; Manuela Rocha de Brito; Delphine Cabannes; Aurélien Clément; Cathy Spataro; Magalie Moinard; Eustáquio Souza Dias; Philippe Callac; Jean-Michel Savoie
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 t...
Sousa-Santos, Carla; Robalo, Joana I; Francisco, Sara M; Carrapato, Carlos; Cardoso, Ana Cristina; Doadrio, Ignacio
Genetic factors have direct and indirect impacts in the viability of endangered species. Assessing their genetic diversity levels and population structure is thus fundamental for conservation and management. In this paper we use mitochondrial and nuclear markers to address phylogeographic and demographic data on the critically endangered Anaecypris hispanica, using a broad sampling set which covered its known distribution area in the Iberian Peninsula. Our results showed that the populations of A. hispanica are strongly differentiated (high and significant ФST and FST values, corroborated by the results from AMOVA and SAMOVA) and genetically diversified. We suggest that the restricted gene flow between populations may have been potentiated by ecological, hydrological and anthropogenic causes. Bayesian skyline plots revealed a signal for expansion for all populations (tMRCA between 68kya and 1.33Mya) and a genetic diversity latitudinal gradient was detected between the populations from the Upper (more diversified) and the Lower (less diversified) Guadiana river basin. We postulate a Pleistocenic westwards colonization route for A. hispanica in the Guadiana river basin, which is in agreement with the tempo and mode of paleoevolution of this drainage. The colonization of River Guadalquivir around 60kya with migrants from the Upper Guadiana, most likely by stream capture, is also suggested. This study highlights the view that critically endangered species facing range retreats (about 47% of its known populations have disappeared in the last 15years) are not necessarily small and genetically depleted. However, the extinction risk is not negligible since A. hispanica faces the combined effect of several deterministic and stochastic negative factors and, moreover, recolonization events after localized extinctions are very unlikely to occur due to the strong isolation of populations and to the patchily ecologically-conditioned distribution of fish. The inferred species
van Oppen, Madeleine J H; Lukoschek, Vimoksalehi; Berkelmans, Ray; Peplow, Lesa M; Jones, Alison M
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
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.
Garay, Erika; Campos, Sergio E; González de la Cruz, Jorge; Gaspar, Ana P; Jinich, Adrian; Deluna, Alexander
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.
T Jacob; T Jebasingh; M N Venugopal; R Usha
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.
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.
Sie, Aisha S; Spruijt, Liesbeth; van Zelst-Stams, Wendy A G; Mensenkamp, Arjen R; Ligtenberg, Marjolijn J L; Brunner, Han G; Prins, Judith B; Hoogerbrugge, Nicoline
According to standard practice following referral to clinical genetics, most high risk breast cancer (BC) patients in many countries receive face-to-face genetic counseling prior to BRCA-mutation testing (DNA-intake). We evaluated a novel format by prospective study: replacing the intake consultation with telephone, written and digital information sent home. Face-to-face counseling then followed BRCA-mutation testing (DNA-direct). One year after BRCA-result disclosure, 108 participants returned long-term follow-up questionnaires, of whom 59 (55 %) had previously chosen DNA-direct (intervention) versus DNA-intake (standard practice i.e., control: 45 %). Questionnaires assessed satisfaction and psychological distress. All participants were satisfied and 85 % of DNA-direct participants would choose this procedure again; 10 % would prefer DNA-intake and 5 % were undecided. In repeated measurements ANOVA, general distress (GHQ-12, p = 0.01) and BC-specific distress (IES-bc, p = 0.03) were lower in DNA-direct than DNA-intake at all time measurements. Heredity-specific distress (IES-her) did not differ significantly between groups. Multivariate regression analyses showed that choice of procedure did not significantly contribute to either general or heredity-specific distress. BC-specific distress (after BC diagnosis) did contribute to both general and heredity-specific distress. This suggests that higher distress scores reflected BC experience, rather than the type of genetic diagnostic procedure. In conclusion, the large majority of BC patients that used DNA-direct reported high satisfaction without increased distress both in the short term, and 1 year after conclusion of genetic testing. PMID:26531312
H. S. Ginwal; Neha Mittal; Arvind Tomar; V. K. Varshney
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.
... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...
Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P
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 tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.
... go for genetic counseling, such as: A family history of a genetic condition To learn about genetic screening for diseases that are more common in certain ethnic groups (e.g., sickle cell disease in African Americans and Tay-Sachs disease in Ashkenazi Jews) To discuss abnormal results ...
The author discusses the basic principles of genetics, including the classification of genetic disorders and a consideration of the rules and mechanisms of inheritance. The most common pitfalls in clinical genetic diagnosis are described, with emphasis on the problem of the negative or misleading family history.
Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.
Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.
Quilot-Turion, Bénédicte; Leppälä, Johanna; Leinonen, Päivi H.; Waldmann, Patrik; Savolainen, Outi; Kuittinen, Helmi
Background and Aims The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses. Methods Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization. Key Results The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions). Conclusions The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas. PMID:23519836
Yuen, R K C; Robinson, W P
Genetic and epigenetic studies of the human placenta can help to clarify the underlying mechanisms of placenta-associated diseases. However, such studies have also revealed a considerable degree of within- and between-placenta variability, which can be attributed to a variety of influences. We illustrate the inherent heterogeneity in the placenta using examples from two types of studies: 1) chromosomal mosaicism and 2) DNA methylation variation. We discuss the factors that may influence the distribution of variation and how, understanding the source of this variation is important for interpreting data used to investigate and predict clinical outcomes.
Fordyce, Sarah L; Avila-Arcos, Maria C; Rockenbauer, Eszter;
The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR...... repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...
Goldstein, J M; Seidman, L J; Buka, S L; Horton, N J; Donatelli, J L; Rieder, R O; Tsuang, M T
Risk factors for schizophrenia, such as genetic vulnerability and obstetric complications, have been associated with cognitive deficits in schizophrenia. We tested the association of these risk factors with general intellectual ability in offspring at high risk for psychoses and normal control subjects. Offspring of 182 parents with DSM-IV schizophrenia or affective psychoses were recruited and diagnosed from the Boston and Providence cohorts of the National Collaborative Perinatal Project (NCPP). Control subjects from the NCPP were selected to be comparable with affected parents based on the parent's age, ethnicity, study site, number of offspring enrolled in the NCPP, and payment status, and on the offspring's age, sex, and history of obstetric complications. Based on data prospectively acquired from pregnancy and events of gestation, labor, delivery, and the neonatal period, we derived a measure of probable hypoxic-ischemic insult. We also report on standardized measures of general intelligence (intelligence quotient [IQ]) collected at age 7. General linear mixed models were used to test for the simultaneous effects of genetic vulnerability, defined as parental diagnosis, and probable hypoxic insult on age 7 IQ. Specificity of the effects for schizophrenia compared with affective psychoses and sex effects were also tested. Low IQ at age 7 was significantly associated with genetic vulnerability to psychoses, in particular with schizophrenia. PMID:10885634
Si, Young-Jae; Choi, Won Suk; Kim, Young-Il; Lee, In-Won; Kwon, Hyeok-Il; Park, Su-Jin; Kim, Eun-Ha; Kim, Se Mi; Kwon, Jin-Jung; Song, Min-Suk; Kim, Chul-Joong; Choi, Young-Ki
The continuous worldwide spread of highly pathogenic avian influenza (HPAI) H5N8 viruses among wild birds and poultry is a potential threat to public health. In the present study, we investigated the genetic characteristics of recent H5N8 viruses continuously isolated from migratory birds over two winters (2013-2014 and 2014-2015) in South Korea. Genetic and phylogenetic analysis demonstrated that the 2014-2015 HPAI H5N8 viruses are closely related to the 2013-2014 viruses, including virulence markers; however, all eight gene segments of 2014-2015 H5N8 viruses clustered in different phylogenetic branches from 2013-2014 H5N8 viruses, except the A/Em/Korea/W492/2015 virus. The H5N8 viruses of Europe and North America belong to sublineages of the 2013-2014 Korean H5N8 viruses but differ from the 2014-2015 Korean H5N8 viruses. Further hemagglutination inhibition (HI) assay results showed that there were 2-to-4 fold differences in HI titer between 2013-2014 and 2014-2015 H5N8 viruses. Taken together, our results suggested that the 2014-2015 Korean H5N8 viruses were genetically and serologically different from those of 2013-2014 winter season H5N8 viruses, including those from Europe and North America. PMID:27424028
Karafet, Tatiana M; Osipova, Ludmila P; Gubina, Marina A; Posukh, Olga L; Zegura, Stephen L; Hammer, Michael F
We examined genetic variation on the nonrecombining portion of the Y chromosome (NRY) to investigate the paternal population structure of indigenous Siberian groups and to reconstruct the historical events leading to the peopling of Siberia. A set of 62 biallelic markers on the NRY were genotyped in 1432 males representing 18 Siberian populations, as well as nine populations from Central and East Asia and one from European Russia. A subset of these markers defines the 18 major NRY haplogroups (A-R) recently described by the Y Chromosome Consortium (YCC 2002). While only four of these 18 major NRY haplogroups accounted for -95% of Siberian Y-chromosome variation, native Siberian populations differed greatly in their haplogroup composition and exhibited the highest phiST value for any region of the world. When we divided our Siberian sample into four geographic regions versus five major linguistic groupings, analyses of molecular variance (AMOVA) indicated higher phiST and phiCT values for linguistic groups than for geographic groups. Mantel tests also supported the existence of NRY genetic patterns that were correlated with language, indicating that language affiliation might be a better predictor of the genetic affinity among Siberians than their present geographic position. The combined results, including those from a nested cladistic analysis, underscored the important role of directed dispersals, range expansions, and long-distance colonizations bound by common ethnic and linguistic affiliation in shaping the genetic landscape of Siberia. The Siberian pattern of reduced haplogroup diversity within populations combined with high levels of differentiation among populations may be a general feature characteristic of indigenous groups that have small effective population sizes and that have been isolated for long periods of time.
Redin, Claire; Le Gras, Stéphanie; Mhamdi, Oussema; Geoffroy, Véronique; Stoetzel, Corinne; Vincent, Marie-Claire; Chiurazzi, Pietro; Lacombe, Didier; Ouertani, Ines; Petit, Florence; Till, Marianne; Verloes, Alain; Jost, Bernard; Chaabouni, Habiba Bouhamed; Dollfus, Helene; Mandel, Jean-Louis; Muller, Jean
Background Bardet-Biedl syndrome (BBS) is a pleiotropic recessive disorder that belongs to the rapidly growing family of ciliopathies. It shares phenotypic traits with other ciliopathies, such as Alström syndrome (ALMS), nephronophthisis (NPHP) or Joubert syndrome. BBS mutations have been detected in 16 different genes (BBS1-BBS16) without clear genotype-to-phenotype correlation. This extensive genetic heterogeneity is a major concern for molecular diagnosis and genetic counselling. While various strategies have been recently proposed to optimise mutation detection, they either fail to detect mutations in a majority of patients or are time consuming and costly. Method We tested a targeted exon-capture strategy coupled with multiplexing and high-throughput sequencing on 52 patients: 14 with known mutations as proof-of-principle and 38 with no previously detected mutation. Thirty genes were targeted in total including the 16 BBS genes, the 12 known NPHP genes, the single ALMS gene ALMS1 and the proposed modifier CCDC28B. Results This strategy allowed the reliable detection of causative mutations (including homozygous/heterozygous exon deletions) in 68% of BBS patients without previous molecular diagnosis and in all proof-of-principle samples. Three probands carried homozygous truncating mutations in ALMS1 confirming the major phenotypic overlap between both disorders. The efficiency of detecting mutations in patients was positively correlated with their compliance with the classical BBS phenotype (mutations were identified in 81% of ‘classical’ BBS patients) suggesting that only a few true BBS genes remain to be identified. We illustrate some interpretation problems encountered due to the multiplicity of identified variants. Conclusion This strategy is highly efficient and cost effective for diseases with high genetic heterogeneity, and guarantees a quality of coverage in coding sequences of target genes suited for diagnosis purposes. PMID:22773737
Rijavec, Matija; Starcic Erjavec, Marjanca; Ambrozic Avgustin, Jerneja; Reissbrodt, Rolf; Fruth, Angelika; Krizan-Hergouth, Veronika; Zgur-Bertok, Darja
One hundred and ten UTI Escherichia coli strains, from Ljubljana, Slovenia, were analyzed for antibiotic resistances, mobile DNA elements, serotype, and phylogenetic origin. A high prevalence of drug resistance and multidrug resistance was found. Twenty-six percent of the isolates harbored a class 1 integron, while a majority of the strains (56%) harbored rep sequences characteristic of F-like plasmids. int as well as rep sequences were found to be distributed in a random manner among strains of the four major phylogenetic groups indicating that all groups have a similar tendency to acquire and maintain mobile genetic elements frequently associated with resistance determinants.
Erkan, Murat Mert; Kong, Bo; Wu, Weiwei; Valkovska, Nataliya; Jager, Carsten; Hong, Xin; Nitsche, Ulrich; Friess, Helmut; Esposito, Irene; Kleeff, Joerg; Michalski, Christoph W.
A common genetic variation of melanoma inhibitory activity-2 labels a subtype of pancreatic adenocarcinoma with high endoplasmic reticulum stress levels Bo Kong1, Weiwei Wu1, Nataliya Valkovska1, Carsten Ja¨ger1, Xin Hong1, Ulrich Nitsche1, Helmut Friess1, Irene Esposito2, Mert Erkan3, Jo¨rg Kleeff1* & Christoph W. Michalski4* 1Department of Surgery, Technische Universita¨t Mu¨nchen, Munich, Germany, 2Institute of Pathology, Technische Universita¨t Mu¨nchen, Munich, Ge...
Velo-Antón, G; Godinho, R; Harris, D J; Santos, X; Martínez-Freiria, F; Fahd, S; Larbes, S; Pleguezuelos, J M; Brito, J C
Phylogeographic studies during the last decade confirmed an internal complexity of the Iberian Peninsula and northern Maghreb as refugial areas during the Miocene to Pleistocene period. Species with low vagility that experienced the complex climatic and palaeogeographic processes occurred in the Western Mediterranean Basin are excellent candidates to study the extent of lineage diversification in this region. We applied phylogenetic analyses based on mitochondrial data to infer the evolutionary history of Vipera latastei/monticola and identify the major biogeographic events structuring the genetic diversity within this group. We obtained a well-resolved phylogeny, with four highly divergent lineages (one African and three Iberian) that originated in the Tertiary. Coalescence-based estimations suggest that the differentiation of the four major lineages in V. latastei/monticola corresponds to the Messinian salinity crisis and the reopening of the Strait of Gibraltar during the Miocene. Subsequent Pliocene and Pleistocene climatic oscillations continued to isolate both Iberian and Maghrebian populations and led to a high genetic structuring in this group, particularly in Southern Iberia, a complex palaeogeographic and topographic region with high endemism levels. This study does not support the current taxonomy of the group, thus suggesting that an integrative evaluation of Iberian and African populations is needed to resolve its systematics. PMID:22982758
Castède, Sophie; Campoy, José Antonio; García, José Quero; Le Dantec, Loïck; Lafargue, Maria; Barreneche, Teresa; Wenden, Bénédicte; Dirlewanger, Elisabeth
The present study investigated the genetic determinism of flowering date (FD), dissected into chilling (CR) and heat (HR) requirements. Elucidation of the genetic determinism of flowering traits is crucial to anticipate the increasing of ecological misalignment of adaptative traits with novel climate conditions in most temperate-fruit species. CR and HR were evaluated over 3 yr and FD over 5 yr in an intraspecific sweet cherry (Prunus avium) F1 progeny, and FD over 6 yr in a different F1 progeny. One quantitative trait locus (QTL) with major effect and high stability between years of evaluation was detected for CR and FD in the same region of linkage group (LG) 4. For HR, no stable QTL was detected. Candidate genes underlying the major QTL on LG4 were investigated and key genes were identified for CR and FD. Phenotypic dissection of FD and year repetitions allowed us to identify CR as the high heritable component of FD and a high genotype × environment interaction for HR. QTLs for CR reported in this study are the first described in this species. Our results provide a foundation for the identification of genes involved in CR and FD in sweet cherry which could be used to develop ideotypes adapted to future climatic conditions. PMID:24417538
Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max
Li, Bin; Tian, Ling; Zhang, Jingying; Huang, Long; Han, Fenxia; Yan, Shurong; Wang, Lianzheng; Zheng, Hongkun; Sun, Junming
Background Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-de...
Full Text Available In this paper, an optimal design of linear phase digital finite impulse response (FIR highpass (HP filter using the L1-norm based real-coded genetic algorithm (RCGA is investigated. A novel fitness function based on L1 norm is adopted to enhance the design accuracy. Optimized filter coefficients are obtained by defining the filter objective function in L1 sense using RCGA. Simulation analysis unveils that the performance of the RCGA adopting this fitness function is better in terms of signal attenuation ability of the filter, flatter passband and the convergence rate. Observations are made on the percentage improvement of this algorithm over the gradient-based L1 optimization approach on various factors by a large amount. It is concluded that RCGA leads to the best solution under specified parameters for the FIR filter design on account of slight unnoticeable higher transition width.
Walter, R B; Kazianis, S
Fishes of the genus Xiphophorus (platyfishes and swordtails) are small, internally fertilizing, livebearing, and derived from freshwater habitats in Mexico, Guatemala, Belize, and Honduras. Scientists have used these fishes in cancer research studies for more than 70 yr. The genus is presently composed of 22 species that are quite divergent in their external morphology. Most cancer studies using Xiphophorus use hybrids, which can be easily produced by artificial insemination. Phenotypic traits, such as macromelanophore pigment patterns, are often drastically altered as a result of lack of gene regulation within hybrid fishes. These fish can develop large exophytic melanomas as a result of upregulated expression of these pigment patterns. Because backcross hybrid fish are susceptible to the development of melanoma and other neoplasms, they can be subjected to potentially deleterious chemical and physical agents. It is thus possible to use gene mapping and cloning methodologies to identify and characterize oncogenes and tumor suppressors implicated in spontaneous or induced neoplasia. This article reviews the history of cancer research using Xiphophorus and recent developments regarding DNA repair capabilities, mapping, and cloning of candidate genes involved in neoplastic phenotypes. The particular genetic complexity of melanoma in these fishes is analyzed and reviewed. PMID:11581522
Eric S J Harris
Full Text Available Oridonin is a diterpenoid with anti-cancer activity that occurs in the Chinese medicinal plant Isodon rubescens and some related species. While the bioactivity of oridonin has been well studied, the extent of natural variation in the production of this compound is poorly known. This study characterizes natural variation in oridonin production in order to guide selection of populations of Isodon with highest oridonin yield. Different populations of I. rubescens and related species were collected in China, and their offspring were grown in a greenhouse. Samples were examined for oridonin content, genotyped using 11 microsatellites, and representatives were sequenced for three phylogenetic markers (ITS, rps16, trnL-trnF. Oridonin production was mapped on a molecular phylogeny of the genus Isodon using samples from each population as well as previously published Genbank sequences. Oridonin has been reported in 12 out of 74 species of Isodon examined for diterpenoids, and the phylogeny indicates that oridonin production has arisen at least three times in the genus. Oridonin production was surprisingly consistent between wild-collected parents and greenhouse-grown offspring, despite evidence of gene flow between oridonin-producing and non-producing populations of Isodon. Additionally, microsatellite genetic distance between individuals was significantly correlated with chemical distance in both parents and offspring. Neither heritability nor correlation with genetic distance were significant when the comparison was restricted to only populations of I. rubescens, but this result should be corroborated using additional samples. Based on these results, future screening of Isodon populations for oridonin yield should initially prioritize a broad survey of all species known to produce oridonin, rather than focusing on multiple populations of one species, such as I. rubescens. Of the samples examined here, I. rubescens or I. japonicus from Henan province
Dubey, J.P.; Velmurugan, G.V.; Ragendran, C.; Yabsley, M.J.; Thomas, N.J.; Beckmen, K.B.; Sinnett, D.; Ruid, D.; Hart, J.; Fair, P.A.; McFee, W.E.; Shearn-Bochsler, V.; Kwok, O.C.H.; Ferreira, L.R.; Choudhary, S.; Faria, E.B.; Zhou, H.; Felix, T.A.; Su, C.
Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study wild animals, from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. gondii was isolated from 31 animals including, to our knowledge for the first time, from a bald eagle (Haliaeetus leucocephalus), five gray wolves (Canis lupus), a woodrat (Neotoma micropus), and five Arctic foxes (Alopex lagopus). Additionally, 66 T. gondii isolates obtained previously, but not genetically characterised, were revived in mice. Toxoplasma gondii DNA isolated from these 97 samples (31+66) was characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers (SAG1, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). A total of 95 isolates were successfully genotyped. In addition to clonal Types II, and III, 12 different genotypes were found. These genotype data were combined with 74 T. gondii isolates previously characterised from wildlife from North America and a composite data set of 169 isolates comprised 22 genotypes, including clonal Types II, III and 20 atypical genotypes. Phylogenetic network analysis showed limited diversity with dominance of a recently designated fourth clonal type (Type 12) in North America, followed by the Type II and III lineages. These three major lineages together accounted for 85% of strains in North America. The Type 12 lineage includes previously identified Type A and X strains from sea otters. This study revealed that the Type 12 lineage accounts for 46.7% (79/169) of isolates and is dominant in wildlife of North America. No clonal Type I strain was identified among these wildlife isolates. These results suggest that T. gondii strains in wildlife from North America have limited diversity, with the occurrence of only a few major clonal types.
Andreas Teufel; Frank Staib; Stephan Kanzler; Arndt Weinmann; Henning Schulze-Bergkamen; Peter R Galle
The completely assembled human genome has made it possible for modern medicine to step into an era rich in genetic information and high-throughput genomic analysis. These novel and readily available genetic resources and analytical tools may be the key to unravel the molecular basis of hepatocellular carcinoma (HCC). Moreover, since an efficient treatment for this disease is lacking, further understanding of the genetic background of HCC will be crucial in order to develop new therapies aimed at selected targets. We report on the current status and recent developments in HCC genetics. Special emphasis is given to the genetics and regulation of major signalling pathways involved in HCC such as p53, Wntsignalling, TGFβ, Ras, and Rb pathways. Furthermore, we describe the influence of chromosomal aberrations as well as of DNA methylation. Finally, we report on the rapidly developing field of genomic expression profiling in HCC, mainly by microarray analysis.
White, Brian T.
The Virtual Genetics Lab II (VGLII) is an improved version of the highly successful genetics simulation software, the Virtual Genetics Lab (VGL). The software allows students to use the techniques of genetic analysis to design crosses and interpret data to solve realistic genetics problems involving a hypothetical diploid insect. This is a brief…
Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao
Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670
Prospero, S; Lutz, A; Tavadze, B; Supatashvili, A; Rigling, D
In this study, we investigated the population genetic structure and possible origins of the plant pathogen Cryphonectria parasitica in Caucasian Georgia, a region within the centre of origin of the host species Castanea sativa. A total of 427 C. parasitica isolates from nine populations were genotyped at 10 microsatellite loci. A high genetic diversity was detected, but the overall Georgian population was dominated by three haplotypes which were present in most individual populations. Two of them have not been previously found in Europe. Bayesian clustering analysis and principal component analysis could not identify their source population, neither in Asia nor in North America. On the other hand, one haplotype is frequent in Central Europe and probably naturally invaded Caucasian Georgia from neighbouring Turkey. Seventy-three haplotypes were unique to specific populations, and 66 of them were represented by a single isolate. Allele patterns suggest that most of these haplotypes emerged locally through sexual recombination between haplotypes of the Georgian and the central European gene pool. Due to the high incidence of haplotypes not otherwise present in Europe, Caucasian Georgia represents an additional source of diversity for the European C. parasitica population.
Weier, Heinz -Ulrich G
Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.
Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil.
Souto, Ana C P; Bonfietti, Lucas X; Ferreira-Paim, Kennio; Trilles, Luciana; Martins, Marilena; Ribeiro-Alves, Marcelo; Pham, Cau D; Martins, Liline; Dos Santos, Wallace; Chang, Marilene; Brito-Santos, Fabio; Santos, Dayane C S; Fortes, Silvana; Lockhart, Shawn R; Wanke, Bodo; Melhem, Márcia S C; Lazéra, Márcia S; Meyer, Wieland
Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Infections due to C. gattii have mainly been described in tropical and subtropical regions, but its adaptation to temperate regions was crucial in the species evolution and highlighted the importance of this pathogenic yeast in the context of disease. Cryptococcus gattii molecular type VGII has come to the forefront in connection with an on-going emergence in the Pacific North West of North America. Taking into account that previous work pointed towards South America as an origin of this species, the present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population in order to gain new insights into its origin and global dispersal from the South American continent using the ISHAM consensus MLST typing scheme. Our results corroborate the finding that the Brazilian C. gattii VGII population is highly diverse. The diversity is likely due to recombination generated from sexual reproduction, as evidenced by the presence of both mating types in clinical and environmental samples. The data presented herein strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil, Amazonia and the Northeast. Numerous genotypes represent a link between Brazil and other parts of the world reinforcing South America as the most likely origin of the C. gattii VGII subtypes and their subsequent global spread, including their dispersal into North America, where they caused a major emergence. PMID:27529479
Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture
Sandra Maria Alkmim-Oliveira
Full Text Available Introduction Determining the genetic similarities among Trypanosoma cruzi populations isolated from different hosts and vectors is very important to clarify the epidemiology of Chagas disease. Methods An epidemiological study was conducted in a Brazilian endemic area for Chagas disease, including 76 chronic chagasic individuals (96.1% with an indeterminate form; 46.1% with positive hemoculture. Results T. cruzi I (TcI was isolated from one child and TcII was found in the remaining (97.1% subjects. Low-stringency single-specific-primer-polymerase chain reaction (LSSP-PCR showed high heterogeneity among TcII populations (46% of shared bands; however, high similarities (80-100% among pairs of mothers/children, siblings, or cousins were detected. Conclusions LSSP-PCR showed potential for identifying similar parasite populations among individuals with close kinship in epidemiological studies of Chagas disease.
Oftedal, Gry; Parkkinen, Veli-Pekka
Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems. PMID:23591049
Fu, Wei; Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Du, Zhixin; Tian, Wenying; Wang, Qin; Wang, Huiyu; Xu, Wentao; Zhu, Shuifang
Digital PCR has developed rapidly since it was first reported in the 1990 s. It was recently reported that an improved method facilitated the detection of genetically modified organisms (GMOs). However, to use this improved method, the samples must be pretreated, which could introduce inaccuracy into the results. In our study, we explored a pretreatment-free digital PCR detection method for the screening for GMOs. We chose the CaMV35s promoter and the NOS terminator as the templates in our assay. To determine the specificity of our method, 9 events of GMOs were collected, including MON810, MON863, TC1507, MIR604, MIR162, GA21, T25, NK603 and Bt176. Moreover, the sensitivity, intra-laboratory and inter-laboratory reproducibility of our detection method were assessed. The results showed that the limit of detection of our method was 0.1%, which was lower than the labeling threshold level of the EU. The specificity and stability among the 9 events were consistent, respectively. The intra-laboratory and inter-laboratory reproducibility were both good. Finally, the perfect fitness for the detection of eight double-blind samples indicated the good practicability of our method. In conclusion, the method in our study would allow more sensitive, specific and stable screening detection of the GMO content of international trading products.
Roulin, Anne C; Mariadassou, Mahendra; Hall, Matthew D; Walser, Jean-Claude; Haag, Christoph; Ebert, Dieter
Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting-stage production is locally adapted--that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life-history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within- and between-population variation for all dormancy-related traits, but no evidence for the hypothesized higher resting-stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation.
Fu, Wei; Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Du, Zhixin; Tian, Wenying; Wang, Qin; Wang, Huiyu; Xu, Wentao; Zhu, Shuifang
Digital PCR has developed rapidly since it was first reported in the 1990 s. It was recently reported that an improved method facilitated the detection of genetically modified organisms (GMOs). However, to use this improved method, the samples must be pretreated, which could introduce inaccuracy into the results. In our study, we explored a pretreatment-free digital PCR detection method for the screening for GMOs. We chose the CaMV35s promoter and the NOS terminator as the templates in our assay. To determine the specificity of our method, 9 events of GMOs were collected, including MON810, MON863, TC1507, MIR604, MIR162, GA21, T25, NK603 and Bt176. Moreover, the sensitivity, intra-laboratory and inter-laboratory reproducibility of our detection method were assessed. The results showed that the limit of detection of our method was 0.1%, which was lower than the labeling threshold level of the EU. The specificity and stability among the 9 events were consistent, respectively. The intra-laboratory and inter-laboratory reproducibility were both good. Finally, the perfect fitness for the detection of eight double-blind samples indicated the good practicability of our method. In conclusion, the method in our study would allow more sensitive, specific and stable screening detection of the GMO content of international trading products. PMID:26239916
Debra A O'Leary
Full Text Available One therapeutic approach to Duchenne Muscular Dystrophy (DMD recently entering clinical trials aims to convert DMD phenotypes to that of a milder disease variant, Becker Muscular Dystrophy (BMD, by employing antisense oligonucleotides (AONs targeting splice sites, to induce exon skipping and restore partial dystrophin function. In order to search for small molecule and genetic modulators of AON-dependent and independent exon skipping, we screened approximately 10,000 known small molecule drugs, >17,000 cDNA clones, and >2,000 kinase- targeted siRNAs against a 5.6 kb luciferase minigene construct, encompassing exon 71 to exon 73 of human dystrophin. As a result, we identified several enhancers of exon skipping, acting on both the reporter construct as well as endogenous dystrophin in mdx cells. Multiple mechanisms of action were identified, including histone deacetylase inhibition, tubulin modulation and pre-mRNA processing. Among others, the nucleolar protein NOL8 and staufen RNA binding protein homolog 2 (Stau2 were found to induce endogenous exon skipping in mdx cells in an AON-dependent fashion. An unexpected but recurrent theme observed in our screening efforts was the apparent link between the inhibition of cell cycle progression and the induction of exon skipping.
Full Text Available Abstract Background To investigate different responses to a high-fat/cholesterol diet and uncover their underlying genetic factors between C57BL/6J (B6 and DBA/2J (D2 inbred mice. Methods B6 and D2 mice were fed a high-fat/cholesterol diet for a series of time-points. Serum and bile lipid profiles, bile acid yields, hepatic apoptosis, gallstones and atherosclerosis formation were measured. Furthermore, a whole genome microarray was performed to screen hepatic genes expression profile. Quantitative real-time PCR, western blot and TUNEL assay were conducted to validate microarray data. Results After fed the high-fat/cholesterol diet, serum and bile total cholesterol, serum cholesterol esters, HDL cholesterol and Non-HDL cholesterol levels were altered in B6 but not significantly changed in D2; meanwhile, biliary bile acid was decreased in B6 but increased in D2. At the same time, hepatic apoptosis, gallstones and atherosclerotic lesions occurred in B6 but not in D2. The hepatic microarray analysis revealed distinctly different genes expression patterns between B6 and D2 mice. Their functional pathway groups included lipid metabolism, oxidative stress, immune/inflammation response and apoptosis. Quantitative real time PCR, TUNEL assay and western-blot results were consistent with microarray analysis. Conclusion Different genes expression patterns between B6 and D2 mice might provide a genetic basis for their distinctive responses to a high-fat/cholesterol diet, and give us an opportunity to identify novel pharmaceutical targets in related diseases in the future.
Background: We tried to evaluate the female fertility and genetic risk to the offspring from the exposure to high-dose 131I by assessing the pregnancy outcomes and health status of the children of female patients with differentiated thyroid cancer who had received therapeutic doses of 131I. Materials and Methods: From 1967 to 2002, a total of 1,282 women had been treated with 131I. Of these patients, 692 (54%) were in the reproductive age group (18-45 years). Forty women had a total of 50 pregnancies after high-dose 131I. Age at presentation ranged from 16 to 36 years (mean, 23 ± 4 years). Histopathology was papillary thyroid cancer in 32 cases and follicular thyroid cancer in 8 cases. Results: Single high-dose therapy was given in 30 cases, 2 doses were given in 7 cases, 3 doses were given in 2 cases, and four doses were given in 1 case in which lung metastases had occurred. In 37 patients (92%), disease was successfully ablated before pregnancy. Ovarian absorbed-radiation dose calculated by the MIRD method ranged from 3.5 to 60 cGy (mean, 12 ± 11 cGy). The interval between 131I therapy and pregnancy varied from 7 to 120 months (37.4 ± 28.2 months). Three spontaneous abortions occurred in 2 women. Forty-seven babies (20 females and 27 males) were born. Forty-four babies were healthy with normal birth weight and normal developmental milestones. Twenty women delivered their first baby after 131I therapy. The youngest child in our series is 11 months of age, and the oldest is 8.5 years of age. Conclusions: Female fertility is not affected by high-dose radioiodine treatment, and the therapy does not appear to be associated with any genetic risks to the offspring
Vorhaus Daniel B
Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by