Genetic analysis of candidate genes modifying the age-at-onset in Huntington’s disease

The expansion of a polymorphic CAG repeat in the HD gene encoding huntingtin has been identified as the major cause of Huntington’s disease (HD) and determines 42–73% of the variance in the age-at-onset of the disease. Polymorphisms in huntingtin interacting or associated genes are thought to modify the course of the disease. To identify genetic modifiers influencing the age at disease onset, we searched for polymorphic markers in the GRIK2, TBP, BDNF, HIP1 and ZDHHC17 genes and analysed seven of them by association studies in 980 independent European HD patients. Screening for unknown sequence variations we found besides several silent variations three polymorphisms in the ZDHHC17 gene. These and polymorphisms in the GRIK2, TBP and BDNF genes were analysed with respect to their association with the HD age-at-onset. Although some of the factors have been defined as genetic modifier factors in previous studies, none of the genes encoding GRIK2, TBP, BDNF and ZDHHC17 could be identified as a genetic modifier for HD.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Notes on the diet of the critically endangered orange–fronted parakeet (Cyanoramphus malherbi) on Maud Island

Abstract

We conducted opportunistic observations on the diet of translocated orange-fronted parakeets (Cyanoramphus malherbi) on Maud Island to provide a first account of the diversity of food types ingested in the wild by this critically endangered species. Orange-fronted parakeets consumed fruits and leaves of 14 plant species as well as non–dietary items such as bark sticks and grit. Of dietary items, 96% were on plant species and 4% invertebrates. Of the plant species ingested 10% were non-natives. A major dietary component consisted of fruits and leaves of mahoe (Melicytus ramiflorus). In contrast to the only other published account of the diet of orange-fronted parakeets, invertebrates constituted a minor part of identified ingested items. This may be related to the different composition of vegetation at the study sites, the low parakeet population density during the time of our study and methodological restrictions during our survey. Our observations on undocumented food items add information about the biology of New Zealands’ rarest parakeet species and indicate dietary flexibility of the species highlighting the potential of other regenerating islands as release sites to expand the geographic distribution of orange–fronted parakeets.     

Genetic mapping of the Lablab purpureus genome suggests the presence of ’cuckoo’ gene(s) in this species

A linkage map of Lablab purpureus consisting of 127 RFLP and 91 RAPD loci was constructed in an F₂ population of 119 individuals. This population was derived from a cross between ’Rongai’ (an annual cultivar) and CPI 24973 (a perennial wild accession). The map comprises 17 linkage groups and covers 1610 centiMorgans (cM) with an average distance of 7 cM between markers. Severe segregation distortions were observed, with the very extreme situation where no paternal type was recovered from the mapping population. These results strongly suggest the presence of a gene conferring preferential transmission from the maternal parent ’Rongai’. It was also clear that, while the majority of RAPD markers are valuable when used together with RFLP or other stringent marker systems, they could be problematic when used solely in mapping exercises. Received: 20 April 1999 / Accepted: 23 August 1999     

Genetic ancestry of participants in the National Children’s Study

Background

The National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes.

Results

We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories.

Conclusions

Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.     

Genetic variation and structure in natural and reintroduced populations of the endangered legume,Pyne’s ground plum (Astragalus bibullatus)

Conservation Genetics - Rare species with limited geographic distributions and small census populations are particularly susceptible to genetic drift and inbreeding. Assessing genetic variation...     

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

The global distribution of the reddish egret is characterized by disjunct colonies occurring from the Pacific side of Northwest Mexico to the Caribbean. We examined distantly isolated colonies of reddish egret to determine global population genetic structure. We used seven polymorphic microsatellites to accomplish five goals: (1) to assess range wide population differentiation among reddish egret (Egretta rufescens) populations, (2) identify extent of gene flow, (3) determine any historical occurrence of bottlenecks, (4) assess genetic differentiation between color morphs, (5) clarify subspecies status of E. r. dickeyi, a completely dark morph population located in and around the Baja California peninsula, Mexico. Genetic differentiation was dramatic (global Fst = 0.161) throughout the reddish egrets range extending from Baja California, Mexico to Great Inagua, Bahamas. Differentiation occurred among three distinct regions (Fst = 0.238) but not among colonies/islands within regions suggesting regional philopatry. Genetic diversity (alleles per locus, and heterozygosity) in Baja California Sur, Mexico and Great Inagua, Bahamas populations is lower than in the Texas/Mexico population due to minimal dispersal between regions and smaller population sizes. Dark and white color morphs when present within the same region showed no differentiation. Patterns of recent population bottlenecks are not evident in each of the three regional populations. With evidence of limited gene flow in addition to low genetic diversity and prospects of habitat loss we recommend that reddish egrets be managed as three distinct or evolutionary significant units.     

Growth and population parameters of the world’s northernmost harbour seals Phoca vitulina residing in Svalbard, Norway

The harbour seals (Phoca vitulina) in Svalbard are the northernmost population of this species. The population size is thought to be less than 1,000 individuals; these animals reside principally within a national park on Prins Karls Forland on the west coast of Spitsbergen, Svalbard, at about 78°20N. The material presented in this study was collected from 367 live-captured animals, aged based on growth layers read from stained, decalcified incisor sections (except for pups of the year). Standard length (F_1,246=45.70, P<0.0001) and body mass (F_1,258=25.28; P<0.0001) were both significantly influenced by sex when age was taken into account. Adult males are both longer [152.9±4.8 (SE) vs 140.1±2.0 cm, standard length] and heavier (104.0±5.0 vs 83.2±2.7 kg, body mass) than adult females in this population. Age at sexual maturity was assessed based on analyses of sex hormones. Testosterone levels in males showed an abrupt increase at 6 years of age, while estradiol levels in females increased from age 4. The reproductive rate of adult females was 0.93. The longevity of Svalbard harbour seals was short compared to harbour-seal populations from other areas. However, these seals are not exposed to terrestrial predation; there is no known mortality due to fisheries or hunting and their pollution burdens are low. Extreme seasonality and perhaps other harsh environmental conditions at the northern edge of this species distribution may exert long-term low levels of stress that result in short life span, or there are currently unknown acute sources of mortality in this population. To our knowledge, this is the first study of population parameters on a pinniped species using cross-sectional, non-terminal sampling.     

Genetic analysis of the ATP1B4 gene in Chinese Han patients with Parkinson’s disease

Parkinson’s disease (PD) is the second most common neurodegenerative disease characterized clinically by bradykinesia, resting tremor, rigidity and postural instability. Mutations in the ATPase 13A2 gene were found to be the causes for the Kufor-Rakeb syndrome, a rare form of recessively inherited atypical juvenile parkinsonism. The ATPase Na⁺/K⁺ transporting beta 4 polypeptide gene (ATP1B4) is located within a 19-centimorgen region of the PARK12 near the marker DXS1001 and it encodes a protein named βm, a member of P-type ATPases β-subunit family. To determine whether mutations in the ATP1B4 gene are associated with PD, we screened the coding region of this gene in 100 Chinese Han patients with PD. A known single nucleotide variant rs2072452 (c.143T > C), predicted to lead to amino acid substitution (p.Val48Ala), was identified. Extended analysis of 202 patients with PD and 400 gender, age, and ethnicity matched healthy controls showed no significant differences between patients and control subjects for genotypic and allelic distributions (P = 0.638 for genotypic distribution; P = 0.685 for allelic distribution in females and P = 0.303 for allelic distribution in males), suggesting the variant in the coding region of the ATP1B4 gene may play little or no role in the development of PD in Chinese Han population.     

Genetic control of “natural” killer lymphocytes in the mouse

Spleens from normal young mice contain lymphocytes that can kill certain in vitro grown Moloney lymphoma lines in a⁵¹Cr-release cytotoxicity test. A lymphoid cell without detectable T- or B-cell markers was previously shown to be responsible. Killing activity shows a marked dependence on the genotype of the donor mouse. When tested against a YAC line of strain A origin maintained in vitro spleens of A, A.CA, and A.SW mice had low activity, whereas CBA, C3H, C57L, and C57Bl spleens were highly active. In semisyngeneic F₁ crosses with strain A as one parent, reactivity resembled the opposite parental strain. Thus, (A×CBA)F₁, (A×C3H)F₁, (A×C57L)F₁, and (A×C57Bl)F₁ were reactive, whereas A×A.CA showed no significant activity. Analysis of the reactivity in (A×C57Bl)F₁×A backcross mice suggests that multiple genes are involved. Preliminary linkage analysis suggests at least oneH-2 linked factor. Another gene appears to be linked to theB (black) locus.     

The world from a cat’s perspective – statistics of natural videos

The mammalian visual system is one of the most intensively investigated sensory systems. However, our knowledge of the typical input it is operating on is surprisingly limited. To address this issue, we seek to learn about the natural visual environment and the world as seen by a cat. With a CCD camera attached to their head, cats explore several outdoor environments and videos of natural stimuli are recorded from the animals perspective. The statistical analysis of these videos reveals several remarkable properties. First, we find an anisotropy of oriented contours with an enhanced occurrence of horizontal orientations, earlier described in the oblique effect as a predominance of the two cardinal orientations. Second, contrast is not elevated in the center of the images, suggesting different mechanisms of fixation point selection as compared to humans. Third, analyzing a sequence of images we find that the precise position of contours varies faster than their orientation. Finally, collinear contours prevail over parallel shifted contours, matching recent physiological and anatomical results. These findings demonstrate the rich structure of natural visual stimuli and its direct relation to extensively studied anatomical and physiological issues.     

Genetic diversity analysis of North Africa’s barley using SSR markers

It was demonstrated that some North Africa barley accessions have diverse tolerance sources for abiotic stresses and a good nutritional quality, but the studies done were incomplete since they were realized separately in each country apart.To implement a more complete analysis, 31 barley accessions originated from North Africa (Algeria, Tunisia and Egypt) were analyzed using 11 SSR markers selected from the seven barley linkage groups for studying the genetic diversity among these chosen barley accessions.Over the 11 SSR markers, a total of 478 reproducible bands were scored with an average of 2.13 alleles/primer and the average polymorphism information content of 0.5.Genetic distance analysis of the 31 accessions showed a large genetic diversity and high number of different groups. The most accessions are clustered according to their eco-geographical origin, according to their pedigree and agronomic characters or according to the caryopsis character (hulled or naked caryopsis). This high number of obtained groups is an invaluable aid in crop improvement strategies and confirms the opinion suggesting that North Africa could be a secondary center of origin of barley. The various growing conditions and the multiple uses of barley in each country may be the cause of the large variability of the barley germplasm in each region.     

Variation of the parameters of natural reproduction and Crow’s indices in the ethnic groups of Dagestan

Using the 2002 All-Russian population census data, the parameters of differential fertility as a component of natural selection (Crow??s indices) have been calculated for women of seven age cohorts of the seven most numerous ethnic groups of the Republic of Dagestan. It has been shown that in the population of Dagestan in the second half of the 20th century the intensities of two types of selection tended to decrease, viz., intragroup selection relaxed in each ethnic group due to considerable reduction of interfamily variance in fertility and intergroup selection relaxed due to reduction of interethnic differences in fertility. A reduction of the average number of offspring (k) was observed in all ethnic groups, suggesting the spread of birth regulation practices (abortion and contraception). Nevertheless, all Muslim groups (aboriginal Dagestan ethnic groups and Azerbaijanis) are still characterized by an extended pattern of reproduction (2.7 < k < 3.3); in Russians k = 2.1. Interethnic differentials in natural reproduction rates, along with migration processes, account for the dynamics of the ethnic composition and gene-pool structure of the population of the Republic of Dagestan.