Detection of rare major genes in lipid levels

Summary A statistical test of polygenic inheritance (TPI) against the alternative of a rare major gene is presented. It is designed for a random sample of quantitative observations on index cases and siblings of those index cases (probands) selected on the basis of the observed measurements of these probands. The test focuses on an increase of the variance of siblings of probands over its value under polygenic inheritance, such an increase being expected in the presence of a major gene producing a shift of the quantitative observations. Certain data on lipids are then analyzed by this test. A major gene can tentatively be confirmed for triglycerides but not for cholesterol. In addition, the values of all index cases are subjected to an analysis of a mixture of normal distributions (NOCOMP computer program), resulting in a significant second component for triglycerides but not for cholesterol. For both TPI and NOCOMP, the exponent in a power transformation is estimated by maximum likelihood simultaneously with all other parameters, so that these analysis methods are robust against a wide range of skewness in the data, which is demonstrated by manipulation of the observations and their reanalyis.     

Flowering patterns in three neotropical mangrove species: Evidence from a Caribbean island

The present study sought to identify the factors that drive flowering in the main neotropical mangrove species. We evaluated the effects of water regime variables and foliar meristematic activity on the flowering intensity of Rhizophora mangle, Laguncularia racemosa, and Avicennia germinans in three physiographic types of San Andres Island, Colombia. The results show that pore salinity regulates flowering intensity and periodicity in all three mangrove species. All species flowering showed significant correlations with water balance and air vapor pressure deficit (VPD). In the fringe and interior mangroves, R. mangle flowering was explained linearly by salinity (25%) and monthly change in salinity (47%), respectively. L. racemosa flowering was linked with stronger periods of foliar meristematic activity and occurred during months of relatively high water balance (54-233 mm) and low VPD (1.18-1.29 kPa). The flowering of A. germinans was triggered by water deficit conditions when the monthly pore salinity increased over 30 g L⁻¹ and, with a month delay response, when the water column height (WCH) was below ground. The flowering of A. germinans was also explained by these variables at 65% and 39%, respectively. The flowering patterns of the studied mangrove species indicate that reproduction within the neotropical mangrove community depends on seasonally contrasting water conditions on an annual basis.     

Phenotypic selection: a successful strategy to fix major genes of hypertension.

Hypertension is dominantly inherited in cross hybrids between hypertensive SHR/Mol and normotensive BB/OK rats. We used these cross hybrids for repeated backcrossing of selected hypertensive animals onto normotensive BB/OK rats to fix high blood pressure and to generate a hypertensive and diabetic BB/OK rat subline. After 8 backcrosses, the backcross parents were genetically analysed with the aid of 259 microsatellite markers to identify SHR genes causing blood pressure of 177 +/- 10 mmHg in this BB/OK rat subline. Loci on chromosomes 1, 14 and 18 showed longest heterozygosity. These loci might contain major genes of the SHR rat causing hypertension in this BB/OK rat subline. This classical strategy seems to be most suitable to fix major genes of hypertension in particular and complex traits in general and therefore to generate new animal models.     

Inbreeding and susceptibility to osteoporosis in Croatian island isolates

The aim of this study was to investigate a recessive genetic component in susceptibility to osteoporosis (OP) by comparing its prevalence in isolated villages of three Croatian islands: Brac, Hvar and Korcula with different levels of inbreeding. A random sample of 20-30% adults from 14 villages was obtained, including a total of 1,389 examinees. The average inbreeding coefficient (F) of examinees from each village population was estimated using Wright's path method (based on genealogical information). The morphometry of the metacarpal bones was performed on hand-wrist radiographs of both hands in all examinees. OP was defined as values of cortical index smaller than 2 standard deviations based on distribution of values in examinees of the same sex under 45 years of age. Mean values of cortical index (CI) and prevalence of OP (both standardized by age and weighted for the sample size) in each village were correlated to the mean inbreeding coefficient (F). The coefficient of correlation (r) between F values and CI was -0.28 in males (p = 0.08) and -0.42 in females (p = 0.005), and between F and OP prevalence 0.32 in males (p < 0.001) and 0.43 in females (p < 0.001). These results indicate a trend of increased susceptibility to osteoporosis with increasing level of inbreeding in isolated communities of Croatian islands.     

Evidence for a major gene controlling susceptibility to tegumentary leishmaniasis in a recently exposed Bolivian population.

Tegumentary leishmaniasis due to Leishmania braziliensis is a parasitic disease that occurs in two stages after the infected sandfly bite: (1) a primary cutaneous lesion followed by (2) a secondary mucosal involvement generally resulting in severe facial deformities. In order to investigate the genetic and environmental factors involved in the development of the cutaneous lesion, a familial study was performed in a region of Bolivia in which the disease is endemic. Complete selection of 118 nuclear families (703 subjects, with 241 patients), each with at least one cutaneous affected subject, was achieved; 41 families were of native origin, and 77 (herein designated "migrant") recently had settled in the area. For the analysis, the trait under study was the time to onset of the primary cutaneous lesion. The start of the follow-up was birth, for native population, or date of arrival in the endemic area, for migrant population. Segregation analysis was performed by use of a model based on survival analysis methods that allows joint estimation of genetic and environmental effects and accounts for gene x covariate interactions. A significant effect of gender, home-forest distance, and forest-related activity was found. In the 77 migrant families there was evidence for a recessive major gene controlling the onset of the primary cutaneous lesion, with residual familial dependences and age x genotype interaction. Penetrance estimations show that young subjects are genetically more susceptible than older subjects, suggesting that this genetic component could concern mechanisms involved in the development of individual protection during childhood. There was also a significant genetic heterogeneity of the sample according to the native/migrant origin of the families, and no major-gene effect was found in the native subsample.     

NOD2 and CCDC122-LACC1 genes are associated with leprosy susceptibility in Brazilians

Leprosy is a complex disease with phenotypes strongly influenced by genetic variation. A Chinese genome-wide association study (GWAS) depicted novel genes and pathways associated with leprosy susceptibility, only partially replicated by independent studies in different ethnicities. Here, we describe the results of a validation and replication study of the Chinese GWAS in Brazilians, using a stepwise strategy that involved two family-based and three independent case–control samples, resulting in 3,614 individuals enrolled. First, we genotyped a family-based sample for 36 tag single-nucleotide polymorphisms (SNPs) of five genes located in four different candidate loci: CCDC122-LACC1, NOD2, TNFSF15 and RIPK2. Association between leprosy and tag SNPs at NOD2 (rs8057431) and CCDC122-LACC1 (rs4942254) was then replicated in three additional, independent samples (combined OR_AA = 0.49, P = 1.39e?06; OR_CC = 0.72, P = 0.003, respectively). These results clearly implicate the NOD2 pathway in the regulation of leprosy susceptibility across diverse populations.     

Detection of resistance genes and susceptibility patterns in Bacteroides and Parabacteroides strains

Susceptibility to five antimicrobials was determined for Bacteroides spp. (n = 52) and Parabacteroides distasonis (n = 8). All isolates were susceptible to metronidazole. The resistance rates to ampicillin, cefoxitin, tetracycline and clindamycin were 98%, 9.6%, 65.3% and 19.2% of the Bacteroides strains, respectively. The genes cepA, cfiA, cfxA, tetQ, ermF and nim were found in 69.2%, 17.3% 9.6%, 50%, 7.7% and 3.8% for these strains respectively. All P. distasonis strains were resistant to ampicilin. Cefoxitin, tetracycline and clindamycin resistance rates were 75%, 87.5% and 50%, respectively. The ermF and nim genes were absent and 37.5%, 12.5%, 12.5% and 87.5% of this strains possessed cepA, cfiA, cfxA and tetQ genes, respectively. Ten cfiA gene positive strains of Bacteroides and Parabacteroides were submitted to E-test with imipenem and amoxicillin–clavulanate. The resistance rate to imipenem was 4.1% and 8.3% to amoxicillin–clavulanate. This feature is for the first time described in Brazil.     

The habitats exploited and the species trapped in a Caribbean island trap fishery

We visually observed fish traps in situ to identify the habitats exploited by the U.S. Virgin Islands fishery and to document species composition and abundance in traps by habitat. Fishers set more traps in algal plains than in any other habitat around St. John. Coral reefs, traditionally targeted by fishers, accounted for only 16 % of traps. Traps in algal plain contained the highest number of fishes per trap and the greatest numbers of preferred food species. Traps on coral reefs contained the most species, 41 of the 59 taxa observed in the study. Acanthurus coeruleus was the most abundant species and Acanthuridae the most abundant family observed in traps. Piscivore numbers were low and few serranids were observed. Traps in algal plain contained the most fishes as a result of: ecological changes such as shifts in habitat use, mobility of species and degradation of nearshore habitat (fishery independent); and, catchability of fishes and long-term heavy fishing pressure (fishery dependent). The low number of serranids per trap, dominance of the piscivore guild by a small benthic predator, Epinephelus guttatus, and dominance of trap contents overall by a small, fast-growing species of a lower trophic guild, Acanthurus coeruleus, all point to years of intense fishing pressure.     

Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

Taxon cycling, i.e. sequential phases of expansions and contractions in species' distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae: Atya lanipes) is geographically restricted and ecologically and morphologically differentiated from other Atya species. Using patterns of nucleotide variation at the COI mtDNA gene in five species of freshwater shrimp (A. lanipes, A. scabra, A. innocuous; Xiphocarididae: Xiphocaris elongata; Palaemonidae: Macrobrachium faustinum) from Puerto Rico, we expected to detect a signature of sequential colonization in these shrimp, consistent with the concept of taxon cycling, and expected that A. lanipes would be at a different taxon stage (i.e. an early stage species) to all other species. We also examined patterns of genetic population structure in each species expected with poor, intermediate and well-developed abilities for among-river dispersal. Population expansions were detected in all species, although the relative timing of the expansions varied among them. Assuming that population expansions followed colonization of Puerto Rico by freshwater shrimp, results bear the hallmarks of sequential colonization and taxon cycling in this fauna. A. lanipes had a star phylogeny, low mean pairwise nucleotide differences and recent (Holocene) estimates for an in situ population expansion in Puerto Rico, and it was inferred as an early stage species in the taxon cycle undergoing a secondary phase of expansion. All other species were inferred as late stage species undergoing regional population expansions, as their mean pairwise nucleotide differences were relatively high and phylogenetic patterns were more complex than A. lanipes. High rates of gene flow without isolation by distance among rivers were detected in all species, although results should be treated cautiously as some populations are unlikely to be in mutation-drift equilibrium. Nested clade analysis produced inconsistent results among species that all have high rates of gene flow and expanding populations.     

Diel differences in the seagrass fish assemblages of a Caribbean island in relation to adjacent habitat types

The fish fauna of Thalassia testudinum (König) seagrass beds was studied at two sites in the Grand Cul-de-Sac Marin Bay (Guadeloupe, French West Indies). The first seagrass bed was located near a coral reef and the second was near coastal mangroves. Both habitats were sampled during day and night, using a purse-seine and a trap net. A total of 98 species belonging to 36 families were observed. Distance-based redundancy analyses revealed two site-specific assemblages of fishes. Diel assemblage shifts were more pronounced in the seagrass beds near coral reefs than in those near mangroves, due to the existence of nocturnal trophic incursions of coral reef fishes into seagrass beds. First-order carnivores dominated the trophic structure of the fish assemblages during both day and night. At night, Haemulidae, Holocentridae and Apogonidae took the place of Labridae, Chaetodontidae and Mullidae present by day near the reef. This switch did not occur near the coast where the exchanges between seagrass beds and mangrove appear to be less important than with the reef ecosystem. Thus, it appears that the adjacent seascape habitat setting affects the intensity in diel variability of the seagrass bed fish community.     

Identification and chromosomal location of major genes for resistance to Pyrenophora teres in a doubled-haploid barley population.

Net blotch, caused by Pyrenophora teres, is one of the most economically important diseases of barley worldwide. Here, we used a barley doubled-haploid population derived from the lines SM89010 and Q21861 to identify major quantitative trait loci (QTLs) associated with seedling resistance to P. teres f. teres (net-type net blotch (NTNB)) and P. teres f. maculata (spot-type net blotch (STNB)). A map consisting of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers was used to identify chromosome locations of resistance loci. Major QTLs for NTNB and STNB resistance were located on chromosomes 6H and 4H, respectively. The 6H locus (NTNB) accounted for as much as 89% of the disease variation, whereas the 4H locus (STNB resistance) accounted for 64%. The markers closely linked to the resistance gene loci will be useful for marker-assisted selection.     

Evaluation of major membrane protein-II as a tool for serodiagnosis of leprosy

As serodiagnosis is the easiest way of diagnosing a disease, the utility of Mycobacterium leprae-derived major membrane protein-II (MMP-II), one of the immuno-dominant antigens, in the serodiagnosis of leprosy was examined. The percent positivity by an enzyme-linked immunosorbent assay for anti-MMP-II antibody was 82.4% for multi-bacillary leprosy, and the specificity of the test was 90.1%. For pauci-bacillary leprosy where cell-mediated immunity predominates, 39.0% showed positive results. These percentage values were significantly higher than these values obtained for existing phenolic glycolipid-I based methods, suggesting that MMP-II antibody detection would facilitate the diagnosis of leprosy.     

Genetic mapping of genes for susceptibility to black spot disease in Japanese pears.

Black spot disease, which is caused by the Japanese pear pathotype of Alternaria alternata (Fr.) Keissler, is one of the most harmful diseases in Japanese pear cultivation. We identified the exact positions and linkage groups (LGs) of the genes for susceptibility to black spot in the Japanese pear (Pyrus pyrifolia Nakai) cultivars 'Osa Nijisseiki' (gene Ani) and 'Nansui' (gene Ana). Segregation of susceptibility and resistance fitted the expected ratio of 1:1 in progeny of 'Nansui' but showed a slight distortion in progeny of 'Osa Nijisseiki'. We mapped the genes for susceptibility to black spot in both populations using a genome scanning approach. The simple sequence repeat (SSR) markers CH04h02 and CH03d02 showed tight linkage to Ani and Ana. Although Ani and Ana are derived from different sources, both genes are located at the top region of LG 11. Information about the positions of the susceptibility genes and the molecular markers linked to them will be useful for marker-assisted selection in pear breeding programs.     

Polymorphisms in autophagy genes and susceptibility to tuberculosis

Recent data suggest that autophagy is important for intracellular killing of Mycobacterium tuberculosis, and polymorphisms in the autophagy gene IRGM have been linked with susceptibility to tuberculosis (TB) among African-Americans, and with TB caused by particular M. tuberculosis genotypes in Ghana. We compared 22 polymorphisms of 14 autophagy genes between 1022 Indonesian TB patients and 952 matched controls, and between patients infected with different M. tuberculosis genotypes, as determined by spoligotyping. The same autophagy polymorphisms were studied in correlation with ex-vivo production of TNF, IL-1β, IL-6, IL-8, IFN-γ and IL-17 in healthy volunteers. No association was found between TB and polymorphisms in the genes ATG10, ATG16L2, ATG2B, ATG5, ATG9B, IRGM, LAMP1, LAMP3, P2RX7, WIPI1, MTOR and ATG4C. Associations were found between polymorphisms in LAMP1 (p = 0.02) and MTOR (p = 0.02) and infection with the successful M. tuberculosis Beijing genotype. The polymorphisms examined were not associated with M. tuberculosis induced cytokines, except for a polymorphism in ATG10, which was linked with IL-8 production (p = 0.04). All associations found lost statistical significance after correction for multiple testing. This first examination of a broad set of polymorphisms in autophagy genes fails to show a clear association with TB, with M. tuberculosis Beijing genotype infection or with ex-vivo pro-inflammatory cytokine production.     

Chronic injury as a major factor in susceptibility to gastric cancer

The etiology of gastric cancer is still unclear. The lesser curvature of stomach is more susceptible to chronic injury due to the anatomical characteristics. Many previous studies demonstrated that the lesser curvature is the most frequent tumor site in gastric cancer. And, precancerous gastric lesions, such as atrophic and intestinal metaplasia were also typically located in the lesser curvature. The lesser curvature is the first part of the stomach to be infected with Helicobacter pylori (H. pylori) infection which was associated with precancerous gastric lesions and gastric cancer. So, chronic injury of the stomach may lead to gastric cancer have hypothesized.     

Phenotypic selection: a successful strategy to fix major genes of hypertension

Spontaneously diabetic BB/OK rats are not genetically susceptible to develop diabetic complications as hypertension or nephropathy. Recently, we generated 5 congenic BB. SHR rat strains by transferring different chromosomal regions of the spontaneously hypertensive rat (SHR) onto the genetic background of BB/OK rats. Four out of 5 strains showed a weak increase of blood pressure (8 mmHg). This weak blood pressure effect indicated that the transferred regions fo not contain major genes for hypertension. That prompted us to choose the classical procedure of phenotypic selection to fix major genes causing hypertension in a BB/OK rat subline generated by cross of BB/OK and SHR and repeated backcrossing of animals with highest blood pressure onto normotensive BB/OK rats. After 7 backcrosses (N8), all backcross parents were genetically analysed with the aid of 259 microsatellites to identify loci causing blood pressure of 177 ± 10 mmHg in this BB/OK rat subline. The data revealed, that loci on chromosome 1, 14 and 18 were heterozygous until BC5, BC6 and BC7, respectively. Considering the relative stable high blood pressure during the backcross procedure, these loci might be of essential importance for the development of hypertension in the SHR.     

Evidence for the segregation of a major gene in human susceptibility/resistance to infection by Schistosoma mansoni.

Severe clinical disease caused by the major human parasite Schistosoma mansoni is the consequence of high and prolonged infections. Epidemiological studies indicate that, for individuals having frequent contacts with cercaria-infested waters, both infection intensities and reinfection after treatment depend, in large part, on their intrinsic susceptibility/resistance to infection, suggesting the role of genetic factors in human resistance to S. mansoni. To investigate whether a major gene controls human susceptibility/resistance to infection by S. mansoni, segregation analysis of infection intensities, adjusted for the factors relevant in schistosomiasis (water contact, age, sex), was performed on 20 Brazilian pedigrees (269 individuals), using both the unified mixed model and the regressive model of analysis. The results are consistent with the hypothesis that there is a codominant major gene controlling human susceptibility/resistance to infection by S. mansoni. Parameter estimates indicate a frequency of .20-.25 for the deleterious allele; thus, about 5% of the population is predisposed to high infections, 60% is resistant, and 35% has an intermediate, although fairly good, level of resistance. These findings provide a genetic basis for earlier observations on the lower resistance and the predisposition to reinfection of certain individuals. In addition to the detection of a major gene effect, the data suggest that immunity to S. mansoni develops progressively during childhood to reach a maximum around the age of puberty. The implications of these results for the strategy to be used in endemic areas to reduce morbidity and to control parasite transmission are discussed.     

dbGAPs: A comprehensive database of genes and genetic markers associated with psoriasis and its subtypes

Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data. The database contains annotation for 202 manually curated genes associated with psoriasis and its subtypes with cross-references. Functional enrichment of these genes, in context of Gene Ontology and pathways, provide insight into their important role in psoriasis etiology and pathogenesis. The dbGAPs interface is enriched with an interactive search engine for data retrieval along with unique customized tools for Single Nucleotide Polymorphism (SNP)/indel detection and SNP/indel annotations. dbGAPs is accessible at http://www.bmicnip.in/dbgaps/.