Urinary selenium in healthy and diabetic Saudi Arabians

We examined Se in urine of 170 Saudi Arabian diabetics (19 insulin-dependent [type 1] and 151 insulin-independent [type 2]) and in an equal number of control subjects of the same origin by measuring the ratio of the concentration of this metal (C_Se) to that of creatinine in urine (C_creat) for each subject. The mean (and SEM) of C_Se/C_creat for the control subjects was 56 (2.9) μmol/mol creat, whereas, the value for the diabetics combined or separated into type 1 and type 2 was 56.7 (3.2), 51.5 (6.3), and 57.4 (3.5) μmol/mol creat, respectively. With the exception of type 2 diabetics who were treated with insulin in addition to oral hypoglycemic and diet (35 patients) (mean [SEM]=43 (4.3) μmol/mol creat), there was no significant difference in C_Se/C_creat between the diabetics and control subjects. Also, there was no significant correlation between C_Se/C_creat and age, sex, or weight of diabetics, whereas, the correlation with the degree of diabetic control was significant (p≤0.0136). Of all diabetes-associated disorders (cardiovascular diseases, neuropathy, ophthalmologic diseases, infections, and hepatic disease), only ophthalmologic diseases appears to cause a significant (p≤0.05) reduction in C_Se/C_creat, but only among type 2 diabetics. Inasmuch as Se status is reflected by urinary Se, healthy Saudi Arabians appear to have Se status that is comparable or higher than those reported for other populations.     

Genetic Variability of Iris setosa

Genetic variability of Iris setosa Pall. ex Link. was studied by the RAPD method. Plants from three different habitats were compared by 135 loci revealed with eight arbitrary primers. The three plant accessions all exhibited a high level of polymorphism, and each was characterized by different frequencies of polymorphic fragments, which probably reflected the geographic isolation of the analyzed populations. The average level of polymorphism detected was 35%.     

Estimation of Genetic Variability in Plantago ovata Cultivars

Five cultivars of Plantago ovata Forsk. (medicinal plant) have been developed by different agricultural universities in India. Genetic variability of these cultivars was estimated using RAPD markers. The data were correlated to morphological characters and a dendrogram was obtained from Jaccard's coefficient. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Variability of PRNP in Chinese Indigenous Goats

Polymorphism of the prion protein gene (PRNP) is usually associated with scrapie susceptibility or resistance. To determine the variability of PRNP in Chinese indigenous goat breeds, we isolated genomic DNA from goat blood and amplified and sequenced the coding region of the gene. We identified 10 polymorphic sites that gave rise to 28 haplotypes. Clear frequency differences were found between northern and southern breeds and confirmed by genetic distance analysis, except for the Tangshan dairy goat. Phylogeographic analysis supported the idea that northern and southern breeds might be considered separate clusters, except for the Tangshan dairy goat. The finding of significant differences in allele distribution in northern and southern goats, especially if involved in modulating resistance/susceptibility, needs to be carefully considered for the feasibility of selection plans for resistance to scrapie.     

Estimating Genetic Variability with Restriction Endonucleases

The estimation of the amount of sequence variation in samples of homologous DNA segments is considered. The data are assumed to have been obtained by restriction endonuclease digestion of the segments, from which the numbers and frequencies of the cleavage sites in the sample are determined. An estimator, p, of the proportion of sites that are polymorphic in the sample is derived without assuming any particular population genetic model for the evolution of the population. The estimator is very close to the EWENS, SPIELMAN and HARRIS (1981) estimator that was derived with the symmetric WRIGHT-FISHER neutral mode. ENGELS (1981) has also recently proposed an estimator of the same quantity, and he arrived at his estimator without assuming a particular population genetic model. The sampling variance of p and ENGELS' estimator are derived. It is found that the sampling variance of p is lower than the sampling variance of ENGELS' estimator. Also, the sampling variance of theta, an estimate of theta (=4Nu) is obtained for the symmetric WRIGHT-FISHER neutral model with free recombination and with no recombination.     

Genetic Variability Under the Seedbank Coalescent

We analyze patterns of genetic variability of populations in the presence of a large seedbank with the help of a new coalescent structure called the seedbank coalescent. This ancestral process appears naturally as a scaling limit of the genealogy of large populations that sustain seedbanks, if the seedbank size and individual dormancy times are of the same order as those of the active population. Mutations appear as Poisson processes on the active lineages and potentially at reduced rate also on the dormant lineages. The presence of “dormant” lineages leads to qualitatively altered times to the most recent common ancestor and nonclassical patterns of genetic diversity. To illustrate this we provide a Wright–Fisher model with a seedbank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seedbank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seedbank, are compared. The effect of a seedbank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seedbank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect from genetic data the presence of a large seedbank in natural populations.     

Genetic diversity of begomoviruses infecting tomato plant in Saudi Arabia

Tomato is known as a highly valuable crop and grown worldwide for various uses. The cultivation and tomato production severely affected globally by several diseases caused by various pathogens. Begomoviruses causes yellow mosaic and leaf curl disease of tomato in the tropical, subtropical, temperate, and semi-arid regions. In Saudi Arabia, the tomato production adversely affected by disease caused by begomoviruses known as TYLCV and ToLCSDV. In this study, the pathogen was identified by Polymerase Chain Reaction using virus-specific primers and transmitted by whiteflies to healthy tomato seedlings. In a field survey, the tomato plants were exhibiting symptoms like viral infection. The infected leaf was randomly collected from various fields of tomato growing areas like Jeddah, Makkah, Tabuk, and Hail. The full-length viral genome was amplified by Rolling Circle Amplification technology (RCA) while betasatellites were amplified by PCR using universal betasatellites primers. The full-length viral genome (∼2.7 kb) and betasatellites (∼1.4 kb) were cloned and sequenced bi-directionally. The generated sequences were assembled and analyzed to find out the genetic variability by using bioinformatics tools and the genetic variability and phylogenetic relationships with selected begomoviruses were analyzed. The sequences showed the highest identity with an isolate of ToLCSDV and TYLCV. The nucleotide similarity and phylogenetic relationship showed the closest cluster with ToLCSDV and TYLCV. The data generated in this study elucidate that the causal organism is a variant of either TYLCV or ToLCSDV. The provided information from this study will be highly valuable for researchers and vegetable growers not only in Saudi Arabia but also in Arabian Peninsula.     

Hidden Genetic Variability within Electromorphs in Finite Populations

The amount of hidden genetic variability within electromorphs in finite populations is studied by using the infinite site model and stepwise mutation model simultaneously. A formula is developed for the bivariate probability generating function for the number of codon differences and the number of electromorph state differences between two randomly chosen cistrons. Using this formula, the distribution as well as the mean and variance of the number of codon differences between two identical or nonidentical electromorphs are studied. The distribution of the number of codon differences between two randomly chosen identical electromorphs is similar to the geometric distribution but more leptokurtic. Studies are also made on the number of codon differences between two electromorphs chosen at random one from each of two populations which have been separated for an arbitrary number of generations. It is shown that the amount of hidden genetic variability is very large if the product of effective population size and mutation rate is large.     

Inter- and Intra-Varietal Genetic Variability in Malvasia Cultivars

The DNA molecular analyses together with ampelography, ampelometry, and biochemistry are essential for grapevine identification and investigation of genetic differences among the Vitis vinifera L. cultivars and clones. Ten Malvasia cultivars (i.e., Istrian Malvasia; M. delle Lipari; M. bianca di Candia; M. di Candia Aromatica; M. del Lazio; M. bianca lunga, also known as Malvasia del Chianti; M. nera di Brindisi/Lecce; M. di Casorzo; M. di Schierano, and M. nera di Bolzano) were analyzed using molecular approaches to study the genetic inter-varietal variability. Thirty Istrian Malvasia genotypes (i.e., 8 Italian clones, such as ISV 1, ISV F6, VCR 4, VCR 113, VCR 114, VCR 115, ERSA 120, ERSA 121, and 22 autochthonous grapevine accessions grown in Istrian Peninsula, Croatia) were investigated to evaluate the morphological and genetic intra-varietal variability. DNA analysis allowed discrimination of all Malvasia genotypes at molecular level using AFLP, SAMPL, and M-AFLP markers. Italian clones and autochthonous Croatian accessions of Istrian Malvasia were grouped according to their different geographic origins. These results showed the great genetic variability of Malvasia genotypes suggesting the need for the preservation of autochthonous grapevine biotypes found on different areas to approve the correct choice and selection of the grape multiplication materials.     

Variability of Some Milk-Associated Genes and Proteins in Several Breeds of Saudi Arabian Camels

To gain knowledge on the molecular basis of diversity of several clans of Saudi camel (Camelus dromedarius) characterization of these animals was conducted at both genetic and protein levels. To this end, blood and milk samples were collected from several camel breeds at different Saudi Arabia locations (northern Jeddah, Riyadh, and Alwagh governorates). Genomic DNA was extracted from blood of four Saudi camel breeds (Majahem, Safra, Wadha, and Hamara), and DNA fragments of the casein and α-lactalbumin genes were amplified. The retrieved DNA sequences were analyzed for genetic variability. The inter-simple sequence repeat technique was used for confirming the relationships among the analyzed camel breeds, and the PCR–RFLP with two restriction enzymes was utilized for exploring their molecular variations. The number of haplotypes, gene diversity, nucleotide diversity, average number of nucleotide differences, and sequence conservation were calculated for all the analyzed DNA sequences. These analyses revealed the presence of several single nucleotide polymorphisms in the analyzed DNA sequences. A group of neighbor joining trees was built for inferring the evolutionary variations among the studied animals. Protein profiling of milk from different camel clans was also conducted, and differences between and within the Saudi camel clans were easily found based on the isoelectric focusing (IEF) profiles using ampholytes with different IEF range. This study revealed that analyzed camel breeds show low levels of genetic differences. This may be a reflection of the evolutionary history of C. dromedarius that was domesticated based on a highly homogeneous ancestor ecotype.     

Genetic variability of the tropical grasshopper Poecilocerus bufonius in Saudi Arabia

Electrophoresis for SDS-proteins and isoenzymes was applied to investigate the genetic variability within the tropical grasshopper Poecilocerus bufonius, which inhabits Saudi Arabia. Samples were selected from different localities that are encompassing the Sarawat Mountains in the west and An-Nafud desert in the north and middle. A range of 2 to 14 protein bands were recorded in the studied samples as measured by SDS-polyacrylamide gel electrophoresis, from which only two were common. The maximum number of protein bands has been recorded in the samples from the west and the minimum number has been recorded in the samples from the north and middle. Six arbitrary chosen enzymes were examined by native-polyacrylamide gel electrophoresis. They were peroxidase (Px), aldehyde oxidase (Ao), acid phosphatase (Acph), alcohol dehydrogenase (Adh), á and â ePsterase (Est). Fourteen presumptive gene loci and 26 polymorphic alleles have been recorded with the highest number of alleles in Taif and minimum number of alleles in Qassim. Adh, Px and Acph have not been recorded in samples from the localities of An-Nafud desert. The samples from Taif (Sarawat Mountains) were more genetically variable than the samples from other localities. Most of alleles were monomeric but only the Px-1 showed trimeric alleles in samples from Taif.     

Dynamics of Genetic Variability in Two-Locus Models of Stabilizing Selection

We study a two locus model, with additive contributions to the phenotype, to explore the dynamics of different phenotypic characteristics under stabilizing selection and recombination. We demonstrate that the interaction of selection and recombination results in constraints on the mode of phenotypic evolution. Let V(g) be the genic variance of the trait and C(L) be the contribution of linkage disequilibrium to the genotypic variance. We demonstrate that, independent of the initial conditions, the dynamics of the system on the plane (V(g), C(L)) are typically characterized by a quick approach to a straight line with slow evolution along this line afterward. We analyze how the mode and the rate of phenotypic evolution depend on the strength of selection relative to recombination, on the form of fitness function, and the difference in allelic effect. We argue that if selection is not extremely weak relative to recombination, linkage disequilibrium generated by stabilizing selection influences the dynamics significantly. We demonstrate that under these conditions, which are plausible in nature and certainly the case in artificial stabilizing selection experiments, the model can have a polymorphic equilibrium with positive linkage disequilibrium that is stable simultaneously with monomorphic equilibria.     

Genetic Variability and Divergence in Grayling, THYMALLUS ARCTICUS

In North America there are two disjunct forms of grayling, Montana and arctic, which have been separated for approximately 75,000 to 100,000 years. Electrophoretic analysis of thirty-six protein loci in these forms has revealed: (1) levels of gene duplication comparable to other salmonids, (2) a level of heterozygosity similar to other salmonids, (3) a fast and a slow evolving set of proteins, and (4) no obvious relationship between genetic variability and enzyme function. The genetic divergence between these populations may warrant subspecific designations for these two forms.     

Genetic Variants Contribute to Gene Expression Variability in Humans

Expression quantitative trait loci (eQTL) studies have established convincing relationships between genetic variants and gene expression. Most of these studies focused on the mean of gene expression level, but not the variance of gene expression level (i.e., gene expression variability). In the present study, we systematically explore genome-wide association between genetic variants and gene expression variability in humans. We adapt the double generalized linear model (dglm) to simultaneously fit the means and the variances of gene expression among the three possible genotypes of a biallelic SNP. The genomic loci showing significant association between the variances of gene expression and the genotypes are termed expression variability QTL (evQTL). Using a data set of gene expression in lymphoblastoid cell lines (LCLs) derived from 210 HapMap individuals, we identify cis-acting evQTL involving 218 distinct genes, among which 8 genes, ADCY1, CTNNA2, DAAM2, FERMT2, IL6, PLOD2, SNX7, and TNFRSF11B, are cross-validated using an extra expression data set of the same LCLs. We also identify ∼300 trans-acting evQTL between >13,000 common SNPs and 500 randomly selected representative genes. We employ two distinct scenarios, emphasizing single-SNP and multiple-SNP effects on expression variability, to explain the formation of evQTL. We argue that detecting evQTL may represent a novel method for effectively screening for genetic interactions, especially when the multiple-SNP influence on expression variability is implied. The implication of our results for revealing genetic mechanisms of gene expression variability is discussed.     

Correlation between Genetic Variability and Body Size in Vertebrates

An analysis of allozymic variation carried out in the main groups of vertebrate animals revealed a tendency towards the increased level of genetic polymorphism in the species of small animals compared to the large ones. This tendency was clearly followed in caudate amphibians, fishes, and mammals. The data are discussed in terms of the integration of monogenic and polygenic systems in the populations. It is hypothesized that this relationship between heterozygosity and body size confirms more general regularity consisting in highly statistically significant correlation between polygenic heterozygosity, maturation rate and life span. It is suggested that high rate of development in small animals resulting in early sexual maturation, can serve as a mechanism determining correlation between heterozygosity and body size at the species level. As a result, compared to large animals, small animals display higher rates of generation change, resulting in accelerated growth of population size and faster accumulation of genetic variability.     

High Genetic Variability of the agr Locus in Staphylococcus Species

The agr quorum-sensing and signal transduction system was initially described in Staphylococcus aureus, where four distinct allelic variants have been sequenced. Western blotting suggests the presence of homologous loci in many other staphylococci, and this has been confirmed for S. epidermidis and S. lugdunensis. In this study we isolated agr-like loci from a range of staphylococci by using PCR amplification from primers common to the six published agr sequences and bracketing the most variable region, associated with quorum-sensing specificity. Positive amplifications were obtained from 14 of 34 staphylococcal species or subspecies tested. Sequences of the amplicons identified 24 distinct variants which exhibited extensive sequence divergence with only 10% of the nucleotides absolutely conserved on multiple alignment. This variability involved all three open reading frames involved in quorum sensing and signal transduction. However, these variants retained several protein signatures, including the conserved cysteine residue of the autoinducing peptide, with the exception of S. intermedius of pigeon origin, which contained a serine in place of cysteine at this position. We discuss hypotheses on the mode of action and the molecular evolution of the agr locus based on comparisons between the newly determined sequences.