DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (?, G) and population differentiation statistics (D, GST ', ? test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society.

Empirical assessment of non-invasive population genetics in bats:Comparison of DNA quality from faecal and tissue samples

Non-invasive population genetics has become a valuable tool in ecology and conservation biology, allowing genetic studies of wild populations without the need to catch, handle or even observe the study subjects directly. We address some of the concerns regarding the limitations of using non-invasive samples by comparing the quality of population genetic information gained through DNA extracted from faecal samples and biopsy samples of two elusive bat species, Myotis mystacinus and Myotis nattereri. We demonstrate that DNA extracted from faeces and tissue samples gives comparable results for frequency based population genetic analyses, despite the occurrence of genotyping errors when using faecal DNA. We conclude that non-invasive genetic sampling for population genetic analysis in bats is viable, and although more labour-intensive and expensive, it is an alternative to tissue sampling, which is particularly pertinent when specimens are rare, endangered or difficult to capture. © 2012 Museum and Institute of Zoology PAS.

Total arsenic, inorganic arsenic, and other elements concentrations in Italian rice grain varies with origin and type

Rice is comparatively efficient at assimilating inorganic arsenic (As _i), a class-one, non-threshold carcinogen, into its grain, being the dominant source of this element to mankind. Here it was investigated how the total arsenic (As_t) and As_i content of Italian rice grain sourced from market outlets varied by geographical origin and type. Total Cr, Cd Se, Mg, K, Zn, Ni were also quantified. As_t concentration on a variety basis ranged from means of 0.18 mg kg^-1 to 0.28 mg kg ^-1, and from 0.11 mg kg^-1 to 0.28 mg kg^-1 by production region. For As_i concentration, means ranged from 0.08 mg kg^-1 to 0.11 mg kg^-1 by variety and 0.10 mg kg ^-1 to 0.06 mg kg^-1 by region. There was significant geographical variation for both As_t and As_i; total Se and Ni concentration; while the total concentration of Zn, Cr, Ni and K were strongly influenced by the type of rice.

Genetics of New-Onset Diabetes after Transplantation

New-onset diabetes after transplantation is a common complication that reduces recipient survival. Research in renal transplant recipients has suggested that pancreatic ß-cell dysfunction, as opposed to insulin resistance, may be the key pathologic process. In this study, clinical and genetic factors associated with new-onset diabetes after transplantation were identified in a white population. A joint analysis approach, with an initial genome-wide association study in a subset of cases followed by de novo genotyping in the complete case cohort, was implemented to identify single-nucleotide polymorphisms (SNPs) associated with the development of new-onset diabetes after transplantation. Clinical variables associated with the development of diabetes after renal transplantation included older recipient age, female sex, and percentage weight gain within 12 months of transplantation. The genome-wide association study identified 26 SNPs associated with new-onset diabetes after transplantation; this association was validated for eight SNPs (rs10484821, rs7533125, rs2861484, rs11580170, rs2020902, rs1836882, rs198372, and rs4394754) by de novo genotyping. These associations remained significant after multivariate adjustment for clinical variables. Seven of these SNPs are associated with genes implicated in ß-cell apoptosis. These results corroborate recent clinical evidence implicating ß-cell dysfunction in the pathophysiology of new-onset diabetes after transplantation and support the pursuit of therapeutic strategies to protect ß cells in the post-transplant period.

Health status and 6 years survival of 552 90+ Italian sib-ships recruited within the EU Project GEHA (GEnetics of Healthy Ageing).

In a scenario of increasing life expectancy worldwide, it is mandatory to identify the characteristics of a healthy aging phenotype, including survival predictors, and to disentangle those related to environment/lifestyle versus those related to familiarity/genetics. To this aim we comprehensively characterised a cohort of 1,160 Italian subjects of 90 years and over (90+, mean age 93 years; age range 90-106 years) followed for 6 years survival, belonging to 552 sib-ships (familiar longevity) recruited (2005-2008) within the EU-funded GEHA project in three Italian geographic areas (Northern, Central and Southern Italy) different for urban/rural and socio-economical characteristics. On the whole, the following factors emerged as significant predictors of survival after 90 years of age: absence of cognitive impairment and physical disability, high hand grip strength scores and body mass index (BMI) values, "excellent/good" self-reported health, high haemoglobin and total cholesterol levels and low creatinine levels. These parameters, excluding BMI values, were also significantly associated within sib-ships, suggesting a strong familial/genetic component. Geographical micro-heterogeneity of survival predictors emerged, such as functional and physical status being more important in Southern than in Central and Northern Italy. In conclusion, we identified modifiable survival predictors related to specific domains, whose role and importance vary according to the geographic area considered and which can help in interpreting the genetic results obtained by the GEHA project, whose major aim is the comprehensive evaluation of phenotypic and genetic data.

Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

Rice (Oryza sativa) cultivar Azucena--belonging to the Japonica subspecies--exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a low-tillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci--qSLB1.1--for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes--SLB1 and SLB2--with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2'-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice.

Arsenic Bioaccessibility in Cooked Rice as Affected by Arsenic in Cooking Water

Rice can easily accumulate arsenic (As) into its grain and is known to be the highest As-containing cereal. In addition, the As burden in rice may increase during its processing (such as when cooking using As-polluted water). The health risk posed by the presence of As in cooked rice depends on its release from the matrix along the digestive system (bioaccessibility). Two types of white polished long-grain rice, namely, nonparboiled and parboiled (total As: 202 and 190 mu g As kg(-1), respectively), were cooked in excess of water with different levels of As (0, 10, 47, 222, and 450 mu g As L-1). The bioaccessibility of As from these cooked rice batches was evaluated with an in vitro dynamic digestion process. Rice cooked with water containing 0 and 10 mu g As L-1 showed lower As concentrations than the raw (uncooked) rice. However, cooking water with relatively high As content (>= 47 mu g As L-1) significantly increased the As concentration in the cooked rice up to 8- and 9-fold for the nonparboiled and parboiled rice, respectively. Parboiled rice, which is most widely consumed in South Asia, showed a higher percentage of As bioaccessibility (59% to 99%) than nonparboiled rice (36% to 69%) and most of the As bioaccessible in the cooked rice (80% to 99%) was released easily during the first 2 h of digestion. The estimation of the As intake through cooked rice based on the As bioaccessibility highlights that a few grams of cooked rice (less than 25 g dry weight per day) cooked with highly As contaminated water is equivalent to the amount of As from 2 L water containing the maximum permissible limit (10 mu g As L-1).

Arsenic Contents in Spanish Infant Rice, Pureed Infant Foods, and Rice

It seems there is a positive correlation between rice content and arsenic level in foods. This is of extraordinary importance for infants below 1 y of age because their diet is very limited and in some cases is highly dependent on rice-based products; this is particularly true for infants with the celiac disease because they have no other option than consume gluten-free products, such as rice or corn. Arsenic contents were significantly higher (P <0.001) in gluten-free infant rice (0.057 mg kg-1) than in products with gluten, based on a mixture of cereals (0.024 mg kg-1). Besides, especial precaution must be taken when preparing rice-based products at home, because arsenic content in Spanish rice was high, with levels being above 0.3 mg kg-1 in some cases.

Effect of cooking method and rice type on arsenic concentration in cooked rice and the estimation of arsenic dietary intake in a rural village in West Bengal, India

Arsenic (As) contamination of rice plants can result in high total As concentrations (t-As) in cooked rice, especially if As-contaminated water is used for cooking. This study examines two variables: (1) the cooking method (water volume and inclusion of a washing step); and (2) the rice type (atab and boiled). Cooking water and raw atab and boiled rice contained 40 g As l-1 and 185 and 315 g As kg-1, respectively. In general, all cooking methods increased t-As from the levels in raw rice; however, raw boiled rice decreased its t-As by 12.7% when cooked by the traditional method, but increased by 15.9% or 23.5% when cooked by the intermediate or contemporary methods, respectively. Based on the best possible scenario (the traditional cooking method leading to the lowest level of contamination, and the atab rice type with the lowest As content), t-As daily intake was estimated to be 328 g, which was twice the tolerable daily intake of 150 g.

Contribution of water and cooked rice to an estimation of the dietary intake of inorganic arsenic in a rural village of West Bengal, India

Arsenic contamination of rice plants by arsenic-polluted irrigation groundwater could result in high arsenic concentrations in cooked rice. The main objective of the study was to estimate the total and inorganic arsenic intakes in a rural population of West Bengal, India, through both drinking water and cooked rice. Simulated cooking of rice with different levels of arsenic species in the cooking water was carried out. The presence of arsenic in the cooking water was provided by four arsenic species (arsenite, arsenate, methylarsonate or dimethylarsinate) and at three total arsenic concentrations (50, 250 or 500 mu g l(-1)). The results show that the arsenic concentration in cooked rice is always higher than that in raw rice and range from 227 to 1642 mu g kg(-1). The cooking process did not change the arsenic speciation in rice. Cooked rice contributed a mean of 41% to the daily intake of inorganic arsenic. The daily inorganic arsenic intakes for water plus rice were 229, 1024 and 2000 mu g day(-1) for initial arsenic concentrations in the cooking water of 50, 250 and 500 g arsenic l(-1), respectively, compared with the tolerable daily intake which is 150 mu g day(-1).

Effect of two different rice dehusking procedures on total arsenic concentration in rice

Pollution of subterranean water by arsenic (As) in Asia has resulted in the worst chemical disaster in human history. For populations living on subsistence rice diets, As contamination of rice grain contributes greatly to dietary As exposure. The main objectives of this study were to compare two dehusking processes: (a) wet process (soaking of rice, boiling and mechanical hulling) and (b) dry process (mechanical hulling), and recommend the method leading to a lower As content in commercial rice. In general, hulling of paddy rice (373 mu g As kg(-1)) significantly decreased As content in rice grain (311 mu g As kg(-1)). The final As concentrations in boiled rice (final product of the wet process) and atab rice (dry process) were 332 and 290 mu g kg(-1). Thus, the dry method is recommended for dehusking paddy rice if not As-free water is available. However, villagers can reduce the As content in the wet system by discarding the soaking water and using new water for the light boiling. Finally, it is not recommended to use rice husk for feeding animals because the As concentration is very high, approximately 1,000 mu g As kg(-1).

Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus

Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 (PRDM5) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus (P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date.

Traces of Peter Rice

A review of the events comprising Peter Rice at Queen's including the Traces of Peter Rice Exhibition at the Naughton Gallery

Urinary excretion of arsenic following rice consumption

Patterns of arsenic excretion were followed in a cohort (n = 6) eating a defined rice diet, 300 g per day d.wt. where arsenic speciation was characterized in cooked rice, following a period of abstinence from rice, and other high arsenic containing foods. A control group who did not consume rice were also monitored. The rice consumed in the study contained inorganic arsenic and dimethylarsinic acid (DMA) at a ratio of 1:1, yet the urine speciation was dominated by DMA (90%). At steady state (rice consumption/urinary excretion) similar to 40% of rice derived arsenic was excreted via urine. By monitoring of each urine pass throughout the day it was observed that there was considerable variation (up to 13-fold) for an individual's total arsenic urine content, and that there was a time dependent variation in urinary total arsenic content. This calls into question the robustness of routinely used first pass/spot check urine sampling for arsenic analysis. (C) 2014 Elsevier Ltd. All rights reserved.