Assessment of genetic diversity in Brazilian barley using SSR markers

Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.     

The quality preserving database: a computational framework for encouraging collaboration, enhancing power and controlling false discovery

The common scenario in computational biology in which a community of researchers conduct multiple statistical tests on one shared database gives rise to the multiple hypothesis testing problem. Conventional procedures for solving this problem control the probability of false discovery by sacrificing some of the power of the tests. We suggest a scheme for controlling false discovery without any power loss by adding new samples for each use of the database and charging the user with the expenses. The crux of the scheme is a carefully crafted pricing system that fairly prices different user requests based on their demands while keeping the probability of false discovery bounded. We demonstrate this idea in the context of HIV treatment research, where multiple researchers conduct tests on a repository of HIV samples.     

Frequency of under- and overweight among children and adolescents during the economic transition in Poland

The aim of this study is to examine the prevalence of underweight, overweight and obesity, using International Obesity Task Force (IOTF) criteria, in four cohorts of children and adolescents living in Poland in different economic eras: communist economy (1977/1978), crisis of the 1980s (1987/1988), political and economic transformation (1992/1994) and the free market economy (2002/2004). Analysis was conducted on a database including 10,934 records for children of the age 7–18 years. In Poland, in the last 26 years of economic and political transformations, the epidemic of obesity was not noticed but the growing incidence of children and adolescents with body mass deficit was observed (p < 0.0001) (20.2% of girls in 2002/2004 vs. 11.0% in 1977/1978 and 12.1% of boys in 2002/2004 vs. 7.2% in 1977/1978). Lower parental education and a higher number of children in a family resulted in a higher prevalence of underweight (odds ratio [OR] fluctuated from 1.26 to 1.63). The social effects of the political transformation in Poland significantly affected families with low socio-economic status (SES), and especially more eco-sensitive boys. This result is opposite to the trends observed in Western countries and makes an important contribution to the current knowledge of the course of further changes in weight-to-height ratio at a global scale.     

Fabrication Process of Silicone-based Dielectric Elastomer Actuators

This contribution demonstrates the fabrication process of dielectric elastomer transducers (DETs). DETs are stretchable capacitors consisting of an elastomeric dielectric membrane sandwiched between two compliant electrodes. The large actuation strains of these transducers when used as actuators (over 300% area strain) and their soft and compliant nature has been exploited for a wide range of applications, including electrically tunable optics, haptic feedback devices, wave-energy harvesting, deformable cell-culture devices, compliant grippers, and propulsion of a bio-inspired fish-like airship. In most cases, DETs are made with a commercial proprietary acrylic elastomer and with hand-applied electrodes of carbon powder or carbon grease. This combination leads to non-reproducible and slow actuators exhibiting viscoelastic creep and a short lifetime. We present here a complete process flow for the reproducible fabrication of DETs based on thin elastomeric silicone films, including casting of thin silicone membranes, membrane release and prestretching, patterning of robust compliant electrodes, assembly and testing. The membranes are cast on flexible polyethylene terephthalate (PET) substrates coated with a water-soluble sacrificial layer for ease of release. The electrodes consist of carbon black particles dispersed into a silicone matrix and patterned using a stamping technique, which leads to precisely-defined compliant electrodes that present a high adhesion to the dielectric membrane on which they are applied.     

Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene

MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African-specific missense mutations (S342G and I384M) in the neighboring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. The APOL1 gene product, apolipoprotein L-1, has been studied for its roles in trypanosomal lysis, autophagic cell death, lipid metabolism, as well as vascular and other biological activities. We also show that the distribution of these newly identified APOL1 risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to MYH9. Mapping by admixture linkage disequilibrium (MALD) localized an interval on chromosome 22, in a region that includes the MYH9 gene, which was shown to contain African ancestry risk variants associated with certain forms of ESKD (Kao et al. 2008; Kopp et al. 2008). MYH9 encodes nonmuscle myosin heavy chain IIa, a major cytoskeletal nanomotor protein expressed in many cell types, including podocyte cells of the renal glomerulus. Moreover, 39 different coding region mutations in MYH9 have been identified in patients with a group of rare syndromes, collectively termed the Giant Platelet Syndromes, with clear autosomal dominant inheritance, and various clinical manifestations, sometimes also including glomerular pathology and chronic kidney disease (Kopp 2010; Sekine et al. 2010). Accordingly, MYH9 was further explored in these studies as the leading candidate gene responsible for the MALD signal. Dense mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a consequence were designated as MYH9-associated nephropathies (Bostrom and Freedman 2010). These included HIV-associated nephropathy (HIVAN), primary nonmonogenic forms of focal segmental glomerulosclerosis, and hypertension affiliated chronic kidney disease not attributed to other etiologies (Bostrom and Freedman 2010). The MYH9 SNP and haplotype associations observed with these forms of ESKD yielded the largest odds ratios (OR) reported to date for the association of common variants with common disease risk (Winkler et al. 2010). Two specific MYH9 variants (rs5750250 of S-haplotype and rs11912763 of F-haplotype) were designated as most strongly predictive on the basis of Receiver Operating Characteristic analysis (Nelson et al. 2010). These MYH9 association studies were then also extended to earlier stage and related kidney disease phenotypes and to population groups with varying degrees of recent African ancestry admixture (Behar et al. 2010; Freedman et al. 2009a, b; Nelson et al. 2010), and led to the expectation of finding a functional African ancestry causative variant within MYH9. However, despite intensive efforts including re-sequencing of the MYH9 gene no suggested functional mutation has been identified (Nelson et al. 2010; Winkler et al. 2010). This led us to re-examine the interval surrounding MYH9 and to the detection of novel missense mutations with predicted functional effects in the neighboring APOL1 gene, which are significantly more associated with ESKD than all previously reported SNPs in MYH9.