Characterization of genetic diversity and population structure in wheat using array based SNP markers

Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder’s Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~?50%), A (~?39%), and D (~?10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon’s information index (I)?=?0.648, expected heterozygosity (He)?=?0.456 and unbiased expected heterozygosity (uHe)?=?0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.

     

Arsenosugar Induced Blood and Brain Oxidative Stress, DNA Damage and Neurobehavioral Impairments

The effect of Arsenosugar on motor function and contextual memory-related to place and event; the extent of DNA damage and oxidative stress in male swiss albino mice was investigated. Passive avoidance test was used for memory test; rota motor test was used for motor function. Several biochemical parameters were used for assessing oxidative stress due to arsenosugar ingestion. Decreased passive avoidance time and decreased retention time in rotating rod indicated disruption of normal neurobehavior. Significant dose-dependent DNA damage was found in mice blood and brain. Decreased super oxide dismutase, increased lipid peroxidation, decreased protein sulfohydryl content, increased protein carbonyl content in blood and hippocampal tissue; glutathione in blood and glutathione peroxidase in hippocampal tissue indicated the ability of arsenosugar to cause oxidative stress. This study concludes with evidence that arsenosugar ingestion causes higher oxidative stress, increases DNA damage in the blood and hippocampus in vivo. This might be responsible for the dysfunction of cognitive and motor functions. However, further investigation is suggested for deciphering the biomolecular mechanism.     

Inhibition of Prolyl Hydroxylase Protects against 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced Neurotoxicity: MODEL FOR THE POTENTIAL INVOLVEMENT OF THE HYPOXIA-INDUCIBLE FACTOR PATHWAY IN PARKINSON DISEASE*

Hypoxia-inducible factor (HIF) plays an important role in cell survival by regulating iron, antioxidant defense, and mitochondrial function. Pharmacological inhibitors of the iron-dependent enzyme class prolyl hydroxylases (PHD), which target α subunits of HIF proteins for degradation, have recently been demonstrated to alleviate neurodegeneration associated with stroke and hypoxic-ischemic injuries. Here we report that inhibition of PHD by 3,4-dihydroxybenzoate (DHB) protects against 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced nigral dopaminergic cell loss and up-regulates HIF-1α within these neurons. Elevations in mRNA and protein levels of HIF-dependent genes heme oxygenase-1 (Ho-1) and manganese superoxide dismutase (Mnsod) following DHB pretreatment alone are also maintained in the presence of MPTP. MPTP-induced reductions in ferroportin and elevations in nigral and striatal iron levels were reverted to levels comparable with that of untreated controls with DHB pretreatment. Reductions in pyruvate dehydrogenase mRNA and activity resulting from MPTP were also found to be attenuated by DHB. In vitro, the HIF pathway was activated in N27 cells grown at 3% oxygen treated with either PHD inhibitors or an iron chelator. Concordant with our in vivo data, the MPP⁺-elicited increase in total iron as well as decreases in cell viability were attenuated in the presence of DHB. Taken together, these data suggest that protection against MPTP neurotoxicity may be mediated by alterations in iron homeostasis and defense against oxidative stress and mitochondrial dysfunction brought about by cellular HIF-1α induction. This study provides novel data extending the possible therapeutic utility of HIF induction to a Parkinson disease model of neurodegeneration, which may prove beneficial not only in this disorder itself but also in other diseases associated with metal-induced oxidative stress.Parkinson disease (PD)² is a neurodegenerative disorder primarily associated with loss of dopaminergic (DAergic) neurons of the pars compacta region of the substantia nigra (SNpc). Dopaminergic neurons are particularly prone to oxidative damage due to high levels of inherent reactive oxygen species that are produced during dopamine synthesis or its breakdown by monoamine oxidases or autoxidation to quinones (1–3). Importantly, iron bound to neuromelanin within DAergic neurons can subsequently react with metabolically liberated hydrogen peroxide through the Fenton reaction to produce extremely toxic hydroxyl radicals. If not properly buffered, hydroxyl radicals can stimulate protein oxidation and lipid peroxidation, which is thought to contribute to macromolecular injury and neuronal death. Iron is the most abundant metal in the brain and some degree of accessible reactive iron is necessary for brain viability as it serves as a cofactor in DNA, RNA, and protein synthesis and for heme and non-heme enzymes involved in both mitochondrial respiration and neurotransmitter synthesis (4). Although iron deficiencies early in life are known to result in impairments in brain development (5), high concentrations of iron may result in cellular toxicity (6) in part due to its ability to catalyze the production of toxic oxygen radicals.An important family of enzymes that require iron as an essential cofactor are the prolyl 4-hydroxylases (PHDs), which serve to hydroxylate proline residues situated within hypoxia-inducible factor proteins (HIFs) (7). Under hypoxic or iron-lacking conditions, PHDs are prevented from hydroxylating proline residues within the alpha (α) subunits of the HIF protein, preventing the ubiquitination and proteasomal degradation of the protein. Stabilization of HIFα results in its accumulation within the cytosol and translocation to the nucleus where it binds HIFβ and then to hypoxia response elements found on a variety of genes including heme oxygenase-1 (Ho-1) and manganese superoxide dismutase (Mnsod).Previous studies have demonstrated that deferoxamine, an iron chelator, can activate HIF-1α and prevent neuronal death in both in vitro and in vivo models of ischemia likely via inhibition of PHDs (8, 9). PHD inhibitors have been demonstrated to prevent oxidative cell death and ischemic injury via HIF pathway activation (10). More recently, it has been shown that inactivation of HIF-1α in specific cortical and striatal neurons exacerbated tissue damage in a mouse model of ischemia (11). With increasing evidence of the protective effects of induction of HIF-dependent gene products involved in iron regulation, cell survival, and energy metabolism, PHD inhibitors have been implicated as targets for neuroprotection in the central nervous system. We demonstrate here that PHD inhibition increases induction of HIF and HIF-related genes, functionally impacts on parameters of iron homeostasis and metabolic function, and, most importantly, significantly reduces the extent of DAergic nigrostriatal injury observed in the well established murine MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) PD model.     

Lymphocyte surface marker genes in fugu

At present, much of the fish adaptive immune system remains unknown due to the paucity of marker-specific reagents (e.g. antibodies) to identify immune cells. The genomic sequence of Takifugu rubripes (fugu) represents an important resource to facilitate the identification of lymphocyte-related genes. Here, we review the recent works on B-lymphocyte markers, the heavy (H) chains of IgM and IgD, and Ig light chain, and T-cell marker gene homologues, CD3ε, CD3γ/δ, CD4, and CD8α in a single fish species, fugu. Expressions of these B- and T-lymphocyte markers homologues in peripheral blood leukocytes and other lymphoid tissues of fugu suggest that these molecules in fish would be available as lymphocyte markers. These findings will lead us to develop reliable reagents for the identification of lymphocyte subpopulations. Fugu holds great promise as one of the model organisms for studies of development and evolution of adaptive and innate immunity in vertebrates.     

Calling SNPs without a reference sequence

Background  

The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies.     

Relationship between anthropometric measures and body composition among Muslim females of West Bengal, India

The human body composition is assessed to determine percent body fat (PBF), fat mass (FM), and lean body mass or fat free mass (FFM). The topological distribution of body fat has been the subject of many studies in the world and India. To the best of our knowledge the present paper is the first report on the body composition in terms of PBF and FM, and their relationship with anthropometric measures in Muslim females in India. The present study examines anthropometric measurements and their relationship with the body composition among Muslim females of West Bengal, India. A cross-sectional study of 100 female, Muslim students of Howrah and Kolkata was undertaken to compare the relationships of biceps and triceps skinfold, waist, hip and upper arm circumference, waist hip ratio and conicity index with their body composition variables (PBF and FM). All anthropometric measures displayed significant (p < 0.05) correlation with body composition measures. The triceps skinfold, however, demonstrated a significant correlation with PBF (r = 0.90) and FM (r = 0.93). The greatest amount of variation of PBF (81.3 %) and FM (89.2 %) was explained by the triceps skinfold. In addition, a considerable amount of variation of PBF (72.8 %) and FM (86.0 %) was explained by the mid upper arm circumference. In conclusion, the present study displays a tendency of regional adiposity in the upper arm, triceps skinfold and mid upper arm circumference are much more strongly associated with body fat.     

Drosophila importin alpha1 performs paralog-specific functions essential for gametogenesis

Importin alpha's mediate nuclear transport by linking nuclear localization signal (NLS)-containing proteins to importin beta1. Animal genomes encode three conserved groups of importin alpha's, alpha1's, alpha2's, and alpha3's, each of which are competent to bind classical NLS sequences. Using Drosophila melanogaster we describe the isolation and phenotypic characterization of the first animal importin alpha1 mutant. Animal alpha1's are more similar to ancestral plant and fungal alpha1-like genes than to animal alpha2 and alpha3 genes. Male and female importin alpha1 (Dalpha1) null flies developed normally to adulthood (with a minor wing defect) but were sterile with defects in gametogenesis. The Dalpha1 mutant phenotypes were rescued by Dalpha1 transgenes, but not by Dalpha2 or Dalpha3 transgenes. Genetic interactions between the ectopic expression of Dalpha1 and the karyopherins CAS and importin beta1 suggest that high nuclear levels of Dalpha1 are deleterious. We conclude that Dalpha1 performs paralog-specific activities that are essential for gametogenesis and that regulation of subcellular Dalpha1 localization may affect cell fate decisions. The initial expansion and specialization of the animal importin alpha-gene family may have been driven by the specialized needs of gametogenesis. These results provide a framework for studies of the more complex mammalian importin alpha-gene family.     

Enhanced Production of Antimicrobial Compounds by Three Salt-Tolerant Actinobacterial Strains Isolated from the Sundarbans in a Niche-Mimic Bioreactor

A novel reactor system, the rotating disk bioreactor (RDBR), was used to mimic the niche environmental conditions of three salt-tolerant estuarine actinobacteria isolated from the Sundarbans region off the Bay of Bengal, designated MS310 (99% similar in its 16S rRNA gene sequence to Streptomyces parvallus), MS3/20 and MS1/7. The RDBR, operated at a rotational speed of one revolution per day, 50% submergence of discs, aeration rate of 1.0 vvm, and with a sucrose-containing medium, faithfully mimicked the intertidal estuarine habitat of these marine isolates, and supported biofilm formation and production of antimicrobial metabolites-in particular, actinomycin D by MS310. Onset of antibiotic production by MS310 occurs at 20 h in the RDBR compared to 55 h in a conventional stirred-tank bioreactor (STBR). Furthermore, peak antimicrobial activity is attained much earlier in the RDBR with MS310 (at 45 h) than that reported with a terrestrial strain of S. parvallus grown in a STBR (at 144 h). Peak antimicrobial activity of metabolites produced by MS1/7 and MS3/20 were also attained earlier in the RDBR (at 25 and 12 h, respectively) than in a STBR (at 80 and 28 h, respectively). Antibiotic synthesis in the three isolates, in general, appears to be associated with their growth. Overall, the RDBR may be considered the preferred alternative to the STBR for production of antimicrobials by biofilm-forming estuarine bacteria for its much higher surface/volume ratio, lower costs, and easy operability.     

Marker-assisted selection for leaf rust resistance genes Lr19 and Lr24 in wheat (Triticum aestivum L.)

Leaf rust caused by Puccinia recondita f.sp. tritici is a wheat disease of worldwide importance. Wheat genotypes known to carry specific rust resistance genes and segregating lines that originated from various cross combinations and derived from distinct F2 lineage, so as to represent a diverse genetic background, were included in the present study for validation of molecular markers for Lr19 and Lr24. STS markers detected the presence of the leaf rust resistance gene Lr19 in a Thatcher NIL (Tc*Lrl9) and Inia66//CMH81A575 and of the gene Lr24 in the genotypes Arkan, Blue Boy II, Agent and CI 17907. Validation of molecular markers for Lr19 and Lr24 in parental lines, followed by successful detection of these genes in F3 lines from various cross combinations, was carried out. The molecular test corresponded well with the host-pathogen interaction test response of these lines.