Encounter rate of large mammals in Thanigebyle range of Bhadra wildlife sanctuary, Karnataka

Estimation of large mammals by using line transact method in the Thanigebyle range of Bhadra Wildlife Sanctuary during May 2009 to April 2010 in Thanigebyle range for four species of large herbivorous mammals viz., Chital (Axis axis), Sambar (Cervus unicolor), Barking deer (Muntiacus muntjak) and Gaur (Bosgaurus). The sanctuary was divided into several zones based on location and habitat types. Four permanent walking transect of 1 km were cut in different habitats of water holes for direct count and walk once in each month and four permanent vehicle transects of 18 kms were made.  A total of 22 kms per month transect was evaluated including both walking transect and permanent vehicle transect of 4 kms and 18 kms respectively. This evaluation indicates that maximum number of individuals was observed in the walking transect when compared to vehicle transect for all the four species. During our study 21 Sambar, 161 Chital, 8 Barking deer and 21 Gaur was encountered. Chital was observed more in the study area. It also reveals that during pre monsoon and post monsoon seasons the number of individuals was observed to be higher. &nbsp

Brown−Vialetto−Van Laere and Fazio−Londe syndromes: SLC52A3 mutations with puzzling phenotypes and inheritance

BACKGROUND: Brown-Vialetto-Van Laere Syndrome (BVVLS) and Fazio-Londe Disease (FLD) are rare neurological disorders presenting with pontobulbar palsy, muscle weakness, and respiratory insufficiency. Mutations in SLC52A2 (hRFVT-2) or SLC52A3 (hRFVT-3) genes can be responsible for these disorders with an autosomal recessive pattern of inheritance. The aim of this study is to screen for mutations in SLC52A2 and SLC52A3 among Indian families diagnosed with BVVLS and FLD. METHODS: SLC52A2 and SLC52A3 were screened in one FLD and three BVVLS patients by exon-specific amplification using PCR and sequencing. In silico predictions using bioinformatics tools and confocal imaging using HEK-293 cells were performed to determine the functional impact of identified mutations. RESULTS: Genetic analysis of a mother and son with BVVLS was identified with a novel homozygous mutation c.710C>T (p.Ala237Val) in SLC52A3. This variant was found to have autosomal pseudo-dominant pattern of inheritance, which was neither listed in the Exome variant server or in 1000 genomes database. In silico analysis and confocal imaging of the p.Ala237Val variant showed higher degree of disorderness in hRFVT3 that could affect riboflavin transport. Furthermore, a common homozygous mutation c.62A>G (p.Asn21Ser) was identified in other BVVLS and FLD patients. Despite having different clinical phenotypes, both BVVLS and FLD disorder can be attributed to this mutation. CONCLUSION: A rare and peculiar pattern of autosomal pseudo-dominant inheritance is observed for the first time in two genetically related BVVLS cases with Indian origin and a common mutation c.62A>G (p.Asn21Ser) in SLC52A3 can be responsible for both BVVLS and FLD with variable phenotypes

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes

Multiomic analysis of oral keratinocytes chronically exposed to shisha

Background: Tobacco is smoked in different form including cigarettes and water pipes. One popular form of water pipe smoking especially in Middle Eastern countries is shisha smoking. Shisha has been associated with various diseases including oral cancer. However, genomic alterations and gene expression changes associated with chronic shisha exposure have not been previously investigated. Objectives: Whole‐exome sequencing and gene expression profiling of immortalized human oral keratinocytes (OKF6/TERT1) cells chronically treated with 0.5% shisha extract for a period of 8 months was undertaken to characterize molecular alterations associated with shisha exposure. Methods: Genomic DNA and RNA were extracted and preprocessed as per manufacturer's instruction and subjected to whole‐exome and transcriptome sequencing using Illumina HiSeq2500 platform. Exome was analyzed using GATK pipeline whereas RNA‐Seq data was analyzed using HiSat2 and HTSeq along with DESeq to elucidate differentially expressed genes. Results: Whole‐exome sequence analysis led to identification of 521 somatic missense variants corresponding to 389 genes RNA‐Seq data revealed 247 differentially expressed genes (≥2‐fold, P‐value<0.01) in shisha treated cells compared to parental cells. Pathway analysis of differentially expressed genes revealed that interferon‐signaling pathway was significantly affected. We predict activation of MAPK1 pathway which is known to play a key role in oral cancer. We also observed allele specific expression of mutant LIMA1 based on RNA‐Seq dataset. Conclusion: Our findings provide insights into genomic alterations and gene expression pattern associated with oral keratinocytes chronically exposed to shisha

Radiometer Footprint Model to Estimate Sunlit and Shaded Components for Row Crops

Th is article describes a geometric model for computing the relative proportion of sunlit vegetation, shaded vegetation, sunlit soil, and shaded soil appearing in a circular or elliptical radiometer footprint for row crops, where the crop rows were modeled as continuous ellipses. Th e model was validated using digital photographs of row crops, where each component was determined by supervised classification. Root mean squared errors (RMSE) between modeled and observed components were 35, 49, 29, and 44% of observed means for sunlit vegetation, shaded vegetation, sunlit soil, and shaded soil, respectively. Mean bias errors (MBE) were, respectively, –5.6, 16.6, –4.0, and –0.5% of observed means. Th e continuous ellipse model was compared to the commonly used clumping index model, where the latter estimates total vegetation and total soil, but does not resolve these into their sunlit or shaded components and does not account for radiometer footprint shape dimensions. Th e continuous ellipse model resulted in RMSE for vegetation and soil of 22 and 19%, respectively, whereas the clumping index model resulted in respective RMSE of 37 and 31%. Th e continuous ellipse model had MBE of 3.3 and –2.6% for vegetation and soil, respectively, which was slightly greater than the respective MBE of –1.5 and 1.4% for clumping index model. Given the model sensitivity and uncertainty of leaf area index (LAI), the RMSE and MBE resulting from the continuous ellipse model would not be expected to be less than 20% of the observed means, and model performance was therefore deemed reasonable in this study

Genetic analysis of pod borer (Helicoverpa armigera) resistance and grain yield in desi and kabuli chickpeas (Cicer arietinum) under unprotected conditions

Half-diallel cross progenies of desi (45F1s and 45F2s) and kabuli (28F1s and 28F2s) chickpeas (Cicer arietinum) along with their parents (10 desi and 8 kabuli) with varying levels of pod borer resistance (PBR) were evaluated in replicated field trials under unprotected conditions during 2001-2002 post-rainy season at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India to study the inheritance of pod borer, Helicoverpa armigera (Hub.), and grain yield. Additive genetic variation was important for the inheritance of PBR in desi chickpea. However, both additive and dominance genetic variations were important in the inheritance of PBR in kabuli chickpea. However, dominance genetic variation was predominant in the inheritance of grain yield in both desi and kabuli chickpeas. The correlation coefficient between general combining ability (gca) effects estimated based on data of F1 and F2 generations was fairly higher, while it was lower for specific combining ability (sca) effects in desi chickpea for PBR. The correlation coefficient between gca effects and between sca effects estimated based on F1 and F2 generations’ data for PBR in kabuli chickpea and for grain yield in desi and kabuli chickpeas were very low. Chickpea lines with significant gca effects for PBR and grain yield in desi and kabuli chickpeas were identified. The implications of study results are discussed in relation to strategies to enhance PBR and grain yield levels

Adult plant development in triticale (× triticosecale wittmack) is controlled by dynamic genetic patterns of regulation

Many biologically and agronomically important traits are dynamic and show temporal variation. In this study, we used triticale (× Triticosecale Wittmack) as a model crop to assess the genetic dynamics underlying phenotypic plasticity of adult plant development. To this end, a large mapping population with 647 doubled haploid lines derived from four partially connected families from crosses among six parents was scored for developmental stage at three different time points. Using genome-wide association mapping, we identified main effect and epistatic quantitative trait loci (QTL) at all three time points. Interestingly, some of these QTL were identified at all time points, whereas others appear to only contribute to the genetic architecture at certain developmental stages. Our results illustrate the temporal contribution of QTL to the genetic control of adult plant development and more generally, the temporal genetic patterns of regulation that underlie dynamic traits.Tobias Würschum, Wenxin Liu, Katharina V. Alheit, Matthew R. Tucker, Manje Gowda, Elmar A. Weissmann, Volker Hahn and Hans Peter Maur

Determination of sex from tooth pulp tissue

Objective: This study was carried out to determine the reliability of sex determination from teeth pulp tissue. Patients and methods: This study was carried on 60 maxillary and mandibular premolars and permanent molars (30 male teeth and 30 female teeth) which were indicated for extraction. The teeth were categorized into three groups of 20 each (10 from males and 10 from females).Group 1-pulp tissue from teeth examined immediately after extraction. Group 2- and Group 3-pulp tissue examined from teeth one and five month after extraction, respectively. Teeth was sectioned and pulpal cells were stained with quinacrine dihydrochloride. The cells were observed with fluorescent microscope for fluorescent body. Gender was determined by identification of Y chromosome fluorescence in dental pulp. Results: Freshly extracted teeth and for those examined one month later, sensitivity, specificity, positive predictive value, negative predictive value, and efficiency were all 100%. Conclusion: The fluorescent Y body test is shown to be a reliable, simple, and cost-effective technique for gender identification in the immediate postmortem period up to one month

A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea