Characterization and potential functional significance of human-chimpanzee large INDEL variation

<p>Abstract</p> <p>Background</p> <p>Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp) may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.</p> <p>Results</p> <p>Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.</p> <p>Conclusions</p> <p>The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.</p

ASSESSMENT OF THE NUTRITIONAL BEHAVIOUR AMONG COLLEGE STUDENTS-A SURVEY

Objective: To assess the nutritional behaviour among college students.Methods: A prospective observational survey was conducted randomly among college students in Guntur. A self-administered data collection form was designed to understand the nutritional behaviour of the subjects.Results: A total of 300 subjects were included in the study, among them 225(75%) were females and 75(25%) were males. The survey revealed that most of them skipped their meals. A majority of 184(61.33%) students opted for high-fat diet and 268(89.33%) opted for starch-rich foods. A total of 222(74%) students usually eat four different varieties of vegetables but only 71(23.66%) of them eat fruits in each week.Conclusion: From this study, it was evident that majority of students have poor dietary habits. Lack of awareness on balanced diet and due to their busy schedules, teenagers were not maintaining a proper diet. This could be reduced by bringing minimum awareness on dietary habits to them. Taking proper diet is very essential to reduce the risk of diseases in future and to improve nourishment

On what scales can GOSAT flux inversions constrain anomalies in terrestrial ecosystems?

This is the final version. Available on open access from European Geosciences Union via the DOI in this recordData availability. CarbonTracker CT2016 results were provided by NOAA ESRL, Boulder, Colorado, USA, from the website at https://www.esrl.noaa.gov/gmd/ccgg/carbontracker/ (National Oceanic and Atmospheric Administration (NOAA) Earth System Laboratory (ESRL), 2019a). CASA GFED 4.1 and CASA CMS NEE fluxes were also downloaded from the CT2016 website. The GOSAT L4 product and VISIT NEE were downloaded from the GOSAT Data Archive Service (https://data2.gosat.nies.go.jp; NIES, 2019). The Dai Global Palmer Drought Severity Index was downloaded from the Research Data Archive at the National Center for Atmospheric Research, Computational and Information Systems Laboratory (https://doi.org/10.5065/D6QF8R93; Dai, 2017). NASA GOME-2 SIF products were obtained from the Aura Validation Data Center (https://avdc.gsfc.nasa.gov/; Aura Validation Data Center, 2019). FLUXCOM products were obtained from the data portal of the Max Planck Institute for Biochemistry (https://www.bgc-jena.mpg.de/geodb/projects/Home.php.; Max Plank Institue for Biogeochemistry, 2019). MERRA-2 products were downloaded from MDISC (https://gmao.gsfc.nasa.gov/reanalysis/MERRA-2/; Global Modeling and Assimilation Office, 2019), managed by the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC). The GEOS-Chem forward and adjoint models are freely available to the public. Instructions for downloading and running the models can be found at http://wiki.seas.harvard.edu/geos-chem (Atmospheric Chemistry Modeling Group at Harvard University , 2019). ACOS GOSAT lite files were obtained from the CO2 Virtual Science Data Environment (https://co2.jpl.nasa.gov/; Jet Propulsion Laboratory, California Institute of Technology, 2019). The SST anomalies were downloaded from the National Oceanic and Atmospheric Administration (NOAA) Earth System Research Laboratory (ESRL) website (https://www.esrl.noaa.gov; National Oceanic and Atmospheric Administration (NOAA) Earth System Laboratory (ESRL), 2019b).Interannual variations in temperature and precipitation impact the carbon balance of terrestrial ecosystems, leaving an imprint in atmospheric CO2. Quantifying the impact of climate anomalies on the net ecosystem exchange (NEE) of terrestrial ecosystems can provide a constraint to evaluate terrestrial biosphere models against and may provide an emergent constraint on the response of terrestrial ecosystems to climate change. We investigate the spatial scales over which interannual variability in NEE can be constrained using atmospheric CO2 observations from the Greenhouse Gases Observing Satellite (GOSAT). NEE anomalies are calculated by performing a series of inversion analyses using the GEOS-Chem adjoint model to assimilate GOSAT observations. Monthly NEE anomalies are compared to "proxies", variables that are associated with anomalies in the terrestrial carbon cycle, and to upscaled NEE estimates from FLUXCOM. Statistically significant correlations (P<0.05) are obtained between posterior NEE anomalies and anomalies in soil temperature and FLUXCOM NEE on continental and larger scales in the tropics, as well as in the northern extratropics on subcontinental scales during the summer (R2≥0.49), suggesting that GOSAT measurements provide a constraint on NEE interannual variability (IAV) on these spatial scales. Furthermore, we show that GOSAT flux inversions are generally better correlated with the environmental proxies and FLUXCOM NEE than NEE anomalies produced by a set of terrestrial biosphere models (TBMs), suggesting that GOSAT flux inversions could be used to evaluate TBM NEE fluxes.Environment and Climate Change CanadaNatural Sciences and Engineering Research Council of CanadaCanadian Space Agenc

Arginine Reverses Ethanol-Induced Inflammatory and Fibrotic changes in Liver despite continued Ethanol Administration

We investigated the potential of arginine to reverse pathological changes in alcohol-induced liver injury. Four groups (six rats/group) of male Wistar rats were fed a fish oil-ethanol diet for 6 (group 2) or 8 (group 1) weeks. Rats in group 3 were fed fish oil-ethanol for 6 weeks, after which they were administered arginine with fish oil-ethanol for an additional 2 weeks. Rats in group 4 were fed fish oil-dextrose for 8 weeks. Liver samples were analyzed for histopathology, lipid peroxidation, cytochrome P4502E1 activity, nuclear factor-κB, and levels of messenger RNA for tumor necrosis factor-α, cyclooxygenase-2, and inducible nitric oxide synthase. Concentrations of endotoxin were measured in plasma. The most severe inflammation and fibrosis was detected in groups 1 and 2, as were the highest levels of endotoxin, lipid peroxidation, cytochrome P450 2E1 activity, activation of nuclear factor-κB, and mRNA levels for tumor necrosis factor-α, cyclooxygenase-2, and inducible nitric oxide synthase. Plasma nitric oxide was also increased as was nitrotyrosine in liver. After arginine was administered, there was marked improvement in the pathological changes accompanied by decreased levels of endotoxin, lipid peroxidation, activation of nuclear factor-κB, tumor necrosis factor-α, cyclooxygenase-2, inducible nitric oxide, and nitrotyrosine staining. The therapeutic effects of arginine are probably secondary to increased levels of nitric oxide but other effects of arginine cannot be excluded

Application of time-dependent density functional theory to optical activity

As part of a general study of the time-dependent local density approximation (TDLDA), we here report calculations of optical activity of chiral molecules. The theory automatically satisfies sum rules and the Kramers-Kronig relation between circular dichroism and optical rotatory power. We find that the theory describes the measured circular dichroism of the lowest states in methyloxirane with an accuracy of about a factor of two. In the chiral fullerene C_76 the TDLDA provides a consistent description of the optical absorption spectrum, the circular dichroism spectrum, and the optical rotatory power, except for an overall shift of the theoretical spectrum.Comment: 17 pages and 13 PostScript figure

Components of resistance to sorghum shoot fly, Atherigona soccata

Sorghum shoot fly, Atherigona soccata is one of the major constraints in sorghum production, and host plant resistance is one of the components to control sorghum shoot fly. Thirty sorghum genotypes were evaluated for different mechanisms of resistance and morphological and agronomic traits during the rainy and postrainy seasons. The sorghum genotypes, Maulee, Phule Anuradha, M 35-1, CSV 18R, IS 2312, Giddi Maldandi, and RVRT 3 suffered lower shoot fly damage, and also exhibited high grain yield potential during the postrainy season. ICSB 433, ICSV 700, ICSV 25019, ICSV 25022, ICSV 25026, ICSV 25039, PS 35805, Akola Kranti, and IS 18551 exhibited antixenosis for oviposition and antibiosis against sorghum shoot fly, A. soccata. Leaf glossiness, plant vigor, leafsheath pigmentation and trichomes were associated with resistance/susceptibility to shoot fly. Path coefficient analysis indicated that direct effects and correlation coefficients of leaf glossiness, plant vigor, plant height, plant color and trichomes were in the same direction, suggesting that these traits can be used to select sorghum genotypes for resistance to shoot fly. Principal co-ordinate analysis based on shoot fly resistance traits and morphological traits placed the test genotypes into different groups. The genotypes placed in different groups can be used to increase the levels and broaden the genetic base of resistance to shoot fly. The environmental coefficient of variation and phenotypic coefficient of variation for shoot fly resistance and morphological traits were quite high, indicating season specific expression of resistance to sorghum shoot fly. High broadsense heritability, genetic advance and genotypic coefficient of variation suggested the predominance of additive nature of genes controlling shoot fly resistance, suggesting that pedigree breeding can be used to transfer shoot fly resistance into high yielding cultivars. This information will be useful for developing shoot fly-resistant high yielding cultivars for sustainable crop production

Heterosis and combining ability for grain Fe and Zn concentration and agronomic traits in sorghum [Sorghum bicolor (L.) Moench]

Studies on genetics and trait relationships with grain yield and other agronomic traits are critical for improving the micronutrients content in the grain and it forms an effective strategy for breeding bio fortified sorghum. It greatly contributes to addressing micronutrient malnutrition in poor people who are dependent on sorghum as a staple food. Development of hybrids with high grain Fe and Zn and higher yield enables delivery of commercial products that address both food and nutrition while bringing profits to farmers. The present study was aimed at developing suitable breeding strategy and improving breeding products using gene action, heterosis and combining ability analysis for improving the grain Iron (Fe) and Zinc (Zn) concentration and grain yield in sorghum. This study was conducted in Line Tester mating design involving seven parents. A total of 12 new hybrids were developed by mating three lines with four testers. The combining ability of the crosses indicated predominance of dominance variance than additive variance for the agronomic traits such as days to 50% flowering, grain yield, grain Fe and Zn concentrations except for plant height and 100 seed weight. Higher magnitude of SCA than GCA variance for grain iron and zinc concentrations indicated the importance of non-additive gene action in the improvement of nutritional traits. Hybrids exhibited heterosis for agronomic traits and for grain Fe concentration and grain Zn. Most of the traits showed significant positive heterosis over mid parent value indicating the predominance of dominant gene action except the trait 100 seed weight. Significant positive mid-parent heterosis for grain iron indicated that there would be an opportunity to exploit heterosis in improving for grain Fe. But for Zn concentration, there is a limited possibility for exploitation of heterosis. This study suggested that simple selection will improve plant height and 100 seed weight in sorghum but heterosis breeding is more useful for improving grain yield. While both parents need to be improved for improving grain Zn concentration, there is good scope for exploiting heterosis for improving grain Fe concentration in sorghum

Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes

Multiple groups of endogenous epsilon-like retroviruses conserved across primates

Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses. IMPORTANCE: Epsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major groups of primates, including humans. These viruses seem to have circulated and infected primate ancestors 42 to 65 million years ago. We are now interested in how these viruses have evolved and whether they have the potential to infect modern humans or other primates