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  • 1
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    Breeding signatures of rice improvement [Genetics] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-09-30
    Description: Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys (2016)
    Oxford University Press
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    Publication Date: 2016-09-17
    Description: Snub-nosed monkeys (genus Rhinopithecus ) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Medium-Range Thermsophere-Ionosphere Storm Forecasts (2015)
    Wiley
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    Publication Date: 2015-02-04
    Description: Quantitative models describing physical processes from the solar corona to the Earth's upper atmosphere can be used to produce numerical space weather forecasts with a lead time of a few days. This article describes research towards such a capability for the thermosphere and ionosphere developed under the NASA/NSF Partnership For Collaborative Space Weather Modeling. Despite enormous scientific progress over the last few years, there is currently no system in place that relies on physics-based models to forecast moderate to intense storms in the Earth's ionosphere caused by solar wind disturbances. Forecasting conditions in the Earth's space environment after the detection of an isolated coronal mass ejection (CME) observed at the solar corona can provide 1-4 days lead time depending on the velocity of the interplanetary CME (ICME). Predicting ionospheric storm impacts due to CMEs is a significant challenge that depends primarily on the accuracy of the forecast for the north-south component of the interplanetary magnetic field at Earth. Geospace storms are also caused by high speed streams (HSS) in the solar wind, emanating from coronal holes. The arrival of HSS and their associated corotating interaction regions (where the high speed flow meets the slower ambient flow) can be forecast also, with lead times of 2-4 days and possibly longer. The thermosphere-ionosphere impacts of these less-intense disturbances may be relatively easier to forecast compared to CMEs at present.
    Print ISSN: 1539-4964
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Chromosome 11q13.3 variant modifies renal cell cancer risk in a Chinese population (2012)
    Oxford University Press
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    Publication Date: 2012-04-25
    Description: A recent genome-wide association study of renal cell carcinoma (RCC) in European population has identified genetic variants in the regions of 2p21 (rs7579899), 11q13.3 (rs7105934) and 12q24.31 (rs4765623) conferred susceptibility to RCC. In our study, we assessed whether these polymorphisms are also associated with RCC risk in a Chinese population. We genotyped these polymorphisms using TaqMan method and assessed their associations with RCC risk in a case–control study of 710 patients with histologically confirmed RCC and 760 cancer-free controls. Normal renal tissues adjacent to tumors were used to evaluate the functional consequences of these polymorphisms. We found that rs7105934 was significantly associated with reduced RCC risk [adjusted odds ratio (OR) = 0.67, 95% confidence intervals (CIs) = 0.47–0.95, GA+AA versus GG], particularly among subgroups of normal-weight individuals (OR = 0.51, 95%CI = 0.29–0.88), never-smokers (OR = 0.53, 95%CI = 0.33–0.85) and non-drinkers (OR = 0.57, 95%CI = 0.370.87). Furthermore, the rs7105934 GA genotype was associated with lower levels of CCND1 mRNA compared with GG genotype, although this association was only marginally significant ( P = 0.055). No significant association between rs7579899 or rs7105934 and RCC risk was observed. Our results suggest that rs7105934 on 11q13.3 may confer susceptibility to RCC in our population. Large population-based prospective and functional studies are required to validate the associations between these loci and RCC risk.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Complete replication of HBV and HCV in HLCZ01 cell [Microbiology] (2014)
    National Academy of Sciences
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    Publication Date: 2014-04-02
    Description: The absence of a robust cell culture system for hepatitis B virus (HBV) and hepatitis C virus (HCV) infection has limited the analysis of the virus lifecycle and drug discovery. We have established a hepatoma cell line, HLCZ01, the first cell line, to the authors’ knowledge, supporting the entire lifecycle...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    A potentially functional polymorphism in the promoter region of miR-34b/c is associated with renal cell cancer risk in a Chinese population (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-15
    Description: Members of the miR-34 family have been shown to be transcriptional targets of the tumour suppressor gene P53 . Aberration expression of miR-34 impairs p53-mediated cell cycle arrest and apoptosis. A single nucleotide polymorphism T 〉 C (rs4938723) located within the CpG island in the promoter region of pri-miR-34b/c may affect its expression and has been suggested to influence cancer risk. In this study, we genotyped rs4938723 using the TaqMan method to explore the relationship between this polymorphism and the risk of renal cell cancer (RCC) in a case-control study of 710 RCC patients and 760 control subjects. We found that individuals carrying the CC genotype had a significantly increased RCC risk compared with those with TT or TT/TC genotypes [odds ratio (OR) = 1.53, 95% confidence interval (CI) = 1.06–2.21 for CC vs. TT and OR = 1.48, 95% CI = 1.05–2.10 for CC vs. TT/TC). Furthermore, the increased risk was more evident in the subgroups of older subjects (OR = 1.80, 95% CI = 1.08–3.01), males (OR = 1.64, 95% CI = 1.08–2.51), smokers (OR = 2.07, 95% CI = 1.16–3.69) and drinkers (OR = 1.94, 95% CI = 1.01–3.73), although no interaction between rs4938723 and these characteristics was observed. Twenty-seven normal tissues adjacent to tumour were used to evaluate the association between the expression level of miR-34b/c and the polymorphism, which revealed higher expression levels of miR-34b/c in normal renal tissues with TT+TC genotypes than in those with CC genotypes ( P 〈 0.01). Furthermore, a luciferase gene assay in 293-T cells showed that the luciferase activities with rs4938723 T allele are higher than that with C allele ( P 〈 0.05). These results suggest that the miR-34b/c rs4938723 C allele may increase susceptibility to RCC by decreasing the activity of pri-miR-34b/c promoter.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Responses of phytoplankton community to the input of different aerosols in the East China Sea (2016)
    Wiley
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    Publication Date: 2016-06-23
    Description: Atmospheric deposition can affect marine phytoplankton by supplying macronutrients and trace elements. We conducted mesocosm experiments by adding aerosols with different composition (dominated by mineral dust, biomass burning and high Cu, and secondary aerosol, respectively) to the surface seawater of the East China Sea. Chlorophyll a concentrations were found to be the highest and lowest after adding aerosols containing the highest Fe and dissolved inorganic nitrogen (DIN), respectively. The relative abundance of Haptophyceae increased significantly after adding mineral dust, whereas diatom, Dinophyceae and Cryptophyceae reached the maximum accompanied with the highest DIN. Our results suggest that Fe may be more important than DIN in promoting primary productivity in the sampled seawater. The input of mineral dust and anthropogenic aerosols may result in distinct changes of phytoplankton community structure.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    Tohoku-Oki Earthquake Caused Major Ionospheric Disturbances at 450 km Altitude Over Alaska (2014)
    Wiley
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    Publication Date: 2014-11-07
    Description: Ionospheric total electron content (TEC) and atmospheric density perturbations were derived from measurements made from instruments onboard the Gravity Recovery and Climate Experiment (GRACE) spacecraft. At the time of the Tohoku-Oki earthquake on March 11, 2011, the twin spacecraft were orbiting at an altitude of ~450 km over Alaska. Significant TEC fluctuations (up to 0.6 TEC units), atmospheric density perturbations (~3.6 · 10 −14  kg/m 3 ), and sudden changes in GRACE acceleration (~4 · 10 −8  m/s 2 ) were observed ~8 minutes after the arrival of seismic and infrasound waves on the ground in Alaska, ~20 minutes after the Tohoku-Oki main shock at 05:46:23 UTC. The results of three-dimensional ionospheric-thermospheric modeling and infrasound ray-tracing simulations are consistent with the arrival time and physical characteristics of the disturbances at GRACE. This is the first time that ionospheric disturbances associated with an earthquake are clearly attributable to perturbations at such high altitudes.
    Print ISSN: 0048-6604
    Electronic ISSN: 1944-799X
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    Global Ionosphere Estimation Based on Data Fusion From Multisource: Multi‐GNSS, IRI Model, and Satellite Altimetry (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Traditionally, the ionosphere determination just uses American Global Positioning System and Russian GLObal NAvigation Satellite System dual‐frequency data and has a low precision particularly on oceans. With the rapid development of Chinese BeiDou and European Galileo systems, they are playing an increasingly important role for modeling global ionosphere. Meanwhile, satellite altimetry provides valuable and precise ionosphere delay over the oceans. Through introducing priori ionosphere values from an advanced empirical ionosphere model, combining the advantages of Global Navigation Satellite System (GNSS) and satellite altimetry technologies, the precision of global ionosphere estimation can be further improved. To assess the improvement, we collect satellite altimetry data from Jason‐2/3 and more than 300 global GNSS stations, the data are processed in 2014 and 2018 when the Sun is in a high and a low activity conditions. The results suggest that the ionosphere determination based on multitechnique fusion in a solar‐geomagnetic reference frame is well suitable to represent the ionosphere and its structure. The determined ionosphere achieves a better global consistency, and its formal accuracy is significantly reduced. By comparing with the International GNSS Service products, evaluating by satellite altimetry measurements, and independently validating with ionosonde techniques, it is proved that the ionosphere results are further improved through employing additional available data, especially for the ionosphere over the oceans.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-16
    Description: Motivation: N 6 -methyl-adenosine (m 6 A) is the most prevalent mRNA methylation but precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide profiling of m 6 A. We previously developed a peak calling algorithm called exomePeak. However, exomePeak over-simplifies data characteristics and ignores the reads’ variances among replicates or reads dependency across a site region. To further improve the performance, new model is needed to address these important issues of MeRIP-seq data. Results: We propose a novel, graphical model-based peak calling method, MeTPeak, for transcriptome-wide detection of m 6 A sites from MeRIP-seq data. MeTPeak explicitly models read count of an m 6 A site and introduces a hierarchical layer of Beta variables to capture the variances and a Hidden Markov model to characterize the reads dependency across a site. In addition, we developed a constrained Newton’s method and designed a log-barrier function to compute analytically intractable, positively constrained Beta parameters. We applied our algorithm to simulated and real biological datasets and demonstrated significant improvement in detection performance and robustness over exomePeak. Prediction results on publicly available MeRIP-seq datasets are also validated and shown to be able to recapitulate the known patterns of m 6 A, further validating the improved performance of MeTPeak. Availability and implementation: The package ‘MeTPeak’ is implemented in R and C ++, and additional details are available at https://github.com/compgenomics/MeTPeak Contact: yufei.huang@utsa.edu or xdchoi@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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