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  • Oxford University Press  (363)
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  • 1
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    Low-frequency germline variants across 6p22.2-6p21.33 are associated with non-obstructive azoospermia in Han Chinese men (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-12
    Description: Genome-wide association studies (GWAS) have identified several common loci contributing to non-obstructive azoospermia (NOA). However, a substantial fraction of NOA heritability remains undefined, especially those low-frequency [defined here as having a minor allele frequency (MAF) between 0.5 and 5%] and rare (MAF below 0.5%) variants. Here, we performed a 3-stage exome-wide association study in Han Chinese men to evaluate the role of low-frequency or rare germline variants in NOA development. The discovery stage included 962 NOA cases and 1348 healthy male controls genotyped by exome chips and was followed by a 2-stage replication with an additional 2168 cases and 5248 controls. We identified three low-frequency variants located at 6p22.2 (rs2298090 in HIST1H1E encoding p.Lys152Arg: OR = 0.30, P = 2.40 x 10 –16 ) and 6p21.33 (rs200847762 in FKBPL encoding p.Pro137Leu: OR = 0.11, P = 3.77 x 10 –16 ; rs11754464 in MSH5 : OR = 1.78, P = 3.71 x 10 –7 ) associated with NOA risk after Bonferroni correction. In summary, we report an instance of newly identified signals for NOA risk in genes previously undetected through GWAS on 6p22.2–6p21.33 in a Chinese population and highlight the role of low-frequency variants with a large effect in the process of spermatogenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Modulation of LSD1 phosphorylation by CK2/WIP1 regulates RNF168-dependent 53BP1 recruitment in response to DNA damage (2015)
    Oxford University Press
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    Publication Date: 2015-07-12
    Description: Proper DNA damage response is essential for the maintenance of genome integrity. The E3 ligase RNF168 deficiency fully prevents both the initial recruitment and retention of 53BP1 at sites of DNA damage. In response to DNA damage, RNF168-dependent recruitment of the lysine-specific demethylase LSD1 to the site of DNA damage promotes local H3K4me2 demethylation and ubiquitination of H2A/H2AX, facilitating 53BP1 recruitment to sites of DNA damage. Alternatively, RNF168-mediated K63-linked ubiquitylation of 53BP1 is required for the initial recruitment of 53BP1 to sites of DNA damage and for its function in repair. We demonstrated here that phosphorylation and dephosphorylation of LSD1 at S131 and S137 was mediated by casein kinase 2 (CK2) and wild-type p53-induced phosphatase 1 (WIP1), respectively. LSD1, RNF168 and 53BP1 interacted with each other directly. CK2-mediated phosphorylation of LSD1 exhibited no impact on its interaction with 53BP1, but promoted its interaction with RNF168 and RNF168-dependent 53BP1 ubiquitination and subsequent recruitment to the DNA damage sites. Furthermore, overexpression of phosphorylation-defective mutants failed to restore LSD1 depletion-induced cellular sensitivity to DNA damage. Taken together, our results suggest that LSD1 phosphorylation modulated by CK2/WIP1 regulates RNF168-dependent 53BP1 recruitment directly in response to DNA damage and cellular sensitivity to DNA damaging agents.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Soil carbon dynamics in a Pinus massoniana plantation following clear-cutting and slash removal (2016)
    Oxford University Press
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    Publication Date: 2016-01-29
    Description: Aims Slash removal is a common practice to prepare recently harvested sites for replanting. However, little is known about its impact on soil carbon (C) dynamics in subtropical plantations. This study evaluates the effects of burning versus manual slash removal site preparation treatments on soil organic carbon (SOC), soil respiration and soil microbial community structure in a Pinus massoniana plantation in southern China. Methods Three areas within a mature P. massoniana plantation were clearcut. Two months following harvesting, slash on one-half of each area was burned (BURN), whereas slash was manually removed (MANR) on the other portion. Slash removal treatments were also compared with adjacent uncut plantation areas (UNCUT). Soil samples, and soil respiration measurements were used to characterize soil properties and microbial communities following slash removal treatments. Important Findings Mean soil respiration rates from the MANR and BURN treatments were 26% and 17% lower, respectively, than the UNCUT treatment over 1 year. The MANR and BURN treatment resulted in soils with 27% and 9% reduction in total phospholipid fatty acids (PLFAs) and 18% and 10% reduction in bacterial PLFAs, respectively, compared with the UNCUT treatment. However, no significant differences existed between slash removal treatments with respect to soil chemical properties, SOC chemical compositions, soil respiration and microbial communities; although PLFA patterns were notably different for the burned plots. Most factors affecting C dynamics and microbial communities were not sensitive to the differences imparted to the ecosystem due to manual slash removal or burning. Our results suggested that low-intensity burning after clear-cutting might have no significant effect on soil C pool and its dynamics compared with manual slash removal in subtropical plantations.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Root tip morphology, anatomy, chemistry and potential hydraulic conductivity vary with soil depth in three temperate hardwood species (2016)
    Oxford University Press
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    Publication Date: 2016-01-23
    Description: Root traits in morphology, chemistry and anatomy are important to root physiological functions, but the differences between shallow and deep roots have rarely been studied in woody plants. Here, we selected three temperate hardwood species, Juglans mandshurica Maxim., Fraxinus mandschurica Rupr. and Phellodendron amurense Rupr., in plantations in northeastern China and measured morphological, anatomical and chemical traits of root tips (i.e., the first-order roots) at surface (0–10 cm) and subsurface (20–30 cm) soil layers. The objectives of this study were to identify how those traits changed with soil depth and to reveal potential functional differences. The results showed that root diameters in deep root tips were greater in J. mandshurica and F. mandschurica , but smaller in P. amurense . However, root stele diameter and the ratio of stele to root diameter in the subsurface layer were consistently greater in all three species, which may enhance their abilities to penetrate into soil. All deep roots exhibited lower tissue nitrogen concentration and respiration rate, which were possibly caused by lower nutrient availability in the subsurface soil layer. Significant differences between shallow and deep roots were observed in xylem structure, with deep roots having thicker stele, wider maximum conduit and greater number of conduits per stele. Compared with shallow roots, the theoretical hydraulic conductivities in deep roots were enhanced by 133% ( J. mandshurica ), 78% ( F. mandschurica ) and 217% ( P. amurense ), respectively, indicating higher efficiency of transportation. Our results suggest that trees’ root tip anatomical structure and physiological activity vary substantially with soil environment.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 5
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    Root diameter variations explained by anatomy and phylogeny of 50 tropical and temperate tree species (2014)
    Oxford University Press
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    Publication Date: 2014-05-06
    Description: Root diameter, a critical indicator of root physiological function, varies greatly among tree species, but the underlying mechanism of this high variability is unclear. Here, we sampled 50 tree species across tropical and temperate zones in China, and measured root morphological and anatomical traits along the first five branch orders in each species. Our objectives were (i) to reveal the relationships between root diameter, cortical thickness and stele diameter among tree species in tropical and temperate forests, and (ii) to investigate the relationship of both root morphological and anatomical traits with divergence time during species radiation. The results showed that root diameter was strongly affected by cortical thickness but less by stele diameter in both tropical and temperate species. Changes in cortical thickness explained over 90% of variation in root diameter for the first order, and ~74–87% for the second and third orders. Thicker roots displayed greater cortical thickness and more cortical cell layers than thinner roots. Phylogenetic analysis demonstrated that root diameter, cortical thickness and number of cortical cell layers significantly correlated with divergence time at the family level, showing similar variation trends in geological time. The results also suggested that trees tend to decrease their root cortical thickness rather than stele diameter during species radiation. The close linkage of variations in root morphology and anatomy to phylogeny as demonstrated by the data from the 50 tree species should provide some insights into the mechanism of root diameter variability among tree species.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 6
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    iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis (2014)
    Oxford University Press
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    Publication Date: 2014-02-26
    Description: :  A challenge in biodata analysis is to understand the underlying phenomena among many interactions in signaling pathways. Such study is formulated as the pathway enrichment analysis, which identifies relevant pathways functional enriched in high-throughput data. The question faced here is how to analyze different data types in a unified and integrative way by characterizing pathways that these data simultaneously reveal. To this end, we developed integrative Pathway Enrichment Analysis Platform, iPEAP , which handles transcriptomics, proteomics, metabolomics and GWAS data under a unified aggregation schema. iPEAP emphasizes on the ability to aggregate various pathway enrichment results generated in different high-throughput experiments, as well as the quantitative measurements of different ranking results, thus providing the first benchmark platform for integration, comparison and evaluation of multiple types of data and enrichment methods. Availability and implementation:   iPEAP is freely available at http://www.tongji.edu.cn/~qiliu/ipeap.html . Contact:   qiliu@tongji.edu.cn or zwcao@tongji.edu.cn 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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  • 7
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    The Transition to Modern Agriculture: Contract Farming in Developing Economies (2014)
    Oxford University Press
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    Publication Date: 2014-09-02
    Description: Recent years have seen considerable interest in the impact of contract farming on farmers in developing countries, motivated out of belief that contract farming spurs transition to modern agriculture. In this article, we provide a thorough review of the empirical literature on contract farming in both developed and developing countries, using China as a special case of the latter. We pay careful attention to broad implications of this research for economic development. We first find empirical studies consistently support the positive contribution of contract farming to production and supply chain efficiency. We also find that most empirical studies identify a positive and significant effect of contract farming on farmer welfare, yet are often unable to reach consistent conclusions as to significant correlates of contract participation.
    Keywords: L23 - Organization of Production, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 8
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    Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer (2016)
    Oxford University Press
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    Publication Date: 2016-03-17
    Description: Most of current gene expression signatures for cancer prognosis are based on risk scores, usually calculated as some summaries of expression levels of the signature genes, whose applications require presetting risk score thresholds and data normalization. In this study, we demonstrate the critical limitations of such type of signatures that the risk scores of samples will change greatly when they are normalized together with different samples, which would induce spurious risk classification and difficulty in clinical settings, and the risk scores of independent samples are incomparable if data normalization is not adopted. To overcome these limitations, we propose a rank-based method to extract a prognostic gene pair signature for overall survival of stage I non-small-cell lung cancer. The prognostic gene pair signature is verified in three integrated data sets detected by different laboratories with different microarray platforms. We conclude that, different from the type of signatures based on risk scores summarized from gene expression levels, the rank-based signatures could be robustly applied at the individualized level to independent clinical samples assessed in different laboratories.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 9
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    CCA2 Attack and Modification of Huang et al.s Public Key Encryption with Authorized Equality Test (2016)
    Oxford University Press
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    Publication Date: 2016-11-05
    Description: In this article, we identify a flaw in Huang et al .'s public key encryption with authorized equality test ( The Computer Journal , 2015). More precisely, we point out that the proof of the indistinguishability under adaptive chosen ciphertext attack (IND-CCA2) security for their scheme has a serious flaw. We illustrate this flaw by presenting a polynomial time CCA2 attack on their scheme. We also provide a solution to correct this flaw by modifying their scheme slightly. Our solution is quite efficient because it provides security against CCA2 attack by exploiting only the hash computation of a two times longer input without any increase in the sizes of ciphertexts and warrants.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway (2015)
    Oxford University Press
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    Publication Date: 2015-09-29
    Description: The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica , a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis . The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon , and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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