Natural variation of salinity response,population structure and candidate genes associated with salinity tolerance in perennial ryegrass accessions

Natural variation in salinity response, effects of population structure on growth and physiological traits and gene–trait association were examined in 56 global collections of diverse perennial ryegrass (Lolium perenne L.) accessions. Three population structure groups were identified with 66 simple sequence repeat markers, which on average accounted for 9 and 11% of phenotypic variation for the control and salinity treatment at 300 mm NaCl. Group 1 (10 accessions) had greater plant height, leaf dry weight and water content, chlorophyll index, K⁺ concentration and K⁺/Na⁺ than group 2 (39 accessions) and group 3 (7 accessions) under salinity stress, while group 3 had higher Na⁺ than groups 1 and 2. Eighty‐seven single nucleotide polymorphisms were detected from four partial candidate genes encoding aquaporin and Na⁺/H⁺ antiporter in both plasma and tonoplast membranes. Overall, rapid decay of linkage disequilibrium was observed within 500 bp. Significant associations were found between the putative LpTIP1 and Na⁺ for the control and between the putative LpNHX1 and K⁺/Na⁺ under the control and salinity treatments after controlling population structure. These results indicate that population structure influenced phenotypic traits, and allelic variation in LpNHX1 may affect salinity tolerance of perennial ryegrass.     

Maintenance of Intestinal Th17 Cells and Reduced Microbial Translocation in SIV-infected Rhesus Macaques Treated with Interleukin (IL)-21

In pathogenic HIV and SIV infections of humans and rhesus macaques (RMs), preferential depletion of CD4⁺ Th17 cells correlates with mucosal immune dysfunction and disease progression. Interleukin (IL)-21 promotes differentiation of Th17 cells, long-term maintenance of functional CD8⁺ T cells, and differentiation of memory B cells and antibody-secreting plasma cells. We hypothesized that administration of IL-21 will improve mucosal function in the context of pathogenic HIV/SIV infections. To test this hypothesis, we infected 12 RMs with SIV_mac239 and at day 14 post-infection treated six of them with rhesus rIL-21-IgFc. IL-21-treatment was safe and did not increase plasma viral load or systemic immune activation. Compared to untreated animals, IL-21-treated RMs showed (i) higher expression of perforin and granzyme B in total and SIV-specific CD8⁺ T cells and (ii) higher levels of intestinal Th17 cells. Remarkably, increased levels of Th17 cells were associated with reduced levels of intestinal T cell proliferation, microbial translocation and systemic activation/inflammation in the chronic infection. In conclusion, IL-21-treatment in SIV-infected RMs improved mucosal immune function through enhanced preservation of Th17 cells. Further preclinical studies of IL-21 may be warranted to test its potential use during chronic infection in conjunction with antiretroviral therapy.     

光受体UVR8对UV-B响应机制研究进展

来自太阳光谱中的UV-B辐射被认为是一种重要的环境信号,可以被植物感受并诱导植物调整自身生长和发育状态以适应环境。人们对植物中光敏色素、隐花色素和蓝光受体向光素的研究已非常深入,但对植物响应UV-B的机制仅在最近才取得一些突破性进展。这些研究发现,植物中存在着UV-B受体UVR8(UV Resistance Locus 8)。目前认为,UVR8二聚体感应UV-B后瞬间解聚为单体,并与E3泛素连接酶COP1(constitutively photomorphogenic 1)相互作用,从而激活UV-B响应基因的表达。该文从UVR8的发现、UVR8的结构和感受UV-B机制、UVR8二聚体重新形成以及UV-B信号传导与可见光信号传导途径间的差异等方面综述了关于UV-B受体UVR8的最新研究成果。     

干旱胁迫对茉莉3个品种叶片光合特性和超微结构的影响

以茉莉3品种为试材,分析干旱胁迫对光合作用相关生理指标和叶肉细胞超微结构的影响。结果表明,在轻度干旱胁迫下, 单瓣茉莉和多瓣茉莉净光合速率（Pn）、蒸腾速率（Tr）、气孔导度（Gs）和胞间 CO2浓度（Ci）呈下降趋势,但叶肉细胞超微结构仅受轻微影响。在中度干旱胁迫下,多瓣茉莉Pn、Tr、Gs持续降低,而Ci 随干旱胁迫的增加反而上升,单瓣茉莉Pn、Tr、Gs和Ci继续呈下降趋势,两品种叶绿体超微结构发生明显变化并出现伤害症状。在重度干旱胁迫下,Pn、Tr、Gs降幅明显,与对照组相比达极显著差异(P<0.01),Ci 持续上升,叶绿体超微结构发生巨大变化,特别是叶绿体发生严重损伤。双瓣茉莉Pn、Tr、Gs、Ci随干旱胁迫的加重也呈现逐渐下降的趋势,但降幅较小,叶肉细胞超微结构无明显变化。因此,与单瓣茉莉和多瓣茉莉相比较,双瓣茉莉对干旱胁迫的耐受力较强。     

江西玉山上奥陶统凯迪阶三衢山组的丛花海绵(Corymbospongia)*

串管海绵在中–晚奥陶世经历了的首次辐射演化事件, 在北美、新南威尔士、哈萨克斯坦、西伯利亚和中国西北等地的上奥陶统地层中皆有报道, 但研究程度较低。本文系华南奥陶系串管海绵首次系统古生物学的报道, 详细描述江西玉山上奥陶统凯迪阶三衢山组的Corymbospongia (丛花海绵属)化石, 并基于C. amplia Rigby, Karl, Blodgett & Baichtal, 2005和C. mica Rigby & Potter, 1986的标本展示该属化石外壁的微孔等特征性结构, 这2个种具有跨板块的生物地理分布。综合串管海绵产出层的碳酸盐岩微相以及伴生钙藻和珊瑚化石等群落分子的指相参照, 识别C. amplia和C. mica均具有明显的生态专属性: C. amplia为造礁生物, 在小型微生物岩中出现; C. mica则代表适应于更浅水生境的平地群落代表。本研究将为从底栖生物群落角度开展扬子区生物地层学及古地理重建提供进一步的依据。     

蓖麻籽提取液对福寿螺毒杀效果及作用机制

采用生物浸泡法, 以草本植物蓖麻籽提取液制备植物源毒杀剂, 研究不同提取液浓度(0、0.5、1.5、3.0、4.5、6.0 g/L)对福寿螺(Pomacea canaliculata Lam)毒杀作用效果, 并通过福寿螺在亚致死浓度1.58(LC₂₅)、3.82(LC₅₀)和6.05 g/L(LC₇₅) 处理条件下的肝脏组织生理生化指标及其相关性, 进一步分析其毒杀作用机制。结果表明: 在提取液处理48h后, 福寿螺死亡率随着时间延长和浓度的增加而增加, 且各浓度处理下福寿螺死亡率差异显著(P<0.05)。福寿螺在亚致死浓度处理48h后, 其肝胰腺组织中蛋白质含量(TP)、丙二醛(MDA)含量和过氧化氢酶(CAT)活性与对照组均存在差异, 过氧化氢酶(CAT)活性与丙二醛(MDA)含量呈显著负相关关系(P<0.05)。蓖麻籽提取液通过影响福寿螺肝脏组织中蛋白质含量(TP)和丙二醛(MDA)含量, 及过氧化氢酶(CAT)活性, 导致螺肝脏组织损伤, 机体代谢紊乱, 从而达到毒杀效果。     

Functional annotation signatures of disease susceptibility loci improve SNP association analysis

Background

Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the phenotype. To date, functional annotations of the genetic variants have rarely played more than an indirect role in assessing evidence for association. Here, we demonstrate how these data can be systematically integrated into an association study’s analysis plan.

Results

We developed a Bayesian statistical model for the prior probability of phenotype–genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a binary regression of association status on a set of annotation variables whose coefficients were estimated through an analysis of associated SNPs in the GWAS Catalog (GC). The functional predictors examined included measures that have been demonstrated to correlate with the association status of SNPs in the GC and some whose utility in this regard is speculative: summaries of the UCSC Human Genome Browser ENCODE super–track data, dbSNP function class, sequence conservation summaries, proximity to genomic variants in the Database of Genomic Variants and known regulatory elements in the Open Regulatory Annotation database, PolyPhen–2 probabilities and RegulomeDB categories. Because we expected that only a fraction of the annotations would contribute to predicting association, we employed a penalized likelihood method to reduce the impact of non–informative predictors and evaluated the model’s ability to predict GC SNPs not used to construct the model. We show that the functional data alone are predictive of a SNP’s presence in the GC. Further, using data from a genome–wide study of ovarian cancer, we demonstrate that their use as prior data when testing for association is practical at the genome–wide scale and improves power to detect associations.

Conclusions

We show how diverse functional annotations can be efficiently combined to create ‘functional signatures’ that predict the a priori odds of a variant’s association to a trait and how these signatures can be integrated into a standard genome–wide–scale association analysis, resulting in improved power to detect truly associated variants.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-398) contains supplementary material, which is available to authorized users.     

Structural Characterization by Multistage Mass Spectrometry (MSn) of Human Milk Glycans Recognized by Human Rotaviruses

We have shown that recombinant forms of VP8* domains of the human rotavirus outer capsid spike protein VP4 from human neonatal strains (N155(G10P[11]) and RV3(G3P[6]) and a bovine strain (B223) recognize unique glycans within the repertoire of human milk glycans. The accompanying study by Yu et al.², describes a human milk glycan shotgun glycan microarray that led to the identification of 32 specific glycans in the human milk tagged glycan library that were recognized by these human rotaviruses. These microarray analyses also provided a variety of metadata about the recognized glycan structures compiled from anti-glycan antibody and lectin binding before and after specific glycosidase digestions, along with compositional information from mass analysis by matrix-assisted laser desorption ionization-mass spectrometry. To deduce glycan sequence and utilize information predicted by analyses of metadata from each glycan, 28 of the glycan targets were retrieved from the tagged glycan library for detailed sequencing using sequential disassembly of glycans by ion-trap mass spectrometry. Our aim is to obtain a deeper structural understanding of these key glycans using an orthogonal approach for structural confirmation in a single ion trap mass spectrometer. This sequential ion disassembly strategy details the complexities of linkage and branching in multiple compositions, several of which contained isomeric mixtures including several novel structures. The application of this approach exploits both library matching with standard materials and de novo approaches. This combination together with the metadata generated from lectin and antibody-binding data before and after glycosidase digestions provide a heretofore-unavailable level of analytical detail to glycan structure analysis. The results of these studies showed that, among the 28 glycan targets analyzed, 27 unique structures were identified, and 23 of the human milk glycans recognized by human rotaviruses represent novel structures not previously described as glycans in human milk. The functional glycomics analysis of human milk glycans provides significant insight into the repertoire of glycans comprising the human milk metaglycome.