湿地植物根系泌氧及其在自然基质中的扩散效应研究进展

湿地植物根系径向泌氧(ROL)是构造根际氧化-还原异质微生态系统的核心要素,其扩散层为好氧、厌氧微生物提供了良好生境并促进其代谢活动,使湿地植物根际成为有机物降解、物质循环及生命活动最为强烈的场所,已有成果证明湿地植物根系ROL的强弱与污染物的去除效果密切相关。因此,开展湿地植物根系ROL及其在自然基质中的扩散效应研究,对于了解湿地植物根系ROL机理及其根际氧环境特征,进而发挥湿地植物的污染去除功能具有十分重要的意义。基于此,首先归纳了湿地植物根系ROL特征及其受影响机制的研究现状,而后从种属差异、时空分布及对微生物的影响等方面对根系ROL在自然基质中的扩散效应国内外研究成果进行了总结,最终根据研究现状与不足对今后的研究方向进行了简要展望。创新之处在于:1)提出影响根系氧供给及氧输送释放通道的环境、生物等因素,阐述了其对根系ROL的影响机制;2)着重阐述了目前研究较少提及的根系ROL扩散效应测定方法。     

Detection of selection signatures in dairy and beef cattle using high-density genomic information

Background

Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs.

Results

Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (F_ST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the F_ST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global F_ST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection.

Conclusions

This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0127-3) contains supplementary material, which is available to authorized users.     

家蚕Bmyan基因的克隆表达和作为microRNA 7靶基因的验证

microRNAs(miRNAs)是一类长约22 nt的非编码RNA,通过与其靶基因3′端非翻译区(3′-UTR)的结合来调节各项生命活动。克隆表达家蚕Bmyan基因,验证其是否是bmo-miR-7的靶基因对于深入研究家蚕变态发育机制有重要意义。基于同源性检索和PCR扩增,克隆了家蚕Bmyan基因CDS全长,编码476个氨基酸。序列分析表明,家蚕YAN蛋白的氨基酸序列保守,含SAM-PNT和ETs结构域。芯片数据、RT-PCR和定量PCR的检测结果表明,Bmyan在五龄3 d的家蚕头部、体壁、卵巢中高量表达,在其余组织中低量表达或不表达。在幼虫期,Bmyan表达水平相对较低,但在上蔟期和蛹期前4 d高量表达。通过3′RACE克隆了Bmyan基因的3′-UTR。RNAhybrid在线软件预测了其3'-UTR上bmo-miR-7的两个靶位点。构建了含有Bmyan基因3′-UTR和荧光素酶报告基因的转染载体,将该载体与bmo-miR-7的mimics序列共转染到家蚕胚胎细胞系BmE中,通过测定荧光素酶的活性,证明了Bmyan基因是bmo-miR-7的靶基因。本研究为进一步揭示bmo-miR-7和Bmyan在家蚕体内的生物学功能奠定了基础。     

马尾松(Pinus massoniana)人工林林窗对土壤不同形态活性有机碳的影响

研究了四川盆地低山丘陵区马尾松人工林不同大小林窗对表层土壤活性有机碳(水溶性有机碳、微生物量碳、易氧化碳)含量、分配比例及碳库管理指数的影响。结果表明:(1)林窗下土壤微生物量碳含量与分配比例较林下土壤有所升高,而水溶性有机碳与易氧化碳含量及水溶性有机碳分配比例有所降低。(2)林窗大小显著影响林窗中心土壤活性有机碳含量与分配比例。随林窗面积增大,水溶性有机碳、微生物量碳与易氧化碳含量呈现较为一致的升高趋势;水溶性有机碳和微生物量碳分配比例也升高,易氧化碳分配比例先下降后升高,稳定态碳先升高后降低;总体表现为较大林窗(900—1225m2)微生物活性强,活性有机碳含量高,且有机碳库稳定性较好。(3)土壤碳库管理指数随林窗面积增大无显著变化,但与各形态活性有机碳含量及总有机碳含量显著相关,说明土壤碳库管理指数能够相对全面地反映林窗大小对土壤碳库的影响。     

A Cytosolic Thioredoxin Acts as a Molecular Chaperone for Peroxisome Matrix Proteins as Well as Antioxidant in Peroxisome

Thioredoxin (TRX) is a disulfide reductase present ubiquitously in all taxa and plays an important role as a regulator of cellular redox state. Recently, a redox-independent, chaperone function has also been reported for some thioredoxins. We previously identified nodulin-35, the subunit of soybean uricase, as an interacting target of a cytosolic soybean thioredoxin, GmTRX. Here we report the further characterization of the interaction, which turns out to be independent of the disulfide reductase function and results in the co-localization of GmTRX and nodulin-35 in peroxisomes, suggesting a possible function of GmTRX in peroxisomes. In addition, the chaperone function of GmTRX was demonstrated in in vitro molecular chaperone activity assays including the thermal denaturation assay and malate dehydrogenase aggregation assay. Our results demonstrate that the target of GmTRX is not only confined to the nodulin-35, but many other peroxisomal proteins, including catalase (AtCAT), transthyretin-like protein 1 (AtTTL1), and acyl-coenzyme A oxidase 4 (AtACX4), also interact with the GmTRX. Together with an increased uricase activity of nodulin-35 and reduced ROS accumulation observed in the presence of GmTRX in our results, especially under heat shock and oxidative stress conditions, it appears that GmTRX represents a novel thioredoxin that is co-localized to the peroxisomes, possibly providing functional integrity to peroxisomal proteins.     

The interaction of Gα13 with integrin β1 mediates cell migration by dynamic regulation of RhoA

Heterotrimeric G protein Gα₁₃ is known to transmit G protein–coupled receptor (GPCR) signals leading to activation of RhoA and plays a role in cell migration. The mechanism underlying the role of Gα₁₃ in cell migration, however, remains unclear. Recently we found that Gα₁₃ interacts with the cytoplasmic domain of integrin β₃ subunits in platelets via a conserved ExE motif. Here we show that a similar direct interaction between Gα₁₃ and the cytoplasmic domain of the integrin β₁ subunit plays a critical role in β₁-dependent cell migration. Point mutation of either glutamic acid in the Gα₁₃-binding ⁷⁶⁷EKE motif in β₁ or treatment with a peptide derived from the Gα₁₃-binding sequence of β₁ abolished Gα₁₃–β₁ interaction and inhibited β₁ integrin–dependent cell spreading and migration. We further show that the Gα₁₃-β₁ interaction mediates β₁ integrin–dependent Src activation and transient RhoA inhibition during initial cell adhesion, which is in contrast to the role of Gα₁₃ in mediating GPCR-dependent RhoA activation. These data indicate that Gα₁₃ plays dynamic roles in both stimulating RhoA via a GPCR pathway and inhibiting RhoA via an integrin signaling pathway. This dynamic regulation of RhoA activity is critical for cell migration on β₁ integrin ligands.