Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase

The X-ray crystal structures of Escherichia coli gamma-aminobutyrate aminotransferase unbound and bound to the inhibitor aminooxyacetate are reported. The enzyme crystallizes from ammonium sulfate solutions in the P3(2)21 space group with a tetramer in the asymmetric unit. Diffraction data were collected to 2.4 A resolution for the unliganded enzyme and 1.9 A resolution for the aminooxyacetate complex. The overall structure of the enzyme is similar to those of other aminotransferase subgroup II enzymes. The ability of gamma-aminobutyrate aminotransferase to act on primary amine substrates (gamma-aminobutyrate) in the first half-reaction and alpha-amino acids in the second is proposed to be enabled by the presence of Glu211, whose side chain carboxylate alternates between interactions with Arg398 in the primary amine half-reaction and an alternative binding site in the alpha-amino acid half-reaction, in which Arg398 binds the substrate alpha-carboxylate. The specificity for a carboxylate group on the substrate side chain is due primarily to the presence of Arg141, but also requires substantial local main chain rearrangements relative to the structurally homologous enzyme dialkylglycine decarboxylase, which is specific for small alkyl side chains. No iron-sulfur cluster is found in the bacterial enzyme as was found in the pig enzyme [Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. B., and Schirmer, T. (2004) J. Biol. Chem. 279, 363-73.]. The binding of aminooxyacetate causes remarkably small changes in the active site structure, and no large domain movements are observed. Active site structure comparisons with pig gamma-aminobutyrate aminotransferase and dialkylglycine decarboxylase are discussed.     

Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

秦巴山区野生百合(Lilium spp.)的育种应用研究

为探索秦巴山区野生百合资源在百合育种中的应用方向及途径, 获得具有其独特遗传背景的育种材料,将秦巴山区野生百合的抗病毒及独特观赏特性等优良遗传性状逐渐渗到栽培品种中去。该研究借助切割柱头杂交及胚抢救技术,选取6种秦巴山区野生百合［岷江百合(Lilium gegale)、宜昌百合(L. leucanthum)、山丹（L. pumilum）、野百合（L. brownii）、宝兴百合（L. duchartrei）、川百合（L. davidii）］以及亚洲百合（Asiatic hybrids,AA）品种‘Elite’、东方百合（Oriental hybrids,OO）品种‘Sorbonne’、‘Siberia’和‘Marlon’、OT百合（Oriental × Trumpet hybrids,OT）品种‘Yelloween’、‘Serano’、‘Corel′door’进行了32组共计263朵花的（品）种间杂交,并针对膨大变软的果实剥离可供离体培养的胚及胚囊进行胚抢救。结果表明：（1）不同杂交组合坐果率、胚获得及萌发率呈现出较大差异,综合坐果率为11.4%,对30个膨大的果实中共计38个可供离体培养的胚及胚囊进行胚抢救,有7株最终萌发。（2）以野生百合为父母本的12组杂交组合中,6组获得了膨大果实,得到6株杂交后代。（3）栽培百合做母本,野生百合做父本的20组杂交组合中,共9组获得了膨大果实,除‘Elite’ × 山丹可直接收获种子外,共得到1株杂交后代。（4）以岷江百合及宜昌百合为亲本的远缘杂交TT × AA及回交OT × TT成功获得杂种后代。（5）秦巴山区6种野生百合在远缘杂交中获得育种后代的几率存在较大差异,宜昌百合和岷江百合获得后代几率较高,宝兴百合获得后代几率较低,野百合未获得后代。以上结果表明,岷江百合和宜昌百合为母本的TT × AA杂交和宝兴百合为父本的TT × AA杂交以及岷江百合和宜昌百合为父本的OT回交,为三种百合的育种利用提供了新途径,野百合的育种应用途径需要继续探索。     

New synthesis of a porous Si/TiO2 photocatalyst: testing its efficiency and stability under visible light irradiation.

TiO(2) nanoparticles were directly coupled with porous silicon and this novel composite material shows very strong photocatalytic activity for the degradation of Rhodamine B with high photochemical stability under visible light irradiation.     

青藏高原火绒草斑块群落空间格局分析

以青藏高原两种生境(阴坡和阶地)和4个斑块大小等级水平(等级1:0.2—0.6m2,G1;等级2:0.6—2 m2,G2;等级3:2—3.6 m2,G3和等级4:3.6—8.6 m2,G4)的火绒草(Leontopodium nanum)群落为对象,利用幂乘方法则,分析了其种群和群落空间异质性和群落物种多样性特征,明晰了优势种、亚优势种、伴生种和偶见种对其植被分布格局的影响。结果表明:各火绒草斑块的群落空间分布格局均呈集群分布,植物种的随机出现频率和实际出现频率的方差对数值与其幂乘方法吻合性较高(R2﹥0.8),幂乘方法能对火绒草斑块植被空间分布格局进行客观分析。优势种火绒草和线叶嵩草(Kobresia capillifolia),亚优势种球花蒿(Artemisia smithii)和珠芽蓼(Polygonum viviparum)等的相对空间异质性(ε)高于群落的空间异质性(δC),位于直线y=0上方,使群落趋于集群分布;伴生种西北针茅(Stipa krylovii)、瑞香狼毒(Stellera chamaejasme)和苔草(Carex sp)等的ε与群落的δC类似,位于直线y=0附近,它们维持群落自身空间分布状态;偶见种的ε低于群落的δC,位于直线y=0下方,降低群落的集群分布。随火绒草斑块等级水平的增加,群落物种数呈增加,丰富度指数DGI呈降低变化。一般火绒草斑块的δc和βw为阶地﹥阴坡,DGI为阶地﹤阴坡;两种生境下,植物种组成的相似性G1斑块较低,G2—G4斑块较高。火绒草斑块的群落分布格局主要由优势种和亚优势种及偶见种的ε决定。     

Detection of Cytomegalovirus Antibodies Using a Biosensor Based on Imaging Ellipsometry

Background

Cytomegalovirus (CMV) is the most common infectious cause of mental disability in newborns in developed countries. There is an urgent need to establish an early detection and high-throughput screening method for CMV infection using portable detection devices.

Methods

An antibody analysis method is reported for the detection and identification of CMV antibodies in serum using a biosensor based on high spatial resolution imaging ellipsometry (BIE). CMV antigen (CMV-3A) was immobilized on silicon wafers and used to capture CMV antibodies in serum. An antibody against human immunoglobulin G (anti-IgG) was used to confirm the IgG antibody against CMV captured by the CMV-3A.

Results

Our results show that this assay is rapid and specific for the identification of IgG antibody against CMV. Further, patient serum was quantitatively assessed using the standard curve method, and the quantitative results were in agreement with the enzyme-linked immunosorbent assay. The CMV antibody detection sensitivity of BIE reached 0.01 IU/mL.

Conclusions

This novel biosensor may be a valuable diagnostic tool for analysis of IgG antibody against CMV during CMV infection screening.