Characterization and its Potential Application of Two Esterases Derived from the Arctic Sediment Metagenome

Two esterase genes (designated as estAT1 and estAT11, respectively) were cloned by activity-based screening of a fosmid library constructed with seashore sediment sample of the Arctic. The sequence analysis of the genes revealed that these esterase genes encoded proteins of 303 and 312 amino acids, respectively, and showed 40-50% identities to members of the hormone-sensitive lipase (HSL) family retaining a catalytic triad with a conserved GDSAG sequence and an oxyanion hole (HGGG). The esterases genes were overexpressed in Escherichia coli by co-expressing GroEL-GroES chaperonine, and the recombinant proteins (rEstAT1 and rEstAT11) were purified to homogeneity. The purified EstAT1 and EstAT11 were active in a broad range of temperature from 20 to 40 degrees C with an optimum temperature at 30 degrees C. The activation energies of rEstAT1 and rEstAT11 to hydrolyze p-nitrophenyl esters of butyrate were determined to be 12.65 kcal/mol and 11.26 kcal/mol, respectively, indicating that they are cold-adapted esterases. The purified EstAT1 and EstAT11 could hydrolyze racemic ofloxacin esters, and further rEstAT11 hydrolyzed preferentially (S)-racemic ofloxacin butyl ester with an enantiomeric excess (ee(p)) value of 70.3%. This work represents an example that develops enzymes from the Arctic using metagenomic approach, potentially applicable to chiral resolution of heat-labile substrates.     

日本对虾c型溶菌酶的高效重组表达及产物分析

从日本对虾(Marsupenaeus japonicus)血液中提取总RNA,根据GenBank已登录的该cDNA序列(AB080238),通过RT-PCR技术扩增出日本对虾溶菌酶(MjLys)成熟肽基因。该基因完整的开放阅读框为477 bp,编码158个氨基酸(aa),前18 aa为信号肽,成熟肽由140 aa组成,分子量为16.4 kD,理论等电点(pI)为8.80。经分析表明,该基因含有一个完整的c型溶菌酶结构域(1-130 aa),包括c型溶菌酶特有的两个活性中心Glu33和Asp50,以及8个保守结构Cys残基。将MjLys成熟肽基因亚克隆至原核表达载体pET-32a(+),在大肠杆菌细胞BL21(DE3)pLysS中诱导发酵,实现了重组MjLys蛋白的高效表达,并测定了该重组蛋白对几种细菌的抑菌活性。结果表明,重组日本对虾溶菌酶对革兰氏阳性菌金黄色葡萄球菌和溶壁微球菌均有显著的溶菌活性。     

Design and Antibacterial Mechanism of Peptides Derived from Sakacin P

Russian Journal of Bioorganic Chemistry - Pseudomonas aeruginosa easily obtains multidrug resistance and forms biofilm. These properties bring more challenges to its control. Antimicrobial peptides...     

水稻籼粳交DH群体籽粒充实度的遗传分析

籽粒充实度差是限制亚种间杂交稻产量潜力发挥的重要因素。作者对籼粳交（圭630／02428）DH群体的籽粒充实度进行了研究,结果表明,籽粒充实度是受多基因控制的数量性状,在该DH群体中发生分离的基因估计数为5－6对。通过估测三级（偏度）和四级（峰度）统计量,检测到控制籽粒充实度的多基因间存在重叠作用。DH群体中籽粒充实度表现出明显的超亲分离,表明基因重组可实现控制籽粒充实度的增效基因的聚合。籽粒充实度与单穗产量、穗均实粒数和干物质／总库容之比呈显著或极显著正相关,与千粒重、穗均颖花数和穗均总库容相关不显著。     

水稻籼粳交DH群体花器性状的遗传分析

水稻花器性状是影响杂交稻制种异交结实率的重要因素之一。利用一个水稻籼粳交(窄叶青8号/京系17)来源的DH群体对水稻柱头外露率、花柱长、柱头长、柱头宽、花药长、花药宽、颖花长、颖花宽和颖花长宽比9个花器性状和穗抽出度进行遗传分析。不论性状在2个亲本间的差异显著与否,在DH群体中10个研究性状在基因型间的差异均达到极显著水平(P<0.01),并表现为连续变异和明显的超亲分离。除花药宽的遗传力较低(50%)、且估计的基因数多达13个之外,其余9个研究性状的遗传力均较高,为68%～93%,控制这些性状的基因数估计为7～10个。这些结果表明,10个研究性状均为受多基因控制的数量性状,其增效和减效基因在2个亲本中均有分布,通过基因重组可产生正向和负向两个方向的超亲基因型。除了柱头长、柱头宽和穗伸出度3个性状未发现有基因间的上位性互作外,其余7个性状均检测到显著的互补性互作。性状相关和通径分析的结果显示,与柱头外露率关系最密切的花器性状为柱头长、柱头宽和颖花长宽比,颖花长和颖花宽主要通过影响颖花长宽比来对柱头外露率产生影响。其次,与柱头外露率关系较密切的为花柱长。柱头外露率高的基因型通常表现为长柱头、长粒型和长花柱。花药长、花药宽与上述花器性状间的相关性较弱。在DH群体中,穗伸     

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins that provides biophysical and biochemical cues that are major regulators of cell proliferation, survival, migration, etc. The ECM plays important roles in development and in diverse pathologies including cardio-vascular and musculo-skeletal diseases, fibrosis, and cancer. Thus, characterizing the composition of ECMs of normal and diseased tissues could lead to the identification of novel prognostic and diagnostic biomarkers and potential novel therapeutic targets. However, the very nature of ECM proteins (large in size, cross-linked and covalently bound, heavily glycosylated) has rendered biochemical analyses of ECMs challenging. To overcome this challenge, we developed a method to enrich ECMs from fresh or frozen tissues and tumors that takes advantage of the insolubility of ECM proteins. We describe here in detail the decellularization procedure that consists of sequential incubations in buffers of different pH and salt and detergent concentrations and that results in 1) the extraction of intracellular (cytosolic, nuclear, membrane and cytoskeletal) proteins and 2) the enrichment of ECM proteins. We then describe how to deglycosylate and digest ECM-enriched protein preparations into peptides for subsequent analysis by mass spectrometry.     

Genome Characterization of a Breeding Line Derived from a Cross Between Oryza sativa and Oryza rufipogon

A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.     

运动负荷对骨基质有机成分的影响及其可能机制

骨基质的有机成分主要为骨Ⅰ型胶原基质金属蛋白酶,该酶是细胞外基质降解的重要酶类;基质金属蛋白酶抑制因子则是基质金属蛋白酶活性的抑制剂,它们均为骨代谢过程中的重要标志性物质。本文通过查阅文献资料,对生理、部分病理状态及运动干预条件下,骨基质的Ⅰ型胶原和基质金属蛋白酶及其抑制因子的变化情况进行综述,并对其变化的机制予以阐释。     

乳链菌肽作用机制及其应用

乳链菌肽作为高效、安全的天然食品防腐剂已得到广泛应用。成熟的乳链菌肽含有34个氨基酸残基,由5个硫醚桥组成独特的内环结构,是研究蛋白质结构与功能的一个很好的材料。本文论述了乳链菌肽的分子结构及其与细胞膜作用的分子机制,详细阐述了乳链菌肽的作用模型。     

Genotypic Mapping Using RFLP Markers on Doubled Haploids Derived from a Cross Between indica and japonica Rice

A rice RFLP map with 233 loci based on a population of 81 doubled haploids (DH) from the indica/japonica hybrid of "Gui 630'/"02428" was used to analyse the genome ratios and graphical genotypes of DH lines. The “Gui 630” genome ratio of the individual DH lines varied from 29.3% to 78.6% with an average of 49% while the ratios of most DH lines ranged between 44% and 49%. Of the mapped RFLP markers 130 showed skewed segregations with a significant deviation from the expected monogenic ratio, but the numbers of the markers deviated towards male and female parent were approximately equal. It was found that the markers with the segregation deviation in the same direction tend to cluster on some chromosomes and some of their regions. The average "Gui 630' genome ratios of different chromosomes in the DH population varied greatly between 29% and 65 %. In addition, several chromosomes were inherited completely from either one of the parents in some DH lines, indicating the rare occurrence of crossover along the pairing homologous chromosomes during meiosis.     

高压静电场在农业中的应用及其作用机理的物理微观解析

本文概括了近几十年来电场处理种子、分选种子、空间电场防病促生技术、电场果蔬保鲜的应用及其产生的电场生物学效应,同时阐述了电场生物效应作用机理及其研究现状.本文重点介绍了近年来一些物理学者对电场作用机理的物理微观解析一介质极化微观理论、一维自由谐振子能级理论、势垒贯穿理论等.指出了电场在农业中的应用非常广泛,但到目前为止对其作用机理还没有统一的理论解释.电场生物学效应作用机理的深入研究需要生物学者、化学学者和物理学者的密切合作.     

Comparison of DABA and GABA Transport into Plasma Membrane Vesicles Derived from Synaptosomes

Abstract: Transport of GABA by a high-affinity transport system ( K _m≃ 10⁻⁵ M) is thought to terminate the action of this postulated neurotransmitter. 2,4-Diaminobutyric acid (DABA), a structural analogue, is taken up by neuronal elements and inhibits GABA uptake. Localization of [³H]DABA by auto-radiography has been used to identify neurons with the GABA high-affinity transport system. After reconstitution of lysed synaptosomal fractions in potassium salts, transfer of these membrane vesicles to sodium salts produces sodium and potassium ion gradients which drive [³H]GABA and [³H]DABA transport. For each, transport requires external sodium, is abolished by ionophores that dissipate the Na⁺ gradient, and is enhanced by conditions which make the intravesicular electromotive force more negative. Some characteristics of the transport of these substances, however, differ. For example, external chloride is required for GABA, but not DABA, transport. Internal potassium is required for DABA, but not GABA, transport. DABA is a competitive inhibitor ( K _i≃ 0.6 MM) of GABA transport into membrane vesicle and synaptosomes. GABA, however, is a feeble inhibitor of DABA uptake into the membrane vesicles. These differences suggest that the two substances are transported by different mechanisms and possibly by different carriers. In addition to these experiments, using enzymatic-fluorometric techniques, it was shown that the artificially imposed ion gradients drive net chemical transport of GABA into the vesicles.     

Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves

Introduction

High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst.

Materials and Methods

We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately.

Results

Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability.

Conclusions

We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.     

Virtual Power Based Algorithm for Decoupling Large Motions from Infinitesimal Strains: Application to Shoulder Joint Biomechanics

New trends of numerical models of human joints require more and more computation of both large amplitude joint motions and fine bone stress distribution. Together, these problems are difficult to solve and very CPU time consuming. The goal of this study is to develop a new method to diminish the calculation time for this kind of problems which include calculation of large amplitude motions and infinitesimal strains. Based on the Principle of Virtual Power, the present method decouples the problem into two parts. First, rigid body motion is calculated. The bone micro-deformations are then calculated in a second part by using the results of rigid body motions as boundary conditions. A finite element model of the shoulder was used to test this decoupling technique. The model was designed to determine the influence of humeral head shape on stress distribution in the scapula for different physiological motions of the joint. Two versions of the model were developed: a first version completely deformable and a second version based on the developed decoupling method. It was shown that biomechanical variables, as mean pressure and von Mises stress, calculated with the two versions were sensibly the same. On the other hand, CPU time needed for calculating with the new decoupled technique was more than 6 times less than with the completely deformable model.     

Identification and Inhibitory Mechanism of Angiotensin I-Converting Enzyme Inhibitory Peptides Derived from Bovine Hemoglobin

Angiotensin I-converting enzyme (ACE, EC.3.4.15.1) inhibitory peptide is an efficacious therapy for hypertension. In this study, four dipeptides, TY, FD, FL and FG, were identified from the desalted fraction of bovine hemoglobin hydrolysate, obtained by in vitro simulated gastrointestinal digestion, via liquid chromatography-tandem mass spectrometry (LC-MS/MS). The IC₅₀ value of TY and FL are 96.43?±?6.17 and 290.66?±?57.92 μM, respectively. The result of molecular docking indicated that TY occupied the ACE subsite S1 and S1′ with a lowest estimated binding energy of ?9.96 Kcal/mol, while FL occupied the subsite S5 with a lowest estimated binding energy of ?9.37 Kcal/mol. The subsite S1′ and S2′ are closer to the ACE active center (Zn²⁺) than S5, and the lowest estimated binding energy of TY is lower than that of FL. This work provided new ACE-inhibitory peptides derived from bovine hemoglobin hydrolysate and explained their inhibitory mechanism.     

来源于海绵的纳米生物硅材料及其相关酶研究进展

水生生物海绵的纳米结构的硅质骨针及其相关酶,在微电子、光纤及生物医学等方面具有诱人的前景,硅生物技术研究的发展有望成为纳米生物技术的一个新亮点。简要综述了海绵骨针的结构、组成及其形态发生过程,骨针合成代谢相关酶——硅聚合酶、骨针分解代谢相关酶——硅分解酶基因的克隆及表达影响因子,海绵骨针硅材料及其相关酶的获得、体外催化活性及潜在应用。     

The Mechanism of Excretion of Drugs into Milk from Untreated Glands after Intramammary Application

It is often maintained that after intramammary application of penicillin the excretion of penicillin via the untreated glands takes place by direct diffusion from treated to untreated glands (vide Hawkins et al. 1962, Jacobs & Pennings 1969, Rollins et al. 1970). Blobel (1960) mentions the possibilities of both direct diffusion from gland to gland and the excretion via the blood.     

Specific Isozyme Marker of a Virus Resistant Barley Derived from Interspecies Cross Between Hordeum vulgare and H. bulbosum

A diploid barley cultivar "Supi 1" was crossed with a tetraploid Hordeum bulbosum “GBC141” to transfer the disease resistant traits. Eleven viable triploid F1 plants were produced by means of embryo rescue technique. The resulting triploid hybrids were backcrossed to diploid barley, and seven BC1 plants were obtained. One of the BC1 plants exhibited barley yellow mosaic virus (BaYMV) resistance when grown in the diseased nursery. Isozyme analysis of H. vulgate, H. bulbosum and their backcross hybrids were made via slab polyacrylamide gel electrophoresis technique. The primary results showed that zymogram variation could be obviously found between diploid barley "Supi 1' and tetraploid H. bulbosurn "GBC141”. A peroxidase isozyme (Rf=0.47) from H. bulbosum was detected in the peroxidase isozyme zymogram of young roots of backcross hybrid BC1-2. This peroxidase isozyme was related to the BaYMV resistance but the linkage relation will be determined by the genetic analysis of the F2 population in the future. The BaYMV resistant line of the backcross with isozyme marker is the important resource of barley disease-resistant breeding.     

Preparative High Performance Chromatography of a Major Browning Compound Derived from Lysine and Glucose

ABSTRACT

A major browning compound derived from lysine and glucose was purified by high performance chromatography on a RP8 column after several extractions in methanol plus acetonitrile. This compound was separated by a main contaminant corresponding to unreacted lysine by extracting the aminoacid after its derivatization with ninhydrin.