葡枝根霉(Rhizopus stolonifer)YF6脂肪酶基因的克隆及其序列分析

筛选并鉴定了1株高产脂肪酶菌株葡枝根霉YF6,并采用简并PCR等分子技术从中克隆到1个新的脂肪酶基因lipRs及其对应的全长cDNA,序列分析表明,该基因编码区全长1173bp,不含内含子序列,编码1段由26个氨基酸残基组成的信号肽和1个由365个氨基酸残基组成的成熟蛋白,该成熟蛋白计算分子量(Mr)为39268.27,等电点为pH7.66,有5个可能的N-糖基化位点,含有脂肪酶特征序列GHSLGGA,与来自米根霉(Rhizopus oryzae)的脂肪酶(AAF32408)同源性最高,一致性为83%,相似性为89%.该基因序列已提交GenBank,登录号为DQ139862.     

解淀粉芽孢杆菌DC-4豆豉溶栓酶成熟肽编码序列的克隆及表达

利用PCR方法从解淀粉芽孢杆菌DC 4总DNA中扩增出豆豉溶栓酶 (DFE)成熟肽编码区片段 .测序结果表明 :DFE成熟肽编码区长 82 5bp,编码 2 75个氨基酸残基 ,分子量为 2 7.7× 10 3 ,推导的N’ -端氨基酸序列与豆豉溶栓酶N’ -端氨基酸测序结果完全一致 ,说明克隆到的基因确实是豆豉溶栓酶基因 .同源性分析表明 ,DFE成熟肽编码区的核苷酸和氨基酸序列与日本纳豆激酶的同源性分别为 80 .0 %和 86 .5 % ,这提示豆豉溶栓酶可能是一种新型的溶栓酶 .将表达质粒pET Nde转化E .coliBL2 1(DE3)中 ,IPTG可诱导表达大量的DFE融合蛋白 ,占菌体可溶性蛋白的 4 0 % ,主要以包涵体的形式存在 .图 3表 1参 19     

红树林沉积物Bt菌株的分离与cry基因型的鉴定（Isolation of Bacillus thuringiensis Strains from Mangrove Sediment Samples and Identification for cry Genes）

从收集自泉州洛江红树林保护区的400个沉积物土壤样品中,分离到18株苏云金芽孢杆菌(Bacillus thuringiensis,Bt).利用PCR-RFLP体系对Bt菌株杀虫晶体蛋白的基因型进行了鉴定,发现15株Bt含有cry1基因,4株含有cry2基因,有3株分别含有cry7、cry8、cry9基因.克隆了一个新型的cry2Ab基因,其编码蛋白与现有Cry2Ab型杀虫晶体蛋白的最高同源性为95%.     

家蚕丝心蛋白轻链cDNA和基因调控片段的克隆及序列分析

从家蚕品种菁松×皓月后部丝腺中提取总RNA ,用RT -PCR扩增技术克隆到家蚕丝心蛋白轻链cDNA .序列分析表明 ,该片段全长为 798个碱基 .比较 4种不同品种来源的家蚕丝心蛋白轻链基因外显子区域序列 ,同源性在98.0 %～ 99.4 %之间 ,推测的氨基酸同源性在 98.0 %～ 99.6 %之间 ,4个品种间发生的变异比较一致地集中在不同位置的 8个碱基上 .提取家蚕品种菁松×皓月后部丝腺总DNA ,进行PCR反应 ,获得家蚕丝心蛋白轻链基因调控片段 ,长度约为 1.2kb,测定了其邻近起始密码子一端包括 5 76个碱基的DNA序列 .结果表明 ,该片段包括一些典型的调控元件和多个可能参与丝蛋白基因特异性表达调控的元件 ,该部分序列与J - 139L链基因相应区域同源性高达 98.8% .图 3参 8     

环境基因组DNA脂肪酶基因克隆与分析

为了建立从环境基因组DNA中直接克隆脂肪酶基因的通用方法,抽提餐馆灶台油污的环境基因组DNA,采用简并PCR等分子技术从中克隆到脂肪酶基因lip42及其对应的全长cDNA.序列分析表明该基因的cDNA编码区序列全长为1692bp,编码1段由19个氨基酸残基组成的信号肽和1段由544个氨基酸残基组成的成熟肽,计算相对分子质量为61541.51,其中含有强碱性氨基酸残基42个,强酸性氨基酸残基56个,等电点pI为5.428,有2个可能的N-糖基化位点.BLAST比对分析表明该序列与已发表的白地霉(Geotrichum geotrichum)脂肪酶基因(U02541)在核苷酸水平的一致性为99%.该基因序列提交GenBank,登录号为DQ313172.将该脂肪酶基因的开放阅读框克隆到毕赤酵母表达载体,转化毕赤酵母GS115,经罗丹明B平板功能筛选得到具脂肪酶活性的重组毕赤酵母菌株[GS115(pAMB768)],验证了直接从环境基因组DNA克隆脂肪酶基因的有效性.图3表1参27     

鸡贫血病毒(CAV)vp1基因的克隆及与其他CAV vp1基因的比较

把一个新鸡贫血病毒(CAV)的vp1基因通过PCR扩增，然后克隆到质粒载体pUC18上．vp1基因包含1347个碱基对，并且推定的VP1蛋白氨基酸序列含有449个氨基酸．通过DNA BLAST软件把该基因的序列数据与在GenBank中发表的其他vp1基因比较显示，克隆的vp1基因与已发表的其他vp1基因之间存在许多核甘酸差异．核甘酸的变异导致其编码蛋白质的某些氨基酸发生改变．氨基酸的改变主要集中在VP1蛋白的29、75、125、141、144、251、254、447位．在这些变异中，许多氨基酸的电荷和／或疏水性发生了改变，例如：Gly→Glu、Val→Glu、Ala→Thr、Leu→Gln、Cys→Trp、Leu→Arg、Arg→Ala、Gly→Ser、Ser→Ala、Glu→Gly、Gly→Thr等．通过CLUSTAL X软件比较了6个不同的vp1基因．该vp1基因已被GenBank登录(登录编号：AF448446)．VP1蛋白是CAV的唯一衣壳蛋白，因此VP1的氨基酸变异可能影响该蛋白质的抗原特征．对该vp1基因进一步进行免疫学研究具有重要意义，并且有可能应用该基因构建CAV基因工程疫苗．图1表3参20     

苏云金芽胞杆菌菌株WB9编码活性因子的基因分析

采用PCR—RFLP及PCR技术对苏云金芽胞杆菌新分离菌株WB9的ICP、VIP、几丁质酶和肠毒素4种活性因子的编码基因进行了分析．结果表明，该菌株含有编码ICP的cry1Aa、cry1Ab、cry1Cb、cry1Fa和cry1GaS个cry1基因型，编码Vip3A蛋白的vip3A基因以及编码3种肠毒素的hblA、bceT和entS基因；不含编码几丁质酶的基因．将vip3A、hblA、bceT和entS基因PCR产物回收纯化后直接测序，经在线的BLAST软件进行同源性分析，前两个基因片段与Bt已公布基因序列的相应片段同源性分别为99％和96％～98％，bceT基因片段与蜡质芽孢杆菌bceT相应片段同源性为97％．     

焦化废水生物膜样品和苯酚降解菌分离株基因盒的分析

使用59-碱基(59be)保守序列和整合酶基因的引物进行PCR扩增,研究了焦化废水处理装置中微生物菌群的基因盒结构,并对两株分离的苯酚降解荫IS-17和IS-46的基因盒进行了扩增测序分析.从5个焦化废水生物膜总DNA样品中均获得了基因盒扩增产物.对IS-17和IS-46的基因盒PCR产物克隆建库并测序,通过序列比对等方法来研究和分析序列的功能.发现本研究获得的基因盒与已报道的基因盒存读码框序列、两端引物结合序列、间隔区大小等方面存在一些不同.本研究结果表明,在焦化废水生物膜菌群中普遍存在基因盒结构,采用基因盒PCR能够从环境或菌株中获取新基因.     

马铃薯X病毒山西分离物外壳蛋白基因的克隆和核苷酸序列分析

对GenBank公布的马铃薯X病毒的基因组核苷酸序列和外壳蛋白基因的核苷酸序列进行了同源性比对分析.结果表明,马铃薯X病毒外壳蛋白基因核苷酸序列的同源性要高于基因组全序列的同源性,并且外壳蛋白基因3'端核苷酸序列的同源性又高于5'端.设计一对特异性引物,以马铃薯感病植株的总RNA为模板,经RT-PCR扩增得到了马铃薯X病毒外壳蛋白基因.该基因含714个核苷酸,编码238个氨基酸.核苷酸序列比对结果表明,该基因与Genbank公布的马铃薯X病毒其他分离物的外壳蛋白基因的同源性为80.2%～97.5%,且3'端的同源性要高于5'端.上述结果预示,RNA干扰抗病毒基因工程中,利用马铃薯X病毒外壳蛋白基因的3'端比用5'端是更好的策略.     

极端嗜热菌海栖热袍菌木聚糖酶B的克隆和表达

极端嗜热菌海栖热袍菌MSB8(ThermotogamaritimaMSB8)能够利用木聚糖代谢 ,并具有两个产木聚糖酶的基因 .本研究首次克隆和在大肠杆菌中表达海栖热袍菌MSB8的第 2个木聚糖酶基因即xynB基因 .以基因组DNA为模板 ,根据xynB基因的全序列设计了两对引物 ,在合适的PCR反应条件下有效地扩增出了xynB基因片段 .选用pET2 8a(+)表达载体 ,NcoI-HindⅢ酶切位点并编码了羧基端 6×His标签的阳性克隆表达成可溶且具有生物活性的蛋白质 .xynB结构基因由 10 4 4对碱基组成 ,编码 347个氨基酸 .根据已知木聚糖酶蛋白质氨基酸的同源性分析 ,XynB与T .sp.strainFjSS3-B .1的XynA的同源性最大 ,为 85 % ,与T .neapolitana的XynB同源性次之 ,为 82 % ,与其它木聚糖酶的同源性小于 4 3% .另外 ,XynB属于F/ 10族木聚糖酶 ,且含有单一功能区 .表 3图 3参 12     

Isolation of novel metal-binding proteins distinct from metallothionein from spotted seatrout (Cynoscion nebulosus) and Atlantic croaker (Micropogonias undulatus) ovaries

Metal-binding proteins were isolated from ovaries of the spotted seatroutCynoscion nebulosus and the Atlantic croakerMicropogonias undulatus collected in 1988 near Port Aransas, Texas, USA. Gel-filtration analysis of spotted seatrout trout ovarian cytosolic fraction on Sephadex G-75 revealed the presence of three zincbinding protein fractions. A major zinc/calcium-binding protein fraction had a low molecular weight (M _r)(6 000 to 10 000), similar to mammalian hepatic metallothionein (MT). All the metals were displaced from this fraction following saturation with exogenous cadmium. After exposure of Atlantic croaker to 2 mg cadmium l^–1 seawater for 2 mo, the majority of the cadmium in the ovarian cytosolic fraction was associated with a similar low molecular weight protein fraction. These proteins were further purified by heat treatment and sequential acetone precipitation. Three isoforms were isolated by reversephase high-performance liquid chromatography. All the isoforms were found to be distinct from mammalian MT, based on amino acid composition. The major isoform contained low amounts of cysteine (approximately 5 residues per molecule) and aromatic amino acids, compared to high amounts of cysteine (typically 17 to 20 residues/molecule) and a lack of aromatic amino acids for mammalian MT. All the ovarian protein isoforms contained more glutamate than mammalian MT. The spotted seatrout and Atlantic croaker ovarian isoforms showed a high degree of homology with metal-binding proteins isolated from mammalian gonadal tissues. The results suggest a physiological role for these metal-binding proteins in developing vertebrate ovaries as well as an involvement in the sequestration of cadmium following environmental exposure.     

A note on some mathematical models on the effects of Bt-maize exposure

Some mathematical models for the estimation of the effects of Cry1Ab and Cry1F Bt-maize exposure in the biodiversity are examined. Novel results about these models are obtained and described in this note. The exact formula for the proportion of population that suffers mortality exposed either to Cry1Ab or Cry1AF pollen is derived. Moreover, regarding Cry1F pollen effects, the species sensitivity of Lepidoptera is discussed.     

Underlying reasons of the controversy over adverse effects of Bt toxins on lady beetle and lacewing larvae

In their recent study, Hilbeck et al. (2012) report that Cry1Ab causes lethal effects on larvae of the ladybird beetle Adalia bipunctata when fed directly to the predator. Such toxic effects were not previously observed in a direct feeding study conducted by us (álvarez-Alfageme et al. 2011). Because Hilbeck et al. (2012) claim that our study design did not allow us to detect any adverse effects we provide arguments for the value and relevance of our study in this commentary. Furthermore we discuss two additional published studies that have not revealed any direct effects of Cry1Ab on larvae of A. bipunctata and are not mentioned by Hilbeck et al. (2012). One of the studies was conducted in our laboratory under more realistic exposure conditions (álvarez-Alfageme et al. 2011). Feeding A. bipunctata larvae with spider mites reared on Bt maize did not reveal any adverse effects on lethal and sublethal parameters of the predator. This was despite the fact that the larvae had ingested high amounts of biologically-active Cry1Ab protein. Thus, we do not see verified evidence that A. bipunctata larvae are sensitive to Cry1Ab at realistic worst-case exposure concentrations. This, together with the fact that A. bipunctata will be little exposed to Cry1Ab under field conditions, allows us to conclude that the risk of Bt maize to this predator is negligible. Support for this comes from the results of many Bt maize field studies that have not revealed evidence for direct Cry1Ab-effects on non-Lepidoptera species.     

Insights into the changes of amino acids,microbial community,and enzymatic activities related with the nutrient quality of product during the composting of food waste

● The highest seed germination index was achieved at 0.3 g/g total solids of food waste. ● Proline was identified as the key amino acid related with the composting process. ● Amino acid metabolism sequences predominated during the whole composting process. This study systematically investigated the changes of amino acids as the composting process of food waste proceeded. It is found that the addition of 0.3 g/g total solids of food waste achieved the highest seed germination index of the product (268 %). The microbial community results indicated that the abundance of amino acid metabolism sequences remained at high levels during the whole composting process. Proline was identified as the key amino acid related with the nutrient quality of product during the composting of food waste. Further plant germination and hydroponic experiments found, that compared with those without the addition of proline, the addition of 50 mg/L proline increased seed germination rate by 20 %, increased shoot length by 3 %, increased root biomass of seedlings by 82 %, and increased leaf biomass of seedlings by 76 %, respectively. Firmicutes, γ-Pseudomonadota, Chloroflexi and Planctomycetes were the key identified bacteria related with the increase of proline during the composting of food waste. Meanwhile, the enzymatic tests of the activities of superoxide dismutase, peroxidase and malondialdehyde indicated that proline did not cause oxidative damage on the growth of plants. This study provided novel insights into the changes of amino acids, microbial community, and enzymatic activities related with the nutrient quality of product during the composting of food waste.     

Reactivity of chlorine dioxide with amino acids, peptides, and proteins

Amino acids, proteins, and peptides are found ubiquitously in waters. They can form harmful byproducts during water treatment by reaction with disinfectants. Chlorination and chloramination of water containing natural organic matter is known to result in the production of toxic substances, often referred to as disinfection byproducts. The main advantage of using chlorine dioxide (ClO₂) over other known chlorine-containing disinfectants is the minimization of the formation of harmful trihalomethanes. Because ClO₂ is a promising alternative to other chlorine-containing disinfectants, the chemistry of ClO₂ interactions with amino acids, proteins, and peptides should be understood to ensure the safety of potable water supplies. Here, we present an overview of the aqueous chemistry of ClO₂ and its reactivity with amino acids, peptides, and proteins. The kinetics and products of the reactions are reviewed. Only a few amino acids have been reported to be reactive with ClO₂, and they have been found to follow second-order kinetics for the overall reaction. The rate constants vary from 10^?2 to 10^7?M^?1?s^?1 and follow an order of reactivity: cysteine?>?tyrosine?>?tryptophan?>?histidine?>?proline. For reactions of histidine, tryptophan, and tyrosine with ClO₂, products vary depending largely on the molar ratios of ClO₂ with the specific amino acid. Products of ClO₂ oxidation differ with the presence or absence of oxygen in the reaction mixture. Excess molar amounts of ClO₂ relative to amino acids are associated with the production of low molecular weight compounds. The oxidation of the biochemically important compounds bovine serum albumin and glucose-6-phosphate dehydrogenase by ClO₂ suggests a denaturing of proteins by ClO₂ by an attack on tryptophan and tyrosine residues and relates to the inactivation of microbes by ClO₂.     

Changes in protein-bound and free amino acids in the muscle of the tiger prawn Penaeus esculentus during starvation

Using the starvation technique, changes in protein and free amino acids were examined in Penaeus esculentus Haswell collected from Moreton Bay, Australia, by trawling in 1985. Prawns of 17.7±0.26 g wet weight were held at 25°C until 2 d after moulting. Groups of seven or eight were then starved fro 5, 10, or 15 d, with appropriate control groups. At the end of each period, ecreted amino acids were collected for 24 h and whole-muscle amino acids and free amino acids (FAA) g^-1 in each prawn were analysed. Concentrations of whole-muscle amino acids showed only minor changes with starvation, but concentrations of many of the FAA changed significantly. Total FAA averaged 1 182±45 mol g^-1 dry weight. Individual FAA, in order of abundance, were glycine, arginine, proline, taurine, threonine, hydroxyproline, alanine, glutamic acid, valine, aspartic acid and lysine; the remaining FAA each contributed <0.2% of the total. Only taurine and alanine did not show significant changes with starvation. Concentrations of glycine, arginine, hydroxyproline, glutamic and aspartic acid increased, while those of proline, threonine, valine and lysine decreased with starvation, that of proline approaching zero after 15 d starvation. Excreted amino acid-nitrogen represented <2% of excreted ammonianitrogen ornithine being the most abundant (35%), followed by leucine (22%) and lysine (17%). The relative abundance of excreted amino acids did not correspond with those of the FAA. It is suggested that, as starvation progresses, the muscle protein is progressively hydrolysed, but with the remaining muscle maintaining its amino acid composition. The liberated amino acids enter the FAA pool and become available for energy production. Proline may have an important role as an energy source, but the ability to synthesise proline may be limited, and thus the artificial food of penaeid prawns may be improved by its addition.     

Amino acid metabolism and protein turnover in larval turbot (Scophthalmus maximus) fed natural zooplankton or Artemia

The present paper studied the influence of different food regimes on the free amino acid (FAA) pool, the rate of protein turnover, the flux of amino acids, and their relation to growth of larval turbot (Scophthalmus maximus L.) from first feeding until metamorphosis. The amino acid profile of protein was stable during the larval period although some small, but significant, differences were found. Turbot larvae had proteins which were rich in leucine and aspartate, and poor in glutamate, suggesting a high leucine requirement. The profile of the FAA pool was highly variable and quite different from the amino acid profile in protein. The proportion of essential FAA decreased with development. High contents of free tyrosine and phenylalanine were found on Day 3, while free taurine was present at high levels throughout the experimental period. Larval growth rates were positively correlated with taurine levels, suggesting a dietary dependency for taurine and/or sulphur amino acids. Reduced growth rates in Artemia-fed larvae were associated with lower levels of free methionine, indicating that this diet is deficient in methionine for turbot larvae. Leucine might also be limiting turbot growth as the different diet organisms had lower levels of this amino acid in the free pool than was found in the larval protein. A previously presented model was used to describe the flux of amino acids in growing turbot larvae. The FAA pool was found to be small and variable. It was estimated that the daily dietary amino acid intake might be up to ten times the larval FAA pool. In addition, protein synthesis and protein degradation might daily remove and return, respectively, the equivalent of up to 20 and 10 times the size of the FAA pool. In an early phase (Day 11) high growth rates were associated with a relatively low protein turnover, while at a later stage (Day 17), a much higher turnover was observed. Received: 19 March 1997 / Accepted: 14 April 1997     

Isolation and characterisation of zinc-binding proteins distinct from metallothionein from the eggs of the sea urchin Strongylocentrotus intermedius

Two low-molecular-weight zinc-binding proteins were purified from eggs of the sea urchin Strongylocentrotus intermedius (Echinodermata: Echinoidea) by gel-permeation and anion-exchange chromatography followed by high performance liquid chromatography. The characteristics of these proteins are distinct from those of metallothionein. Amino acid compositions show a low or intermediate content of cysteine and high amounts of acidic amino acids, glycine and histidine; they also contain methionine and aromatic residues. On the basis of these characteristics, the S. intermedius zinc-binding proteins appear similar to other metalloproteins isolated from both vertebrates and invertebrates. No typical metallothionein was detected in the extracts from S. intermedius eggs.