华支睾吸虫糖基转移酶基因全长序列的克隆和生物信息学分析

目的分析和预测华支睾吸虫囊蚴全长cDNA质粒文库中编号为cs091c06的糖基转移酶基因EST序列结构和功能特征及其编码蛋白的理化性质,预测该基因的生物学意义和应用前景。方法利用NCBI网站和ExPaSy等生物信息学在线分析工具和Vector NTI suite等软件包,分析华支睾吸虫囊蚴全长cDNA质粒文库中cs091c06的EST序列及编码蛋白的理化性质、结构与功能特征。结果 BLASTx工具分析该EST序列是糖基转移酶的同源基因,序列全长为1 402bp,其完整的编码框为37～1 011bp,编码325个氨基酸。Target P和Signal P软件预测该编码氨基酸前30个氨基酸是分泌信号肽,蛋白的理化性质较稳定。蛋白质一级结构扫描发现两个糖基转移酶的保守功能区分别位于67～178aa和69～253aa,且在该基因的N端发现明显的蛋白质糖基化位点,分别位于76～79aa和190～193aa。在该基因的氨基酸序列中,共发现8个B细胞表位和6个T细胞表位。RT-PCR结果显示,该基因在华支睾吸虫成虫阶段高表达,囊蚴和虫卵阶段低表达。结论华支睾吸虫糖基转移酶基因与多个物种同源,编码蛋白可能是华支睾吸虫重要的虫体分泌排泄抗原成分;阶段特异性表达特征提示该基因很可能参与华支睾吸虫重要虫源蛋白糖基化过程,可作为华支睾吸虫病疫苗候选分子和药物靶标。     

华支睾吸虫组织蛋白酶Cathepsin L1 样基因全长序列的克隆和生物信息学分析

目的预测华支睾吸虫全长cDNA质粒文库中cs002d09号EST序列的结构和功能特征及编码蛋白的应用前景。方法利用NCBI和ExPaSy等生物信息学网站在线分析工具和Vector NTIsuite及PcGene等软件包，分析华支睾吸虫全长cDNA质粒文库中cs002d09号EST序列及其编码蛋白的理化性质、结构与功能特征。结果BLASTx分析该ESF序列是组织蛋白酶Cathepsin L1的同源基因，全序列长为1458bp，包含完整的编码区80～1191，编码371个氨基酸，前18个氨基酸是分泌信号肽，蛋白的理化性质较稳定。该蛋白有2个空间构象相对独立功能域：N端的抑制功能域和C端的活性功能域，抑制功能域含有3个线性B细胞抗原表位，同源性较低；C端活性功能域同源性较高，Cys177，His318和Asn338组成催化中心，位于底物结合裂缝的底部。结论华支睾吸虫Cathepsin Ll基因与多个物种的Cathepsin L1基因同源，编码蛋白可能是重要的虫体分泌排泄抗原成分，在华支睾吸虫病的免疫诊断和疫苗研究方面有较好的应用前景。     

华支睾吸虫组织蛋白酶Cathepsin L1样基因全长序列的克隆和生物信息学分析

目的预测华支睾吸虫全长cDNA质粒文库中cs002d09号EST序列的结构和功能特征及编码蛋白的应用前景。方法利用NCBI和ExPaSy等生物信息学网站在线分析工具和Vector NTIsuite及PcGene等软件包，分析华支睾吸虫全长cDNA质粒文库中cs002d09号EST序列及其编码蛋白的理化性质、结构与功能特征。结果BLASTx分析该ESF序列是组织蛋白酶Cathepsin L1的同源基因，全序列长为1458bp，包含完整的编码区80～1191，编码371个氨基酸，前18个氨基酸是分泌信号肽，蛋白的理化性质较稳定。该蛋白有2个空间构象相对独立功能域：N端的抑制功能域和C端的活性功能域，抑制功能域含有3个线性B细胞抗原表位，同源性较低；C端活性功能域同源性较高，Cys177，His318和Asn338组成催化中心，位于底物结合裂缝的底部。结论华支睾吸虫Cathepsin Ll基因与多个物种的Cathepsin L1基因同源，编码蛋白可能是重要的虫体分泌排泄抗原成分，在华支睾吸虫病的免疫诊断和疫苗研究方面有较好的应用前景。     

华支睾吸虫表膜相关蛋白基因的扩增、序列分析和克隆

目的识别华支睾吸虫新基因,并将所发现的华支睾吸虫表膜相关蛋白(tegumental protein ofClonorchis sinensis,CsTP)的cDNA序列克隆到原核载体中,为进一步的研究奠定基础。方法对华支睾cDNA质粒文库进行随机筛选并测序,用在线生物信息学工具进行序列分析,识别CsTP基因,并对其进行同源性、物理性质及结构分析。设计引物,从华支睾cD-NA质粒文库中扩增目的基因cDNA序列,并构建原核重组质粒,相同引物从华支睾吸虫基因组中扩增出CsTP的DNA序列。结果发现CsTP基因,其cDNA完整阅读框含555个碱基,编码184个氨基酸,理论分子量为20.7kDa;其DNA序列含1393个碱基,含有3个外显子、2个内含子。序列分析表明,CsTP蛋白与其它物种的表皮蛋白或膜相关蛋白有一定的同源性。所构建的重组原核表达质粒PGEX-4T-1-CsTP经PCR、双酶切及测序证实与目的基因相符。结论发现华支睾吸虫表膜相关蛋白基因,成功构建其重组原核表达质粒为进一步研究该基因的功能提供了条件。     

华支睾吸虫19kDa分泌型蛋白(CsSP19)基因的克隆、表达与免疫学功能研究

目的对一个新发现的华支睾吸虫分泌型蛋白的未知基因,进行克隆表达和重组产物的免疫学鉴定,确定其免疫学功能。方法利用生物信息学方法从华支睾吸虫成虫全长cDNA质粒文库中发现一个编码分泌型蛋白的新基因（克隆号Cs004f03）,将去除信号肽序列的编码序列克隆到原核表达质粒pET-28a（＋）中,IPTG诱导表达,产物经亲和层析纯化,并制备大鼠免疫血清,Western-blot方法分析其抗原性和分泌性。结果CsSP19开放阅读框（ORF）有564bp,编码188个氨基酸,理论分子量为21.2kDa,成熟肽的理论分子量为19kDa。该基因的成熟肽编码区在大肠杆菌中可获得高表达,重组蛋白能被华支睾吸虫病人血清所识别,同时,重组蛋白免疫血清也能识别华支睾吸虫分泌排泄抗原中分子量约19kDa的蛋白条带。结论CsSP19蛋白是华支睾吸虫分泌排泄抗原中一个有潜在诊断价值的分泌蛋白。     

华支睾吸虫蛋白酶体α2新基因的生物信息学分析与克隆表达

目的发现华支睾吸虫成虫蛋白酶体新基因,应用生物信息学方法预测其结构和功能,表达重组蛋白为进一步确定其功能特征奠定基础。方法通过华支睾吸虫成虫cDNA文库的大规模测序,获取全长cDNA序列,利用生物信息学软件ORFfinder,BLAST,Conserved Domains和ExPASy等识别华支睾吸虫蛋白酶体α2(CsPSMA2)新基因,分析其基因和编码蛋白结构,同源性比对并构建系统发育树。将CsPSMA2基因克隆到pGEX-4T-1原核表达载体中,在大肠杆菌BL21(DE3)中诱导表达,表达产物经SDS-PAGE鉴定。结果确定了编码CsPSMA2的新基因并成功登录到GenBank(Accession NO.:EU223819)。该基因全长833bp,编码235个氨基酸,第5-232aa之间含有蛋白酶体α2全长结构域,理论分子量为26.0kDa,分子进化分析显示CsPSMA2的蛋白与日本血吸虫亲缘关系最近,重组质粒融合表达了带有GST标签的CsPSMA2蛋白。结论发现了华支睾吸虫蛋白酶体α2新基因,确定了其重要的功能域和结构特征,成功进行了该基因在大肠杆菌中的克隆表达。     

华支睾吸虫Rap2B样基因的生物信息学分析及其克隆、表达

目的从华支睾吸虫cDNA文库中筛选Rap2B样基因并分析其结构和功能,初步进行克隆和表达纯化,为进一步研究其功能奠定基础。方法利用多种生物信息学分析软件,分析华支睾吸虫Rap2B蛋白的拓扑学结构、生物学和免疫学功能特征。设计引物,从华支睾cDNA质粒文库中扩增目的基因cDNA序列,构建原核重组质粒并初步表达纯化。结果华支睾吸虫Rap2B样基因长度为847bp,其全长编码序列为426bp,编码141个氨基酸,理论分子量是15851.1。重组的原核表达质粒pET-28a(+)-Rap2B经PCR、双酶切及DNA测序结果均表明重组质粒构建成功。该基因在大肠杆菌中能高效表达。经His亲和层析柱获得了纯化的重组蛋白,Western blotting证实Rap2B重组蛋白能被感染华支睾吸虫的大鼠血清识别。结论华支睾吸虫Rap2B蛋白经生物信息学预测为ras原癌基因家族成员,可能在华支睾吸虫致癌过程中有一定作用。该基因可在原核表达系统中高效表达,并得到了纯化的重组蛋白,为进一步研究该蛋白的功能以及在致病尤其是可能促发肿瘤的作用方面奠定一定基础。     

华支睾吸虫磷脂酶A2基因生物学特性的初步研究

目的对新发现的华支睾吸虫磷脂酶A2（CsPLA2）基因进行生克隆、原核表达,确定该蛋白是否为成虫分泌/排泄蛋白（excretory-secretory protein,ESP）。方法利用多种生物信息学分析软件,从华支睾吸虫全长cDNA质粒文库中识别出CsPLA2样基因,分析该基因表达蛋白的生物学功能特征;将CsPLA2克隆入原核表达质粒pET28a（＋）,并在大肠埃希菌BL21/DE3中诱导表达,蛋白表达产物经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（SDS-PAGE）进行鉴定;应用Western blot确定CsPLA2是否为ESP;应用免疫荧光方法观察CsPLA2在成虫的组织定位。结果该基因编码307个氨基酸,含有信号肽序列,具有PLA2功能域和活化位点,与谷蛀虫同源蛋白相比,一致性为45%,相似性为52%。PCR、双酶切及DNA测序结果表明pET28a-CsPLA2重组质粒构建成功,SDS-PAGE显示目的基因在大肠埃希菌BL21/DE3中高效表达,表达产物为包涵体。Western blot结果表明CsPLA2是华支睾吸虫的ESP组分之一。虫体免疫组织化学定位显示CsPLA2定位于虫体的腹吸盘、肠支、睾丸处。结论新发现一个CsPLA2基因,其表达的蛋白定位于虫体的腹吸盘、肠支、睾丸处,为华支睾吸虫成虫ESP组分之一。该基因可在原核表达系统中高效表达。     

华支睾吸虫HMGB1同源分子的识别及其进化研究北大核心CSCD

目的识别华支睾吸虫HMGB1同源分子的CDS及其蛋白序列,并分析其进化特征。方法分别用基于麝猫后睾吸虫HMGB1预测序列的5'和3'RACE以及基于华支睾吸虫HMGB1基因组预测序列的PCR法扩增华支睾吸虫成虫来源的cDNA,对扩增产物进行克隆测序,并进行序列的同源性比较和拼接,分析其ORFs,据此对华支睾吸虫成虫来源的cDNA进行PCR扩增验证其转录;构建进化树,对识别出的HMGB1同源分子进行进化分析。结果识别出两个华支睾吸虫HMGB1同源蛋白CDS,大小分别为381和477 bp,二者均在华支睾吸虫成虫转录,产物均一;推测其编码蛋白分别为127和159个氨基酸,其分子序列与血吸虫同源性较高,而与人及其他脊椎动物同源性低。结论成功识别出华支睾吸虫HMGB1同源蛋白CDS序列,为研究其与肝胆管癌发生的关联性和机制奠定了基础。     

华支睾吸虫CsSCCRO基因的克隆表达和蛋白纯化

目的原核表达华支睾吸虫鳞状上皮癌相关肿瘤基因(SCCRO)全长编码区序列,获得纯化的重组蛋白,为进一步功能研究做好准备。方法用生物信息学方法从华支睾吸虫成虫全长cDNA文库中识别出与人鳞状上皮癌相关基因的同源序列及其全长编码区,将其编码区序列克隆到原核表达载体PET-30a(+),测序鉴定重组质粒,在大肠杆菌BL-21/DE3中用IPTG诱导表达,重组产物用His-镍蛋白纯化柱纯化。结果华支睾吸虫鳞状上皮癌相关基因长度为1 218bp,其全长编码序列长度为780bp,编码259个氨基酸,1-22位为分泌信号肽,在羧基端有一个高度保守的区域。该基因在大肠杆菌中得到了高效的可溶性表达,重组蛋白达总蛋白的39%,纯化后的重组蛋白纯度可达98%。结论鳞状上皮癌相关基因的PET-30a(+)原核重组质粒在大肠杆菌BL-21/DE3中可以稳定高效地表达可溶性蛋白。     

Gallbladder cancer epidemiology,pathogenesis and molecular genetics: Recent update

Gallbladder cancer is a malignancy of biliary tract which is infrequent in developed countries but common in some specific geographical regions of developing countries. Late diagnosis and deprived prognosis are major problems for treatment of gallbladder carcinoma. The dramatic associations of this orphan cancer with various genetic and environmental factors are responsible for its poorly defined pathogenesis. An understanding to the relationship between epidemiology, molecular genetics and pathogenesis of gallbladder cancer can add new insights to its undetermined pathophysiology. Present review article provides a recent update regarding epidemiology, pathogenesis, and molecular genetics of gallbladder cancer. We systematically reviewed published literature on gallbladder cancer from online search engine Pub Med(http://www.ncbi.nlm.nih.gov/pubmed). Various keywords used for retrieval of articles were Gallbladder, cancer Epidemiology, molecular genetics and bullion operators like AND, OR, NOT. Cross references were manually searched from various online search engines(http://www.ncbi.nlm.nih.gov/pubmed,https://scholar.google.co.in/, http://www.medline.com/home.jsp). Most of the articles published from 1982 to 2015 in peer reviewed journals have been included in this review.     

Safety of tumor necrosis factor inhibitors use for rheumatoid arthritis and ankylosing spondylitis in Africa, the Middle East, and Asia: focus on severe infections and tuberculosis

Multiple studies of patients in Western countries with rheumatoid arthritis (RA) and ankylosing spondylitis (AS) have indicated increased risk for active tuberculosis (TB) and other infections among these individuals. It has also been consistently reported that patients receiving tumor necrosis factor (TNF) inhibitors for these conditions have higher rates of active TB and other infections than RA or AS patients not receiving these medications. These issues have been studied less extensively in the Asia and Africa–Middle East regions, and information from these regions is important because of higher rates of TB in the general population. This paper reviews studies of RA and AS patients from Asia, Africa, and the Middle East who received TNF inhibitors. A literature search was conducted using http://www.ncbi.nlm.nih.gov/pubmed to collect and report these data. The years included in the PubMed literature search ranged from January 2000 to October 2011. Additionally, information from the China Hospital Knowledge Database was used to report data from Chinese patients with RA and AS treated with TNF inhibitors. Results from these studies indicate that the risk for active TB and other infections in AS and RA patients from Asia, Africa, and the Middle East are increased in patients receiving TNF inhibitors and that the risk is higher among those treated with monoclonal antibodies versus soluble TNF receptor.     

亚洲带绦虫成虫谷胱甘肽S-转移酶基因的克隆及生物信息学分析

目的分析亚洲带绦虫成虫谷胱甘肽S-转移酶（GST,glutathione S-transferase）基因结构并预测其编码蛋白的结构和功能。方法利用生物信息网站如美国国家生物技术信息中心（NCBI,http：//www.ncbi.nl m.nih.gov/）和瑞士生物信息学研究所的蛋白分析专家系统（ExPASY,http：//ca.expasy.org/）中生物信息学分析工具,并结合其它分析软件,从获得亚洲带绦虫成虫全长cDNA质粒文库的表达序列标签（EST,expression sequence tag）中识别GST基因,分析该基因的结构并预测其编码的蛋白质的结构和功能特征。结果该基因与猪带绦虫GST的一致性为94%,相似性为97%;全长810bp,编码区为28-687bp,编码219个氨基酸,无各种亚细胞定位序列,具有多个潜在的磷酸化位点,蛋白的理化性质稳定;预测三个主要的抗原表位89aa-94aa,27aa-32aa,119aa-124aa位于空间结构上相距较远的分子表面,前面两个表位属于绦虫共有的线性抗原表位。结论从亚洲带绦虫成虫cDNA文库中筛选出GST基因,预测为胞浆型蛋白,可能具有较好的免疫诊断抗原应用前景。     

日本血吸虫乳酸脱氢酶(SjLDH)结构与功能的生物信息学分析

目的 应用生物信息学分析软件预测日本血吸虫乳酸脱氢酶（SjLDH）氨基酸序列的结构与功能。 方法 应用NCBI、Expasy等在线生物信息学网站及Vector NTI、PCgene等软件包分析SjLDH与其他物种的同源序列，进行多序列同源比对，分析相同的保守位点及催化活性位点，构建分子进化树；预测二级结构、拓扑结构；同源模建预测三级结构；预测主要抗原表位等。 结果 SjLDH与其他物种的同源序列含相同的保守位点及催化活性位点，与华支睾吸虫LDH（CsLDH）同源性最高为75％，与阴道毛滴虫LDH（TvLDH）同源性最低为17%，与人LDH（HsLDH-A，-B，-C）的同源性为58%~60％； SjLDH与果蝇（DmLDH）的进化距离较秀丽隐杆线虫（CeLDH）为近，3种人LDH中与HsLDH-B、-C的进化距离较HsLDH-A为近；该蛋白具有3个跨膜区域，3个高亲水性区域，主要的线性表位98aa~106aa位于膜外，与原虫LDH相同区域差异显著，而与其他LDH有1~3个氨基酸的差异，关键催化位点之一及底物丙酮酸结合区域位于该区域，蛋白质同源模建分析表明该区域位于蛋白表面形成环状结构，3个关键催化位点位于该区域或在其附近。 结论 生物信息学预测结果提示LDH是研究物种分子进化理想的分子；SjLDH可能是免疫诊断、药物作用及疫苗潜在的靶分子。     

BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.

The amino acid sequence rules that specify beta-sheet structure in proteins remain obscure. A subclass of beta-sheet proteins, parallel beta-helices, represent a processive folding of the chain into an elongated topologically simpler fold than globular beta-sheets. In this paper, we present a computational approach that predicts the right-handed parallel beta-helix supersecondary structural motif in primary amino acid sequences by using beta-strand interactions learned from non-beta-helix structures. A program called BETAWRAP (http://theory.lcs.mit.edu/betawrap) implements this method and recognizes each of the seven known parallel beta-helix families, when trained on the known parallel beta-helices from outside that family. BETAWRAP identifies 2,448 sequences among 595,890 screened from the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/) nonredundant protein database as likely parallel beta-helices. It identifies surprisingly many bacterial and fungal protein sequences that play a role in human infectious disease; these include toxins, virulence factors, adhesins, and surface proteins of Chlamydia, Helicobacteria, Bordetella, Leishmania, Borrelia, Rickettsia, Neisseria, and Bacillus anthracis. Also unexpected was the rarity of the parallel beta-helix fold and its predicted sequences among higher eukaryotes. The computational method introduced here can be called a three-dimensional dynamic profile method because it generates interstrand pairwise correlations from a processive sequence wrap. Such methods may be applicable to recognizing other beta structures for which strand topology and profiles of residue accessibility are well conserved.     

Cardiac injury biomarkers in paediatric age: Are we there yet?

The aim of this article is to evaluate the clinical utility of cardiac injury biomarkers in paediatric age. In December 2015, a literature search was performed (PubMed access to MEDLINE citations; http://www.ncbi.nlm.nih.gov/PubMed/). The search strategy included the following medical subject headings and text terms for the key words: “cardiac injury biomarkers”, “creatine kinase-MB”, “myoglobin”, “troponin”, “children”, “neonate/s”, “newborn/s”, “infant/s” and echocardiography. In the paediatric population, troponins show a good correlation with the extent of myocardial damage following cardiac surgery and cardiotoxic medication and can be used as predictors of subsequent cardiac recovery and mortality. Elevation of cardiac injury biomarkers may also have diagnostic value in cases when cardiac contusion or pericarditis is suspected. Cardiac injury biomarkers are very sensitive markers for the detection of myocardial injury and have been studied in healthy newborns, after tocolysis, intrauterine growth restriction, respiratory distress and asphyxia. The proportion of newborns with elevated troponin was higher than that in ill infants, children, and adolescents and in healthy adults, suggesting that myocardial injury, although clinically occult, is common in this young age group. Results suggest that significant elevation of cord troponin is an excellent early predictor of severity of hypoxic-ischaemic encephalopathy and mortality in term infants. Cardiac biomarkers may also benefit centres without on-site echocardiography with evidence showing good correlation with echo-derived markers of myocardial function. Further studies are needed to better clarify the role of cardiac biomarkers in paediatric age and their correlation with echocardiographic parameters.     

Coagulation factor XI: a database of mutations and polymorphisms associated with factor XI deficiency.

Hereditary factor XI deficiency is a rare bleeding disorder that is found worldwide. Rapidly increasing numbers of mutations and polymorphisms in various populations have been reported. However, the number of identified mutations given in recent literature and available databases is named to be not more than 35. We assumed that this is clearly too low and that to date no comprehensive survey of mutations associated with factor XI deficiency is available. To provide a complete database of mutations and polymorphisms associated with factor XI deficiency we collected all available data on hereditary factor XI deficiency from main biological and medical databases [http://ncbi.nlm.nih.gov/pubmed and http://ncbi.nlm.nih.gov/omim (OMIM reference 264900) and the Human Gene Mutation Database for F11 mutations http://uwcmml1s.uwcm.ac.uk/uwcm/mg/search/119891.html] as well as from contributions to international congresses. As of 8 June 2004 the number of reported causative mutations is 81, of which 12 have been described in unrelated individuals by more than one study group. For three frequently observed mutations [type II and type III mutations (Gln116Stop and Phe283Leu) and Cys38Arg] common founders have been described. Furthermore, 20 polymorphisms have been described in association with factor XI deficiency, three of which have been reported by two independent study groups. For the majority, allele frequencies have been published for in the Caucasian and/or Black population.     

Adenosine release from stimulated mast cells.

Adenosine release has been documented in lung tissue exposed to hypoxic conditions or antigen challenge. Exogenous adenosine potentiates mediator release from stimulated rat serosal and mouse bone marrow-derived mast cells. To investigate the production and release of adenosine from stimulated mast cells, rat serosal mast cells were purified on metrizamide gradients, sensitized with anti-dinitrophenol IgE for 30 min at 37 degrees C, and challenged in the presence of 1 microM deoxycoformycin with either dinitrophenol-conjugated bovine serum albumin antigen, the calcium ionophore A23187, or compound 48/80. Reactions were terminated by centrifugation, and the supernatants and pellets were assayed for adenosine and ATP content, respectively, by high performance liquid chromatography. The adenosine concentration of the supernatants increased from 0.036 +/- 0.003 nmol per 10(6) cells to 0.049, 0.056, and 0.129 nmol per 10(6) cells 60 sec after challenge with antigen, 48/80, or A23187, respectively. After ionophore stimulation, increased extracellular adenosine was evident by 15 sec, peaked by 60 sec, and remained constant for at least 5 min. A significant decline in stimulated ATP levels was observed within 30 sec, suggesting that the enhanced adenosine concentrations may result from the breakdown of ATP. Cultured mouse bone marrow-derived mast cells under similar conditions also displayed augmented extracellular adenosine levels with A23187 challenge. This endogenous source of adenosine may act locally through a positive feedback mechanism to potentiate immediate hypersensitivity reactions.