杨柳田头菇B交配型基因信息素受体片段的克隆与分析

利用简并PCR及DNA步移法,从杨柳田头菇Agrocybe salicacola YAASM0711菌株中扩增得到了一个4 231 bp的核酸片段.经过比对及序列预测,所获得序列中含有杨柳田头菇交配型编码基因中的信息素受体部分,其序列长度为1194 bp,包含4个内含子,5个外显子的长度分别为217 bp,113 bp,67 bp,138bp,449 bp.拼接后的ORF全长984 bp,编码327个氨基酸残基.该序列与灰盖鬼伞Coprinus cinerea、双色蜡蘑Laccaria bicolor信息素受体氨基酸序列较为相似,含有7个跨膜区.信息素受体遗传进化分析显示,其与多个物种信息素受体聚集在一起,可能与真菌信息素受体的多种起源有关.     

棉花GhZIP4基因的克隆及表达分析

根据EST拼接的序列设计引物,利用RT-PCR和PCR方法,从陆地棉‘苏棉18’-cDNA和基因组DNA中分别克隆获得了GhZIP4基因片段.结果表明:(1)GhZIP4基因cDNA序列全长1 487 bp,包含1 269 bp ORF,编码422个氨基酸残基,其氨基酸序列具有典型的ZIP蛋白特征,预测具有8个跨膜结构域,第Ⅲ和第Ⅳ跨膜结构域间存在可变区,在可变区有2个富含His的结构域“HRHSHPHG”和“HSHGHGHD”.(2)氨基酸进化树分析显示,GhZIP4同拟南芥ZIP家族AtZIP4的相似性较高.(3)GhZIP4 DNA序列编码区全长1 778 bp,包含4个外显子和3个内含子,所有外显子/内含子交接点都遵从gt/ag剪接规则.(4)半定量分析显示,GhZIP4基因在茎中表达量最高,表明该基因有可能在某些金属离子地上部和根部的动态平衡分布过程中具有重要作用.     

无核小枣木质素合成基因Zj4CL的克隆和表达分析

为研究无核小枣果实无核形成机理,应用RT-PCR扩增技术首次从无核小枣果实中克隆得到4-香豆酸辅酶A连接酶(4CL,4-Coumarate:Coenzyme A Ligase)基因,该序列长度1819 bp,包含1776 bp的完整开放阅读框,编码591个氨基酸,命名为Zj4CL(登陆号KP279930)。Zj4CL与基因组序列比对发现,该基因组含有5个外显子,4个内含子。序列比对和结构域分析表明,Zj4CL包含4CL基因家族的Box I和Box II保守区。进化树分析显示,Zj4CL与苹果(XP_008362825)的亲缘关系最近。实时荧光定量PCR分析表明,无核小枣在花后30 d左右基因表达量达到最大值,到花后40 d以后表达量明显下降。     

藏酋猴达菲抗原/趋化因子受体基因的克隆与序列分析

利用GenBank公布的恒河猴达菲抗原/趋化因子受体基因(FY)核苷酸序列设计2对特异引物,采用PCR方法克隆藏酋猴Macaca thibetana FY基因,分别得到1.0kb和1.1kb的DNA片段,通过DNA测序和序列拼接获得藏酋猴FY基因1491bp片段,该片段包含2个外显子(21bp和990bp)和1个内含子(480bp)。该基因开放阅读框长1011bp,编码336个氨基酸,该蛋白等电点是5.77,分子量是35.52kDa,分子半衰期30h,不稳定指数是39.84,总平均疏水性是0.689,是疏水性蛋白。拓扑结构预测显示该基因编码氨基酸有15个潜在的功能位点:3个N-糖基化位点,2个酪蛋白激酶Ⅱ磷酸化位点,10个N-肉豆蔻酰化位点。整个蛋白质多肽链含有7个跨膜螺旋区,4个细胞外区和4个细胞内区。同源性比较结果显示,与人、恒河猴、牛、兔、犬、大熊猫6个物种FY基因编码区核苷酸序列间同源性分别为94.7%、99%、75.2%、80.2%、74.5%、71.7%,氨基酸序列间同源性分别为92%、99%、89.8%、78.2%、90%、89.3%。系统进化树结果表明:藏酋猴与恒河猴亲缘关系最近,与人类亲缘关系较近。     

斑点叉尾鮰巨噬细胞移动抑制因子(MIF)基因多态性及表达分析

巨噬细胞移动抑制因子(MIF)是一类主要由T细胞产生、负责机体在环境协迫和炎症反应中进行免疫应答的细胞因子。根据斑点叉尾鮰MIF基因EST序列,应用RACE技术克隆了MIF 3'UTR和5'UTR序列,利用Genome Walking技术克隆了MIF启动子序列,通过特异PCR克隆MIF内含子序列,并对多个体MIF基因组序列进行多态性分析,利用荧光定量PCR研究MIF的组织分布。结果显示,斑点叉尾鮰MIF基因组序列共3 918 bp,其中编码区348 bp,编码115个氨基酸,5'UTR为70 bp,3'UTR为434 bp,启动子为1 382 bp,共有2个内含子,分别为243 bp和1 441 bp。MIF基因组序列中包含4个重复单元序列和60个多态性位点,其中共有6个SNP位于转录因子结合位点上。斑点叉尾鮰MIF mRNA在肠中表达量最高,肌肉中表达量最低。     

辽宁碱蓬甜菜碱醛脱氢酶基因(BADH)启动子分离及序列分析

根据已知的辽宁碱蓬BADHcDNA5′端序列设计两个基因特异的反向引物(BR1,BR2),通过衔接头PCR获得了BADH基因起始密码子上游265bp的序列。根据所获得的序列设计两个基因特异的反向引物(BR3,BR4),用BR2、BR3、BR4分别与4个简并引物配对,通过TAILPCR扩增,获得了约2kb的序列。经Sequencer软件拼接上述两段序列,获得了BADH基因起始密码子上游2055bp的序列。用TSSPTCM软件分析此序列,预测出转录起始点(T)位于起始密码子上游62bp处,由此获得了1993bp的SlBADH启动子序列。用PLACE软件分析此序列,发现该序列具有启动子的基本元件TATAbox、CAATbox,包含多个胁迫诱导元件,如盐诱导元件GAAAAA,抗冻、缺水、脱落酸、抗寒元件CANNTG,伤害诱导元件ANATTNCNN,热激元件ATAAATGT等,是一个强的胁迫诱导启动子。     

一色齿毛菌锰过氧化物酶2基因克隆及生物信息学分析

摘要 锰过氧化物酶（manganese peroxidase,MnP）是由一系列同功酶组成的木质素降解酶。我们前期工作克隆了一色齿毛菌（Cerrena unicolor) MnP1基因序列。在此基础上,本研究采用简并PCR、染色体步移和RACE等技术对C. unicolor mnp2基因(Cu-mnp2)序列进行克隆。同时,采用生物信息学软件对Cu-mnp2的基因结构、Cu-MnP2的蛋白质结构及多物种MnPs蛋白质序列的系统进化关系进行分析。克隆得到3 053 bp的Cu-mnp2 DNA序列(GenBank:JX270806.1)和1 429 bp的Cu-mnp2 cDNA序列(GenBank: JQ782580.1)。序列分析结果显示,Cu-mnp2 DNA序列包含14个外显子和13个内含子,启动子区域包含TATA-BOX、SP1和AP1等作用元件;Cu-mnp2 cDNA序列包含71 bp的5′UTR、230 bp的3′ UTR以及1 128 bp的开放阅读框(ORF)。Cu-mnp2 ORF序列的BLAST比对结果表明,Cu-mnp2与Trametes versicolor FP-101664 SS1 mnp序列覆盖度为53%,序列相似性为65%;与Heterobasidion irregulare mnp、C. unicolor mnp1等cDNA序列都有较高的序列相似性。Cu-mnp2的ORF编码(GenBank:AFK91530.1)由340个氨基酸残基组成的多肽链(Cu-MnP2)。Cu-MnP2蛋白质序列的BLAST比对和蛋白质三维结构均显示,Cu-MnP2包含Mn ²⁺ 、Ga ²⁺ 、血红素及芳香底物结合位点。对包含Cu-MnP1、Cu-MnP2蛋白质序列在内的多物种MnPs蛋白质序列的系统发育分析表明,多物种的MnPs分为两大类群,分别为包含4个二硫键的短MnPs和包含5个二硫键的长MnPs。其中,Cu-MnP1与Cu-MnP2均属于短MnPs,Cu-MnP2与Trametes versicolor MrP 的蛋白质序列亲缘关系最近。通过Cu-mnp2基因的克隆和序列分析,对继续研究C. uniclor的MnP同工酶基因结构和功能奠定基础。     

TCR组库及其在肿瘤免疫中的应用前景与挑战

TCR组库是指机体在特定时间内免疫循环中T细胞克隆的总和,其多样性程度与机体健康密切相关。借助免疫组库测序技术(immune repertoire sequencing, IR-seq),靶向扩增TCR抗原互补决定区(complementarity determining region, CDR) 1-3可有效获取特定时期内疾病患者TCR组库完整的多样性信息。基于此,TCR组库分析可为肿瘤免疫研究提供新型生物标记物,用于监测免疫状态和评估患者预后;同时,TCR组库也可为TCR-T过继免疫疗法的检测与追踪提供有效途径。另外,基于靶向抗原的TCR CDR3序列特征,通过机器学习算法开发"TCR-抗原"识别预测的生物信息学工具,将有利于促进肿瘤免疫研究和治疗应用方面的发展。该文综述了当前TCR组库的检测技术与分析方法,及其在肿瘤免疫中的应用前景与挑战。     

桃中两个MADS box基因的克隆与表达分析

为研究李属(Prunus sp．)果树生殖调控的相关基因,对国际公共数据库中的李属植物的EST(expressed sequence tags)序列进行了电子拼接,获得了8个MADS box基因的cDNA序列,并利用PCR技术从桃中克隆出其中的两个cDNA,分别命名为PpMDS4和PpMADS6,在GenBank中的登录号为AY705972和AY705973。PpMADS4基因长850bp,包含一个732bp的开放阅读框,编码243个氨基酸。PpMADS6基因长1190bp,包含1个768bp的开放阅读框,编码256个氨基酸。PpMADS4和PpMADS6在序列上分别与拟南芥中的AGAMOUS基因和矮牵牛中的PFG基因高度同源。RT-PCR分析表明,PpMADS4基因在桃的花瓣、心皮、果实及果仁中表达,应属于控制花器官发育的C类MADS box基因。PpMADS6基因在桃的叶、萼片、花瓣、心皮及果实中表达,应属于调控植物由营养生长向生殖生长过渡的A类MADSbox基因。     

2株WU多瘤病毒全基因组序列测定和分析

WU多瘤病毒(WUPyV)是多瘤病毒科多瘤病毒属的新成员,近来发现与人呼吸道感染等有关。本研究对2株WUPyV进行全基因组序列测定和拼接,获得这2株病毒全基因组序列,并与已上传到GenBank的国内外几株WUPyV的全基因组序列和氨基酸序列进行比对和系统进化分析。这2株WUPyV是环状、双链DNA病毒,基因组全长5 228bp,比GenBank已知WUPyV全序列少1bp。缺失的一对碱基位于位点4 536处,属于大T抗原的非编码区。病毒全基因组编码5个蛋白,分别是3个衣壳蛋白VP2、VP3、VP1与大T抗原和小T抗原。系统进化分析显示相对中国福建福州的FZ18株,另一株FZTF株与参考株-澳大利亚的B0株关系较近。     

Distribution of N,P, K,Ca, Mg,S, Zn,Fe, Mn and Cu in groundnut

Summary Concentration of N, P, K, Ca, Mg and S in summer groundnut crop was higher than in kharif while Zn, Fe, Mn and Cu contents were higher in summer crop. Kernel's N, P and Zn; Leaflet's Ca and Mn; Stem's K and Fe; Root's S and Cu and Petiole's Mg contents were highest. Shell's N, P, K, Mg, S, Zn and Cu; Kernel's Ca, Fe and Mn contents were the least. N, P, K, S, Zn and Cu concentrations decreased linearly as the crop grew. Ca, Mg, Fe and Mn concentrations did not display any distinct pattern. Ca concentration was positively correlated with pod yield in both the seasons.     

Simultaneous measurement of the trace elements Al, As, B, Be, Cd, Co, Cu, Fe, Li, Mn, Mo, Ni, Rb, Se, Sr, and Zn in human serum and their reference ranges by ICP-MS

The goal of this article was to establish reference ranges of the concentration of trace elements in human serum and to compare these results with those reported by other authors. We describe the sample preparation and measurement conditions that allow the rapid, precise, and accurate determination of Al, As, B, Be, Cd, Co, Cu, Fe, Li, Mn, Mo, Ni, Rb, Se, Sr, and Zn in human serum samples (n=110) by inductively coupled plasma-mass spectrometry (ICP-MS). Accuracy and precision were determined by analyzing three reconstituted reference serum samples by comparison with other methods and by the standard addition procedure. The advantages of the ICP-MS method include short time of analysis of the elements mentioned, low detection limit, high precision, and high accuracy. Disadventages include a high risk of contamination due to the presence of some of the elements of interest in the environment, the relatively delicate sample handling, and the high cost of the equipment.     

Reference values for the concentrations of As,Cd, Co,Cr, Cu,Fe, I,Hg, Mn,Mo, Ni,Pb, Se,and Zn in selected human tissues and body fluids

This report attempts to formulate reference ranges of elemental concentrations for 15 trace elements in selected human tissues and body fluids. A set of samples consisting of whole blood, blood serum, urine, milk, liver, and hair were chosen and considered for 15 elements of biological significance: As, Cd, Co, Cr, Cu, F, Fe, I, Hg, Mn, Mo, Ni, Pb, Se, and Zn. The results represent wholly or partially data received from 40 countries of the global regions of Africa, Asia, Europe, North, South, and Central America, Australia, and New Zealand. This survey, even if qualitative, has been useful in demonstrating certain trends of trace-element scenarios around the world. It is of course recognized that both diet and environment exert a strong influence on the distribution pattern of several elements, such as As, Cd, Mn, Pb, Se, and Zn. A limited comparison of the available information on soil status of different countries reflected some interesting associations for elements, such as Mn and Zn. Importantly, this study revealed that only a few countries were in a position to identify a reasonable amount of data on samples requested for this project. Regretably, for a number of countries, any dependable data for even such essential elements as Cu, Fe, and Zn were not available. In view of the nutritional importance of many elements, the time is ripe for concerted efforts by intergovernmental agencies to initiate investigations or commission task forces/projects to generate reliable reference data for selected global regions, which sadly lack data of any kind at present.     

Crystal structure, detonation performance, and thermal stability of a new polynitro cage compound: 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptacyclo [5.5.1.13, 11. 15, 9] pentadecane

A new polynitro cage compound 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptcyclo [5.5.1.1(3,11).1(5,9)] pentadecane (NNNAHP) was designed in the present work. Its molecular structure was optimized at the B3LYP/6-31 G(d,p) level of density functional theory (DFT) and crystal structure was predicted using the Compass and Dreiding force fields and refined by DFT GGA-RPBE method. The obtained crystal structure of NNNAHP belongs to the P-1 space group and the lattice parameters are a = 9.99 ?, b = 10.78 ?, c = 9.99 ?, α = 90.01°, β = 120.01°, γ = 90.00°, and Z = 2, respectively. Based on the optimized crystal structure, the band gap, density of state, thermodynamic properties, infrared spectrum, strain energy, detonation characteristics, and thermal stability were predicted. Calculation results show that NNNAHP has detonation properties close to those of CL-20 and is a high energy density compound with moderate stability.     

Monovalent Cation Permeation through the Connexin40 Gap Junction Channel : Cs,Rb, K,Na, Li,TEA, TMA,TBA, and Effects of Anions Br,Cl, F,Acetate, Aspartate,Glutamate, and NO3

The unitary conductances and permeability sequences of the rat connexin40 (rCx40) gap junction channels to seven monovalent cations and anions were studied in rCx40-transfected neuroblastoma 2A (N2A) cell pairs using the dual whole cell recording technique. Chloride salt cation substitutions (115 mM principal salt) resulted in the following junctional maximal single channel current-voltage relationship slope conductances (γ_j in pS): CsCl (153), RbCl (148), KCl (142), NaCl (115), LiCl (86), TMACl (71), TEACl (63). Reversible block of the rCx40 channel was observed with TBA. Potassium anion salt γ_j are: Kglutamate (160), Kacetate (160), Kaspartate (158), KNO₃ (157), KF (148), KCl (142), and KBr (132). Ion selectivity was verified by measuring reversal potentials for current in rCx40 gap junction channels with asymmetric salt solutions in the two electrodes and using the Goldman-Hodgkin-Katz equation to calculate relative permeabilities. The permeabilities relative to Li⁺ are: Cs⁺ (1.38), Rb⁺ (1.32), K⁺ (1.31), Na⁺ (1.16), TMA⁺ (0.53), TEA⁺ (0.45), TBA⁺ (0.03), Cl⁻ (0.19), glutamate⁻ (0.04), and NO₃− (0.14), assuming that the monovalent anions permeate the channel by forming ion pairs with permeant monovalent cations within the pore thereby causing proportionate decreases in the channel conductance. This hypothesis can account for why the predicted increasing conductances with increasing ion mobilities in an essentially aqueous channel were not observed for anions in the rCx40 channel. The rCx40 effective channel radius is estimated to be 6.6 Å from a theoretical fit of the relationship of relative permeability and cation radius.     

Competitive inhibition and selectivity enhancement by Ca in the uptake of inorganic elements (Be, Na, Mg, K, Ca, Sc, Mn, Co, Zn, Se, Rb, Sr, Y, Zr, Ce, Pm, Gd, Hf) by carrot (Daucus carota cv. U.S. harumakigosun)

We investigated the uptake of inorganic elements (Be, Na, Mg, K, Ca, Sc, Mn, Co, Zn, Se, Rb, Sr, Y, Zr, Ce, Pm, Gd, and Hf) and the effect of Ca on their uptake in carrots (Daucus carota cv. U.S. harumakigosun) by the radioactive multitracer technique. The experimental results suggested that Na, Mg, K, and Rb competed for the functional groups outside the cells in roots with Ca but not for the transporter-binding sites on the plasma membrrane of the root cortex cells. In contrast, Y, Ce, Pm, and Gd competed with Ca for the transporters on the plasma membrane. The selectivity, which was defined as the value obtained by dividing the concentration ratio of an elemental pair, K/Na, Rb/Na, Be/Sr, and Mg/Sr, in the presence of 0.2 and 2 ppm Ca by that of the corresponding elemental pair in the absence of Ca in the solution was estimated. The selectivity of K and Rb in roots was increased in the presence of Ca. The selectivity of Be in roots was not affected, whereas the selectivity of Mg was increased by Ca. These observations suggest that the presence of Ca in the uptake solution enhances the selectivity in the uptake of metabolically important elements against unwanted elements.     

Potential Compounds for Oral Cancer Treatment: Resveratrol,Nimbolide, Lovastatin,Bortezomib, Vorinostat,Berberine, Pterostilbene,Deguelin, Andrographolide,and Colchicine

Oral cancer is one of the main causes of cancer-related deaths in South-Asian countries. There are very limited treatment options available for oral cancer. Research endeavors focused on discovery and development of novel therapies for oral cancer, is necessary to control the ever rising oral cancer related mortalities. We mined the large pool of compounds from the publicly available compound databases, to identify potential therapeutic compounds for oral cancer. Over 84 million compounds were screened for the possible anti-cancer activity by custom build SVM classifier. The molecular targets of the predicted anti-cancer compounds were mined from reliable sources like experimental bioassays studies associated with the compound, and from protein-compound interaction databases. Therapeutic compounds from DrugBank, and a list of natural anti-cancer compounds derived from literature mining of published studies, were used for building partial least squares regression model. The regression model thus built, was used for the estimation of oral cancer specific weights based on the molecular targets. These weights were used to compute scores for screening the predicted anti-cancer compounds for their potential to treat oral cancer. The list of potential compounds was annotated with corresponding physicochemical properties, cancer specific bioactivity evidences, and literature evidences. In all, 288 compounds with the potential to treat oral cancer were identified in the current study. The majority of the compounds in this list are natural products, which are well-tolerated and have minimal side-effects compared to the synthetic counterparts. Some of the potential therapeutic compounds identified in the current study are resveratrol, nimbolide, lovastatin, bortezomib, vorinostat, berberine, pterostilbene, deguelin, andrographolide, and colchicine.     

New Coleoptera records from New Brunswick, Canada: Stenotrachelidae, Oedemeridae, Meloidae, Myceteridae, Boridae, Pythidae, Pyrochroidae, Anthicidae, and Aderidae

We report 19 new species records for the faunal list of Coleoptera in New Brunswick, Canada, six of which are new records for the Maritime provinces, and one of which is new Canadian record. We also provide the first recent records for five additional species in New Brunswick. One new species of Stenotrachelidae, Cephaloon ungulare LeConte, is added to the New Brunswick faunal list. Additional records are provided for Cephaloon lepturides Newman, as well the first recent record of Nematoplus collaris LeConte. Two species of Oedemeridae, Asclera puncticollis (Say) and Asclera ruficollis (Say), are newly reported for New Brunswick, and additional locality and bionomic data are provided for Calopus angustus LeConte and Ditylus caeruleus (Randall). The records of Ditylus caerulus are the first recent records for the province. Three species of Meloidae, Epicauta pestifera Werner, Lytta sayi LeConte, and Meloe augustcollis Say are reported the first time for New Brunswick; Epicauta pestifera is newly recorded in Canada. Lacconotus punctatus LeConte and the family Mycteridaeis newly recorded for New Brunswick. The first recent records of Borus unicolor Say (Boridae) are reported from the province. One new species of Pythidae, Pytho siedlitzi Blair, and the first recent records of Pytho niger Kirby are added to the faunal list of New Brunswick. Three species of Pyrochroidae are newly reported for the province, including Pedilus canaliculatus (LeConte) and Pedilus elegans (Hentz), which are new for the Maritime provinces. Five species of Anthicidae and the first recent record of Anthicus cervinus LaFerté-Sénectére are newly reported for New Brunswick. Anthicus melancholicus LaFerté-Sénectère, Sapintus pubescens (LaFerté-Sénectère), Notoxus bifasciatus (LeConte), and Stereopalpus rufipes Casey are new to the Maritime provinces faunal list. Ambyderus granularis (LeConte) is removed from the faunal list of the province. Three species of Aderidae, Vanonus huronicus Casey, Zonantes fasciatus (Melsheimer), and Zonantes pallidusWerner, are newly recorded for New Brunswick; Zonantes fasciatus and Vanonus huronicus are new for the Maritime provinces' faunal list. Collection data, bionomic data, and distribution maps are presented for all these species.