高糖土壤微生物宏基因组文库的构建及β-葡萄糖苷酶基因鉴定

采用宏基因组技术构建了高糖土壤微生物的DNA文库,该文库约含9万个克隆,文库外源DNA总容量为3.1×10~9bp。利用活性筛选策略,对文库进行筛选,获得11个β-葡萄糖苷酶的阳性克隆,并对其中2个表达β-葡萄糖苷酶的克隆进行亚克隆和序列分析,获得两个编码新型β-葡萄糖苷酶的基因分别命名为:unbgl3A和unbgl3B。生物信息学分析表明:unbgl3A基因由2241个碱基对组成,unbgl3B基因由2292个碱基对组成。在核苷酸水平上,unbgl3A、unbgl3B与已知数据库中的β-葡萄糖苷酶基因没有任何相似性。在氨基酸水平上,与GenBank数据库中已知β-葡萄糖苷酶的相似性分别为73%和69%。     

解淀粉芽孢杆菌SYBC H47铁载体合成酶基因dhbA、dhbB、dhbC的克隆表达与序列分析

铁载体是微生物在缺铁环境中产生的小分子螯合物,利用CAS双平板法鉴定出已有菌株产铁载体,经鉴定所产铁载体为儿茶酚型。以解淀粉芽孢杆菌SYBC H47基因组DNA序列为模板,通过PCR克隆得到了铁载体产生途径中前体物质2,3-二羟基苯甲酸(DHB)合成所需酶的3个基因dhb A、dhb B、dhb C,结果表明三基因全长分别为786 bp、927 bp、1 197 bp,诱导表达,经SDS-PAGE电泳表明三蛋白大小分别为27.1 k D、34.3 k D、42.9 k D。用KMB培养基诱导表达三株重组菌株,表明三株重组菌株铁载体产量均有明显提高。经同源性比对和生物信息学分析发现,dhb A、dhb B、dhb C三基因分别编码2,3-二氢-2,3-二羟基苯甲酸脱氢酶、异分支酸酶、异分支酸合酶,dhb A、dhb C蛋白结构稳定,而dhb B蛋白结构则不是很稳定,其二级结构主要由α螺旋、β折叠、延伸链及无规卷曲构成但比例各不相同。以上结果为铁载体合成的研究提供了理论依据。     

D类碳青霉烯酶的研究进展

碳青霉烯酶（carbapenemases）是指能够明显水解亚胺培南或美罗培南的一类β-内酰胺酶,它包括AMBLER分子分类的A、B和D三类酶。其中,B类为金属酶,属于BUSH功能分类的3群;A、D类为丝氨酸酶,分别属于BUSH分类的2f和2d亚群^[1,2]。本文主要针对D类碳青霉烯酶的发现与分群、生化特性、耐药特征以及流行病学等问题进行综述。     

植物查耳酮异构酶生物信息学分析

查耳酮异构酶（CHI）是黄酮类化合物合成途径中的关键酶之一。利用生物信息学方法对该酶基因及编码蛋白进行系统的分析,将为深入开展研究打下基础。本文利用NCBI数据库中注册的CHI基因的核酸及氨基酸序列,以葡萄CHI为主,对其组成成分、疏水性／亲水性、翻译后修饰、蛋白质二级及三级结构等进行预测和推断。结果表明：葡萄CHI不具有明显的亲水或疏水区域;二级结构主要由α-螺旋、不规则卷曲和β-折叠组成,β-转角散布于整个肽链中;β3a—β3f连同α1—α7构成了蛋白三级结构的核心;包含CHI结构域;在高级结构、活性位点等方面具有较高的保守性。     

体外培养主动脉细胞钙化作用研究

目的：初步探讨主动脉钙化的机制。方法：外殖块法分离培养家兔主动脉平滑肌细胞,进行vonKossa染色以显示钙化,生化法检测细胞内外不溶性钙。放兔法测定培养上清骨钙素的含量。RT-PCR方法检测X型胶原mR-NA的表达。结果：25-羟基胆固醇（A组）和β-甘油磷酸盐（B组）分别培养的传代细胞均可见多个细胞结节,且细胞结节von kossa染色阳性;而对照组（C组）无细胞结节形成,von kossa染色阴性,前二者每孔不溶性钙沉积量,以及培养上清中骨钙素含量明显高于后者,且A、B两组X型胶原mRNA的表达为阳性。结论：25-羟基胆固醇、β-甘油磷酸盐均可促进主动脉中膜细胞发生钙化,主动脉中膜在钙化过程中与成骨细胞相似,骨钙素分泌增多且有X型胶原mRNA的表达。     

利尿剂联合β受体阻滞剂治疗慢性心力衰竭的临床效果评价

目的:评价利尿剂联合β受体阻滞剂(β-RB)治疗慢性心力衰竭(CHF)的临床疗效.方法:将127例CHF患者随机分为三组,分别以利尿剂(A组)、β-RB(B组)和利尿剂+β-RB(C组)治疗,比较各组患者治疗后心功能指标、心室重塑情况及临床疗效.结果:治疗8周后,C组LVEF、SV、CO的水平均显著高于A组和B组,但其HR水平显著低于A组和B组,差异均具有统计学意义(P＜0.05);C组LVESV、LVS、LVEDV、LVD水平均显著低于A组和B组,差异均具有统计学意义(P＜0.05);A组治疗总有效率为77.5％,B组治疗总有效率为78.0％,C组治疗总有效率为93.5％,C组治疗总有效率显著高于与A组和B组,差异均具有统计学意义(P＜0.05).结论:利尿剂联合β-RB治疗CHF的临床效果显著优于利尿剂和β-RB单用的临床效果.     

A7—B7二硫键缺失对胰岛素原重折叠及结构的影响

为研究A7 B7二硫键在胰岛素原结构和折叠中的作用 ,构建了A7 B7二硫键缺失的胰岛素原突变体 ,研究了其与野生型胰岛素原在体外重折叠产率、自由巯基氧化速度、CD谱、受体及抗体结合活性 ,以及对胰蛋白酶酶切敏感性的差别。结果表明 ,A7 B7二硫键缺失可导致胰岛素原α 螺旋明显减少以及对胰蛋白酶的酶切敏感性显著增加 ,其对胰岛素原结构的影响主要导致了受体结合活性的大幅度降低。突变体在体外重折叠 1h后巯基氧化速率较野生型明显减慢 ,但其最终折叠产率与野生型相当。由此提出一个胰岛素原折叠的可能途径 ,即A链链内二硫键最先形成 ,然后是两对链间二硫键。且A2 0 B19二硫键比A7 B7二硫键很可能先形成 ,在折叠中更重要。     

三种方法制备的猪小肠黏膜下层支架的生物相容性和免疫原性的对比研究

目的:采用三种不同的脱细胞方法制备小肠黏膜下层(small intestinal submucosa,SIS)支架,研究其生物相容性、免疫原性以及构建真皮替代物等方面,为组织工程化皮肤的细胞载体支架提供优选方案。方法:将新鲜猪小肠分别采用单纯机械法、机械-化学法、机械-酶消化法制备三种不同的SIS,分别作为A、B、C组;通过复合成纤维细胞构建真皮替代物,利用HE染色观察支架组织学形态以及细胞粘附情况、MTT法检测细胞增殖情况,同时观察支架移植SD大鼠皮下1、2、4周后炎症反应及血管化程度。结果:组织学观察A组有细胞残留,B、C组未见细胞残留。MTT结果显示细胞在支架上生长旺盛增殖能力强,其中A组优于B、C组;皮下移植后的HE结果表明B组引起炎症反应较A、C组弱,而C组血管化程度较A、B组更明显。结论:机械-化学法以及机械-酶消化法制备的SIS具有良好的生物相容性以及免疫原性,可作为构建组织工程化皮肤细胞载体的选择。     

7-木糖紫杉烷糖基水解酶LXYL-P1-1和LXYL-P1-2活性中心预测及初步的功能分析

7-木糖紫杉烷糖基水解酶LXYL-P1-1和LXYL-P1-2是克隆自真菌香菇的两个双功能酶(序列一致性97%),具有β-木糖苷酶/β-葡萄糖苷酶双重活性,能特异性地水解移除7-木糖-10-去乙酰紫杉醇等紫杉烷上的木糖基。采用生物信息学方法对两个酶蛋白进行酶活性中心预测,初步确定Asp300和Glu529分别为亲核试剂和一般酸/碱催化剂,而Asn172-Gly173-Arg174和Lys207-His208为底物结合结构域。以LXYL-P1-2为研究对象,以毕赤酵母细胞为表达宿主,应用定点突变技术获得了N172A、G173A、R174A、K207A、H208A、D300N和E529Q突变体,并进行了酶活性分析。结果显示:在分别以PNP-Xyl、PNP-Glc和7-木糖-10-去乙酰紫杉醇为底物时,N172A、G173A、R174A、K207A、D300N和E529Q的β-木糖苷酶与β-葡萄糖苷酶活性大幅度下降甚至完全消失;H208A的β-木糖苷酶活性也显著下降,但仍保持98%的β-葡萄糖苷酶活性。其结果初步验证了对上述两个酶蛋白的活性中心的预测,为进一步揭示7-木糖紫杉烷糖基水解酶结构与功能的关系提供了实验依据。     

决明查尔酮合成酶的同源模建和分子模拟对接

查尔酮合成酶(chalcone synthase,CHS)是植物中类黄酮生物合成途径的关键酶,其催化对-香豆酰辅酶A和丙二酸单酰辅酶A发生缩合反应.本研究以苜蓿CHS的晶体为模板,利用同源建模构建决明CHS的三维模型.经过动力学优化后,决明CHS的三维模型与苜蓿CHS的结构极为相似,主要由α-螺旋和β-折叠构成,其中有13个α螺旋,占32.82％,15个β折叠,占19.23％,无规则卷曲占47.95％.模型验证结果表明决明CHS的三维模型具有合理的立体化学性质与氨基酸相容性.决明CHS含有两个重要的结构域:对-香豆酰辅酶A结合域与丙二酸单酰辅酶A结合域.决明CHS与对-香豆酰辅酶A、丙二酸单酰辅酶A的结合主要通过氢键与范德华力.决明CHS中Cys164、His303与活性中心的H2O能够形成电子传递体系,参与对-香豆酰辅酶A形成CHS-对-香豆酰基中间产物.本研究结果为利用此类CHS三维模型研究其催化机理和分子工程改造奠定基础.     

REDUCTION OF THE PECTORAL SPINE AND GIRDLE IN DOMESTICATED CHANNEL CATFISH IS LIKELY CAUSED BY CHANGES IN SELECTION PRESSURE

Locked pectoral spines of the Channel Catfish Ictalurus punctatus more than double the fish's width and complicate ingestion by gape‐limited predators. The spine mates with the pectoral girdle, a robust structure that anchors the spine. This study demonstrates that both spine and girdle exhibit negative allometric growth and that pectoral spines and girdles are lighter in domesticated than in wild Channel Catfish. This finding could be explained by changes in selection pressure for spine growth during domestication or by an epigenetic effect in which exposure to predators in wild fish stimulates pectoral growth. We tested the epigenetic hypothesis by exposing domesticated Channel Catfish fingerlings to Largemouth Bass Micropterus salmoides predators for 13 weeks. Spines and girdles grow isometrically in the fingerlings, and regression analysis indicates no difference in proportional pectoral growth between control and predator‐exposed fish. Therefore a change in selection pressure likely accounts for smaller pectoral growth in domesticated Channel Catfish. Decreasing spine growth in older fish suggests anti‐predator functions are most important in smaller fish. Additionally, growth of the appendicular and axial skeleton is controlled differentially, and mechanical properties of the spine and not just its length are an important component of this defensive adaptation.     

Bacterial diversity and community structure of the intestinal microbiome of Channel Catfish (Ictalurus punctatus) during ontogenesis

The acquisition of gut microbes does not occur randomly and is highly dependent on host factors, environmental cues, and self-assembly rules exerted by the microbes themselves. The main objective of this project was to characterize how the gut microbiome develops during the early life stages of Channel Catfish and to identify i) which bacteria are the main constituents of the gut microbiome at different ontogenesis stages, and ii) at which time point(s) the gut microbiome stabilizes. High-throughput Illumina Miseq DNA sequencing of the V4 domain of the 16S rRNA gene was used to assess the microbial community composition during the life stages of Channel Catfish along with water and feed samples. Microbiomes from fertilized eggs, sac fry, swim up fry, pre-fingerlings, and fingerlings were all significantly distinct. OTUs analyses showed that the phylum Proteobacteria, Firmicutes, Fusobacteria and Cyanobacteria dominated the Channel Catfish gut microbiome. During the early stages of ontogenesis, the fish microbiome was dynamic and highly diverse, with significant shifts occurring between fertilized eggs to sac fry (6 dph), and from sac fry to swim up fry (15 dph). The gut microbiome stabilized between the pre-fingerlings and fingerlings stage (≤90 dph) with an observed reduction in species richness. Feed had a more significantly contribution to the microbial colonization of the gut than water. We have identified the period in which the gut microbiome changes rapidly from 15 dph until 21 dph before stabilizing after 90 dph.     

Hydroxylation-induced stabilization of the collagen triple helix. Further characterization of peptides with 4(R)-hydroxyproline in the Xaa position

4(R)-Hydroxyproline in the Yaa position of the -Gly-Xaa-Yaa-repeated sequence of collagen plays a crucial role in the stability of the triple helix. Since the peptide (4(R)-Hyp-Pro-Gly)10 does not form a triple helix, it was generally believed that polypeptides with a -Gly-4(R)-Hyp-Yaa-repeated sequence do not form a triple helix. Recently, we found that acetyl-(Gly-4(R)-Hyp-Thr)10-NH2 forms a triple helix in aqueous solutions. To further study the role of 4(R)-hydroxyproline in the Xaa position, we made a series of acetyl-(Gly-4(R)-Hyp-Yaa)10-NH2 peptides where Yaa was alanine, serine, valine, and allo-threonine. We previously hypothesized that the hydroxyl group of threonine might form a hydrogen bond to the hydroxyl group of 4(R)hydroxyproline. In water, only the threonine- and the valine-containing peptides were triple helical. The remaining peptides did not form a triple helix in water. In 1,2- and in 1,3-propanediol at 4 degrees C, all the soluble peptides were triple helical. From the transition temperature of the triple helices, it was found that among the examined residues, threonine was the most stable residue in the acetyl-(Gly-4(R)-Hyp-Yaa)10-NH2 peptide. The transition temperatures of the valine- and allo-threonine-containing peptides were 10 degrees lower than those of the threonine peptide. Surprisingly, the serine-containing peptide was the least stable. These results indicate that the stability of these peptides depends on the presence of a methyl group as well as the hydroxyl group and that the stereo configuration of the two groups is essential for the stability. In the threonine peptide, we hypothesize that the methyl group shields the interchain hydrogen bond between the glycine and the Xaa residue from water and that the hydroxyl groups of threonine and 4(R)hydroxyproline can form direct or water-mediated hydrogen bonds.     

The Cysteine-rich Region of Type VII Collagen Is a Cystine Knot with a New Topology

Collagens are a group of extracellular matrix proteins with essential functions for skin integrity. Anchoring fibrils are made of type VII collagen (Col7) and link different skin layers together: the basal lamina and the underlying connective tissue. Col7 has a central collagenous domain and two noncollagenous domains located at the N and C terminus (NC1 and NC2), respectively. A cysteine-rich region of hitherto unknown function is located at the transition of the NC1 domain to the collagenous domain. A synthetic model peptide of this region was investigated by CD and NMR spectroscopy. The peptide folds into a collagen triple helix, and the cysteine residues form disulfide bridges between the different strands. The eight cystine knot topologies that are characterized by exclusively intermolecular disulfide bridges have been analyzed by molecular modeling. Two cystine knots are energetically preferred; however, all eight disulfide bridge arrangements are essentially possible. This novel cystine knot is present in type IX collagen, too. The conserved motif of the cystine knot is CX₃CP. The cystine knot is N-terminal to the collagen triple helix in both collagens and therefore probably impedes unfolding of the collagen triple helix from the N terminus.     

Polyamine-linked oligonucleotides for DNA triple helix formation.

The concept of antigene therapy of disease is based on the ability of an oligonucleotide (the therapeutic agent) to bind to double-stranded genomic DNA (the target associated with the disease). Examples are herein given of the linkage of a series of polyamines to a 21-mer homopyrimidine oligonucleotide. These conjugated 21-mers can each form a triple helix with an appropriate double-stranded homopurine-homopyrimidine DNA according to Hoogsteen base-pairing rules. No triple helix was found when unmodified third strand was used at 10 mM sodium phosphate, pH 6.5, 100 mM sodium chloride solution. In contrast, the spermine-conjugated oligonucleotide had a melting temperature of 42 degrees C. According to the melting profile, the appended spermine moiety was found to affect the Tm only of the triple helix, but not of the subsequent melting of the underlying double helix. The Tm enhancing ability of the spermine-conjugate was found to be better than that of other polyamine-conjugates.     

A calorimetric study of the triple helix formation: interaction of poly(C) - guanosine - protonated poly(C).]

The triple helix formation of poly(C) - guanosine - poly(C+) was investigated by the help of an LKB scanning micro-calorimeter. The existence of the triple helix could also be shown by recording the melting curves. The ultraviolet absorption at different wave lengths namely 275 nm, 260 nm, and 245 nm was plotted as a function of the temperature. Furthermore formation of the triple helix was shown by plotting the ultraviolet absorption at 245 nm during the increasing addition of guanosine solution to a fixed amount of poly(C) in the solution. Finally the formation of the triple helix was demonstrated by plotting the ultraviolet absorption at 245 nm of a certain mixture of the components while the pH value of the solution was continuously lowered. All these methods show that the monomer interacts with the polymer double helix to form a triple helix. The calorimetric measurements show that the reaction enthalpy is concentration dependent. Above a threshold concentration a rapid increase of the reaction enthalpy is observed. This increase occurs in a very narrow concentration interval. Above this interval a final value of the reaction enthalpy is reached. The amount of the reaction enthalpy for the interaction of guanosine with poly(C) - poly(C+) double helix is 5.5 Kcal (mol base triplet)-1.     

Properties of film from splendid squid (Loligo formosana) skin gelatin with various extraction temperatures

Properties of film from splendid squid (Loligo formosana) skin gelatin extracted at different temperatures (50-80°C) were investigated. Tensile strength (TS) and elongation at break (EAB) of films decreased, but water vapour permeability (WVP) increased (P<0.05) as the extraction temperature increased. Increase in transparency value with coincidental decrease in lightness was observed with increasing extraction temperatures. Electrophoretic study revealed that degradation of gelatin became more pronounced with increasing extraction temperatures. As a consequence, their corresponding films had the lower mechanical properties. FTIR spectra of obtained gelatin films revealed the significant loss of molecular order of the triple helix. Thermogravimetric analysis indicated that F80 exhibited the higher heat susceptibility and weight loss. Loosen structure was observed in film prepared from gelatin with increasing extraction temperatures. Thus, the temperature used for gelatin extraction from splendid squid skin directly affected the properties of corresponding films.     

A directional nucleation-zipping mechanism for triple helix formation

A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T·A base pair by a C·G pair at either the 5′ or the 3′ end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5′ side of the triplex (referred to as the 5′ side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5′ end to the 3′ end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5′ than at the 3′ duplex–triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression.     

Substitutions for glycine alpha 1-637 and glycine alpha 2-694 of type I procollagen in lethal osteogenesis imperfecta. The conformational strain on the triple helix introduced by a glycine substitution can be transmitted along the helix

Two substitutions for glycine in the triple-helical domain were found in type I procollagen synthesized by skin fibroblasts from two probands with lethal osteogenesis imperfecta. One was a substitution of valine for glycine alpha 1-637, and the other was a substitution of arginine for glycine alpha 2-694. The effects of the mutations on the zipper-like folding of the collagen triple helix were similar, since there was post-translational overmodification of the collagenase A fragments (amino acids 1-775) but not of more COOH-terminal fragments of the protein. The mutations differed markedly, however, on their effects on thermal unfolding of the triple helix. The collagenase A fragment from the collagen containing the arginine alpha 2-694 substitution was cleaved at about amino acid 700 when incubated with trypsin at 30-35 degrees C. Therefore, there was micro-unfolding of the triple helix at a site close to the glycine substitution. Surprisingly, however, the collagenase A fragment with the valine alpha 1-637 substitution was also cleaved at about amino acid 700 under the same conditions. The results, therefore, demonstrated that although most glycine substitutions delay folding of the triple helix in regions that are NH2-terminal to the site of the substitution, the effects on unfolding can be transmitted to regions that are COOH-terminal to the site of the glycine substitution.     

乌贼皮胶原蛋白的提取及结构表征

为了充分利用乌贼加工废弃物,分析了乌贼皮的基本组成成分,优化了从乌贼皮中提取胶原蛋白的工艺条件,并利用SDS-PAGE垂直电泳、紫外扫描和傅里叶变换红外光谱对所提取的胶原蛋白进行了结构表征.结果表明,乌贼皮中含有大量胶原蛋白,可作为胶原蛋白来源的补充.采用酸酶复合提取胶原蛋白的最佳条件为:酒石酸浓度为0.1mol/L,胃蛋白酶添加量为1400U/g,料液比为1:20(m:V,原料),4℃提取18h,提取率为12.08％.SDS-PAGE垂直电泳、紫外扫描和傅里叶变换红外光谱的结果表明,采用酸酶复合法从乌贼皮中提取的胶原蛋白为I型胶原蛋白,保持了完整的三螺旋结构.