Molecular cloning and characterization of the oprQ gene coding for outer membrane protein OprE3 of Pseudomonas aeruginosa.

We cloned and characterized the oprQ gene coding for outer membrane protein OprE3 of Pseudomonas aeruginosa PAO1. The oprQ gene was composed of 1,275 base pairs including a sequence encoding for the signal sequence and a mature protein with a Mr of 44,602. Computer-aided alignment and hydropathy analyses of the predicted amino acid sequences suggested that OprE3 is a transmembrane protein homologous to outer membrane proteins of P. aeruginosa such as OprD2 (OprD) porin and OprE1 (OprE) porin. Susceptibility to several antibiotics of the strains lacking or overproducing OprE3 was indistinguishable from that of the wild-type strain, suggesting that OprE3 is unlikely involved in the diffusion of carbapenems and other beta-lactam antibiotics.     

Quality assessed nonculture techniques for detection and typing of meningococci

PCR protocols are increasingly used in laboratories worldwide for the diagnosis and confirmation of invasive meningococcal infection. Protocols are now available for the identification of Neisseria meningitidis, for genogrouping, susceptibility to antibiotics and genotyping of the corresponding isolates. The implementation of quality assurance (QA) schemes and standardization of protocols are required. Diagnostic and confirmatory PCRs should perform consistently in clinical and reference microbiology laboratories. General QA schemes address the issues of sample preparation, PCR laboratory environment, equipment and validation of protocols. Moreover, external QA interlaboratory studies are essential. The European Monitoring Group on Meningococci has provided a good forum to conduct such studies through the development and distribution of samples and protocols for nonculture detection and typing of N. meningitidis.     

Molecular cloning and nucleotide sequence analysis of the maltose-inducible porin gene of Aeromonas salmonicida

Abstract The gene for the Aeromonas salmonicida maltose-inducible porin (maltoporin) was cloned into phagemid pTZ18R in two restriction fragments, 0.6-kb Pst I/ Kpn I and 1.7-kb Sph I, of genomic DNA and their nucleotide sequences were determined. Open reading frames of 1329 and 1335 bp translated into sequences of 443 and 445 amino acids, with a 23 or 25 amino acid signal sequence and a 420 amino acid mature protein of molecular mass 46424 Da. Putative ribosome binding sites, AGGA and GGGAA, occurred 9 bp upstream of two possible ATG initiation codons. The A. salmonicida gene product showed a high degree of similarity with Escherichia coli LamB, and codon usage was very similar to that of another A. salmonicida outer membrane protein but markedly different from those of extracellular proteins.     

分子分型技术用于流脑疫情的同源性分析

目的 应用多位点序列分型（Multilocus sequence typing,MLST）技术和脉冲场凝胶电泳（pulsed-field gel electrophoresis,PFGE）技术对大连市2014年4月同一工地两起流脑疫情得到的脑膜炎奈瑟氏菌株进行分子分型图谱分析,了解各菌株之间的亲缘关系。方法 对病例的脑脊液标本进行脑膜炎奈瑟菌PCR分群,对另一病例和所有密切接触者分离菌株进行多位点序列分型（MLST）试验和脉冲场凝胶电泳（PFGE）鉴定实验。结果 疑似病例标本PCR结果为脑膜炎奈瑟氏菌A群阳性,另一病例和所有密切接触者分离到的菌株PFGE图谱基本相同,表明来自同一克隆系。多位点序列分析结果为ST7。结论 两起疫情分离到的菌株型别之间具有高度的同源性,该病原菌类型为ST7的A群脑膜炎奈瑟氏菌。     

Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

Molecular analysis of a cruciferin storage protein gene family of Brassica napus

We have isolated a five-member gene subfamily which encodes cruciferin, a legumin-like 12S storage protein of Brassica napus L., and have analyzed the structure and expression of the family members in developing embryos. Sequence analysis has shown that the coding regions of all five genes are highly similar, with the two most divergent members of the family retaining 89% sequence identity. The analysis of this cruciferin gene family's expression indicates that the developmental pattern of expression of each gene is similar, and the steady-state mRNA levels of each gene are approximately equivalent to each other at all developmental stages.     

苹果炭疽菌的分子鉴定与检测

测定苹果炭疽菌rDNA全序列,比对苹果炭疽菌和其它炭疽菌ITS序列以及构建系统关系树,发现苹果炭疽菌与胶孢炭疽菌的ITS序列相似性高达99．8％,并与胶孢炭疽菌聚在一起,可以明确苹果炭疽菌应属于胶孢炭疽菌。进一步的序列比对发现,苹果炭疽菌的18S rDNA3’端比其它胶孢炭疽菌多出一段379bp的序列,根据这一特有片段设计引物CgF1与通用引物ITS4配对,结果仅能从苹果炭疽菌中扩增出1232bp的特异性条带。用苹果炭疽菌接种离体苹果,以接种发病的病组织总DNA为模板,利用引物CgF1／ITS4进行PCR扩增,同样可以扩增出1232bp的特异性条带,而健康苹果组织DNA中未能扩增出任何条带,表明该方法可用于苹果炭疽菌的鉴定和快速检测。     

Molecular Comparison of Dengue Type 1 Mochizuki Strain Virus and Other Selected Viruses Concerning Nucleotide and Amino Acid Sequences of Genomic RNA: A Consideration of Viral Epidemiology and Variation

Dengue-1 (D1) Mochizuki strain was examined for its nucleotide and amino acid sequences of genomic RNA and the data obtained were compared with those of other selected virus strains reported previously. Genomic regions corresponding to C, preM and M proteins were the major subjects of study. Parts of E protein were additionally examined. Among the D1 viruses investigated, the Mochizuki virus which was isolated in 1943 in Japan was shown to be close to Philippine 836-1 strain isolated in 1984 and Nauru Island strain isolated in 1974 at the respective places, in contrast with Thai AHF 82-80 strain isolated in 1980 and Caribbean CV1636/77 strain isolated in 1977. At the same time, a difference was noted between the Mochizuki and Philippine/Nauru strains at the cleavage site of preM/M junction: Mochizuki possessed RRGKR/S sequence whereas the Philippine/Nauru had RRDKR/S. The glycosylation site in preM and hydrophobic regions at the carboxyl termini of M and E were well conserved. Significances of the data are discussed in connection with viral epidemiology and variation.     

核酸、氨基酸分类和蛋白质二级结构关系的分析与分子设计

核酸序列中包含一定的蛋白质结构信息。根据通常情况下遗传密码表中密码子中间位的碱基配对时产生的氢键数目,尝试将20种氨基酸划分为两类,并用自编的计算机软件对蛋白质二级结构数据库中两类氨基酸的类聚现象进行了统计分析。结果表明,使用这种方法对氨基酸进行划分后,氨基酸残基具有较大概率与划入同一类的氨基酸残基相邻出现,并且这种聚集体对二级结构具有一定的偏好性。最后按照该方法设计了一段氨基酸序列并给出了预测服务器预测得到的结构。     

核酸、氨基酸分类和蛋白质二级结构关系的分析与分子设计

核酸序列中包含一定的蛋白质结构信息。根据通常情况下遗传密码表中密码子中间位的碱基配对时产生的氢键数目,尝试将20种氨基酸划分为两类,并用自编的计算机软件对蛋白质二级结构数据库中两类氨基酸的类聚现象进行了统计分析。结果表明,使用这种方法对氨基酸进行划分后,氨基酸残基具有较大概率与划入同一类的氨基酸残基相邻出现,并且这种聚集体对二级结构具有一定的偏好性。最后按照该方法设计了一段氨基酸序列并给出了预测服务器预测得到的结构。     

199株猪链球菌临床分离株血清型、毒力基因及多位点序列分型分析

【背景】猪链球菌（Streptococcus suis,SS）血清型、基因型众多,毒力因子复杂。【目的】了解SS临床分离株血清型、毒力基因分布、分子分型特征及其之间的相关性。【方法】针对199株SS临床分离株,应用PCR技术进行血清分型和毒力基因检测,采用多位点序列分型方法（multilocus sequence typing,MLST）进行基因分型,并分析SS血清型、毒力基因型和序列型（sequence type,ST型）的流行特点及其关联性。【结果】199株SS临床分离株分属于16种血清型（1、2、3、4、6、7、8、9、10、12、15、16、21、24、29和30型）,主要以2、4、3型为主,分别占26.13%（52/199）、14.57%（29/199）和12.06%（24/199）,未定型（NT）菌株占21.61%（43/199）。共鉴定出72种ST型,其中ST1、ST94、ST117、ST7、ST28和ST87为主要ST型,分别占12.56%（25/199）、11.56%（23/199）、9.56%（19/199）、9.04%（18/199）、6.03%（12/199）和3.01%（6/199）,另有24种新发现的ST型（ST1224—ST1227,ST1229—ST1235,ST1241—ST1242,ST1300—ST1310）;分为12个克隆群（cloning complexes,CC）和32个单个ST型。199株SS分离株中毒力基因fbps的检出率最高,为96.98%（193/199）;共有19种毒力基因型,其中66株（33.17%）epf-/mrp-/sly-/gapdh+/fbps+/orf2+型SS为优势毒力基因型。【结论】近年来SS的优势血清型为2、4和3型;ST型具有明显的遗传异质性,种内分化程度较高且与ST型存在一定交叉性;毒力基因分布情况存在差异,毒力基因型呈现多样化。本研究对SS临床分离株的流行特征进行探究,为猪SS病诊断、治疗和制定防控措施提供科学依据。     

Congenital analbuminaemia: Molecular defects and biochemical and clinical aspects

Background

DNA and mRNA sequencing of the coding regions of the human albumin gene (ALB) and of its intron/exon junctions has revealed twenty-one different molecular defects causing congenital analbuminaemia (CAA).

Scope of review

To describe the mutations in molecular terms and to present the current knowledge about the most important biochemical and clinical effects of CAA.

Major conclusions

CAA is rare, but its frequency seems to be significantly higher in restricted and minimally admixed populations. The condition affects especially the lipid metabolism but apart from a possible increased risk for atherosclerotic complications, it is generally associated with mild clinical symptoms in adults. By contrast, several reports indicate that analbuminaemic individuals may be at risk during the perinatal and childhood periods, in which they seem to show increased morbidity and mortality. The twenty-one causative defects include seven nonsense mutations, seven changes affecting splicing, five frame-shift/deletions, one frame-shift/insertion and one mutation in the start codon. These results indicate that the trait is an allelic heterogeneous disorder caused by homozygous (nineteen cases) or compound heterozygous (single case) inheritance of defects. Most mutations are unique, but one, named Kayseri, is responsible for about half of the known cases.

General significance

Study of the defects in the ALB resulting in CAA allows the identification of “hot spot” regions and contributes to understanding the molecular mechanism underlying the trait. Such studies could also give molecular information about different aspects of ALB regulation and shed light on the regulatory mechanisms involved in the synthesis of the protein. This article is part of a Special Issue entitled Serum Albumin.     

Identification of regions in which positive selection may operate in S-RNase of Rosaceae: Implication for S-allele-specific recognition sites in S-RNase

A stylar S-RNase is associated with gametophytic self-incompatibility in the Rosaceae, Solanaceae, and Scrophulariaceae. This S-RNase is responsible for S-allele-specific recognition in the self-incompatible reaction, but how it functions in specific discrimination is not clear. Window analysis of the numbers of synonymous (d_S) and non-synonymous (d_N) substitutions in rosaceous S-RNases detected four regions with an excess of d_N over d_S in which positive selection may operate (PS regions). The topology of the secondary structure of the S-RNases predicted by the PHD method is very similar to that of fungal RNase Rh whose tertiary structure is known. When the sequences of S-RNases are aligned with the sequence of RNase Rh based on the predicted secondary structures, the four PS regions correspond to two surface sites on the tertiary structure of RNase Rh. These findings suggest that in S-RNases the PS regions also form two sites and are candidates for the recognition sites for S-allele-specific discrimination.     

Synthesis and biological properties of polysaccharide-peptide conjugates as potential antigens for a vaccine against meningococci of serogroups A and B

A new approach to the development of a vaccine against meningococci of serogroups A and B was proposed. It involves the synthesis of conjugates of high-molecular capsule polysaccharides of the serogroup A meningococcus (PsA) with earlier synthesized protective fragments of membrane proteins from serogroup B meningococci. The conjugates were synthesized using a method that consists of the generation of aldehyde groups by oxidizing free vicinal hydroxyl groups of PsA and subsequent reaction of these groups with amino groups of the peptide. The reaction proceeds with the intermediate formation of the Schiff base, which is reduced to the stable secondary amine. The main parameters of the reaction were optimized in the synthesis of a PsA conjugate with a model peptide and methods of their characterization were developed. The reproducibility and efficiency of the synthetic procedure were demonstrated by the example of synthesis of PsA conjugates with fragments of protein PorA from the outer membrane of the serogroup B meningococcus. It was shown that, when administered without adjuvant, a conjugate of PsA with a protective peptide, which represents an exposed conserved fragment 306–332 of protein PorA, stimulates the formation of antibodies to the peptide and polysaccharide moieties of the molecule and is also capable of decreasing the degree of bacteremia in animals infected with serogroup A and serogroup B meningococci. The approach can be applied to the development of a complex vaccine for serogroup A and serogroup B meningococci.     

Molecular cloning and nucleotide sequence of cDNA for sporamin,the major soluble protein of sweet potato tuberous roots

Summary Sporamin accounts for more than 80% of the total soluble proteins of tuberous roots of sweet potato, but very little, if any, in other tissues of the same plant. In vitro translation of RNA fractions from the tuberous roots in wheat germ extract and subsequent immunoprecipitation with the antibody to sporamin indicated that this protein is synthesized by membrane-bound polysomes as a precursor 4 000 daltons larger than the mature protein. A cDNA expression library was constructed from the total poly(A)⁺ RNA from the tuberous roots by a vector-primer method, and an essentially full-length cDNA clone for the sporamin mRNA was selected by direct immunological screening of the colonies. Northern blot analysis showed that sporamin mRNA is approximately 950 nucleotides in length and is specifically present in tuberous roots and very little, if any, in leaves, petioles and non-tuberous roots. Nucleotide sequence of the cDNA predicts a 37 amino acid extension in the precursor at the amino-terminus of the mature protein.     

Isolation and characterization of a tomato cDNA clone which codes for a salt-induced protein

The cDNA clone (pNP24) coding for a protein induced by exogenous NaCl has been isolated from a tomato root cDNA library with the use of an inosine containing synthetic oligomer. The authenticity of the clone has been established by comparing the sequence of the clone to the NH₂-terminal sequence of the protein which has been purified to homogeneity by HPLC. The nucleotide sequence of pNP24 reveals a 5 signal sequence, an open reading frame of 718 nucleotides, a 3 AT rich untranslated region containing a probable polyadenylation signal sequence, and a poly A stretch. The mature polypeptide sequence as deduced from the nucleotide sequence reveals a protein with a molecular weight of 24226. This protein has been named NP24. It is slightly basic and has an unusually high number of cysteines (15). Northern blot analyses reveal that the abundance of mRNA for NP24 is at least 100-fold greater in tomato suspension cells in log phase grown in medium with NaCl than in cells grown in the control medium. The mRNA for NP24 is below the level of detection in roots of young control tomato plants until several weeks after germination but it is induced earlier and to higher levels in roots stressed by 0.171 M NaCl. Thus salt stress accelerates the accumulation of message in tomato roots. A comparison of the steady state levels of mRNA for NP24 to the accumulation of NP24 by immuno analyses indicates that the accumulation of this protein is determined by its mRNA level. The protein is not secreted and is localized within the cytoplasm or the soluble fraction of the nucleus, vacuole, or microbodies. NP24 has a high degree of homology (58%) with thaumatin, a protein which has considerable value as an artificial sweetener.     

The cation-selective substate of the mitochondrial outer membrane pore: Single-channel conductance and influence on intermembrane and peripheral kinases

The polyanion-induced substate of the outer mitochondrial membrane was studiedin vivo andin vitro. Study of the substate in artificial bilayers showed that it is highly cation selective. The induction of the substate in intact mitochondria leads to a complete inhibition of the intermembrane kinases, such as creatine kinase and adenylate kinase, which were excluded from the external ATP pool. Peripheral kinases, such as hexokinase, were blocked when they utilized internal ATP. The results with intact mitochondria suggested the existence of two regions of the outer membrane containing channels of different states, which may be involved in the regulation of intermembrane and peripheral kinases.     

Hexokinase-binding properties of the mitochondrial VDAC protein: Inhibition by DCCD and location of putative DCCD-binding sites

The outer mitochondrial membrane receptor for hexokinase binding has been identified as the VDAC protein, also known as mitochondrial porin. The ability of the receptor to bind hexokinase is inhibited by pretreatment with dicyclohexylcarbodiimide (DCCD). At low concentrations, DCCD inhibits hexokinase binding by covalently labeling the VDAC protein, with no apparent effect on VDAC channel-forming activity. The stoichiometry of [¹⁴C]-DCCD labeling is consistent with one to two high-affinity DCCD-binding sites per VDAC monomer. A comparison between the sequence of yeast VDAC and a conserved sequence found at DCCD-binding sites of several membrane proteins showed two sites where the yeast VDAC amino acid sequence appears to be very similar to the conserved DCCD-binding sequence. Both of these sites are located near the C-terminal end of yeast VDAC (residues 257–265 and 275–283). These results are consistent with a model in which the C-terminal end of VDAC is involved in binding to the N-terminal end of hexokinase.