The core element of the EcoRII methylase as defined by protease digestion and deletion analysis.

Binding of the EcoRII DNA methyltransferase to azacytosine-containing DNA protects the enzyme from digestion by proteases. The limit digest yields a product having a Mr on SDS-PAGE 20% less than the intact protein. The N terminus of the tryptic digestion product was sequenced and found to be missing the N terminal 82 amino acids. Under the conditions used unbound enzyme was digested to small peptides. Protection of the enzyme from protease digestion implies that the enzyme undergoes major conformational changes when bound to DNA. The trypsin sensitive region of the EcoRII methyltransferase occurs prior to the first constant region shared with other procaryotic DNA(cytosine-5)methyltransferases. To determine if this region played a role in substrate binding or specificity, N-terminal deletion mutants were studied. Deletion of 97 amino acids resulted in a decrease of enzyme activity. Further deletions caused a complete loss of activity. Enzyme deleted through amino acid 85 was purified and found to have the same specificity as wild type however there was an increase in Km for both S-adenosylmethionine (AdoMet) and DNA of 27 and 18 fold respectively. The N-terminus of the EcoRII methylase, although a variable region present in many procaryotic DNA(cytosine-5)methylases, plays no role in determining enzyme specificity, although it does contribute to the interaction with both AdoMet and DNA.     

Effect of gluco-monosaccharides and different conditions on digestion of hyaluronan by testicular hyaluronidase

The changes of molecular size of hyaluronan during enzymatic reaction of bovine testicular hyaluronidase at different conditions are monitored by size exclusion high performance liquid chromatography. The effect of glucuronate, galacturonate, glucosamines and pyridoxin as potential inhibitors of hydrolysis is evaluated. The most effective of all tested inhibitors was the presence of glucuronate which not only inhibited the hydrolysis, but also initiated enzymatic reconstruction by transglycosylation reaction at pH 7.0 and absence of any buffer or salt. That effect was not found in the presence of a salt or with any other of the compounds tested.     

Effects of cultural conditions on protease production by Aeromonas hydrophila

Production of extracellular proteolytic activity by Aeromonas hydrophila was influenced by temperature, pH, and aeration. Conditions which produced maximal growth also resulted in maximal protease production. Enzyme production appeared to be modulated by an inducer catabolite repression system whereby NH4+ and glucose repressed enzyme production and complex nitrogen and nonglucose, carbon energy sources promoted it. Under nutritional stress, protease production was high, despite poor growth.     

Effects of nuclease and protease digestion on the ultrastructure of Paramecium basal bodies

The action of deoxyribonuclease, ribonuclease, perchloric acid, and pronase on the fine structure of basal bodies of sectioned Paramecium was observed as part of a more extensive autoradiographic electron microscope analysis directed toward the problem of basal body DNA. DNase was found to have no detectable effect on basal body fine structure. Pronase first solubilized the linkers and C tubules of the triplets, then attacked the protein portion of the axosome, a localized portion of the ciliary axoneme adjacent to the distal end of the basal body, the rim fiber, and newly described lumen spiral complex. Prolonged pronase treatment disrupted the remaining microtubular elements, basal body plates, and cartwheel. RNase removed material from the axosome and the lumen complex, a conspicuous structure occupying the central portion of the basal body and consisting of a twisted or looped 90-A diam fiber or, more probably, pair of fibers, in association with large, dense granules. The apparent removal of both RNA and protein from this basal body structure by either of the two corresponding enzymes suggests an unusual organization of the two components. Observations from this and other laboratories suggest that the basal body RNA is single stranded. Its function is unknown but alternatives are discussed.     

Beyond strain typing and molecular epidemiology: integrated genetic epidemiology of infectious diseases

In the past 20 years, genetic and molecular methods for characterizing pathogen strains have taken a major place in modern approaches to epidemiology of parasitic and other infectious diseases. Here, Michel Tibayrenc explains the main concepts used in this field of research, with special emphasis on the approaches developed in his team, and suggests future avenues to explore.     

Effects of cultural conditions on protease production by Aeromonas hydrophila.

Production of extracellular proteolytic activity by Aeromonas hydrophila was influenced by temperature, pH, and aeration. Conditions which produced maximal growth also resulted in maximal protease production. Enzyme production appeared to be modulated by an inducer catabolite repression system whereby NH4+ and glucose repressed enzyme production and complex nitrogen and nonglucose, carbon energy sources promoted it. Under nutritional stress, protease production was high, despite poor growth.     

Conformational strain in the hydrophobic core and its implications for protein folding and design

We have designed de novo 13 divergent spectrin SH3 core sequences to determine their folding properties. Kinetic analysis of the variants with stability similar to that of the wild type protein shows accelerated unfolding and refolding rates compatible with a preferential stabilization of the transition state. This is most likely caused by conformational strain in the native state, as deletion of a methyl group (Ile-->Val) leads to deceleration in unfolding and increased stability (up to 2 kcal x mol(-1)). Several of these Ile-->Val mutants have negative phi(-U) values, indicating that some noncanonical phi(-U) values might result from conformational strain. Thus, producing a stable protein does not necessarily mean that the design process has been entirely successful. Strained interactions could have been introduced, and a reduction in the buried volume could result in a large increase in stability and a reduction in unfolding rates.     

Review. The origin of the prion agent of kuru: molecular and biological strain typing

Kuru is an acquired human prion disease that primarily affected the Fore linguistic group of the Eastern Highlands of Papua New Guinea. The central clinical feature of kuru is progressive cerebellar ataxia and, in sharp contrast to most cases of sporadic Creutzfeldt-Jakob disease (CJD), dementia is a less prominent and usually late clinical feature. In this regard, kuru is more similar to variant CJD, which also has similar prodromal symptoms of sensory disturbance and joint pains in the legs and psychiatric and behavioural changes. Since a significant part of the clinicopathological diversity seen in human prion disease is likely to relate to the propagation of distinct human prion strains, we have compared the transmission properties of kuru prions with those isolated from patients with sporadic, iatrogenic and variant CJD in both transgenic and wild-type mice. These data have established that kuru prions have prion strain properties equivalent to those of classical (sporadic and iatrogenic) CJD prions but distinct from variant CJD prions. Here, we review these findings and discuss how peripheral routes of infection and other factors may be critical modifiers of the kuru phenotype.     

Effects of oxygenation conditions on the respiratory activity generated by medullo-spinal preparations of rats

On isolated medullo-spinal preparations (IMSP) of newborn rats that generate rhythmic respiratory activity, we observed specific features of the reactions to a decrease in the O₂ tension in the superfusing medium (saturation with an isocapnic anoxic gas mixture) manifested in a standard configuration of the preparation, after separation of the rostral part of the medulla and after pH modifications. Using microelectrode amperometric measurements of pO₂ above the ventral medullary surface and of pO₂ profiles into the medullary tissues, we demonstrated the dependence of oxygen supply of IMSP on the rate of superfusion and the existence of hypoxic and anoxic zones in its tissues. The mechanisms of sensitivity of the IMSP-generated respiratory rhythm to hypoxia are discussed.     

地衣芽孢杆菌碱性蛋白酶的研究 Ⅰ.碱性蛋白酶高产菌的筛选及产酶条件初探

从成都佳丰食品厂等处采集的样品中平板分离初筛到124株碱性蛋白酶产生菌,进一步复筛出一株高产,且稳定的碱性蛋白酶产生菌株B．L．JF-ld,初步鉴定为地衣穿孢杆菌（Bacilluslicheniformis）。该菌的最适产酶条件为：培养基（％）为麦芽糖7．5,酵母膏3,NaCl0．5,K2HPO4·3H2O0．53,NaHPO4·2H2O0．03,Na2CO30．056,MnSO4l×10－4mol／L,pH8．7,通气量为（1：0．5）～（1：1）（v／v）,37℃发酵40h,酶活力单位高达7180U／ml。     

Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks

We developed a computational method to predict the retention times of peptides in HPLC using artificial neural networks (ANN). We performed stepwise multiple linear regressions and selected for ANN input amino acids that significantly affected the LC retention time. Unlike conventional linear models, the trained ANN accurately predicted the retention time of peptides containing up to 50 amino acid residues. In 834 peptides, there was a strong correlation (R2 = 0.928) between measured and predicted retention times. We demonstrated the utility of our method by the prediction of the retention time of 121,273 peptides resulting from LysC-digestion of the Escherichia coli proteome. Our approach is useful for the proteome-wide characterization of peptides and the identification of unknown peptide peaks obtained in proteome analysis.     

HLA-DQA1 and HLA-DQB1 in Celiac disease predisposition: practical implications of the HLA molecular typing

Celiac disease (CD) is a multifactorial disorder with an estimated prevalence in Europe and USA of 1:100 and a female:male ratio of approximately 2:1. The disorder has a multifactorial etiology in which the triggering environmental factor, the gluten, and the main genetic factors, Human Leukocyte Antigen (HLA)-DQA1 and HLA-DQB1 loci, are well known. About 90-95% of CD patients carry DQ2.5 heterodimers, encoded by DQA1*05 and DQB1*02 alleles both in cis or in trans configuration, and DQ8 molecules, encoded by DQB1*03:02 generally in combination with DQA1*03 variant. Less frequently, CD occurs in individuals positive for the DQ2.x heterodimers (DQA1≠*05 and DQB1*02) and very rarely in patients negative for these DQ predisposing markers. HLA molecular typing for Celiac disease is, therefore, a genetic test with a negative predictive value. Nevertheless, it is an important tool able to discriminate individuals genetically susceptible to CD, especially in at-risk groups such as first-degree relatives (parents, siblings and offspring) of patients and in presence of autoimmune conditions (type 1 diabetes, thyroiditis, multiple sclerosis) or specific genetic disorders (Down, Turner or Williams syndromes).     

Extracellular protease activity of different Pseudomonas strains: dependence of proteolytic activity on culture conditions

AIMS: This study investigated the effect of growth conditions on proteolytic activity of a Pseudomonas strain, named Pseudomonas sp. LBSA1, isolated from bulk raw milk. It was compared with three Pseudomonas chlororaphis and one Pseudomonas fluorescens strain from culture collections. METHODS AND RESULTS: Bacteriae were grown in a minimal salt medium. For all the strains, addition of 1% (v/v) skim milk to the growth medium was sufficient to induce protease production in 48-h culture. Addition of 1 mmol l(-1) calcium chloride permitted the detection of proteolytic activity of four strains in 48-h cultures but not for Pseudomonas sp. LBSA1. The five strains presented two patterns of proteolytic activity when grown in the minimal salt medium supplemented with 2% (v/v) skim milk at various temperatures for 48 h. Two electrophoretic protease patterns were also obtained from the zymogram of extracellular medium for the five strains. CONCLUSIONS: The growth conditions permitting protease production are variable and do not depend on the genus of the producing strain. SIGNIFICANCE AND IMPACT OF THE STUDY: For the first time a study on proteolytic activity of P. chlororaphis strains is reported. Among the tested criteria, zymograms of extracellular medium were the only ones that permitted distinguishing the P. chlororaphis strains from the P. fluorescens strain.     

Development of a molecular method for the typing of Brettanomyces bruxellensis (Dekkera bruxellensis) at the strain level

AIMS: In recent years, Brettanomyces/Dekkera bruxellensis has caused increasingly severe quality problems in the wine industry. A typing method at the strain level is needed for a better knowledge of the dispersion and the dynamics of these yeasts from grape to wine. METHODS AND RESULTS: Three molecular tools, namely random-amplified polymorphic DNA, PCR fingerprinting with microsatellite oligonucleotide primers and SAU-PCR, were explored for their relevance to typing strains of Brettanomyces bruxellensis. The results indicated that discrimination of each individual strain was not possible with a single PCR typing technique. We described a typing method for B. bruxellensis based on restriction enzyme analysis and pulse field gel electrophoresis (REA-PFGE). Results showed that electrophoretic profiles were reproducible and specific for each strain under study. CONCLUSIONS: Consequently, REA-PFGE should be considered for the discrimination of B. bruxellensis strains. This technique allowed a fine discrimination of B. bruxellensis, as strains were identified by a particular profile. SIGNIFICANCE AND IMPACT OF THE STUDY: This study constitutes a prerequisite for accurate and appropriate investigations on the diversity of strains throughout the winemaking and ageing process. Such studies will probably give clearer and more up-to-date information on the origin of the presence of Brettanomyces in wine after vinification when they are latent spoilage agents.     

A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution

Background

Tortricidae, one of the largest families of microlepidopterans, comprise about 10,000 described species worldwide, including important pests, biological control agents and experimental models. Understanding of tortricid phylogeny, the basis for a predictive classification, is currently provisional. We present the first detailed molecular estimate of relationships across the tribes and subfamilies of Tortricidae, assess its concordance with previous morphological evidence, and re-examine postulated evolutionary trends in host plant use and biogeography.

Methodology/Principal Findings

We sequenced up to five nuclear genes (6,633 bp) in each of 52 tortricids spanning all three subfamilies and 19 of the 22 tribes, plus up to 14 additional genes, for a total of 14,826 bp, in 29 of those taxa plus all 14 outgroup taxa. Maximum likelihood analyses yield trees that, within Tortricidae, differ little among data sets and character treatments and are nearly always strongly supported at all levels of divergence. Support for several nodes was greatly increased by the additional 14 genes sequenced in just 29 of 52 tortricids, with no evidence of phylogenetic artifacts from deliberately incomplete gene sampling. There is strong support for the monophyly of Tortricinae and of Olethreutinae, and for grouping of these to the exclusion of Chlidanotinae. Relationships among tribes are robustly resolved in Tortricinae and mostly so in Olethreutinae. Feeding habit (internal versus external) is strongly conserved on the phylogeny. Within Tortricinae, a clade characterized by eggs being deposited in large clusters, in contrast to singly or in small batches, has markedly elevated incidence of polyphagous species. The five earliest-branching tortricid lineages are all species-poor tribes with mainly southern/tropical distributions, consistent with a hypothesized Gondwanan origin for the family.

Conclusions/Significance

We present the first robustly supported phylogeny for Tortricidae, and a revised classification in which all of the sampled tribes are now monophyletic.     

产脂肪酶菌株C7828-5的筛选、鉴定以及产酶条件的优化

以花生油为唯一碳源,从海口市各地被油脂污染土样中分离筛选出1株中温碱性脂肪酶菌株C7828-5。形态学、生理生化特征和分子生物学鉴定结果表明,该菌株为铜绿假单胞菌(Pseudomonas aeruginosa)。该菌所产脂肪酶的最适温度为37℃,最适pH为8.0。优化了菌株的产酶条件,最适产酶培养基(g/L)为:蔗糖5、牛肉膏20、(NH_4)_2SO_41、MgSO_4·7H_2O 0.5、CaCl_20.5,聚乙烯醇花生油乳化液120 mL,发酵72 h,获得高达8.08 U/mL的脂肪酶表达量。