The role of a single N-linked glycosylation site for a functional epitope of herpes simplex virus type 1 envelope glycoprotein gC

A monoclonal antibody, B1C1, binding to an epitope of antigenic site II of the herpes simplex virus type 1 (HSV-1) glycoprotein gC-1, is a potent inhibitor of two important biological functions of gC-1: its binding to cell surface heparan sulfate and its binding to the receptor for complement factor C3b. Here, we have analyzed a B1C1-resistant HSV- 1 variant (HSV-12762/B1C1B4.2), obtained after passage of wild type HSV- 1 (HSV-12762) in the presence of high concentrations of B1C1. The transport of newly synthesized mutant gC-1 to the cell surface was comparable to that of wild type glycoprotein, but no binding of surface- associated mutant gC-1 to B1C1 was detected. However, mutant and wild type gC-1 bound equally well to other site II Mabs. Attachment of wild type but not mutant virus was inhibited by B1C1. Sequencing of the mutant gC-1 gene revealed only one nucleotide change, resulting in replacement of Thr150 by an Ile, in turn destroying an N-glycosylation site at Asn148. Loss of one complex type N-linked glycan was confirmed by endoglycosidase digestion and subsequent SDS-polyacrylamide gel electrophoresis. Circular dichroism analysis of purified gC-1 from cells infected with mutant or wild type virus did not reveal any difference in secondary structure between mutant and wild type gC-1. It was not possible to obtain a B1C1-resistant phenotype by nucleotide- directed mutagenesis of gC-1 where Asn148 was changed to a glutamine. These data demonstrated that the threonine of the glycosylation site and not the N-linked glycan in itself was essential for B1C1 binding      

Mathematical model for the homeostasis of alpha-macroglobulins in the rat

Alpha-macroglobulins (AM) are proteins that inactivate proteinases. Sodium monofluorophosphate (MFP) binds to AM and transiently changes AM plasma levels. As a consequence MFP is useful to modify AM homeostasis. A mathematical model to study the homeostasis of AM is proposed in this paper. The model describes changes in plasma concentration of AM, MFP concentration in the gastrointestinal tract, MFP plasma concentration, plasma concentration of AMMFP and includes rate constants of the processes involved in AM homeostasis. Estimation of the rate constants values was achieved using experimental and mathematical resources. The homeostasis of AM after an oral dose of 80 μmol of MFP was analyzed with a simulation tool. Experimental conditions that modify the homeostasis of AM had been simulated and validated using specific drugs that change some parameter of the system.The mathematical model describes accurately the behavior of the biological model. The results allow concluding that the simplifications made did not underestimate the main processes involved in the homeostasis and, also that the assumptions made were correct.     

白色生物技术在可持续大规模化学生产中的应用

目前几乎所有有机化学品和塑料是从原油和天然气中生产的, 而生物技术的应用使得利用可再生资源进行大规模化工生产成为可能。以下主要综述了白色生物技术, 即利用细菌、酵母或酶将可发酵糖转化为特定的化学产品的技术。白色生物技术极大节省了不可再生能源的消耗, 减少了温室气体的排放。在有利条件下, 如果化工生产中相关技术有了发展并且可以成功以木质纤维素为原料, 那么到2050年不可再生能源的消耗将减少将近2/3 (67%)。欧洲（EU-25）地区的分析表明, 白色生物技术相关的用地在未来几年的欧洲不会受到制约, 尤其是有大量闲置资源的东欧。另外, 虽然原则上可以在白色生物技术中使用自然的细菌和酶, 但是很多专家认为, 利用经遗传改造生物体(GMO)可以达到高产量、高浓度、高效率, 这对实现经济活力是必要的。值得注意的是, 目前并不是所有的重组基因和其他物种间的相互作用所带来的后果都可预见, 因此化工生产释放的GMOs的安全失活和处理非常重要, 但是如果采取足够的预防措施, 在白色生物技术中应用GMOs的风险是可以控制的。我们认为, 生物生产过程的技术突破、下游生产过程的控制、化石燃料的高价格、可发酵糖的低价获得是生物质化学产业发展中的关键因素, 这4个因素及其他伴随策略是发展整体白色生物技术的要求。     

Directed evolution of cellobiose utilization in Escherichia coli K12

The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and salicin. Such Bgl+ mutants do not use cellobiose, which is the most common beta-glucoside in nature. We have isolated a Cel+ (cellobiose-utilizing) mutant from a Bgl+ mutant of E. coli K12. The Cel+ mutant grows well on cellobiose, arbutin, and salicin. Genes for utilization of these beta-glucosides are located at 37.8 min on the E. coli map. The genes of the bgl operon are not involved in cellobiose utilization. Introduction of a deletion covering bgl does not affect the ability to utilize cellobiose, arbutin, or salicin, indicating that the new Cel+ genes provide all three functions. Spontaneous cellobiose negative mutants also become arbutin and salicin negative. Analysis of beta-glucoside positive revertants of these mutants indicates that there are separate loci for utilization of each of the beta-glucoside sugars. The genes are closely linked and may be activated from a single locus. A fourth gene at an unknown location increases the growth rate on cellobiose. The cel genes constitute a second cryptic system for beta-glucoside utilization in E. coli K12.      

Authors index

An analysis was made of specific richness (S), specific diversity (H), equitability (J), frequency (F), dominance (Dm) and density (D) of the macroinvertebrates associated with the invasive species Limnoperna fortunei (Dunker, 1857), was made. Limnoperna fortunei caused an increase in the specimen number on the rocky environment studied. The species richness and abundance of different taxa of macroinvertebrates, except mollusks was positively related to the presence and density of L.fortunei. Autochthonous gastropod species conversely, tended to be displaced. This revised version was published online in July 2006 with corrections to the Cover Date.     

Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium

Tumor progression alters the composition and physical properties of the extracellular matrix. Particularly, increased matrix stiffness has profound effects on tumor growth and metastasis. While endothelial cells are key players in cancer progression, the influence of tumor stiffness on the endothelium and the impact on metastasis is unknown. Through quantitative mass spectrometry, we find that the matricellular protein CCN1/CYR61 is highly regulated by stiffness in endothelial cells. We show that stiffness‐induced CCN1 activates β‐catenin nuclear translocation and signaling and that this contributes to upregulate N‐cadherin levels on the surface of the endothelium, in vitro. This facilitates N‐cadherin‐dependent cancer cell–endothelium interaction. Using intravital imaging, we show that knockout of Ccn1 in endothelial cells inhibits melanoma cancer cell binding to the blood vessels, a critical step in cancer cell transit through the vasculature to metastasize. Targeting stiffness‐induced changes in the vasculature, such as CCN1, is therefore a potential yet unappreciated mechanism to impair metastasis.     

Eicosapentaenoic and docosahexaenoic acids production by and okara-utilizing potential of thraustochytrids

Nine thraustochytrid strains isolated from subtropical mangroves were screened for their eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) production potential in a glucose yeast extract medium. Their ability to utilize okara (soymilk residue) for growth and EPA and DHA production was also evaluated. EPA yield was low in most strains, while DHA level was high on glucose yeast extract medium, producing 28.1–41.1% of total fatty acids, for all strains, with the exception of Ulkenia sp. KF13. The DHA yield of Schizochytrium mangrovei strains ranged from 747.7 to 2778.9 mg/l after 52 h of fermentation at 25°C. All strains utilized okara as a substrate for growth, but DHA yield was lower when compared with fermentation in a glucose yeast extract medium. Journal of Industrial Microbiology & Biotechnology (2001) 27, 199–202. Received 11 December 2000/ Accepted in revised form 29 June 2001     

HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling

MOTIVATION: The search for genetic variants that are linked to complex diseases such as cancer, Parkinson's;, or Alzheimer's; disease, may lead to better treatments. Since haplotypes can serve as proxies for hidden variants, one method of finding the linked variants is to look for case-control associations between the haplotypes and disease. Finding these associations requires a high-quality estimation of the haplotype frequencies in the population. To this end, we present, HaploPool, a method of estimating haplotype frequencies from blocks of consecutive SNPs. RESULTS: HaploPool leverages the efficiency of DNA pools and estimates the population haplotype frequencies from pools of disjoint sets, each containing two or three unrelated individuals. We study the trade-off between pooling efficiency and accuracy of haplotype frequency estimates. For a fixed genotyping budget, HaploPool performs favorably on pools of two individuals as compared with a state-of-the-art non-pooled phasing method, PHASE. Of independent interest, HaploPool can be used to phase non-pooled genotype data with an accuracy approaching that of PHASE. We compared our algorithm to three programs that estimate haplotype frequencies from pooled data. HaploPool is an order of magnitude more efficient (at least six times faster), and considerably more accurate than previous methods. In contrast to previous methods, HaploPool performs well with missing data, genotyping errors and long haplotype blocks (of between 5 and 25 SNPs).     

A phylogenetic survey of myotubularin genes of eukaryotes: distribution,protein structure,evolution, and gene expression

Background  

Phosphorylated phosphatidylinositol (PtdIns) lipids, produced and modified by PtdIns kinases and phosphatases, are critical to the regulation of diverse cellular functions. The myotubularin PtdIns-phosphate phosphatases have been well characterized in yeast and especially animals, where multiple isoforms, both catalytically active and inactive, occur. Myotubularin mutations bring about disruption of cellular membrane trafficking, and in humans, disease. Previous studies have suggested that myotubularins are widely distributed amongst eukaryotes, but key evolutionary questions concerning the origin of different myotubularin isoforms remain unanswered, and little is known about the function of these proteins in most organisms.     

The origin of behavioral bursts in decision-making circuitry

From ants to humans, the timing of many animal behaviors comes in bursts of activity separated by long periods of inactivity. Recently, mathematical modeling has shown that simple algorithms of priority-driven behavioral choice can result in bursty behavior. To experimentally test this link between decision-making circuitry and bursty dynamics, we have turned to Drosophila melanogaster. We have found that the statistics of intervals between activity periods in endogenous activity-rest switches of wild-type Drosophila are very well described by the Weibull distribution, a common distribution of bursty dynamics in complex systems. The bursty dynamics of wild-type Drosophila walking activity are shown to be determined by this inter-event distribution alone and not by memory effects, thus resembling human dynamics. Further, using mutant flies that disrupt dopaminergic signaling or the mushroom body, circuitry implicated in decision-making, we show that the degree of behavioral burstiness can be modified. These results are thus consistent with the proposed link between decision-making circuitry and bursty dynamics, and highlight the importance of using simple experimental systems to test general theoretical models of behavior. The findings further suggest that analysis of bursts could prove useful for the study and evaluation of decision-making circuitry.