Sequence divergence and open regions of RNA secondary structures in the envelope regions of the 17 human immunodeficiency virus isolates.

Genetic variation during the course of infection of an individual is a remarkable feature of the acquired immune deficiency syndrome (AIDS) disease. This variation has been studied for the envelope protein encoding regions of seventeen different sequences from various isolates of human immunodeficiency virus (HIV) using multiple sequence comparison and calculation of variability. The open regions with little intramolecular base pairing in these envelope sequences are predicted by a recently developed statistical method. The minimum length L for a run of hypervariable sites, conserved sites, or open regions that gives significance at the 1% (or 0.1%) level is then determined by a scan statistical method. The results show that significant clusters of open regions predicted at the RNA levels correlate with significant clusters of hypervariable sites in the HIV envelope gene. Those significant genomic variations in HIVs seem to be manifested mainly in the extracellular portion of the envelope protein. Twelve potential antigenic determinants are predicted using an antigenic index method. Interestingly, the majority of the significant hypervariable regions in the exterior envelope protein (gp120) were predicted potential epitopes.     

The glycosylphosphatidyl inositol-anchored adhesion molecule F3/contactin is required for surface transport of paranodin/contactin-associated protein (caspr)

Paranodin/contactin-associated protein (caspr) is a transmembrane glycoprotein of the neurexin superfamily that is highly enriched in the paranodal regions of myelinated axons. We have investigated the role of its association with F3/contactin, a glycosylphosphatidyl inositol (GPI)-anchored neuronal adhesion molecule of the Ig superfamily. Paranodin was not expressed at the cell surface when transfected alone in CHO or neuroblastoma cells. Cotransfection with F3 resulted in plasma membrane delivery of paranodin, as analyzed by confocal microscopy and cell surface biotinylation. The region that mediates association with paranodin was mapped to the Ig domains of F3 by coimmunoprecipitation experiments. The association of paranodin with F3 allowed its recruitment to Triton X-100-insoluble microdomains. The GPI anchor of F3 was necessary, but not sufficient for surface expression of paranodin. F3-Ig, a form of F3 deleted of the fibronectin type III (FNIII) repeats, although GPI-linked and expressed at the cell surface, was not recovered in the microdomain fraction and was unable to promote cell surface targeting of paranodin. Thus, a cooperative effect between the GPI anchor, the FNIII repeats, and the Ig regions of F3 is required for recruitment of paranodin into lipid rafts and its sorting to the plasma membrane.     

The search for polyprenols in dendroflora of Vietnam

The occurrence of polyprenols in leaves of over 340 species of dendroflora in natural habitats in the regions of Hanoi and Hue in Vietnam was studied. Plant material was collected in the late autumn (October/November) during the end of a vegetation season. Leaves of about 200 plant species did not contain detectable amounts of polyprenols in contrast to few systematic families, e.g. Moraceae, Euphorbiaceae, where polyprenols were highly abundant and their pattern could be used as a chemotaxonomic criterion. Most often dominating polyprenols were prenol-11 and prenol-12. In several angiosperm species prenol-13 and detectable amounts of prenol-14 were also found. The incidence of prenol-13 and -14 was not restricted to a specific taxonomic group since species exhibiting domination of such longer chain polyprenols belonged to various systematic families. In some plants (e.g. Ceiba pentandra) alpha-cis polyprenols were accompanied by alpha-trans counterparts. This report describes several new plant species that may serve as natural sources of long chain polyprenols.     

In situ molecular level studies on membrane related peptides and proteins in real time using sum frequency generation vibrational spectroscopy

Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interactions between different peptides/proteins (melittin, G proteins, alamethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling.     

Proteomic analysis of the bacterial induction of resistance to atrazine in soybean leaves

Atrazine is a photosystem-II-inhibiting herbicide that interferes with photosynthetic electron transport, resulting in oxidative stress. Soybean (Glycine max (L.) Merrill) is an atrazine-sensitive crop, and its productivity is severely impacted by soils containing atrazine residues. Our previous study indicated that the bacteria Klebsiella pneumoniae strain SnebYK-induced resistance to atrazine in soybean, both before and after pasteurization. In order to study the molecular mechanisms of this induced resistance, proteins change in soybean leaves induced by SnebYK was investigated using two-dimensional gel electrophoresis. Differentially expressed proteins (relative to a non-induced control) were identified using MALDI-TOF MS. Differential expression patterns were detected in soybean leaves that had been induced by the bacterium. Analysis of relative expression levels indicated up-regulation of most of the mRNAs in these samples relative to the control. The corresponding proteins were observed to be involved primarily in physiological processes, including active oxygen removal, resistance signal transduction, and photosynthesis. This is the first study to conduct proteomic analysis of a soybean resistance response induced by bacteria. It is plausible that these differentially expressed proteins may interact to play a major role in defense and/or resistance responses.     

Biodegradation of DDT by stimulation of indigenous microbial populations in soil with cosubstrates

Stimulation of native microbial populations in soil by the addition of small amounts of secondary carbon sources (cosubstrates) and its effect on the degradation and theoretical mineralization of DDT [l,l,l-trichloro-2,2-bis(p-chlorophenyl)ethane] and its main metabolites, DDD and DDE, were evaluated. Microbial activity in soil polluted with DDT, DDE and DDD was increased by the presence of phenol, hexane and toluene as cosubstrates. The consumption of DDT was increased from 23 % in a control (without cosubstrate) to 67, 59 and 56 % in the presence of phenol, hexane and toluene, respectively. DDE was completely removed in all cases, and DDD removal was enhanced from 67 % in the control to ~86 % with all substrates tested, except for acetic acid and glucose substrates. In the latter cases, DDD removal was either inhibited or unchanged from the control. The optimal amount of added cosubstrate was observed to be between 0.64 and 2.6 mg C $ {\text{g}}^{ - 1}_{\text{dry soil}} $ . The CO₂ produced was higher than the theoretical amount for complete cosubstrate mineralization indicating possible mineralization of DDT and its metabolites. Bacterial communities were evaluated by denaturing gradient gel electrophoresis, which indicated that native soil and the untreated control presented a low bacterial diversity. The detected bacteria were related to soil microorganisms and microorganisms with known biodegradative potential. In the presence of toluene a bacterium related to Azoarcus, a genus that includes species capable of growing at the expense of aromatic compounds such as toluene and halobenzoates under denitrifying conditions, was detected.     

Apport de la TEMP/TDM pour la détection du ganglion sentinelle dans les cancers du col utérin et de l’endomètre

The sentinel lymph node procedure is still under evaluation for the management of cervical and endometrial carcinomas. The aim of our study was to determine the diagnostic accuracy of single-photon emission computed tomography/computed tomography (SPECT/CT) for preoperative sentinel lymph node mapping in uterine cancers. Sixty-eight patients with cervical (n = 42) or endometrial carcinoma (n = 26) underwent preoperative lymphoscintigraphy for sentinel node mapping. Sentinel node detection rate with conventional planar imaging was similar to that of SPECT/CT (87.1 versus 91.8 %) in the whole cohort. However, SPECT/CT detected a higher number of sentinel nodes in more than one third of patients, affected by either cervical or endometrial carcinoma. The rate of non or insufficiently contributive procedures (lack of uptake or unilateral uptake) in endometrial carcinomas was 47 % with conventional planar imaging, and 30 % with SPECT/CT. Sensitivity of both procedures for the detection of metastatic nodes was 81.8 %, compared to 100 % for the intraoperative combined detection (gamma probe sonde and blue dye). The impact of SPECT/CT for the sentinel lymph node detection in cervical and endometrial carcinomas needs further evaluation. Nevertheless, SPECT/CT may provide additional information when conventional planar imaging detects only unilateral uptake, may improve identification of atypical localizations, and facilitate surgical approach.     

Techniques de recherche des polymorphismes génétiques

Sequencing the human genome has allowed the discovery of millions of DNA sequence variants. Sequence variations in human DNA are mainly present asSingle Nucleotide Polymorphisms (SNPs); this common form of variation is found about once every 1,000 bases in the human genome and 1.8 million SNPs have now been identified and located. The accessibility of databases of SNPs opens the possibility of studying the influence of these polymorphisms on disease risks as well as on drug responses. Numerous approaches have been set up for the identification of SNPs. In this review we describe the main techniques used for the identification of these polymorphisms. They rely on two major consequences of sequence variations: the apparition or the disappearance of restriction enzyme sites or the alteration of DNA strand hybridization due to the presence of a mismatch. Southern blotting and restriction endonucleases have allowed the development of the technique ofrestriction fragment length polymorphisms (RFLPs), now performed on PCR products. Several other approaches such as denaturing high-performance liquid chromatography or real-time PCR can detect allele differences upon re-hybridization and heteroduplex formation. However, DNA sequencing remains the obligate step for the positive identification of known or unknown SNPs. At last, the development of high-throughput methods allows a large increase in the rate of discovery of SNPs likely.     

Heterogeneity,Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission

The Ross-Macdonald model has dominated theory for mosquito-borne pathogen transmission dynamics and control for over a century. The model, like many other basic population models, makes the mathematically convenient assumption that populations are well mixed; i.e., that each mosquito is equally likely to bite any vertebrate host. This assumption raises questions about the validity and utility of current theory because it is in conflict with preponderant empirical evidence that transmission is heterogeneous. Here, we propose a new dynamic framework that is realistic enough to describe biological causes of heterogeneous transmission of mosquito-borne pathogens of humans, yet tractable enough to provide a basis for developing and improving general theory. The framework is based on the ecological context of mosquito blood meals and the fine-scale movements of individual mosquitoes and human hosts that give rise to heterogeneous transmission. Using this framework, we describe pathogen dispersion in terms of individual-level analogues of two classical quantities: vectorial capacity and the basic reproductive number, . Importantly, this framework explicitly accounts for three key components of overall heterogeneity in transmission: heterogeneous exposure, poor mixing, and finite host numbers. Using these tools, we propose two ways of characterizing the spatial scales of transmission—pathogen dispersion kernels and the evenness of mixing across scales of aggregation—and demonstrate the consequences of a model''s choice of spatial scale for epidemic dynamics and for estimation of , both by a priori model formulas and by inference of the force of infection from time-series data.