猕猴模型在HIV疫苗研究中的应用

对HIV疫苗的研究一直是国际上艾滋病方面研究的热点和难点。动物模型则为疫苗研究必不可缺少的重要工具,缺乏合适的动物模型很大程度上制约了AIDS疫苗的研究。目前在国际上SIV或SHIV感染的猕猴模型为最常用的AIDS研究模型,受猕猴背景及病毒特性等多种因素的影响,使得以上两种模型在HIV疫苗研究中仍存在一定的局限性。为了更好地发挥猕猴模型在HIV疫苗研究中的巨大潜力,开发理想的AIDS猕猴模型已成为目前HIV疫苗研究的首要任务。本文简要介绍了AIDS疫苗的研发策略、研发概况以及SIV/SHIV猕猴模型在HIV疫苗中的应用,并对其中存在的问题及其应用前景进行了探讨。     

Neurite Fasciculation Mediated by Complexes of Axonin-1 and Ng Cell Adhesion Molecule

Neural cell adhesion molecules composed of immunoglobulin and fibronectin type III-like domains have been implicated in cell adhesion, neurite outgrowth, and fasciculation. Axonin-1 and Ng cell adhesion molecule (NgCAM), two molecules with predominantly axonal expression exhibit homophilic interactions across the extracellular space (axonin- 1/axonin-1 and NgCAM/NgCAM) and a heterophilic interaction (axonin-1–NgCAM) that occurs exclusively in the plane of the same membrane (cis-interaction). Using domain deletion mutants we localized the NgCAM homophilic binding in the Ig domains 1-4 whereas heterophilic binding to axonin-1 was localized in the Ig domains 2-4 and the third FnIII domain. The NgCAM–NgCAM interaction could be established simultaneously with the axonin-1–NgCAM interaction. In contrast, the axonin-1–NgCAM interaction excluded axonin-1/axonin-1 binding. These results and the examination of the coclustering of axonin-1 and NgCAM at cell contacts, suggest that intercellular contact is mediated by a symmetric axonin-1₂/NgCAM₂ tetramer, in which homophilic NgCAM binding across the extracellular space occurs simultaneously with a cis-heterophilic interaction of axonin-1 and NgCAM. The enhanced neurite fasciculation after overexpression of NgCAM by adenoviral vectors indicates that NgCAM is the limiting component for the formation of the axonin-1₂/NgCAM₂ complexes and, thus, neurite fasciculation in DRG neurons.     

Protein contact prediction using patterns of correlation

We describe a new method for using neural networks to predict residue contact pairs in a protein. The main inputs to the neural network are a set of 25 measures of correlated mutation between all pairs of residues in two "windows" of size 5 centered on the residues of interest. While the individual pair-wise correlations are a relatively weak predictor of contact, by training the network on windows of correlation the accuracy of prediction is significantly improved. The neural network is trained on a set of 100 proteins and then tested on a disjoint set of 1033 proteins of known structure. An average predictive accuracy of 21.7% is obtained taking the best L/2 predictions for each protein, where L is the sequence length. Taking the best L/10 predictions gives an average accuracy of 30.7%. The predictor is also tested on a set of 59 proteins from the CASP5 experiment. The accuracy is found to be relatively consistent across different sequence lengths, but to vary widely according to the secondary structure. Predictive accuracy is also found to improve by using multiple sequence alignments containing many sequences to calculate the correlations.     

Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states

We have previously shown that the metabolism for most efficient cell growth can be realized by a combination of two types of elementary modes. One mode produces biomass while the second mode generates only energy. The identity of the four most efficient biomass and energy pathway pairs changes, depending on the degree of oxygen limitation. The identification of such pathway pairs for different growth conditions offers a pathway-based explanation of maintenance energy generation. For a given growth rate, experimental aerobic glucose consumption rates can be used to estimate the contribution of each pathway type to the overall metabolic flux pattern. All metabolic fluxes are then completely determined by the stoichiometries of involved pathways defining all nutrient consumption and metabolite secretion rates. We present here equations that permit computation of network fluxes on the basis of unique pathways for the case of optimal, glucose-limited Escherichia coli growth under varying levels of oxygen stress. Predicted glucose and oxygen uptake rates and some metabolite secretion rates are in remarkable agreement with experimental observations supporting the validity of the presented approach. The entire most efficient, steady-state, metabolic rate structure is explicitly defined by the developed equations without need for additional computer simulations. The approach should be generally useful for analyzing and interpreting genomic data by predicting concise, pathway-based metabolic rate structures.     

Enzymatic surface modification and functionalization of PET: A water contact angle,FTIR, and fluorescence spectroscopy study

The purpose of this study was to investigate the changes induced by a lypolytic enzyme on the surface properties of polyethylene terephthalate (PET). Changes in surface hydrophilicity were monitored by means of water contact angle (WCA) measurements. Fourier Transform Infrared spectroscopy (FTIR) in the Attenuated Total Reflectance mode (ATR) was used to investigate the structural and conformational changes of the ethylene glycol and benzene moieties of PET. Amorphous and crystalline PET membranes were used as substrate. The lipolytic enzyme displayed higher hydrolytic activity towards the amorphous PET substrate, as demonstrated by the decrease of the WCA values. Minor changes were observed on the crystalline PET membrane. The effect of enzyme adhesion was addressed by applying a protease after‐treatment which was able to remove the residual enzyme protein adhering to the surface of PET, as demonstrated by the behavior of WCA values. Significant spectral changes were observed by FTIR–ATR analysis in the spectral regions characteristic of the crystalline and amorphous PET domains. The intensity of the crystalline marker bands increased while that of the amorphous ones decreased. Accordingly, the crystallinity indexes calculated as band intensity ratios (1,341/1,410 cm^?1 and 1,120/1,100 cm^?1) increased. Finally, the free carboxyl groups formed at the surface of PET by enzyme hydrolysis were esterified with a fluorescent alkyl bromide, 2‐(bromomethyl)naphthalene (BrNP). WCA measurements confirmed that the reaction proceeded effectively. The fluorescence results indicate that the enzymatically treated PET films are more reactive towards BrNP. FTIR analysis showed that the surface of BrNP‐modified PET acquired a more crystalline character. Biotechnol. Bioeng. 2009;103: 845–856. © 2009 Wiley Periodicals, Inc.     

Contrasted patterns of mitochondrial and nuclear structure among nursery colonies of the bat Myotis myotis

Thirteen nursery colonies of Myotis myotis were sampled in central Europe to investigate the dispersal behaviour of this bat species. Mitochondrial DNA sequences of 260 bats reveal the occurrence of three evolutionary lineages that have probably originated in distinct glacial refugia and meet in a contact zone near the Alps. Moreover, the strong haplotypic segregation (Φ_ST=0.540) suggests that breeding females are philopatric. Contrastingly, the low population structure at 15 microsatellite loci (F_ST=0.022), suggests the homogenizing effect of nuclear gene flow. The different perspectives given by these two markers are consistent with strong male‐biased dispersal. As a result of female philopatry, the local haplotypic variability seems to be largely influenced by historical processes of colonization. Conversely, the homogeneity of nuclear variability within roosts that are located north of the Alps seems to mainly reflect contemporary gene flow. Finally, despite the fact that females are faithful to their natal colony, movements of both males and females occur outside the breeding period. Mitochondrial survey of individuals sampled exclusively in nurseries may thus poorly reflect the metapopulation dynamics of this species.     

A Preliminary Study of the Surface Properties of Earthworms and Their Relations to Non-Stain Behaviour

The surface properties of earthworms were studied using nitrogen adsorption/desorption isotherm and dynamic contact angle measurement with the aim to understand their non-stain behaviour. The results obtained by applying dynamic contact angle technique using water, glycerol, cooking oil and dimethylsilicone show that the surface properties of earthworms are a function of time. The critical surface energy, calculated using advancing angle, is as low as 11 × 10~(-3) J·m~(-2). However this hydrophobic behaviour at the initial contact moment changes progressively into hydrophilic as time goes by. This behaviour together with the creeping movement of corrugated surface is believed to be responsible for the non-stain behaviour of earthworms. The nitrogen adsorption isotherm of dried skin of earthworms at 77.3 K exhibits more or less Type V isotherm with surface area of 13 m~2·g~(-1) calculated using the α_s plot. The Type V isotherm is the indication of weak interaction between nitrogen and the worm surface.     

Pleistocene climatic cycling drives intra‐specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China

The repeated formation and loss of land‐bridges during the Pleistocene have had lasting impacts on population genetic structure. In the tropics, where island populations persisted through multiple glacial cycles, alternating periods of isolation and contact are expected to have driven population and taxonomic divergence. Here, we combine mitochondrial and nuclear sequence data with microsatellites to dissect the impact of Pleistocene climate change on intra‐specific diversification in the horseshoe bat Rhinolophus affinis. This taxon shows considerable morphological and acoustic variation: two parapatric subspecies (himalayanus and macrurus) occur on mainland China and a third (hainanus) on Hainan Island. Our phylogeographic reconstruction and coalescent analyses suggest the island subspecies formed from an ancestral population of himalayanus via two colonization events c. 800 000 years before present. R. a. hainanus then recolonized the mainland, forming macrurus and thus a secondary contact zone with himalayanus. Finally, macrurus recolonized Hainan following the LGM. We found that all three biological events corresponded to known periods of land‐bridge formation. Evidence of introgression was detected between macrurus and both its sister taxa, with geographical proximity rather than length of separation appearing to be the biggest determinant of subsequent genetic exchange. Our study highlights the important role of climate‐mediated sea level changes have had in shaping current processes and patterns of population structure and taxonomic diversification.     

Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants

Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants’ increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti‐aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains.