In vivo evolution of human immunodeficiency virus type 1 toward increased pathogenicity through CXCR4-mediated killing of uninfected CD4 T cells

The destruction of the immune system by progressive loss of CD4 T cells is the hallmark of AIDS. CCR5-dependent (R5) human immunodeficiency virus type 1 (HIV-1) isolates predominate in the early, asymptomatic stages of HIV-1 infection, while CXCR4-dependent (X4) isolates typically emerge at later stages, frequently coinciding with a rapid decline in CD4 T cells. Lymphocyte killing in vivo primarily occurs through apoptosis, but the importance of apoptosis of HIV-1-infected cells relative to apoptosis of uninfected bystander cells is controversial. Here we show that in human lymphoid tissues ex vivo, apoptosis of uninfected bystander CD4 T cells is a major mechanism of lymphocyte depletion caused by X4 HIV-1 strains but is only a minor mechanism of depletion by R5 strains. Further, X4 HIV-1-induced bystander apoptosis requires the interaction of the viral envelope glycoprotein gp120 with the CXCR4 coreceptor on CD4 T cells. These results emphasize the contribution of bystander apoptosis to HIV-1 cytotoxicity and suggest that in association with a coreceptor switch in HIV disease, T-cell killing evolves from an infection-restricted stage to generalized toxicity that involves a high degree of bystander apoptosis.     

Metabolic Engineering of Ammonium Assimilation in Xylose-Fermenting Saccharomyces cerevisiae Improves Ethanol Production

Cofactor imbalance impedes xylose assimilation in Saccharomyces cerevisiae that has been metabolically engineered for xylose utilization. To improve cofactor use, we modified ammonia assimilation in recombinant S. cerevisiae by deleting GDH1, which encodes an NADPH-dependent glutamate dehydrogenase, and by overexpressing either GDH2, which encodes an NADH-dependent glutamate dehydrogenase, or GLT1 and GLN1, which encode the GS-GOGAT complex. Overexpression of GDH2 increased ethanol yield from 0.43 to 0.51 mol of carbon (Cmol) Cmol⁻¹, mainly by reducing xylitol excretion by 44%. Overexpression of the GS-GOGAT complex did not improve conversion of xylose to ethanol during batch cultivation, but it increased ethanol yield by 16% in carbon-limited continuous cultivation at a low dilution rate.     

Bi- and tricyclic nucleoside derivatives restricted in S-type conformations and obtained by RCM-reactions

Ring-closing metathesis (RCM) is applied as a new and powerful technology in the construction of nucleoside analogues that are conformationally restricted in S-type conformations due to additional 3',4'- and/or 3',5'-linkages.     

Fragile site long arm chromosome 16

Summary A fragile site at the long arms (q21) of chromosome 16 was found in two persons, each of whom became the parent of a child with a de novo structural chromosome abnormality—a balanced autosomal translocation and an autosomal deletion. The question of an increased risk of structural chromosome abnormalities in the offspring of persons with fragile site long arm 16 is discussed.     

Patterns of niche conservatism among non-native birds in Europe are dependent on introduction history and selection of variables

Recently, the study of niche dynamics using spatial environmental data and species occurrences has become an active field of research. Several studies report niche shifts between native and invasive populations, but it is debated whether these shifts are biologically meaningful or result from methodological artefacts. Using data on the occurrence of non-native birds in Europe, we assess the prevalence of niche shifts along a selected number of climatic variables and find that although niche differences are frequent, biological explanations are often not necessary. Niche shifts occurred more frequently along variables that were of little ecological importance in the non-native range, and about 75 % of the shifts detected do not result from range expansion into different environments but only reflect climatic conditions at introduction locations. Excluding variables exhibiting a niche shift increases the accuracy of predictions of invasion risk generated by native-range based distribution models, evidencing that selection of variables is a crucial step when studying niche changes during biological invasions.     

Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus

Nitrogen-fixing root nodules develop on legumes as a result of an interaction between host plants and soil bacteria collectively referred to as rhizobia. The organogenic process resulting in nodule development is triggered by the bacterial microsymbiont, but genetically controlled by the host plant genome. Using T-DNA insertion as a tool to identify novel plant genes that regulate nodule ontogeny, we have identified two putatively tagged symbiotic loci, Ljsym8 and Ljsym13, in the diploid legume Lotus japonicus. The sym8 mutants are arrested during infection by the bacteria early in the developmental process. The sym13 mutants are arrested in the final stages of infection, and ineffective nodules are formed. These two plant mutant lines were identified in progeny from 1112 primary transformants obtained after Agrobacterium tumefaciens T-DNA-mediated transformation of L. japonicus and subsequent screening for defects in the symbiosis with Mesorhizobium loti. Additional nontagged mutants arrested at different developmental stages were also identified and genetic complementation tests assigned all the mutations to 16 monogenic symbiotic loci segregating recessive mutant alleles. In the screen reported here independent symbiotic loci thus appeared with a frequency of ～1.5%, suggesting that a relatively large set of genes is required for the symbiotic interaction.     

A comparison of calibration methods for stereo fluoroscopic imaging systems

Stereo (biplane) fluoroscopic imaging systems are considered the most accurate and precise systems to study joint kinematics in vivo. Calibration of a biplane fluoroscopy system consists of three steps: (1) correction for spatial image distortion; (2) calculation of the focus position; and (3) calculation of the relative position and orientation of the two fluoroscopy systems with respect to each other. In this study we compared 6 methods for calibrating a biplane fluoroscopy system including a new method using a novel nested-optimization technique. To quantify bias and precision, an electronic digital caliper instrumented with two tantalum markers on radiolucent posts was imaged in three configurations, and for each configuration placed in ten static poses distributed throughout the viewing volume. Bias and precision were calculated as the mean and standard deviation of the displacement of the markers measured between the three caliper configurations. The data demonstrated that it is essential to correct for image distortion when sub-millimeter accuracy is required. We recommend calibrating a stereo fluoroscopic imaging system using an accurately machined plate and a calibration cube, which improved accuracy 2-3 times compared to the other calibration methods. Once image distortion is properly corrected, the focus position should be determined using the Direct Linear Transformation (DLT) method for its increased speed and equivalent accuracy compared to the novel nested-optimization method. The DLT method also automatically provides the 3D fluoroscopy configuration. Using the recommended calibration methodology, bias and precision of 0.09 and 0.05 mm or better can be expected for measuring inter-marker distances.