CD1 antigen presentation by human dendritic cells as a target for herpes simplex virus immune evasion

In contrast to MHC molecules, which present peptides, the CD1 molecules have been discovered to present lipid Ags to T cells. CD1-restricted T lymphocytes have been recently associated with resistance to virus infection. The mechanisms underlying activation of CD1-restricted T cells in the course of virus infection are not defined. In this study, we wanted to investigate the interaction of HSV with the antiviral CD1 Ag presentation system in human dendritic cells (DC). In response to low titers of HSV, the surface expression of CD1b and CD1d on human DC was up-regulated. These phenotypic changes enhanced the capacity of infected DC to stimulate proliferation of CD1-restricted T lymphocytes. High titers of HSV, however, lead to strong down-regulation of all surface CD1 molecules. This modulation of surface expression was associated with intracellular accumulation, colocalization with viral proteins, and disruption of the CD1 recycling machinery. Finally, even at low titers HSV interfered with the capacity of infected DC to stimulate the release of important cytokines by CD1d-restricted NKT cells. Thus, we demonstrate both the existence of a CD1 pathway allowing human DC to react to viral infection, as well as its blockage by a human herpesvirus.     

Similarities of ordered gene lists

MOTIVATION: Many applications of microarray technology in clinical cancer studies aim at detecting molecular features for refined diagnosis. In this paper, we follow an opposite rationale: we try to identify common molecular features shared by phenotypically distinct types of cancer using a meta-analysis of several microarray studies. We present a novel algorithm to uncover that two lists of differentially expressed genes are similar, even if these similarities are not apparent to the eye. The method is based on the ordering in the lists. RESULTS: In a meta-analysis of five clinical microarray studies we were able to detect significant similarities in five of the ten possible comparisons of ordered gene lists. We included studies, where not a single gene can be significantly associated to outcome. The detection of significant similarities of gene lists from different microarray studies is a novel and promising approach. It has the potential to improve upon specialized cancer studies by exploring the power of several studies in one single analysis. Our method is complementary to previous methods in that it does not rely on strong effects of differential gene expression in a single study but on consistent ones across multiple studies.     

Identification of cardiac malformations in mice lacking <Emphasis Type="Italic">Ptdsr</Emphasis>using a novel high-throughput magnetic resonance imaging technique

Background  

Congenital heart defects are the leading non-infectious cause of death in children. Genetic studies in the mouse have been crucial to uncover new genes and signaling pathways associated with heart development and congenital heart disease. The identification of murine models of congenital cardiac malformations in high-throughput mutagenesis screens and in gene-targeted models is hindered by the opacity of the mouse embryo.     

Maternal-fetal transplacental leakage of mitochondrial DNA in bovine nuclear transfer pregnancies: potential implications for offspring and recipients

The synepitheliochorial placenta of ruminants is constructed of multiple tissue layers that separate maternal and fetal blood. In nuclear transfer cloned ruminants, however, placental anomalies such as abnormal vascular development and hemorrhagic cotyledons have been reported. We have investigated the possible exchange of genetic material between somatic cell nuclear transfer cloned (SCNT) bovine fetuses and recipients at day 80 of gestation using mitochondrial DNA (mtDNA) as a marker. Twenty-three recovered SCNT-fetuses and their recipients were screened for divergent and thus informative mtDNA combinations. Twenty-one fetuses generated by in vitro fertilization (IVF) or multiple ovulation embryo transfer (MOET) and the corresponding recipients served as controls. A search for recipient mtDNA haplotype in DNA extracts from fetal blood by PCR-RFLP analysis revealed three cases of chimerism (two SCNT, one IVF) among a total of 19 informative fetus-recipient pairs (eight SCNT, seven IVF, four MOET). Placental anomalies have also been observed in some IVF fetuses and the present data therefore suggests transplacental leakage of cell components or cells from the recipient into some fetuses generated by in vitro techniques. Further studies are necessary to determine (i) the nature of leaked material, (ii) whether there is bi-directional leakage, and (iii) whether leaked material is present in recipients and calves after parturition, i.e. whether leakage takes place in vivo. If recipients were chimeric for DNA or cells derived from genetically modified SCNT (or IVF) embryos, their subsequent utilization might be affected.     

Chlorophyll breakdown in tobacco: on the structure of two nonfluorescent chlorophyll catabolites

In extracts of senescent leaves of the tobacco plant Nicotiana rustica, two colorless compounds with UV/VIS characteristics of nonfluorescent chlorophyll catabolites (NCCs) were detected and tentatively identified as Nr-NCCs. These two polar NCCs were found in similar amounts in the fresh extracts, and their constitutions could be determined by spectroscopic analysis. The data showed both of the two Nr-NCCs to have the same tetrapyrrolic core structure, as reported previously for all other NCCs from senescent higher plants. In the less polar catabolite, named Nr-NCC-2, this core structure was conjugated with a glucopyranose unit, as similarly discovered earlier in Bn-NCC-2, an NCC from oilseed rape (Brassica napus). The more polar NCC from tobacco leaves, Nr-NCC-1, carried an additional malonyl substituent at the 6'-OH group of the glucopyranosyl moiety. Partial (enzyme-catalyzed) hydrolysis of Nr-NCC-1 gave Nr-NCC-2, while enzyme-catalyzed malonylation of Nr-NCC-2 gave Nr-NCC-1, establishing the identity of their basic tetrapyrrole structure. In earlier work (on the polar NCCs from oilseed rape), only separate glucopyranosyl and malonyl functionalities were detected. Nr-NCC-1, thus, represents a further variant of the structures of NCCs from senescent higher plants and exhibits an unprecedented peripheral refunctionalization in chlorophyll catabolites.     

Dendritic cell immunization route determines CD8+ T cell trafficking to inflamed skin: role for tissue microenvironment and dendritic cells in establishment of T cell-homing subsets

The effector/memory T cell pool branches in homing subsets selectively trafficking to organs such as gut or skin. Little is known about the critical factors in the generation of skin-homing CD8+ T cells, although they are crucial effectors in skin-restricted immune responses such as contact hypersensitivity and melanoma defense. In this study, we show that intracutaneous, but not i.v. injection of bone marrow-derived dendritic cells induced skin-homing CD8+ T cells with up-regulated E-selectin ligand expression and effector function in contact hypersensitivity. The skin-homing potential and E-selectin ligand expression remained stable in memory phase without further Ag contact. In contrast, i.p. injection induced T cells expressing the gut-homing integrin alpha(4)beta(7). Although differential expression of these adhesion molecules was strictly associated with the immunization route, the postulated skin-homing marker CCR4 was transiently up-regulated in all conditions. Interestingly, dendritic cells from different tissues effectively induced the corresponding homing markers on T cells in vitro. Our results suggest a crucial role for the tissue microenvironment and dendritic cells in the instruction of T cells for tissue-selective homing and demonstrate that Langerhans cells are specialized to target T cells to inflamed skin.     

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.     

Similarity of binding sites of human matrix metalloproteinases

Tissue components hydrolyzing matrix metalloproteinases (MMPs) exhibit a high sequence similarity (56-64% in catalytic domains) and yet a significant degree of functional specificity. The hexapeptide-binding sites of 24 known human MMPs were compared in terms of their force field interaction energies with five probes that are most frequently encountered in substrates and inhibitors. The probes moved along a grid enclosing partially flexible binding sites in rigid catalytic domains that were represented by published experimental structures and comparative models and new comparative models for nine most recently characterized MMPs. For individual MMPs, representative interaction energies were obtained as averages for all suitable experimental structures. Correlations of the representative energies for all MMP pairs were succinctly catalogued for individual probes, subsites, and correlation levels. Among the probes (neutral sp(3) carbon and sp(3) oxygen, positive sp(3) nitrogen and hydrogen, and negative carbonyl oxygen), the last probe is least distinctive. Similarities of subsites are decreasing as S1 ' > S2 > S3 ' > S1 approximately S3 > S2 '. Most interesting, occupancies of subsites in published structures of MMP-inhibitor complexes follow an almost parallel trend, alluding to overall low selectivity of known MMP inhibitors. Flexible subsite S1 ' that appears as the specificity pocket in rigid x-ray structures is actually very similar among individual MMPs. Several correlations indicated that MMPs 3, 8, and 12 have similar binding sites. Modeling results are corroborated with published experimental data on MMP inhibition and substrate specificities. The results provide numerous clues for development of specific inhibitors and substrates, as well as for selection of MMPs for testing that provides maximum information without redundant experiments.