Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine. Horton and Gibson contributed equally to this work.     

A ferrocene-perfluoroarene molecular complex

Perfluorophenanthrene and decamethylferrocene cocrystallize as a molecular adduct in monoclinic space group P2₁/c with a = 8.842(2), b = 11.262(1), c = 30.695(8) Å, β = 95.89(2)°, V = 3040.3(8) ų, Z = 4. The structure was refined to R = 0.0537 for 1567 observed reflections. The perfluoroarene is twisted and chiral; the crystal is a racemate, however.     

Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium.

In Salmonella typhimurium, the genetic loci and biochemical reactions necessary for the conversion of aminoimidazole ribotide (AIR) to the 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) moiety of thiamine remain unknown. Preliminary genetic analysis indicates that there may be more than one pathway responsible for the synthesis of HMP from AIR and that the function of these pathways depends on the availability of AIR, synthesized by the purine pathway or by the purF-independent alternative pyrimidine biosynthetic (APB) pathway (L. Petersen and D. Downs, J. Bacteriol. 178:5676-5682, 1996). An insertion in rseB, the third gene in the rpoE rseABC gene cluster at 57 min, prevented HMP synthesis in a purF mutant. Complementation analysis demonstrated that the HMP requirement of the purF rseB strain was due to polarity of the insertion in rseB on the downstream rseC gene. The role of RseC in thiamine synthesis was independent of rpoE.     

Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea

ABSTRACT: BACKGROUND: Monitoring drug resistance in Mycobacterium tuberculosis is essential to curb the spread of tuberculosis (TB). Unfortunately, drug susceptibility testing is currently not available in Papua New Guinea (PNG) and that impairs TB control in this country. We report for the first time M. tuberculosis mutations associated with resistance to first and second-line anti-TB drugs in Madang, PNG. A molecular cluster analysis was performed to identify M. tuberculosis transmission in that region. RESULTS: Phenotypic drug susceptibility tests showed 15.7% resistance to at least one drug and 5.2% multidrug resistant (MDR) TB. Rifampicin resistant strains had the rpoB mutations D516F, D516Y or S531L; isoniazid resistant strains had the mutations katG S315T or inhA promoter C15T; streptomycin resistant strains had the mutations rpsL K43R, K88Q, K88R), rrs A514C or gidB V77G. The molecular cluster analysis indicated evidence for transmission of resistant strain. CONCLUSIONS: We observed a substantial rate of MDR-TB in the Madang area of PNG associated with mutations in specific genes. A close monitoring of drug resistance is therefore urgently required, particularly in the presence of drug-resistant M. tuberculosis transmission. In the absence of phenotypic drug susceptibility testing in PNG, molecular assays for drug resistance monitoring would be of advantage.     

Turnover of O-Glucosides of Dihydrozeatin and Dihydrozeatin-9-riboside During the Cell Growth Cycle of Photoautotrophic Cell Suspension Cultures of Chenopodium rubrum

The cellular levels of O-glucosides of ³H-(diH)Z and ³H-(diH)[9R]Z, the major short-term metabolites of ³H-(diH)Z having been exogenously supplied to photoautotrophically growing suspension cell cultures of Chenopodium rubrum, decreased significantly during further culture, irrespective of whether the cells were maintained in the stationary phase or were transferred to conditions restoring cell divison. Metabolism of both compounds was more pronounced during the active growth phase than during the stationary phase. The O-glucosides were converted preferentially to polar compounds of as yet unknown nature, which were partly excreted into the medium. The cellular pools of both glycosides remained compartmented within the vacuole. In contrast to the O-glycosides, the small cellular pools of the aglycones ³H-(diH)Z and ³H-(diH)[9R]Z maintained their level during the experimental period of 30 days. Small amounts of the glucosides, as well as of the aglycones, were recovered from the medium and could have resulted from the lysis of a few cells. The results demonstrate, for the first time, that O-glucosides of cytokinins are not irreversibly deposited within the vacuole of plant cells but may serve to maintain a small, but more or less constant pool of extra-vacuolar, presumably cytosolic, aglycones. (DiH)Z and its derivatives could be demonstrated to be endogenous cytokinins of Chenopodium rubrum suspension cultured cells occurring along with those of the isopentenyladenine and zeatin types.     

H2O2 destruction by ascorbate-dependent systems from chloroplasts.

Washed lamellae from isolated spinach chloroplasts exhibited peroxidative activity with 3,3'-diaminobenzidine or ascorbate as electron donors. By heat treatment or by incubation of the chloroplasts with pronase a heat-labile enzymic activity (system A) and a heat-stable non-enzymic peroxidative activity (system B) could be differentiated. System A is membrane-bound, reacts with 3,3'-diaminobenzidine and with ascorbate as electron donors, shows a sharp pH optimum between 7.5 and 8.0 with both substrates and is inhibited competitively by cyanide. The heat-stable factor can be extracted from the chloroplast lamellae by heat treatment, reacts only with ascorbate as electron donor, shows increasing activity with higher pH values but no optimum and is not inhibited by cyanide. Both peroxidative systems in connection with a relatively high concentration of ascorbate in chloroplasts should represent an important tool for the detoxification of H2O2 which is produced in these organelles by photosynthetic O2 reduction.