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1.
J Gastrointest Surg ; 19(1): 56-64; discussion 64, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25183407

ABSTRACT

PURPOSE: The enteric microbiome is known to play a major role in healthy gut homeostasis and several disease states. It may also contribute to both the intestinal recovery and complications that occur in patients with short bowel syndrome. The extent and nature of alterations to the gut microbiota following intestinal resection, however, are not well studied in a controlled setting. The purpose of this investigation is to characterize the effects of massive small bowel resection on the murine enteric microflora. METHODS: Wild-type C57BL6 mice, following a week of acclamation to a liquid rodent diet, underwent either 50% proximal small bowel resection (SBR) or a sham operation. Mice were sacrificed, and enteric contents from the small bowel, cecum, and stool were harvested at 7 and 90 days post-operatively. DNA was isolated, and the V3-V5 regions of the 16s rRNA gene amplified and pyrosequenced on a Roche 454 platform. Sequences were clustered into operation taxonomic units and classified. Communities were then analyzed for diversity and phylogenic composition. RESULTS: In the long-term group, the microbes inhabiting the ileum of mice undergoing SBR and sham operation differed significantly at the genus level (p < 0.001). Small bowel contents collected before and after SBR also differed significantly (p = 0.006). This was driven by an increase in Lactobacillus and decrease in Enterobacteriaceae species in mice undergoing SBR. No difference was seen in the long-term stool or in stool, cecal, or ileal contents in the short-term. No difference in microbial community diversity was found in any group. CONCLUSION: Bowel resection induces long-term changes in the microbial community of the murine ileum, but not at more distal sites of the gastrointestinal tract. The increase in Lactobacillus encountered small bowel of resected mice correlates with limited previous studies. These changes may reflect an adaptive response of the microbiota to maximize energy extraction, but further studies are needed to establish the role played by this altered community.


Subject(s)
Bacteria/isolation & purification , Intestinal Mucosa/microbiology , Intestine, Small/surgery , Microbiota/physiology , Short Bowel Syndrome/microbiology , Animals , Disease Models, Animal , Follow-Up Studies , Intestinal Mucosa/surgery , Intestine, Small/microbiology , Mice , Mice, Inbred C57BL
2.
Anim Genet ; 37(2): 121-9, 2006 Apr.
Article in English | MEDLINE | ID: mdl-16573526

ABSTRACT

The bovine major histocompatibility complex (MHC) or BoLA is organized differently from typical mammalian MHCs in that a large portion of the class II region, called class IIb, has been transposed to a position near the centromere on bovine chromosome 23. Gene mapping indicated that the rearrangement resulted from a single inversion, but the boundaries and gene content of the inverted segment have not been fully determined. Here, we report the genomic sequence of BoLA IIb. Comparative sequence analysis with the human MHC revealed that the proximal inversion breakpoint occurred approximately 2.5 kb from the 3' end of the glutamate-cysteine ligase, catalytic subunit (GCLC) locus and that the distal breakpoint occurred about 2 kb from the 5' end from a divergent class IIDRbeta-like sequence designated DSB. Gene content, order and orientation of BoLA IIb are consistent with the single inversion hypothesis when compared with the corresponding region of the human class II MHC (HLA class II). Differences with HLA include the presence of a single histone H2B gene located between the proteasome subunit, beta type, 9 (PSMB9) and DMB loci and a duplicated TAP2 with a variant splice site. BoLA IIb spans approximately 450 kb DNA, with 20 apparently intact genes and no obvious pseudogenes. The region contains 227 simple sequence repeats (SSRs) and approximately 167 kb of retroviral-related repetitive DNA. Nineteen of the 20 genes identified in silico are supported by bovine EST data indicating that the functional gene content of BoLA IIb has not been diminished because it has been transposed from the remainder of BoLA genes.


Subject(s)
Cattle/genetics , Chromosome Inversion , Genes, MHC Class II , Animals , Chromosomes, Mammalian , Contig Mapping , Evolution, Molecular , Histones/genetics , Humans , Molecular Sequence Data , Sequence Analysis, DNA
3.
Nature ; 435(7038): 43-57, 2005 May 05.
Article in English | MEDLINE | ID: mdl-15875012

ABSTRACT

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.


Subject(s)
Dictyostelium/genetics , Genome , Genomics , Social Behavior , ATP-Binding Cassette Transporters/genetics , Animals , Base Composition , Cell Adhesion/genetics , Cell Movement/genetics , Centromere/genetics , Conserved Sequence/genetics , DNA Transposable Elements/genetics , DNA, Ribosomal/genetics , Dictyostelium/cytology , Dictyostelium/enzymology , Dictyostelium/metabolism , Eukaryotic Cells/metabolism , Gene Duplication , Gene Transfer, Horizontal/genetics , Humans , Molecular Sequence Data , Phylogeny , Proteome , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , RNA, Transfer/genetics , Repetitive Sequences, Nucleic Acid/genetics , Sequence Analysis, DNA , Signal Transduction/genetics , Telomere/genetics
4.
Eur J Clin Nutr ; 55(11): 922-31, 2001 Nov.
Article in English | MEDLINE | ID: mdl-11641740

ABSTRACT

OBJECTIVE: To compare the effects of a rapeseed oil-based diet containing an increased proportion of easily oxidised polyunsaturated fatty acids such as alpha-linolenic acid with a diet rich in saturated fatty acids on the degree of lipid peroxidation in the human body. DESIGN: A randomised cross-over study. SUBJECTS AND INTERVENTIONS: Nineteen healthy moderately hyperlipidemic subjects (six women and 13 men, age 50+/-8 y and body mass index (BMI) 24.5+/-2.6 kg/m(2)) were given a rapeseed oil-based diet (RO) and a control diet (SAT) rich in saturated fatty acids during two consecutive 4 week periods separated by a 4 week wash-out period. Biomarkers of lipid peroxidation and antioxidants were analysed in plasma and urine. RESULTS: No significant differences in plasma or urinary levels of free 8-iso-prostaglandin F(2alpha), plasma total 8-iso-prostaglandin F(2alpha) plasma hydroperoxides or plasma malondialdehyde were observed between the RO and SAT diets (P=0.14-0.95). A higher concentration of serum gamma-tocopherol was detected after the RO diet compared to the SAT diet (P<0.001), whereas the serum alpha-tocopherol concentration and plasma antioxidative capacity did not differ between the two test diets. The total cholesterol, LDL cholesterol and LDL/HDL ratio were lower after the RO diet compared to the SAT diet (P<0.001), while HDL cholesterol and total triglyceride levels were similar after the two diets. CONCLUSION: These results suggest that a rapeseed oil-based diet rich in alpha-linolenic acid does not seem to increase the degree of lipid peroxidation in plasma and urine compared to a diet rich in saturated fats. This is possibly due to a sufficient content of antioxidants in the rapeseed oil diet to increase circulating concentrations of antioxidants that may protect unsaturated fatty acids from oxidation. SPONSORSHIP: Swedish Council for Forestry and Agricultural Research and Foundation for Geriatric Research.


Subject(s)
Dietary Fats/administration & dosage , Fatty Acids, Unsaturated/administration & dosage , Lipid Peroxidation/drug effects , Plant Oils/administration & dosage , Antioxidants/analysis , Biomarkers/blood , Biomarkers/urine , Cross-Over Studies , Diet , Fatty Acids/administration & dosage , Fatty Acids/blood , Fatty Acids, Monounsaturated , Female , Humans , Lipid Peroxidation/physiology , Lipid Peroxides/blood , Lipoproteins/blood , Male , Middle Aged , Oxidation-Reduction , Plant Oils/pharmacology , Rapeseed Oil
5.
Eur J Nutr ; 40(1): 10-6, 2001 Feb.
Article in English | MEDLINE | ID: mdl-11315500

ABSTRACT

BACKGROUND AND AIMS: Lipid peroxidation is believed to be involved in the pathophysiology of a number of diseases and in the process of aging. This study investigates the effects of dietary supplementation with vitamin E (20 g/kg diet of all-rac-alpha-tocopheryl succinate for 3 weeks) on both non-enzymatic and enzymatic lipid peroxidation in experimental rats with carbon tetrachloride (CCl4)-induced hepatotoxicity (2.5 mL/kg body). METHODS: Plasma, urine and liver samples from control rats (n = 6), CCl4-treated rats (n = 6), and rats supplemented with vitamin E prior to CCl4 treatment (n = 8) were collected. Non-enzymatic lipid peroxidation induced by free radicals was investigated by measurement of a major F2-iso-prostane, 8-iso-prostaglandin F2 alpha (8-iso-PGF2 alpha). Cyclooxygenase-catalyzed enzymatic lipid peroxidation was measured with a major PGF2 alpha metabolite, 15-keto-13,14-dihydro-prostaglandin F2 alpha (15-K-DH-PGF2 alpha). Malondialdehyde and antioxidants in plasma were also quantified. RESULTS: CCl4 treatment alone resulted in significantly higher levels of plasma, urinary and liver 8-iso-PGF2 alpha, and of plasma and urinary 15-K-DH-PGF2 alpha compared to controls. Rats supplemented with vitamin E prior to CCl4 treatment had significantly lower levels of urinary and liver 8-iso-PGF2 alpha, urinary 15-K-DH-PGF2 alpha, and plasma malondialdehyde than rats treated with CCl4 alone. However, plasma 8-iso-PGF2 alpha and plasma 15-K-DH-PGF2 alpha were not affected by vitamin E supplementation. CONCLUSION: Thus, both non-enzymatic and enzymatic lipid peroxidation during experimental hepatic oxidative injury were suppressed by dietary vitamin E supplementation in rats.


Subject(s)
Dinoprost/analogs & derivatives , Lipid Peroxidation/drug effects , Liver/drug effects , Vitamin E/pharmacology , Animals , Antioxidants/analysis , Carbon Tetrachloride/toxicity , Dietary Supplements , Dinoprost/analysis , Dinoprost/blood , Dinoprost/metabolism , F2-Isoprostanes , Liver/metabolism , Male , Malondialdehyde/blood , Radioimmunoassay , Rats , Rats, Sprague-Dawley , Vitamin E/administration & dosage
6.
Nature ; 409(6822): 934-41, 2001 Feb 15.
Article in English | MEDLINE | ID: mdl-11237014

ABSTRACT

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.


Subject(s)
Contig Mapping , Genome, Human , Chromosomes, Artificial, Bacterial , Cloning, Molecular , DNA Fingerprinting , Gene Duplication , Humans , In Situ Hybridization, Fluorescence , Repetitive Sequences, Nucleic Acid
7.
Article in English | MEDLINE | ID: mdl-10991772

ABSTRACT

8-Iso-prostaglandin F(2 alpha)(8-iso-PGF(2 alpha)) is a major isoprostane formed in vivo mainly by non-enzymatic peroxidation of arachidonic acid and a potential biomarker of oxidative injury. We have recently reported development of a specific radioimmunoassay for the measurement of free 8-iso-PGF(2 alpha)in plasma and urine. The aim of this study was to employ this radioimmunoassay to analyze the total amount of 8-iso-PGF(2 alpha)(sum of free and esterified) in liver tissues by using alkaline hydrolysis, and to apply it in an experimental model of carbon tetrachloride-induced lipid peroxidation in rats. Basal levels of total 8-iso-PGF(2 alpha)in hydrolyzed liver tissues of control rats were 6.5 times higher than the levels of free 8-iso-PGF(2 alpha). At maximum formation of total 8-iso-PGF(2 alpha)in the livers of carbon tetrachloride-treated rats, total levels of 8-iso-PGF(2 alpha)were almost 13 times higher than the levels of free 8-iso-PGF(2 alpha). In conclusion, high levels of 8-iso-PGF(2 alpha)in tissues can be quantified after hydrolysis both at basal conditions and in a model of increased lipid peroxidation. The methodology for measurement of total levels of 8-iso-PGF(2 alpha)in tissues may be suitable for future investigations of the location of oxidative injury in the body.


Subject(s)
Arachidonic Acid/metabolism , Dinoprost/analogs & derivatives , Dinoprost/metabolism , Lipid Metabolism , Liver/metabolism , Radioimmunoassay/methods , Animals , Biomarkers , Dinoprost/biosynthesis , F2-Isoprostanes , Hydrolysis , Male , Oxidative Stress , Rats , Rats, Sprague-Dawley , Time Factors
8.
Int J Obes Relat Metab Disord ; 24(5): 652-7, 2000 May.
Article in English | MEDLINE | ID: mdl-10849590

ABSTRACT

OBJECTIVE: To estimate the reliability of anthropometric measurements in overweight and lean subjects, and to examine the influence of this reliability on correlations to other variables, since low reliability leads to underestimation of correlations. DESIGN: Replicate measurements by two observers in 26 overweight and 25 lean subjects measured at two occasions. MEASUREMENTS: Sagittal abdominal diameter (SAD), waist circumference (waist), waist-to-hip ratio (W/H) and skinfold measurements. RESULTS: Intra-class correlation coefficients (ICCs) for SAD and waist were higher than for W/H (0.98 vs. 0.90, P<0.001, and 0.97 vs. 0.90, P = 0.001, respectively). For waist, the ICC was lower for overweight than for lean subjects (0.85 vs 0.95, P=0.030), but the ICC values were comparable for SAD and W/H (0.92 vs. 0.95 and 0.78 vs. 0.83, respectively). Intra-observer variations (IOV) for SAD and waist were lower than for W/H (coefficients of variation; 1.6%, 1.4% and 2.3%, respectively), as were intra-subject variations (ISV) (2.7%, 3.0% and 3.4%, respectively). ICC values ranged from 0.84 to 0.93 and were lower for overweight than for lean subjects for biceps, subscapular and umbilical skinfolds (P=0.031, P<0.001 and P=0.048, respectively). Coefficients of variations for skinfold measurements ranged between 7.3% and 16.0% for IOV and between 14.9% and 20.8% for ISV. CONCLUSIONS: The low ICC values imply that correlations can be underestimated in overweight groups. We propose that, because of their higher reliability, SAD and waist have a higher predictive capacity for cardiovascular risk than W/H. SAD is the only measurement with high reliability in both weight groups and its use is recommended.


Subject(s)
Anthropometry , Body Weight , Abdomen , Adult , Body Constitution , Body Mass Index , Female , Humans , Male , Middle Aged , Sensitivity and Specificity , Skinfold Thickness
9.
J Nutr ; 130(1): 10-4, 2000 Jan.
Article in English | MEDLINE | ID: mdl-10613758

ABSTRACT

Lipid peroxidation is thought to be an important factor in the pathophysiology of a number of diseases and in the process of aging. We investigated the effects of supplementation with vitamin E on lipid peroxidation in rats. Both free radical-induced nonenzymatic- and cyclooxygenase-catalyzed enzymatic lipid peroxidation were investigated by measuring the levels of F(2)-isoprostanes (8-iso-PGF(2alpha)) and PGF(2alpha)-metabolite (15-K-DH-PGF(2alpha)), respectively, in blood, urine and liver. Samples were collected from control rats (n = 6) and from rats supplemented with vitamin E in the diet for 3 wk (n = 8, 20 g/kg diet of DL-alpha-tocopherol hydrogen succinate). Plasma alpha-tocopherol concentration and antioxidative capacity were greater in the vitamin E-supplemented rats than in the control rats (17.9 +/- 1.7 vs. 50.4 +/- 10.4 micromol/L, P < 0.001 and 181 +/- 6 vs. 275 +/- 27 micromol/L trolox equivalents, P < 0.001). Urine 8-iso-PGF(2alpha) tended to be lower in the vitamin E-supplemented rats (0.72 +/- 0.40 vs. 0.34 +/- 0.19 nmol/mmol creatinine, P = 0.056). Urine 15-K-DH-PGF(2alpha) was lower due to vitamin E supplementation (0.97 +/- 0.38 vs. 0.56 +/- 0. 21 nmol/mmol creatinine, P < 0.05), as was liver-free 8-iso-PGF(2alpha) concentration (0.47 +/- 0.11 vs. 0.18 +/- 0.04 nmol/g, P < 0.001). Supplementation with vitamin E did not affect plasma 8-iso-PGF(2alpha) or 15-K-DH-PGF(2alpha) concentrations, liver total 8-iso-PGF(2alpha) or plasma malondialdehyde levels. Thus, vitamin E supplementation reduced urine basal levels of biomarkers of both nonenzymatic and enzymatic lipid peroxidation. In liver, vitamin E reduced the basal level of free 8-iso-PGF(2alpha) but not total 8-iso-PGF(2alpha).


Subject(s)
Dinoprost/analogs & derivatives , Dinoprost/metabolism , Lipid Peroxidation/drug effects , Oxytocics/metabolism , Vasoconstrictor Agents/metabolism , Vitamin E/pharmacology , Animals , Body Weight/drug effects , Chromatography, High Pressure Liquid , Diet , Dinoprost/blood , Dinoprost/urine , F2-Isoprostanes , Liver/metabolism , Male , Malondialdehyde/blood , Oxytocics/blood , Oxytocics/urine , Radioimmunoassay , Rats , Rats, Sprague-Dawley , Vasoconstrictor Agents/blood , Vasoconstrictor Agents/urine
10.
FEMS Microbiol Rev ; 22(4): 323-32, 1998 Oct.
Article in English | MEDLINE | ID: mdl-9862125

ABSTRACT

Treponema pallidum subsp, pallidum, the causative agent of the sexually transmitted disease syphilis, is a fastidious, microaerophilic obligate parasite of humans. This bacterium is one of the few prominent infectious agents that has not been cultured continuously in vitro and consequently relatively little is known about its virulence mechanisms at the molecular level. T. pallidum therefore represented an attractive candidate for genomic sequencing. The complete genome sequence of T. pallidum has now been completed and comprises 1,138,006 base pairs containing 1041 predicted protein coding sequences. An important goal of this project is to identify possible virulence factors. Analysis of the genome indicates a number of potential virulence factors including a family of 12 proteins related to the Msp protein of Treponema denticola, a number of putative hemolysins, as well as several other classes of proteins of interest. The results of this analysis are reviewed in this article and indicate the value of whole genome sequences for rapidly advancing knowledge of infectious agents.


Subject(s)
Genome, Bacterial , Treponema pallidum/genetics , Genes, Bacterial , Hemolysin Proteins/genetics , Nuclear Pore Complex Proteins , Proto-Oncogene Proteins/genetics , Syphilis/microbiology , Treponema pallidum/pathogenicity , Virulence/genetics
11.
J Biochem Biophys Methods ; 37(3): 137-46, 1998 Nov 18.
Article in English | MEDLINE | ID: mdl-9870188

ABSTRACT

The ferrous oxidation in xylenol orange version 2 (FOX2) assay coupled with triphenylphosphine has recently been employed for the measurement of total plasma hydroperoxides (ROOHs). In this study, we have evaluated sample handling and the effect of storage conditions on ROOH levels in human plasma (n = 32). Mean level of ROOHs in fresh plasma was 8.35 +/- 3.09 mumol/l (range 4.03-19.5 mumol/l). Addition of butylated hydroxytoluene (BHT) immediately after sample collection had no effect on the concentration of ROOHs. Storage of samples at -70 degrees C for 6 weeks was associated with a variable degree of loss of detectable ROOHs. A mean ROOH level of 6.00 +/- 2.23 mumol/l (range 2.88-13.5 mumol/l) was recorded after 6 weeks of storage at -70 degrees C. There was no difference in the mean level of ROOHs between samples stored for 6 and 60 weeks at -70 degrees C. Inclusion of BHT had no effect on the stability of plasma ROOHs during prolonged storage. Intra-assay coefficients of variation were < 12%, with the lowest variation in fresh samples (7.6%). In conclusion, these results suggest that the FOX2 assay should be a useful tool for measurement of ROOHs in fresh plasma samples but not in stored samples.


Subject(s)
Fluorescent Dyes , Hydrogen Peroxide/blood , Lipid Peroxidation/physiology , Xylenes , Adult , Aged , Antioxidants/pharmacology , Blood Preservation , Butylated Hydroxytoluene/pharmacology , Diabetes Mellitus, Type 2/blood , Evaluation Studies as Topic , Female , Humans , Male , Metabolic Diseases/blood , Middle Aged , Phenols , Reproducibility of Results , Sulfoxides
12.
Science ; 281(5375): 375-88, 1998 Jul 17.
Article in English | MEDLINE | ID: mdl-9665876

ABSTRACT

The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.


Subject(s)
Genome, Bacterial , Sequence Analysis, DNA , Treponema pallidum/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Base Sequence , Borrelia burgdorferi Group/genetics , Carrier Proteins/genetics , Carrier Proteins/metabolism , DNA Repair/genetics , DNA Replication/genetics , DNA Restriction Enzymes/genetics , Energy Metabolism/genetics , Genes, Bacterial , Genes, Regulator , Heat-Shock Response/genetics , Lipoproteins/genetics , Membrane Proteins/genetics , Molecular Sequence Data , Movement , Open Reading Frames , Oxygen Consumption/genetics , Protein Biosynthesis , Recombination, Genetic , Replication Origin , Transcription, Genetic , Treponema pallidum/metabolism , Treponema pallidum/pathogenicity
13.
Genomics ; 40(2): 247-52, 1997 Mar 01.
Article in English | MEDLINE | ID: mdl-9119391

ABSTRACT

Two frequent protein variants of glutamate pyruvate transminase (GPT) (E.C.2.6.1.2) have been used as genetic markers in humans for more than two decades, although chromosomal mapping of the GPT locus in the 1980s produced conflicting results. To resolve this conflict and develop useful DNA markers for this gene, we isolated and characterized cDNA and genomic clones of GPT. We have definitively mapped human GPT to the terminus of 8q using several methods. First, two cosmids shown to contain the GPT sequence were derived from a chromosome 8-specific library. Second, by fluorescence in situ hybridization, we mapped the cosmid containing the human GPT gene to chromosome band 8q24.3. Third, we mapped the rat gpt cDNA to the syntenic region of rat chromosome 7. Finally, PCR primers specific to human GPT amplify sequences contained within a "half-YAC" from the long arm of chromosome 8, that is, a YAC containing the 8q telomere. The human GPT genomic sequence spans 2,7 kb and consists of 11 exons, ranging in size from 79 to 243 bp. The exonic sequence encodes a protein of 495 amino acids that is nearly identical to the previously reported protein sequence of human GPT-1. The two polymorphic GPT isozymes are the results of a nucleotide substitution in codon 14, coding for a histidine in GPT-1 and an asparagine in GPT-2, which causes a gain or loss of an NlaIII restriction site. In addition, a cosmid containing the GPT sequence also contains a previously unmapped, polymorphic microsatellite sequence, D8S421. The cloned GPT gene and associated polymorphisms will be useful for linkage and physical mapping of disease loci that map to the terminus of 8q, including atypical vitelliform macular dystrophy (VMD1) and epidermolysis bullosa simplex, type Ogna (EBS1). In addition, this will be a useful system for characterizing the telomeric region of 8q. Finally, determination of the molecular basis of the GPT isozyme variants will permit PCR-based detection of this world-wide polymorphism.


Subject(s)
Alanine Transaminase/genetics , Chromosome Mapping , Chromosomes, Human, Pair 8/genetics , DNA, Complementary/genetics , Polymorphism, Restriction Fragment Length , Amino Acid Sequence , Animals , Base Sequence , Chromosome Mapping/methods , Exons/genetics , Genes/genetics , Genetic Variation/genetics , Humans , Isoenzymes/genetics , Microsatellite Repeats , Molecular Sequence Data , Rats , Sequence Analysis, DNA
14.
J Bacteriol ; 177(11): 3027-35, 1995 Jun.
Article in English | MEDLINE | ID: mdl-7768798

ABSTRACT

The genome of the photosynthetic eubacterium Rhodobacter sphaeroides 2.4.1 comprises two chromosomes and five endogenous plasmids and has a 65% G+C base composition. Because of these characteristics of genome architecture, as well as the physiological advantages that allow this organism to live in sunlight when in an anaerobic environment, the sensitivity of R. sphaeroides to UV radiation was compared with that of the more extensively studied bacterium Escherichia coli. R. sphaeroides was found to be more resistant, being killed at about 60% of the rate of E. coli. To begin to analyze the basis for this increased resistance, a derivative of R. sphaeroides, strain 2.4.1 delta S, which lacks the 42-kb plasmid, was mutagenized with a derivative of Tn5, and the transposon insertion mutants were screened for increased UV sensitivity (UVs). Eight UVs strains were isolated, and the insertion sites were determined by contour-clamped homogeneous electric field pulsed-field gel electrophoresis. These mapped to at least five different locations in chromosome I. Preliminary analysis suggested that these mutants were deficient in the repair of DNA damage. This was confirmed for three loci by DNA sequence analysis, which showed the insertions to be within genes homologous to uvrA, uvrB, and uvrC, the subunits of the nuclease responsible for excising UV damage.


Subject(s)
DNA Repair , Endodeoxyribonucleases/genetics , Escherichia coli Proteins , Rhodobacter sphaeroides/genetics , Amino Acid Sequence , Base Sequence , Chromosome Mapping , DNA Transposable Elements , DNA, Bacterial/genetics , Genes, Bacterial , Molecular Sequence Data , Sequence Alignment , Sequence Homology, Amino Acid
15.
J Bacteriol ; 176(24): 7694-702, 1994 Dec.
Article in English | MEDLINE | ID: mdl-8002595

ABSTRACT

Although multiple chromosomes occur in bacteria, much remains to be learned about their structural and functional interrelationships. To study the structure-function relationships of chromosomes I and II of the facultative photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T, auxotrophic mutants were isolated. Five strains having transposon insertions in chromosome II showed requirements for p-aminobenzoic acid (pABA)-dihydroxybenzoic acid (dHBA), serine, thymine, uracil, or histidine. The His, Thy, and pABA-dHBA mutants reverted to prototrophy at low frequency and concordantly lost their transposon insertions from the genome. The Ser, Ura, and pABA-dHBA mutants were complemented by cosmids that carried the region of chromosome II where the transposon insertions were located. The cosmids used for complementation analysis were selected, on the basis of map position, from a set of overlapping clones that had been ordered by a combination of hybridization and restriction endonuclease mapping. These experiments provide the basis for detailed studies of the structure, function, and interaction between each chromosome, and they demonstrate at this early stage of investigation that no fundamental differences exist between each chromosome.


Subject(s)
Chromosome Mapping , Chromosomes, Bacterial , Genome, Bacterial , Rhodobacter sphaeroides/genetics , 4-Aminobenzoic Acid/metabolism , Base Sequence , Cloning, Molecular , Cosmids , DNA Mutational Analysis , Genetic Complementation Test , Histidine/metabolism , Hydroxybenzoates/metabolism , Molecular Sequence Data , Mutagenesis, Insertional , Restriction Mapping , Serine/metabolism , Thymine/metabolism , Uracil/metabolism
16.
J Biol Chem ; 263(31): 16156-62, 1988 Nov 05.
Article in English | MEDLINE | ID: mdl-3053688

ABSTRACT

Nitrate reductase, released and purified from membrane fractions of Escherichia coli, is composed of three subunits. Formation of the enzyme depends on induction of the nar operon, narGHJI, which is composed of four open reading frames (ORF). Previous studies established that the first two genes in the operon narG and narH encode the alpha and beta subunits, respectively, while formation of the gamma subunit, cytochrome bNR, depends on expression of the promoter distal genes. The narJ and narI genes were subcloned separately into plasmids where each was under the control of the nar promoter. Expression of these plasmids in a mutant which forms only alpha and beta subunits revealed that expression of the narI gene is sufficient to restore normal levels of cytochrome bNR, but expression of both genes is required for assembly of fully active, membrane-bound nitrate reductase. The amino acid composition, the N-terminal sequence, and the sequence of cyanogen bromide fragments derived from the isolated gamma subunit corresponds to that expected for a protein produced by the narI ORF. A protein corresponding to the narJ ORF did not appear to be associated with the purified nitrate reductase complex or with the complex immunoprecipitated from Triton X-100-solubilized membrane preparations. We conclude that narI encodes the gamma subunit (cytochrome bNR) and that while the product of the narJ gene is required for assembly of fully active membrane-bound enzyme it is not tightly associated with the active enzyme.


Subject(s)
Escherichia coli/genetics , Genes, Bacterial , Genes , Nitrate Reductases/genetics , Transcription, Genetic , Amino Acid Sequence , Cloning, Molecular , Escherichia coli/enzymology , Genetic Complementation Test , Macromolecular Substances , Molecular Sequence Data , Mutation , Operon , Plasmids , Restriction Mapping
17.
J Bacteriol ; 170(4): 1721-9, 1988 Apr.
Article in English | MEDLINE | ID: mdl-2832376

ABSTRACT

In previous studies it has been established that in Escherichia coli the three known subunits of anaerobic nitrate reductase are encoded by the narGHI operon. From the nucleotide sequence of the narI region of the operon we conclude that, in addition to the narG and narH genes, the nar operon contains two other open reading frames (ORFs), ORF1 and ORF2, that encode proteins of 26.5 and 25.5 kilodaltons, respectively. Protein fusions to each of the genes in the operon showed that expression of all four genes was similarly regulated. The reading frames of ORF1 and ORF2 were verified, and the N-terminal sequence for the ORF1 fusion protein was determined. The nar operon therefore contains four genes designated and ordered as narGHJI.


Subject(s)
Escherichia coli/genetics , Genes, Bacterial , Nitrate Reductases/genetics , Operon , Anaerobiosis , Base Sequence , Cloning, Molecular , DNA Restriction Enzymes , DNA, Bacterial/genetics , Escherichia coli/enzymology , Gene Expression Regulation , Molecular Sequence Data , Nitrate Reductase , Nitrates/metabolism , Plasmids , Repetitive Sequences, Nucleic Acid , Transformation, Bacterial , beta-Galactosidase/genetics
18.
J Bacteriol ; 162(3): 1047-53, 1985 Jun.
Article in English | MEDLINE | ID: mdl-2987179

ABSTRACT

Strains in which the lacZ gene (which specifies beta-galactosidase) is fused to a gene encoding an envelope protein often exhibit a phenotype termed overproduction lethality. In such strains, high-level synthesis of the cognate hybrid protein interferes with the process of protein export, and this leads ultimately to cell death. A variation of this phenomenon has been discovered with lacZ fusions to the gene specifying the major outer membrane porin protein OmpF. In this case, we find that lambda transducing phage carrying an ompF-lacZ fusion will not grow on a host strain that constitutively overexpresses ompF. We have exploited this observation to develop a selection for ompF mutants. Using this protocol, we have isolated mutants altered in ompF expression and have identified mutations that block OmpF export. Our results suggest that it should be possible to adapt this selection for use with other genes specifying exported proteins.


Subject(s)
Bacterial Outer Membrane Proteins/genetics , Mutation , Base Sequence , Chromosome Mapping , Operon , Plasmids , Porins , beta-Galactosidase/genetics
19.
J Bacteriol ; 162(3): 1054-60, 1985 Jun.
Article in English | MEDLINE | ID: mdl-2987180

ABSTRACT

Expression of the major porin structural genes, ompF and ompC, is influenced by medium osmotic strength and requires the products of two regulatory genes, ompR and envZ. To help define the sites required for the expression of both porin genes, we have used a novel selection to identify mutations that decrease ompF transcription. From our assignment of the mRNA start site by the primer extension method, these mutations appear to delineate poorly conserved -10 and -35 consensus promoter regions. In addition, one mutation provides the first genetic evidence that an A residue at position -45 may be important for RNA polymerase recognition.


Subject(s)
Bacterial Outer Membrane Proteins/genetics , Genes, Bacterial , Mutation , Operon , Bacteriophages/genetics , Base Sequence , DNA, Bacterial/analysis , Porins , RNA, Messenger/analysis , Transcription, Genetic
20.
Genetics ; 105(2): 281-91, 1983 Oct.
Article in English | MEDLINE | ID: mdl-17246160

ABSTRACT

To test genetic recombination in the vicinity of insertions of the transposon Tn5, crosses were performed by transduction between M. xanthus strains carrying different insertions of Tn5. One member of each pair carried resistance to kanamycin (Tn5-Km); the other carried resistance to tetracycline (Tn5-Tc). The distance between each pair of Tn5 insertions was also measured by restriction mapping. The physical distance corresponding to each recombination frequency was calculated from the transductional linkage and compared with distance on the restriction map. A good correspondence between the two measures of distance was obtained for a pair of Tn5 insertions near the cglB locus and for another pair near the mgl locus. Correspondence between the two measurements of distance, the observed allelic behavior of Tn5-Km and Tn5 -Tc at the same locus and the finding of the same frequencies of recombinants in reciprocal crosses implied that recombination in the vicinity of Tn 5 was normal.

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