Search

We report the construction and analysis of a mouse gene trap mutant resource created in the C57BL/6N genetic background containing more than 350,000 sequence-tagged embryonic stem (ES) cell clones. We also demonstrate the ability of these ES cell clones to contribute to the germline and produce knockout mice. Each mutant clone is identified by a genomic sequence tag representing the exact insertion location, allowing accurate prediction of mutagenicity and enabling direct genotyping of mutant alleles. Mutations have been identified in more than 10,000 genes and show a bias toward the first intron. The trapped ES cell lines, which can be requested from the Texas A&M Institute for Genomic Medicine, are readily available to the scientific community.

The third postnatal week of mouse development is characterized by dramatic changes of gene expression in the small intestine. Although these changes are often assumed to reflect regulation at the level of transcription, to date there have been no direct investigations of this. In the current study we have used trehalase as a marker of intestinal maturation. Highly sensitive reverse transcriptase-polymerase chain reaction methods were developed for semi-quantitative analysis of both initial and mature transcripts, i.e., hnRNA and mRNA. Jejunums collected during normal development (specifically from postnatal days 8-21) showed parallel increases in the levels of trehalase hnRNA and mRNA. Likewise, when precocious gut maturation was elicited by dexamethasone administration on days 8-10, both initial and mature trehalase transcripts were significantly increased, although with a relatively slow time course. We conclude that both normal and glucocorticoid-induced maturation of trehalase expression reflect transcriptional activation. However, the slow time course of the glucocorticoid effect suggests that trehalase may not be a primary response gene.

Trehalase is the least studied of the membrane-bound alpha- glucosidase enzymes. Here we report the isolation and characterization of the mouse trehalase (Treh) gene. Initially, PCR using primers based on published rat cDNA sequence was used to clone a partial mouse cDNA. This allowed design of mouse primers which identified a single positive clone in a bacterial artificial chromosome (BAC) library of mouse genomic DNA. Analysis of BAC subclones showed that the Treh structural gene spans approximately 13 kb and comprises 15 exons. Data from genomic Southern blotting were consistent with mouse Treh being a single copy gene. The transcription initiation site was determined by both S1 nuclease mapping and 5' rapid amplification of cDNA ends (5' RACE) to be located 25 nt upstream of the ATG in exon 1. The mouse Treh exons were found to have an open reading frame of 1728 nt and the encoded protein of 576 amino acids showed 81, 82 and 93% amino acid sequence identity with rabbit, human and rat trehalase, respectively. The trehalase signature sequence found at amino acids 162 to 175 had 100% identity with the corresponding region of rabbit, human and rat and 79% identity with that for yeast trehalase. When a mouse Treh cDNA was used for Northern blot analysis of RNA from 12 mouse tissues, Treh mRNA expression was detected only in kidney and small intestine. The size of the mRNA in both of these tissues was estimated to be approximately 2.1 kb, furthermore both tissues appear to have the same transcription initiation site as determined by nuclease protection. Using the T31 radiation hybrid panel, mouse Treh was shown to be located on Chromosome 9 in a broad region that is orthologous with human Chromosome 11q23. The human trehalase gene (TREH) was identified in the latter location via database searching, which also revealed the overall structure of the human gene as being similar to that of the mouse.

bicaudal was the first Drosophila mutation identified as producing mirror-image pattern duplications along the anteroposterior axis of the embryo. However the mutation has been little studied due to its low penetrance and suppressibility. We undertook cloning of the bicaudal locus together with studies of the mutation's effects on key elements of the posterior embryonic patterning pathway. Our mapping studies place the bicaudal mutation within a approximately 2 kb region, 3' to the protein coding sequence of the Drosophila homolog of beta NAC, a subunit of Nascent polypeptide Associated Complex (NAC). Genomic DNA encoding beta NAC completely rescues the bicaudal phenotype. The lethal phenotype of Enhancer of Bicaudal, E(Bic), a mutation hypothesized to affect the bicaudal locus, is also completely rescued by the beta NAC locus. We further demonstrate that the E(Bic) mutation is caused by a P element insertion into the transcribed region of the beta NAC gene. NAC is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. In contrast to other bicaudal-embryo-producing mutations, bicaudal leads to ectopic translation of mRNA for the posterior determinant nanos, without affecting the localization of mRNA for its upstream regulator, oskar, in the embryo. These findings suggest that repression of nanos mRNA translation occurs on the ribosome and involves a role for beta NAC.

Cell wall-defective bacteria which later reverted to acid-fast bacilli have been isolated from sarcoid tissue. These have not been conclusively shown to be mycobacteria. Specific PCR assays were applied to identify mycobacterial nucleic acids in these cultured isolates and in fresh specimens obtained from patients with sarcoidosis. Positive amplification and hybridization were observed with Mycobacterium avium complex- and/or Mycobacterium paratuberculosis-specific probes in five of the six cultured isolates and two fresh skin biopsy samples and one cerebrospinal fluid specimen. There was no amplification or hybridization with Mycobacterium tuberculosis or M. avium subsp. silvaticum probes, respectively. Patients' sera were also tested for antibody reactivities by immunoblotting with M. paratuberculosis recombinant clones expressing the 36,000-molecular-weight antigen (36K antigen) (p36) and the 65K heat shock protein (PTB65K). All seven sarcoidosis, four of six tuberculosis, and all six leprosy patient serum specimens showed strong reactivity with p36 antigen. In contrast, 13 of 38 controls showed only weak reactivity with p36 (P = 0.002 for controls versus sarcoidosis samples). Similarly, PTB65K reacted with high intensity with sera from 5 of 5 sarcoidosis, 5 of 6 tuberculosis, and 5 of 6 leprosy patients, compared with its low-intensity reaction with 5 of 22 controls (P = 0.001 for controls versus sarcoidosis samples). This study demonstrates the isolation and/or identification of M. paratuberculosis or a closely related M. avium complex strain from sarcoid skin lesions and cerebrospinal fluid. Furthermore, the reactivity of antibodies in sarcoid patient sera against p36 and PTB65K antigens was comparable to the reactivity of sera obtained from patients with known mycobacterial disease. Collectively, these data provide further support for the theory of the mycobacterial etiology of sarcoidosis.

The mechanism by which Helicobacter pylori undermines host defence mechanisms is unclear. Several in vitro studies using soluble mucins have suggested that H pylori may compromise mucus function. Gastric mucus gel was obtained from 13 H pylori infected patients; six untreated subjects and seven after eradication of the infection. Gastric mucus is a non-Newtonian substance in that its viscosity changes with changing rates of shear, requiring mucus viscosity to be measured in a rotational cone-plate microviscometer. Viscosity was measured at shear rates varying from 1.15 s-1 to 46 s-1. The gastric mucus viscosity was significantly higher in patients infected with H pylori compared with mucus gel obtained after eradication of the infection. The results of our study suggest that the previous studies using in vitro methods involving soluble mucins or its components may have lead to erroneous conclusions about the in vivo interactions of H pylori and gastric mucus gel. The present findings argue against the hypothesis that degradation of gastric mucus by H pylori is important in the pathogenesis of peptic ulcer.

Thirty one cultures were established in MG3 medium from the intestinal tissues of 29 patients, including 18 with Crohn's disease, five with ulcerative colitis, and six non-inflammatory bowel disease controls. All cultures grew either acid fast bacilli or uncharacterized spheroplasts. Pellets from these cultures were coded and assayed blind for M paratuberculosis and M avium subsp silvaticum using IS900- and IS902-PCR (polymerase chain reaction) assays, respectively. IS900 and IS902 are multicopy DNA insertion elements specific for these two organisms. Six Crohn's disease cultures and a single non-inflammatory bowel disease control were positive for M paratuberculosis. A further six cultures were positive for M avium subsp silvaticum, of which two each were from Crohn's disease, ulcerative colitis, and non-inflammatory bowel disease controls. The intensity of the IS900-PCR signals indicated very low numbers of M paratuberculosis organisms and bore no relation to visible spheroplastic or bacillary mycobacterial growth. The results suggest that M paratuberculosis isolated from man exists in a form which hardly replicates if at all when cultured in MG3 medium in vitro, and are consistent with the involvement of this known animal enteric pathogen in a proportion of chronic enteritis in man.

Many investigators have tried to prove a relationship between Crohn's disease and Mycobacteria. Recent evidence suggests that some autoimmune diseases may be initiated through "molecular mimicry" between mycobacterial stress protein antigens and their human homologs. We investigated whether antibody to stress proteins was more frequent in patients with Crohn's disease than controls. We used ATP binding to separate stress proteins (heat-shock-induced, de novo-synthesized, and constitutively expressed ATP-binding proteins) from crude extracts obtained from Mycobacteria and from an SV40-transformed human epithelial cell line that expresses a heat-shock protein, hsp73, as a complex with SV40 T antigen. We used immunoblots to compare sera from 34 patients with Crohn's disease, 14 with ulcerative colitis, and 14 with duodenal or gastric ulcers (noninflammatory bowel disease control patients). We found no statistically significant pattern or frequency of antibodies against single proteins or a combination of mycobacterial or human stress proteins. These observations do not support the hypothesis that a humoral immune response to stress proteins of Mycobacteria is important in the pathogenesis of Crohn's disease.

The efficiency of culture media was compared for the culture and subculture of very slowly growing acid-fast bacilli and spheroplast forms obtained from intestinal tissues of patients with Crohn's disease and ulcerative colitis and from controls without inflammatory bowel disease. Media were developed by modifying a nutrient broth medium based on veal infusion broth and yeast extract. We evaluated the effects of pH and the addition of Tween 80, Dubo oleic albumin complex, an extract from intestinal tissue from a patient with Crohn's disease, horse serum, sucrose, magnesium sulfate, ferrous ammonium sulfate, and sodium citrate. All media contained mycobactin J (2 micrograms/ml). We developed a medium (MG3) which was highly successful in promoting the growth of very fastidious organisms and promoted reversion of spheroplasts to acid-fast rods. MG3 contained veal infusion broth, 1% yeast extract, 10% horse serum, 0.3 M sucrose, 0.2% MgSO4, 0.1% ferrous ammonium sulfate, 0.1% sodium citrate, and 2 mg of mycobactin J per liter. We were able to obtain quantities of organisms sufficient for examination of the organisms by molecular techniques. Successful cultivation of all isolates and reversion of spheroplasts to acid-fast forms encourage further studies of the possibility of a complex association of mycobacteria and Crohn's disease.

We have been able to isolate mycobacteria from intestinal specimens obtained by surgical resection or endoscopic biopsy from patients with Crohn's disease, ulcerative colitis, and noninflammatory bowel diseases. Nineteen slow-growing (Runyon groups I and III) and 17 rapid-growing (Runyon group IV) mycobacterial isolates were obtained. Slow-growing mycobacteria were recovered from approximately one-third of intestinal biopsy specimens from Crohn's disease, one-quarter of ulcerative colitis biopsies, and 40% of biopsies from noninflammatory bowel disease patients. Isolates were most commonly members of the Mycobacterium avium-complex. One isolate (from an ulcerative colitis patient) was biochemically similar to the Mycobacterium strain previously associated with Crohn's disease, and one from a Crohn's disease patient was Mycobacterium kansasii. The rapid-growing organisms were members of the Mycobacterium fortuitum-complex. In addition to conventional mycobacteria, spheroplasts (cell wall-defective forms) were isolated from 12 patients with Crohn's disease (most often from surgically resected colon) and 3 patients with ulcerative colitis; none were isolated from non-inflammatory bowel disease patients. We have been unable to identify a consistent relationship between the presence, or the species, of Mycobacterium and Crohn's disease. Our results do not support the proposed role of a specific mycobacterium in the pathogenesis of Crohn's disease. The cause of Crohn's disease remains unclear.

Experiments were designed to determine the role of heme and the importance of other factors in the growth of Campylobacter pylori. Campylobacter pylori strains were tested for their ability to synthesize porphyrin, for their ability to grow and be maintained on basal medium and basal medium supplemented with blood or blood products, and for the influence of bovine serum albumin and catalase on viability. Results indicated that Campylobacter pylori does not require heme as a source of porphyrin. Growth of Campylobacter pylori could not be sustained on media containing starch or hemoglobin, but was sustained on media containing erythrocytes, serum, bovine serum albumin or catalase. The ability to grow on media containing bovine serum albumin and catalase suggests that protection from toxic fatty acids and the prevention of toxic product formation may be important factors in the growth and survival of Campylobacter pylori in vitro. Both bovine serum albumin and catalase combined provide the minimum requirements which allow the spectrum of Campylobacter pylori present in a single culture to grow on blood-free media.