A validated web-based tool to display individualised Crohn's disease predicted outcomes based on clinical, serologic and genetic variables.

BACKGROUND: Early treatment for Crohn's disease (CD) with immunomodulators and/or anti-TNF agents improves outcomes in comparison to a slower 'step up' algorithm. However, there remains a limited ability to identify those who would benefit most from early intensive therapy. AIM: To develop a validated, individualised, web-based tool for patients and clinicians to visualise individualised risks for developing Crohn's disease complications. METHODS: A well-characterised cohort of adult patients with CD was analysed. Available data included: demographics; clinical characteristics; serologic immune responses; NOD2 status; time from diagnosis to complication; and medication exposure. Cox proportional analyses were performed to model the probability of developing a CD complication over time. The Cox model was validated externally in two independent CD cohorts. Using system dynamics analysis (SDA), these results were transformed into a simple graphical web-based display to show patients their individualised probability of developing a complication over a 3-year period. RESULTS: Two hundered and forty three CD patients were included in the final model of which 142 experienced a complication. Significant variables in the multivariate Cox model included small bowel disease (HR 2.12, CI 1.05-4.29), left colonic disease (HR 0.73, CI 0.49-1.09), perianal disease (HR 4.12, CI 1.01-16.88), ASCA (HR 1.35, CI 1.16-1.58), Cbir (HR 1.29, CI 1.07-1.55), ANCA (HR 0.77, CI 0.62-0.95), and the NOD2 frameshift mutation/SNP13 (HR 2.13, CI 1.33-3.40). The Harrell's C (concordance index for predictive accuracy of the model) = 0.73. When applied to the two external validation cohorts (adult n = 109, pediatric n = 392), the concordance index was 0.73 and 0.75, respectively, for adult and pediatric patients. CONCLUSIONS: A validated, web-based tool has been developed to display an individualised predicted outcome for adult patients with Crohn's disease based on clinical, serologic and genetic variables. This tool can be used to help providers and patients make personalised decisions about treatment options.

Housing conditions and respiratory health in a Boston public housing community.

OBJECTIVES: To determine frequency of and possible associations between environmental housing factors and self-reported respiratory symptoms in public housing. METHODS: We used a community-participatory method in which trained residents conducted in-person interviews with a random sample of 53 households in one housing development in Boston, Massachusetts. RESULTS: Environmental factors suspected of affecting respiratory health that were reported by more than 30 percent of respondents included: Moisture (43 percent), mold (43 percent), cracks in walls, floors and ceilings (49 percent), sewage leaks (33 percent), unexplained odor (35 percent), use of air fresheners (91 percent), use of gas ovens for heating (38 percent), no vent for the oven (74 percent), stuffy air (66 percent), overheating at least part of the winter (73 percent), cockroaches (70 percent), rodents (40 percent), pets (39 percent), frequent renovations (40 percent), repeated requests for repairs (52 percent), dust from construction (45 percent), use of more than three hazardous household products (32 percent), vehicle traffic nearby (81 percent), and smoking in the household (57 percent). Forty percent of respondents reported having asthma. Respondents also reported that 56 percent of their children had asthma. Forty percent of respondents reported wheeze and 48 percent reported coughing or sneezing episodes in the preceding month. We found the following positive statistically significant associations, adjusted for age, sex, Black or Hispanic origin, and years lived in public housing: wheeze with moisture problems (OR = 4.8; CI = 1.2, 19.3), sewage leaks (OR = 6.3; CI = 1.3, 30.3), odor (OR = 7.5; CI = 1 .4, 39.0), cracks in walls,floors and ceilings (OR = 8.6; CI 1.9, 38.0), and frequency of renovations (OR = 9.8; CI = 1.8, 54.4); cough with moisture problems (OR = 5.3; CI = 1.3, 20.8), stuffy air (OR = 4.4; CI = 1.2, 16.7), cockroaches (OR = 5.4; CI = 1.2, 24.2), smoking (OR = 5.0; CI = 1.2, 20.5), odor (OR = 10.9; CI = 2.3, 53.0), cracks in walls, floors and ceilings (OR = 6.2; CI = 1.8, 22.3) and frequency of renovations (OR = 4.4; CI = 1.1, 17.5); and sneeze with cockroaches (OR = 5.2; CI = 1.1, 24.2), stuffy air (OR = 6.3; CI = 1.5, 26.5), cracks in walls, floors and ceilings (OR = 6.3; CI = 1.7, 23.1), repeated requests for repairs (OR = 5.6; CI = 1.4, 21.5), and construction dust (OR = 15.6; CI = 2.2, 112.3). CONCLUSIONS: Housing conditions that affect respiratory health were common in this public housing development. Self-reported rates of respiratory symptoms and asthma were extremely high. Statistical associations between housing conditions and respiratory symptoms in the preceding month were frequently positive and sometimes statistically significant. Engaging community residents strengthened the research process.

An efficient, automatable template preparation for high throughput sequencing.

We have developed a 96-well format for DNA template isolation that can be readily automatable. The template isolation protocol involves simple alkaline lysis chemistry and reversible capture on a silica solid phase. After the cells are lysed, no centrifugation is necessary, as lysate purification, DNA binding, washing, and release occur in 96-well filter plates. Large numbers of templates prepared using the silica purification method have been sequenced and analyzed. The quality of sequence resulting from our method has been compared with that generated from several commercial plasmid preparation protocols. We found sequence quality of the silica bead preparations to be equivalent to or, in some cases, better than those prepared by other methods. This method offers many advantages over other protocols we have used. First, the silica purifications have allowed us to more than double overall laboratory throughput while decreasing our template isolation materials cost at least five-fold. Second, because we have eliminated all centrifugation steps in the protocol, automation has been much simpler. The protocol has also been adapted to purify PCR products for use as templates in subsequent sequencing reactions.

Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome.

The nucleotide sequence of 1.5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to approximately 66% completion. The sequences, derived from 43 recombinant cosmids, contain 1046 putative protein-coding genes, 44 repetitive regions, 3 tRNAs, and 15 tRNAs. The gene density of one per 1.4 kb is slightly lower than that of Mycoplasma (1.2 kb). Of the protein coding genes, 44% have significant matches to genes with well-defined functions. Comparison of 1157 M. leprae and 1564 Mycobacterium tuberculosis proteins shows a complex mosaic of homologous genomic blocks with up to 22 adjacent proteins in conserved map order. Matches to known enzymatic, antigenic, membrane, cell wall, cell division, multidrug resistance, and virulence proteins suggest therapeutic and vaccine targets. Unusual features of the M. leprae genome include large polyketide synthase (pks) operons, inteins, and highly fragmented pseudogenes.

A TEF-1-independent mechanism for activation of the simian virus 40 (SV40) late promoter by mutant SV40 large T antigens.

Simian virus 40 (SV40) large tumor antigen (T antigen) stimulates the activity of the SV40 late promoter and a number of cellular and other viral promoters. We have characterized the ability of T antigens with mutations in the DNA-binding domain and within the N-terminal 85 residues to activate the SV40 late promoter. T antigens lacking both nonspecific and sequence-specific DNA-binding activities were able to induce the late promoter. Mutations within the N-terminal 85 residues of T antigen diminished activation by less than twofold. Activation by wild-type and most of the mutant T antigens required intact binding sites for the cellular transcription factor TEF-1 in the late promoter. Curiously, two mutants altered in the N-terminal region and an additional mutant altered in the DNA-binding domain activated a late promoter derivative lacking TEF-1 binding sites, indicating the existence of a TEF-1-independent pathway for activation of the late promoter. A consensus binding site for the TATA binding protein, TBP, was created in variants of late promoters either containing or lacking TEF-1 binding sites. Basal expression was increased by the consensus TBP binding site only when TEF-1 binding sites were present, leading to a reduction in the degree of activation by T antigen. However, activation by a mutant T antigen of the promoter lacking TEF-1 sites was unchanged or slightly enhanced by the consensus TBP binding site. These results suggest that some mutant T antigens can stabilize an interaction between TBP and additional factors bound to the late promoter.

Efficient transcriptional activation of many simple modular promoters by simian virus 40 large T antigen.

Simian virus 40 (SV40) large T antigen is a multifunctional protein which plays central roles during both lytic and transforming infections by SV40. It is a potent transcriptional activator and increases expression from the SV40 late promoter and from several cellular promoters. To understand better the transcriptional activation activity of large T antigen, we examined its ability to transactivate a set of simple modular promoters containing one of four upstream activation sequences coupled with one of three different TATA box sequences originally constructed and studied by Taylor and Kingston (Mol. Cell. Biol. 10:165-175, 1990). Large T antigen activated transcription from all of these simple promoters. The identity of the TATA box was a more important determinant of the final level of gene expression than was the identity of the upstream activating sequence element. We also determined the ability of a set of mutant SV40 large T antigens to activate a subset of these promoters. Several mutant SV40 large T antigens which had reduced ability to activate the complex SV40 late and Rous sarcoma virus long terminal repeat promoters showed reduced transcriptional activation activity on all of the modular promoters tested. We used a set of promoter derivatives of the human U6 small nuclear RNA promoter containing different TATA boxes and found that wild-type large T antigen could activate transcription from all of them, although to widely different levels of expression.

Transformation of a continuous rat embryo fibroblast cell line requires three separate domains of simian virus 40 large T antigen.

Mouse C3H 10T1/2 cells and the established rat embryo fibroblast cell line REF-52 are two cell lines widely used in studies of viral transformation. Studies have shown that transformation of 10T1/2 cells requires only the amino-terminal 121 amino acids of simian virus 40 (SV40) large T antigen, while transformation of REF-52 cells requires considerably more of large T antigen, extending from near the N terminus to beyond residue 600. The ability of a large set of linker insertion, small deletion, and point mutants of SV40 T antigen to transform these two cell lines and to bind p105Rb was determined. Transformation of 10T1/2 cells was greatly reduced by mutations within the first exon of the gene for large T antigen but was only modestly affected by mutations affecting the p105Rb binding site or the p53 binding region. All mutants defective for transformation of 10T1/2 cells were also defective for transformation of REF-52 cells. In addition, mutants whose T antigens had alterations in the Rb binding site showed a substantial reduction in transformation of REF-52 cells, and the degree of this reduction could be correlated with the ability of the mutant T antigens to bind p105Rb. There was a tight correlation between the ability of mutants to transform REF-52 cells and the ability of their T antigens to bind p53. These results demonstrate that multiple regions of large T antigen are required for full transformation by SV40.

The ability of simian virus 40 large T antigen to immortalize primary mouse embryo fibroblasts cosegregates with its ability to bind to p53.

The large T antigen encoded by simian virus 40 (SV40) plays essential roles in the infection of permissive cells, leading to production of progeny virions, and in the infection of nonpermissive cells, leading to malignant transformation. Primary mouse embryo fibroblasts (MEFs) are nonpermissive for SV40, and infection by wild-type SV40 leads to immortalization and transformation of a small percentage of infected cells. We examined the ability of an extensive set of mutants whose lesions affect SV40 large T antigen to immortalize MEFs. We found that immortalization activity was retained by all mutants whose lesions are located upstream of codon 346. This includes a mutant lacking amino acids 168 to 346. We previously showed (M. J. Tevethia, J. M. Pipas, T. Kierstead, and C. Cole, Virology 162:76-89, 1988) that sequences downstream of amino acid 626 are not required for immortalization of primary MEFs. Studies by Thompson et al. (D. L. Thompson, D. Kalderon, A. Smith, and M. Tevethia, Virology 178:15-34, 1990) indicate that all sequences upstream of residue 250, including the domain for binding of tumor suppressor protein Rb, are not required for transformation of MEFs. Together, these studies demonstrate that the immortalization activity of large T antigen for MEFs maps to sequences between 347 and 626. Several mutants with lesions between 347 and 626 retained the ability to immortalize at nearly the wild-type frequency, while others, with small insertions at amino acid 409 or 424 or a deletion of residues 587 to 589, failed to immortalize. The abilities of mutant T antigens to form a complex with tumor suppressor protein p53 were examined. We found that all mutants able to immortalize retained the ability to complex with p53, while all mutants which lost the ability to immortalize were no longer able to bind p53. This suggests that inactivation of the growth-suppressive properties of p53 is essential for immortalization of MEFs.

Mapping the transcriptional transactivation function of simian virus 40 large T antigen.

T antigen is able to transactivate gene expression from the simian virus 40 (SV40) late promoter and from several other viral and cellular promoters. Neither the mechanisms of transactivation by T antigen nor the regions of T antigen required for this activity have been determined. To address the latter point, we have measured the ability of a set of SV40 large T antigen mutants to stimulate gene expression in CV-1 monkey kidney cells from the SV40 late promoter and Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter. Transactivation, although reduced, was retained by an N-terminal 138-amino-acid fragment of T antigen. Mutants with alterations at various locations within the N-terminal 85 amino acids transactivated the RSV LTR promoter less well than did wild-type T antigen. Most of these were also partially defective in their ability to transactivate the SV40 late promoter. Two mutants with lesions in the DNA-binding domain that were unable to bind to SV40 DNA were completely defective for transactivation of both promoter, while a third mutant with a lesion in the DNA-binding domain which retained origin-binding activity transactivated both promoters as well as did wild-type T antigen. Only a low level of transactivation was seen with mutant T antigens which had lesions in or near the zinc finger region (amino acids 300 to 350). Mutations which caused defects in ATPase activity, host range/helper function, binding to p53, binding to the retinoblastoma susceptibility protein, or nuclear localization had little or no effect on transactivation. These results suggest that N-terminal portion of T antigen possesses an activation activity. The data are consistent with the idea that the overall conformation of T antigen is important for transactivation and that mutations in other regions that reduce or eliminate transactivation do so by altering the conformation or orientation of the N-terminal region so that its ability to interact with various targets is diminished or abolished.

Cyclic AMP-cyclic AMP receptor protein as a repressor of transcription of the spf gene of Escherichia coli.

The spf gene of Escherichia coli encodes an unstable 109-nucleotide RNA, spot 42 RNA; the level of this RNA was reduced three- to fivefold when cells were grown in the presence of 3',5'-cyclic AMP (cAMP). We show that this regulation occurs through reduction in transcription and depends on both cAMP and the cAMP receptor protein (CRP) but is independent of the de novo protein synthesis. Through deletion analysis of the spf gene promoter, we have identified sequences that are important in the synthesis of spot 42 RNA. Deletion of sequences upstream of -77 completely eliminated the negative control of cAMP-CRP and resulted in high constitutive levels of transcription. This region contained a sequence that both conformed to the consensus binding site for cAMP-CRP in positively regulated promoters and acted as a cAMP-CRP binding site in a gel retardation assay. Deletion of sequences between positions -77 and -60 greatly reduced the level of transcription in the presence or absence of cAMP-CRP, indicating that at least part of this region is a binding site for a positive-acting transcription factor (or RNA polymerase itself). We propose that the proximity of the two sites defined here allows for the negative control of spf gene transcription by cAMP-CRP. In particular, if only one site at a time can be occupied, the binding of cAMP-CRP would interfere with the binding of a transcription factor.

DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA.

We have shown that the level of DNA polymerase I (Pol I) activity in Escherichia coli is influenced by the level of a 109-nucleotide RNA, spot 42 RNA. Deletion of the gene for spot 42 RNA results in a 20 to 25% decrease in Pol I activity, as assayed by nucleotide incorporation in cell extracts and a decrease in the ability of cells to grow in the presence of the DNA-alkylating agent methyl methanesulfonate. Also, a physiological reduction of the level of spot 42 RNA, by growth in media containing poor carbon sources, results in a corresponding decrease in Pol I activity. Conversely, overproduction of spot 42 RNA results in a 10 to 15% increase in Pol I activity in vitro. Thus, changes in the amount of spot 42 RNA result in relatively small but significant changes in Pol I activity.

Spot 42 RNA of Escherichia coli is not an mRNA.

Spot 42 RNA of Escherichia coli, a 109-nucleotide RNA that influences the level of DNA polymerase I, has an AUG triplet preceded by a purine-rich potential ribosome-binding site and is followed by a short (14-triplet) potential open reading frame. Although the RNA bound to ribosomes, it did so inefficiently and nonproductively. When fused to lacZ sequences, spot RNA did not support the synthesis of beta-galactosidase. Also, the biological effects of spot 42 RNA were not altered by mutation of the tyrosine UAU codon to the chain termination UAG. We conclude that the effects of spot 42 RNA are mediated by the RNA itself and not by a spot 42 RNA-encoded peptide.

A gene between polA and glnA retards growth of Escherichia coli when present in multiple copies: physiological effects of the gene for spot 42 RNA.

We have isolated the single gene for spot 42 RNA of Escherichia coli on a 20-kilobase DNA fragment. Physical characterization of this cloned DNA fragment showed that it is homologous to a region at 86 min on the genetic map and extends from the 23S to 5S rRNA coding region of rrnA to the coding region of glnA, the gene for glutamine synthetase. Other genes included on this cloned DNA fragment are polA, ntrC (glnG), and ntrB (glnL). E coli cells transformed with a multicopy plasmid clone of the gene for spot 42 RNA had about a 10-fold increase in the amount of spot 42 RNA they contained. The amount of 6S RNA in these cells was increased about twofold, although the gene for 6S RNA was not located on this plasmid or on the larger 20-kilobase fragment. Presence of this multicopy plasmid also affected the growth of cells. The generation time was increased under a variety of growth conditions, especially when cells were grown in medium with succinate as the carbon source. In addition, some strains of E. coli which have multicopy plasmids carrying the gene for spot 42 RNA were unable to respond normally to a shift into richer medium: upon upshift from minimal glucose to LB broth or minimal glucose plus 1% Casamino Acids, there was a 3- to 4-h lag before the culture adapted to the new medium. More than 90% of the cells in such cultures stopped dividing, although they remained viable. The plating efficiency of minimal-glucose-grown cells was 100-fold less on rich media than on minimal glucose medium. One revertant was isolated which regained the phenotype of pBR322-transformed cells. Analysis of this strain showed that the plasmid it contained had an insertion of an IS1 element into the 5' end of the coding region for the gene for spot 42 RNA.

Arrangement of the genes coding for ribosomal ribonucleic acids in Neurospora crassa.

We have cloned and characterized Neurospora crassa ribosomal deoxyribonucleic acid (rDNA). The rDNA is found as a tandemly repeated 6.0-megadalton sequence. We have mapped a portion of the rDNA repeat unit with respect to its sites for 13 restriction endonucleases and defined those regions coding for the 5. 8S, 17S, and 26S ribosomal ribonucleic acids (rRNA's). We have also isolated several clones containing 5S rRNA sequences. The 5S rRNA coding sequences are not found within the rDNA repeat unit. We found that the sequences surrounding the 5S rRNA coding regions are highly heterogeneous.