An antagonist decoy receptor and a death domain-containing receptor for TRAIL

TRAIL, also called Apo2L, is a cytotoxic protein that induces apoptosis of many transformed cell lines but not of normal tissues, even though its death domain-containing receptor, DR4, is expressed on both cell types. An antagonist decoy receptor (designated as TRID for TRAIL receptor without an intracellular domain) that may explain the resistant phenotype of normal tissues was identified. TRID is a distinct gene product with an extracellular TRAIL-binding domain and a transmembrane domain but no intracellular signaling domain. TRID transcripts were detected in many normal human tissues but not in most cancer cell lines examined. Ectopic expression of TRID protected mammalian cells from TRAIL-induced apoptosis, which is consistent with a protective role. Another death domain-containing receptor for TRAIL (designated as death receptor-5), which preferentially engaged a FLICE (caspase-8)-related death protease, was also identified.

[GC-MS analysis of constituents of essential oils from stems of Ephedra sinica Stapf, E. intermedia Schrenk et C.A. Mey. and E. equisetina Bge]

The essential oils from the dried stems of Ephedra sinica, E. intermedia and E. equisetina were analyzed by GC-MS qualitatively and GC quantitatively. One hundred and twenty-seven constituents were identified, l-alpha-terpineol (31.64%) in E. sinica, 1,4-cineole (12.80%) in E. intermedia and hexadecanoic acid (26.22%) in E. equisetina being the main constituents.

Test for qualitative interaction of clinical significance

We generalize the problem of detecting qualitative interaction between treatments and subsets in a two treatment clinical trial to the more practical problem of detecting a qualitative interaction greater than a non-negative value d, corresponding to the minimal treatment difference of clinical significance. We develop a test based on simultaneous confidence intervals for the generalized problem under the assumption of normality. The proposed test is easy to implement, either by hand calculation or through the use of virtually any existing statistical software. We derive explicit power function for the proposed test and give examples to illustrate the procedures.

The receptor for the cytotoxic ligand TRAIL

TRAIL (also known as Apo-2L) is a member of the tumor necrosis factor (TNF) ligand family that rapidly induces apoptosis in a variety of transformed cell lines. The human receptor for TRAIL was found to be an undescribed member of the TNF-receptor family (designated death receptor-4, DR4) that contains a cytoplasmic "death domain" capable of engaging the cell suicide apparatus but not the nuclear factor kappa B pathway in the system studied. Unlike Fas, TNFR-1, and DR3, DR4 could not use FADD to transmit the death signal, suggesting the use of distinct proximal signaling machinery. Thus, the DR4-TRAIL axis defines another receptor-ligand pair involved in regulating cell suicide and tissue homeostasis.

Relationship between Asbestos Exposures and 8-Hydroxydeoxyguanosine Levels in Leukocytic DNA of Workers at a Chinese Asbestos-material Plant

The objective of the study was to evaluate the level of 8-hydroxydeoxyguanosine (8-OHdG) in DNA of peripheral-blood leukocytes as a biological marker of asbestos exposure and/or its fibrotic effects in an occupational population exposed to asbestos. The setting was a large-scale asbestos plant in China producing brake linings, asbestos rubber, and textile using chrysotile. From a base population of active and retired workers with various levels of cumulative exposure to asbestos and grades of asbestosis, 39 study subjects were randomly selected to reflect incremental grades of asbestosis based on Chinese diagnostic standards. They consisted of 19 "normal" (control) and ten "suspected" and ten "definite" asbestosis-grade subjects, group-matched for age and sex. Leukocytic DNA was extracted from 5-mL samples of peripheral blood and 8-OHdG level measured by high-pressure liquid chromatography. A cumulative asbestos exposure index (CEI) was calculated for each subject as the summed product of duration and level of asbestos exposure per job, incorporating a job-exposure matrix. Geometric mean 8-OHdG levels showed a positive gradient in relation to increasing grades of asbestosis (control: 1.78, suspected: 2.21, definite: 2.58), with a significant difference between the control and definite-asbestosis subgroups (p < 0.05). The 8-OHdG level of the two subgroups combined as one "asbestosis" group was significantly higher than that of the control group (control: 1.78, asbestosis: 2.39, p = 0.01). Further, 8-OHdG levels were moderately correlated with CEIs for all subjects (r = 0.35, p < 0.05) and with grades of asbestosis for all (r = 0.47, p < 0.01) and for male subjects (r = 0.43, p < 0.05). In multiple regression analyses, grade of asbestosis explained 27% of the total variation in 8-OHdG and was a better predictor than CEI or duration of exposure. Thus, the 8-OHdG level in leukocytic DNA is related to grade of asbestosis and to individual cumulative exposure and may serve as a biologic marker reflecting the status of oxidative DNA damage by asbestos.

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

Messenger RNA is produced by RNA polymerase II (pol II) transcription, followed by processing of the primary transcript. Transcription, splicing and cleavage-polyadenylation can occur independently in vitro, but we demonstrate here that these processes are intimately linked in vivo. We show that the carboxy-terminal domain (CTD) of the pol II large subunit is required for efficient RNA processing. Splicing, processing of the 3' end and termination of transcription downstream of the poly(A) site, are all inhibited by truncation of the CTD. We found that the cleavage-polyadenylation factors CPSF and CstF specifically bound to CTD affinity columns and copurified with pol II in a high-molecular-mass complex. Our demonstration of an association between the CTD and 3'-processing factors, considered together with reports of a similar interaction with splicing factors, suggests that an mRNA 'factory' exists which carries out coupled transcription, splicing and cleavage-polyadenylation of mRNA precursors.

[Potential role of gut peptides in stress-induced colonic motor disorder]

OBJECTIVE

To explore the potential role of gut peptide in stress-induced colonic motor disorder.

METHODS

In 9 conscious Wistar rats pre-equipped with strain-gauge transducers on ascending and descending colon, colonic motility was recorded before, during and after stress. And colonic transit was evaluated by instilling Cr into the cecum through chronically implanted cannula in each group of 16 rats with or without stress, and then calculating the geometric center (GC) of radioactivity. The contents of VIP, SP, NT, SST, MOT and Leu-ENK in plasma, colonic mucosa and muscle layer were assessed in 16 stressed and 16 control rats. Exogenous peptides (VIP, SP, SST, NT) were intravenously administered in 9 rats to determine the colonic motor response. Also, the effects of peptides on colonic circular muscle strips were investigated.

RESULTS

Motor activity was increased after stress, whereas colonic transit was delayed. In the stressed rats, plasma levels of VIP and Leu-ENK were higher than those in controls. The content of Leu-ENK in muscle tissue decreased. Both in vivo and in vitro studies showed that SP and NT excited, whereas VIP and SST inhibited colonic motor activity.

CONCLUSION

Release of certain peptides is altered by stress. Increased release of ENK and VIP may be involved in stress-induced colonic motor disorder and in the regulation of "stress hormone" release.

Subset selection with additional order information

Traditional subset selection procedures were developed without assuming any order information about the response variable. However, in some applications there is additional, even though incomplete, order information about the treatment effects at increasing treatment levels. One important example is the up-then-down umbrella ordering with an unknown peak. This type of additional order information is utilized explicitly in this paper to construct subset selection procedures for several settings studied in the literature where only order restricted tests are known to exist. This paper also proposes a straightforward algorithm to compute the isotonic regression with respect to umbrella orderings, which can be used to carry out the proposed procedures. Examples are given to illustrate the procedures and algorithm.

Characterization of the interaction between the acidic activation domain of VP16 and the RNA polymerase II initiation factor TFIIB

Contact between a transcriptional activator and one or more components of the RNA polymerase II transcription initiation machinery is generally believed important for activators to function. Several different molecular targets have been suggested for direct contact by herpes simplex virus virion protein VP16, including the general initiation factor TFIIB. In this report we have used several strategies to critically assess this interaction between VP16 and TFIIB. Affinity columns of VP16 bound TFIIB activity from HeLa cell extracts and the binding was reduced by mutations in the activation domain of VP16. In assays of direct binding, VP16 bound recombinant human TFIIB but not Drosophila or yeast TFIIB. Unlike binding from an extract, however, we found that the interaction between VP16 and recombinant human TFIIB was not affected by mutations in VP16 that reduce transactivation. Point mutations within human TFIIB that reduce transactivation by VP16 have been shown to reduce VP16 binding, but we show here that these same mutations critically affect both the important TBP-TFIIB interaction and the ability of TFIIB to support activator-independent basal transcription in vitro. Taken together our results suggest more evidence is needed to support the notion that TFIIB is a functionally important target for the activator VP16.

[Diagnosis of chylous ascites with oral administration of 13C-palmitic acid]

12 cases of chylous ascites in PUMC hospital in the recent 30 years were analysed. The etiology of this disease includes non-traumatic (83.3%) and traumatic (16.7%) causes. All the patients received isotope examination or lymphangiography, but only in 8 patients the site of the lesion was found. As these two kinds of examination can only show the lesions in the right and left lumbar lymph trunks, cisterna chyli and throacic duct but not the intestinal lymph truck, the authors set up a method by administering orally 13C-palmitic acid to detect the lesion of intestinal lymph trunk. Palmitic acid is a long-chain fatty acid, which enters directly into the intestinal lymph trunk after absorption. Palmitic acid labelled with 13C could be detected in the ascitic fluid if there is a leak from intestinal lymph trunk. This new method was used to examine a patients who had negative results with isotope examination and lymphangiography; 13C could be detected in the ascitic fluid 30 minutes after oral administration but not in exhaled air. It can be concluded that cyhle leaked into the peritoneal cavity from the intestinal lymph trunk. This method is also of help to determine the possible site of leakage and the degree of obstruction, so it is quite useful for the diagnosis of chylous ascities.

The syndrome of lung hemorrhage and nephritis is usually an ANCA-associated condition

BACKGROUND

In the absence of evidence of arteritis or Wegener's granulomatosis, the syndrome of lung hemorrhage and nephritis has been commonly associated with anti-glomerular basement membrane (GBM) antibodies. However, it has been increasingly recognized that many cases are associated with antineutrophil cytoplasmic antibodies (ANCAs).

OBJECTIVE

To review available clinical and pathologic findings to determine the diseases accounting for lung hemorrhage and nephritis.

METHODS

We studied the records of 750 patients from whom serum samples were sent to our laboratory for anti-GBM antibody assays between 1981 and 1993 and found 88 patients with evidence of lung hemorrhage and nephritis. Serum samples were retested, using current methods, for anti-GBM antibodies (against noncollagenous 1 domain of the alpha 3 chain of type IV collagen) and for antibodies to proteinase 3 and myeloperoxidase--the two types of ANCA of diagnostic value.

RESULTS

Of 88 patients with evidence of lung hemorrhage and nephritis, 48 had ANCAs, six had anti-GBM antibodies, and seven had both. In 48 patients with ANCAs, the pathologic findings that accounted for the pulmonary renal syndrome were pauci-immune necrotizing and crescentic glomerulonephritis and pulmonary capillaritis. Only eight had convincing evidence (during life) of Wegener's granulomatosis and only one other had documented arteritis. In 27 patients without ANCAs or anti-GBM antibodies, a variety of unrelated renal and pulmonary diseases were found.

CONCLUSIONS

The largest group of patients who present with the syndrome of lung hemorrhage and nephritis have ANCAs and not anti-GMB antibodies. Appropriate tests for antibodies to proteinase 3, antibodies to myeloperoxidase, and anti-GBM antibodies provide reliable guides for making a diagnosis in patients with this pulmonary renal syndrome.

[Lactulose hydrogen breath test in small intestinal bacterial overgrowth]

Lactulose hydrogen breath test (LHBT) was evaluated in 21 patients suspected of having small intestinal bacterial overgrowth syndrome and 10 healthy volunteers as control. After dietary preparation and a 12-hour fast, subjects received 15g of lactulose mixed with 40% barium sulfate. The purpose of the barium meal was to reveal the position of lactulose in the intestines. End-expiratory samples of breath were taken at 15 minutes intervals at least for 4 hours. Breath hydrogen was measured with gas chromatography. A positive LHBT was defined as increase of hydrogen concentration in the breath more than 10 x 10(-6) above the baseline value before barium reached the sixth group of small intestine. Cultures were considered positive for bacterial overgrowth when anaerobic counts > or = 10(6) CFU/ml of aspirate. The procedure was carried out under sterile condition. Compared with the bacteriologic culture, LHBT has a sensitivity of 71.4%, specificity of 88.2% and accuracy of 80.6%. These results show that the LHBT is a simple, non-invasive and relatively reliable method for diagnosis of small intestinal bacterial overgrowth.

Homology requirements for ligation and strand exchange by the FLP recombinase

The FLP recombinase of the 2-microns plasmid of Saccharomyces cerevisiae belongs to the integrase family whose members form a covalent bond between a conserved tyrosine of the recombinase and the 3'-phosphoryl group at the site of cleavage. Ligation takes place when the 5'-OH generated during the cleavage step attacks the phosphotyrosine bond and reforms a phosphodiester bond. When the incoming 5'-OH is from the partner duplex, strand exchange occurs. The FLP recognition target (FRT) contains two inverted 13-base pair (bp) FLP binding sequences that surround an 8-bp core region. It has been shown that heterology in the core regions of the recombinase FLP recognition target sites can dramatically impair recombination. Therefore, it was of interest to study the homology requirements of the core sequence for FLP-mediated ligation. Using nicked duplex substrates containing mismatches in the core sequence, we have demonstrated that the FLP ligation reaction can tolerate mismatches at all positions in the 8-bp core except the position immediately adjacent to the cleavage site. Using half-FRT substrates that contain a single-stranded core sequence, we showed that 4 base pairs adjacent to the cleavage site in the core are required for FLP to execute ligation with a single-stranded oligonucleotide. FLP is also able to ligate the protruding single strand on a half-FRT site to the opposite strand to form a hairpin. We have studied the effect of the base composition of the protruding 8-nucleotide single strand upon the efficiency of hairpin ligation. These studies revealed the importance of intrastrand complementarity in the formation of hairpin by FLP. Hence we conclude that the homology in the position adjacent to the cleavage site is most important, and the degree of the homology required is dependent on the nature of the ligation assay.

Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site

To further elucidate the mechanism of transcriptional initiation, we used synthetic oligonucleotides to prepare templates containing heteroduplex regions of varying size and location along the DNA of the adenovirus major late promoter. Unlike closed, linear DNA, or DNA with a downstream mismatch, DNA with a mismatch upstream of the initiation site only required the general factors TATA box-binding protein and transcription factor (TF) IIB to direct specific and accurate initiation in vitro by calf thymus RNA polymerase II. In the presence of TFIIF, initiation was possible on closed, linear DNA, but an upstream mismatch region still stimulated transcriptional initiation by more than 100-fold, leading to production of approximately 0.5 transcript/template in the absence of TFIIE, TFIIH, or ATP. The presence of a DNA mismatch was most effective in the -9 to -1 region; furthermore, stimulation by a mismatch did not require that the initiation site be included in the heteroduplex region. Efficient initiation at the immunoglobulin heavy chain promoter in the presence of TATA box-binding protein and TFIIB was also achieved when a mismatch region was introduced from -9 to +3. Our results suggest that initiation by RNA polymerase II in the absence of transcriptional activation is limited by melting of the promoter DNA upstream of the initiation site.

Identification of the functional domains of the FLP recombinase. Separation of the nonspecific and specific DNA-binding, cleavage, and ligation domains

The FLP recombinase of the 2-microns plasmid of Saccharomyces cerevisiae binds to its recognition target (FRT) site, induces a bend in the DNA, and promotes DNA cleavage and strand ligation. We have subjected this protein to limited proteolysis and have purified three polypeptides: P13 (13 kDa), P21 (21 kDa), and P32 (32 kDa). These peptides are derived from the following regions of FLP: P13, amino acids 2-123; P21, amino acids 148-346; P32, amino acids 124-423. In this report, we show that P13 binds to DNA nonspecifically and P32, like P21, binds to the FRT site specifically. A single molecule of P32 is able to induce a bend in the DNA of 55 degrees, similar to that induced by intact FLP (63 degrees). P13 enhances the binding of P21 or P32 to the FRT site. Both P32 and P21 can catalyze DNA ligation in combination with P13. P32 can cleave and covalently attach to the FRT site in combination with P13, whereas P21 cannot. These results suggest that FLP contains two DNA-binding domains. A nonspecific DNA-binding region is located in the NH2-terminal 123 amino acids, whereas the region that imparts specific DNA-binding resides in amino acids 148-346. Only the regions in P13 and P21 are needed for ligation activity, but those in P13 and P32 are required for cleavage.

Mechanism of cleavage and ligation by FLP recombinase: classification of mutations in FLP protein by in vitro complementation analysis

The FLP recombinase of the 2 microns plasmid of Saccharomyces cerevisiae is a member of the integrase family of site-specific recombinases. Recombination catalyzed by members of this family proceeds via the ordered cleavage and religation of four strands of DNA. Although the amino acid sequences of integrase family members are quite different, each recombinase maintains an absolutely conserved tetrad of amino acids (R-191, H-305, R-308, Y-343; numbers are those of the FLP protein). This tetrad is presumed to reflect a common chemical mechanism for cleavage and ligation that has evolved among all family members. The tyrosine is the nucleophile that causes phosphodiester bond cleavage and covalently attaches to the 3'-PO4 terminus, whereas the other three residues have been implicated in ligation of strands. It has recently been shown that cleavage by FLP takes place in trans; that is, a FLP molecule binds adjacent to the site of cleavage but receives the nucleophilic tyrosine from a molecule of FLP that is bound to another FLP-binding element (J.-W. Chen, J. Lee, and M. Jayaram, Cell 69:647-658, 1992). These studies led us to examine whether the ligation step of the FLP reaction is performed by the FLP molecule bound adjacent to the cleavage site (ligation in cis). We have found that FLP promotes ligation in cis. Furthermore, using in vitro complementation analysis, we have classified several mutant FLP proteins into one of two groups: those proteins that are cleavage competent but ligation deficient (group I) and those that are ligation competent but cleavage defective (group II). This observation suggests that the active site of FLP is composed of several amino acid residues from each of two FLP molecules.

Ligation of synthetic activated DNA substrates by site-specific recombinases and topoisomerase I

The FLP protein of the 2-microns plasmid of Saccharomyces cerevisiae is a conservative site-specific recombinase that is involved in the amplification of the plasmid. This recombination reaction proceeds via the covalent attachment of the protein to the 3'-phosphoryl group at the site of the breaks through a phosphotyrosine linkage. We have recently developed an assay that measures FLP-mediated strand ligation independent of FLP-mediated cleavage and covalent attachment to the DNA. The substrate for ligation was produced by FLP-induced cleavage of the FLP recognition site followed by digestion with Pronase and was shown to contain (at least) a tyrosine residue at the 3'-PO4 terminus adjacent to the FLP cleavage sites. We have now synthesized artificial substrates that bear a tyrosine residue on the 3'-PO4 of an appropriate oligonucleotide and find that this substrate is ligated as efficiently as the previous ligation substrates that were isolated after FLP cleavage of the substrate. Analogous substrates for other members of the integrase family of recombinases (lambda integrase protein, P1-Cre protein) as well as for mammalian topoisomerase I are also active as ligation substrates with their cognate protein. This class of activated substrates should be useful in the study of breakage and reunion reactions involving DNA.

Mutations of the FLP recombinase gene that cause a deficiency in DNA bending and strand cleavage

We have used site-directed mutagenesis to change several amino acids of the C-terminal portion of the FLP recombinase of Saccharomyces cerevisiae. These residues are absolutely conserved among the six FLP-like proteins from various yeast strains. We have examined the ability of the altered proteins to catalyze recombination in vivo and in vitro and to perform various partial steps of the reaction in vitro. Two of the mutations produced a partial defect in DNA binding but the remainder resulted in normal binding. All of these mutations caused impairment of the ability of the protein to induce the type II bend of the FRT site, and some of these proteins were also defective in DNA strand cleavage. None of the mutations affected the ability of the proteins to perform synapsis between two FRT sites, but some were defective in strand ligation. Interestingly, some mutant proteins showed impairment of the initial stages of the recombination reaction on a linear substrate and yet they maintained the ability to resolve a Holliday intermediate in the reaction. We conclude that this conserved region of the FLP protein is important for the early stage(s) of the recombination reaction.

Ligation activity of FLP recombinase. The strand ligation activity of a site-specific recombinase using an activated DNA substrate

The FLP protein of the 2-microns plasmid of yeast belongs to the integrase family of site-specific recombinases whose members form a covalent bond between a conserved tyrosine of the recombinase and the 3'-phosphoryl group at the site of cleavage. We have made an activated DNA substrate and have shown that FLP can promote efficient strand ligation without forming a covalent intermediate with the DNA substrate. The strand ligation activity of FLP is independent of its ability to cleave DNA. Since site-specific recombinases are members of the larger class of topoisomerases, these findings may be generally applicable to other members of this class of enzymes.