Lactate dehydrogenase-immunoglobulin G complex in the serum of the postburn patient.
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Adolescent↗
Biomedical subjects
X Huang
Publications and source records attributed to X Huang.
Piecewise exponential survival trees with time-dependent covariates.
Survival trees methods are nonparametric alternatives to the semiparametric Cox regression in survival analysis. In this paper, a tree-based method for censored survival data with time-dependent covariates is proposed. The proposed method assumes a very general model for the hazard function and is fully nonparametric. The recursive partitioning algorithm uses the likelihood estimation procedure to grow trees under a piecewise exponential structure that handles time-dependent covariates in a parallel way to time-independent covariates. In general, the estimated hazard at a node gives the risk for a group of individuals during a specific time period. Both cross-validation and bootstrap resampling techniques are implemented in the tree selection procedure. The performance of the proposed survival trees method is shown to be good through simulation and application to real data.
Biometry↗
Architecture for a Web-based clinical information system that keeps the design open and the access closed.
We are developing the Patient Clinical Information System (PatCIS) project at Columbia-Presbyterian Medical Center to provide patients with access to health information, including their own medical records (permitting them to contribute selected aspects to the record), educational materials and automated decision support. The architecture of the system allows for multiple, independent components which make use of central services for managing security and usage logging functions. The design accommodates a variety of data entry, data display and decision support tools and provides facilities for tracking system usage and questionnaires. The user interface minimizes hypertext-related disorientation and cognitive overload; our success in this regard is the subject of on-going evaluation.
Computer Security↗
An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences.
We describe herein the use of a 2H-labeling strategy to achieve specific assignments of considerably overlapped cross peaks in the 1H-NMR spectrum of a DNA trinucleotide repeat sequence. Our strategy focuses on site-specific 2H-labeling of base moieties to simplify the NMR spectral regions which contain the major portion of the structural information. To achieve efficient preparation of 2H8- or 2H6-labeled DNA and RNA nucleosides and nucleotides, the existing synthetic and purification procedures were significantly improved. Our experiments demonstrate that pyrimidine H6 deuteration reactions may be carried out using non-deuterated base reagents with DMSO-d6 as a 2H donor. These reactions are simple and economic to perform and produce base deuterated nucleosides and nucleotides in high yield. The 2H-labeled residues have been incorporated into oligonucleotides with minor modifications of the existing reaction conditions. Using the homologous CGG repeat sequence, d(CGG)5, as an example, the effectiveness of the site-specific base deuteration strategy is demonstrated. In the otherwise extensively overlapped spectra of d(CGG)5, 2H-labeling has permitted unambiguous identification of a sequential connectivity at a central CG step and confirmation of several other NOE assignments. This information is critical for elucidation of the structure and the folding of the CGG repeat sequences and will contribute to the intensive effort to understand the mechanisms of triplet expansion, which has been implicated in the development of a number of hereditary neurodegenerative diseases. In addition to the two dimensional spectral simplification in a key spectral region using site-specific 2H8/2H6-labeling, the potential applications of the prescribed strategy in homonuclear three dimensional experiments are also discussed.
DNA↗
A tool for analyzing and annotating genomic sequences.
We describe a tool for analyzing and annotating large genomic sequences containing introns. The analysis and annotation tool (AAT) includes two sets of programs, one for comparing the query sequence with a protein database and the other for comparing the query with a cDNA database. Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region. On a data set of 570 DNA sequences, AAT identified 94% of coding nucleotides correctly and 74% of exons exactly. Results of analyzing a human BAC sequence with the AAT tool are also presented. The AAT tool reduces the labor-intensive work of locating the exons of the query sequence and improves the process of defining intron-exon boundaries by using the wealth of available protein and cDNA data.
Amino Acid Sequence↗
Capillary zone electrophoresis with fluid-impervious polymer tubing inside a fused-silica capillary.
A fused-silica capillary was used as a mold in the in situ formation of, and as a sheath for, a highly crosslinked poly(styrene-divinylbenzene) inner tubing having 3-5 microns wall thickness. This 'tube-in-the-tube' construction with the thin-walled, fluid-impervious polymer inner tubing precluded contact between the aqueous buffer solution and the inner wall of the fused-silica capillary. As a result, this structure withstood long-term treatment with highly alkaline solutions without deterioration. In order to hydrophilize the inner surface of the polymer tube, a polyoxyethylene oligomer was grafted to its inner wall and subsequently crosslinked. The inner tube with such hydrophilic coating was also stable to hydrolytic attack by 1 M NaOH. Although the nonpolar polymeric inner surface generated electrosmotic flow as if it had some fixed negative charges, the flow velocity became almost negligibly small once it had been hydrophilized. As illustrated by electropherograms, the hydrophilization of the polymeric inner tube greatly facilitated the CZE of basic proteins in the pH range from 3 to 6 without the need for additives in the electrophoretic medium to mask the silanol groups at the surface of quartz capillaries.
Chemical Phenomena↗
Zinc-induced Alzheimer's Abeta1-40 aggregation is mediated by conformational factors.
The heterogeneous precipitates of Abeta that accumulate in the brain cortex in Alzheimer's disease possess varying degrees of resistance to resolubilization. We previously found that Abeta1-40 is rapidly precipitated in vitro by physiological concentrations of zinc, a neurochemical that is highly abundant in brain compartments where Abeta is most likely to precipitate. We now present evidence that the zinc-induced precipitation of Abeta is mediated by a peptide dimer and favored by conditions that promote alpha-helical and diminish beta-sheet conformations. The manner in which the synthetic peptide is solubilized was critical to its behavior in vitro. Zinc-induced Abeta aggregation was dependent upon the presence of NaCl, was enhanced by alpha-helical-promoting solvents, but was abolished when the peptide stock solution was stored frozen. The Abeta aggregates induced by zinc were reversible by chelation, but could then be reprecipitated by zinc for several cycles, indicating that the peptide's conformation is probably preserved in the zinc-mediated assembly. In contrast, Abeta aggregates induced by low pH (5.5) were not resolubilized by returning the pH milieu to 7.4. The zinc-Abeta interaction exhibits features resembling the gelation process of zinc-mediated fibrin assembly, suggesting that, in events such as clot formation or injury, reversible Abeta assembly could be physiologically purposive. Such a mechanism is contemplated in the early evolution of diffuse plaques in Alzheimer's disease and suggests a possible therapeutic strategy for the resolubilization of some forms of Abeta deposit in the disease.
Alzheimer Disease↗
Genomic organization of the human PP4 gene encoding a serine/threonine protein phosphatase (PP4) suggests a common ancestry with PP2A.
Serine/threonine protein phosphatase type 4 (PP4) belongs to a family of okadaic acid and microcystin-LR-sensitive protein phosphatases. In this study, we report the cloning and characterization of the human PP4 gene. The gene spans about 10 kb and includes one untranslated and eight translated exons. The 5' flanking region of the gene is rich in G and C (60.1%) and lacks TATA and CAAT boxes. Sequence analysis of the 5'-flanking region reveals potential binding sites for transcription factors SP1, AP1, AP2, and several gamma-IRE-CS sites. Two transcription initiation sites were mapped by ribonuclease protection analysis, one to 54 and the other to 84 bp upstream of the ATG initiation codon. PCR analysis of a human/rodent somatic cell hybrid panel maps PP4 to chromosome 16, and comparison of the PP4 gene structure with that of PP2A and PP1 suggests that PP4 is more closely related to PP2A than PP1.
Amino Acid Sequence↗
Glycosylation affects both the three-dimensional structure and antibody binding properties of the HIV-1IIIB GP120 peptide RP135.
We have prepared glycosylated analogues of the principal neutralizing determinant of gp120 and studied their conformations by NMR and circular dichroism spectroscopies. The 24-residue peptide from the HIV-1IIIB isolate (residues 308-331) designated RP135, which contains the immunodominant tip of the V3 loop, was glycosylated with both N- and O-linked sugars. The structures of two glycopeptides, one with an N-linked beta-glucosamine (RP135NG) and the other with two O-linked alpha-galactosamine units (RP135digal), were studied by NMR and circular dichroism spectroscopies. Molecular dynamics calculations based on the NMR data obtained in water solutions were performed to explore the conformational substates sampled by the glycopeptides. The data showed that covalently linking a carbohydrate to the peptide has a major effect on the local conformation and imparts additional minor changes at more distant sites of partially defined secondary structure. In particular, the transient beta-type turn comprised of the -Gly-Pro-Gly-Arg- segment at the "tip" of the V3 loop is more highly populated in RP135digal that in the native peptide and N-linked analogue. Binding data for the glycopeptides with 0.5beta, a monoclonal antibody mapped to the RP135 sequence, revealed a significant enhancement in binding for RP135digal as compared with the native peptide, whereas binding was reduced for the N-linked glycopeptide. These data show that glycosylation of V3 loop peptides can affect their conformations as well as their interactions with antibodies. The design of more ordered and biologically relevant conformations of immunogenic regions from gp120 may aid in the design of more effective immunogens for HIV-1 vaccine development.
Amino Acid Sequence↗
Obliterative airway disease after heterotopic tracheal xenotransplantation: pathogenesis and prevention using new immunosuppressive agents.
BACKGROUND: The purpose of this study was to investigate whether obliterative bronchiolitis might occur after xenogenic pulmonary transplantation. A model for obliterative airway disease (OAD) after tracheal allograft transplantation in the rat undergoes tracheal obliteration with histologic features characteristic of obliterative bronchiolitis in human lung transplant recipients. Using this model, the pathogenesis of OAD and its prevention with immunosuppressive drugs was studied in rat recipients of hamster tracheal grafts. METHODS: Tracheae from 30 hamsters (xenografts) or 23 Brown-Norway rats (allografts) were implanted and wrapped in the greater omentum of untreated Lewis rats. The grafts were removed on day 1, 3, 7, 14, 21, or 28 after transplantation and stained with hematoxylin and eosin and Masson's trichrome and by immunohistochemistry and immunofluorescence (IFL) techniques. In addition, 25 recipients were treated with cyclosporine (CsA, 10 mg/kg p.o.), leflunomide (LFM, 20 mg/kg p.o.), or rapamycin (RPM, 6 mg/kg i.p.) for 14 or 21 days (5 animals per treatment group). Visual and morphometric analyses were used to evaluate the extent of airway obliteration, luminal coverage by respiratory or flattened cuboidal epithelium, and extent and density of peritracheal cellular inflammation. RESULTS: In all xenografts, a neutrophilic infiltration of the mucosa and submucosa was observed from day 1 until day 14 and was associated with complete loss of tracheal epithelium by day 14. A marked peritracheal mononuclear cellular infiltrate mixed with plasma cells and eosinophils was seen on days 7 and 14. Both the extent of peritracheal inflammation and the density of the mononuclear cell infiltrate were significantly increased in xenograft tracheae when compared with the allografts. Tracheal obliteration began on day 14 and reached a maximum of 43% on day 21 with evidence of intraluminal fibrosis. In contrast to IFL of allografts, IFL of xenografts demonstrated marked deposition of rat immunoglobulin in the peritracheal tissue on days 7 and 14. The effects of treatment with immunosuppressive drugs on tracheal graft narrowing and protection of respiratory epithelium were as follows: After 14 days of treatment, the percentage of tracheal graft narrowing was 12%, 23%, and 19% in the no treatment, CsA, and LFM groups, respectively; the percentage of respiratory epithelium at 14 days was 0%, 21%, and 95%. After 21 days of treatment, the percentage of tracheal graft narrowing was 43%, 49%, 12%, and 5% for the no treatment, CsA, LFM, and RPM groups, respectively; the percentage of respiratory epithelium at 21 days was 0%, 39%, 86%, and 0%. Using computerized morphometry, the extent and densities of the peritracheal cellular infiltrates were significantly reduced in LFM- and CsA-treated groups when compared with untreated xenograft controls. LFM and RPM, but not CsA, significantly reduced the degree of luminal obliteration compared with no treatment (P<0.05). LFM and, to a lesser extent, CsA were able to prevent the loss of normal respiratory epithelium. Analysis by IFL revealed a marked decrease in rat immunoglobulin deposition in xenografts from LFM- and RPM-treated groups compared with xenografts from CsA-treated or untreated rats. CONCLUSIONS: (1) OAD occurs not only after tracheal allotransplantation but also after xenotransplantation. (2) Subepithelial infiltration of neutrophils and the appearance of plasma cells and eosinophils in the peritracheal infiltrates distinguished the histology of rejected xenografts from allografts. (3) Antibody deposition was detected by IFL only in xenografts. (4) Treatment with LFM or RPM significantly decreased the severity of luminal obliteration. Importantly, LFM also prevented the loss of respiratory epithelium.
Airway Obstruction↗
Neurokinin-1 receptor antagonist SR140333: a novel type of drug to treat cerebral ischemia.
Substance P (SP) has been implicated in immune responses and could increase glutamate release, and inflammatory reactions are known to be able to potentiate ischemic damage. We have previously found that SP was over-expressed in cerebral ischemia and speculated that SP may play a role in exacerbating ischemic damage. In this study, we examined whether a neurokinin-1 (NK-1) receptor antagonist, SR140333, would have an effect on brain ischemia. Intra-cerebroventricular (i.c.v.) administration of SR140333 (30 micrograms) markedly reduced (37.1 +/- 7.8%, p < 0.001) infarct volume measured 24 h after focal cerebral ischemia in the rat. The SR140333-treated group also exhibited a significantly improved neurological function reflected by the neurological deficit score. The results represented the first demonstration that a NK-1 receptor antagonist may be a novel type of drug for treatment of cerebral ischemia.
Animals↗
sigma factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA.
Thesigmasubunit of RNA polymerase determines promoter recognition and catalyzes DNA strand separation. The -35 promoter region is recognized by a helix-turn-helix motif in region 4, while the -10 region is specified, at least in part, by an amphipathic helix in region 2. We have proposed that conserved aromatic residues insigmaregion 2.3 interact with the non-template strand of the -10 element to drive open complex formation. We now report that Bacillus subtilis sigmaA holoenzyme, but neither core nor sigmaA alone, binds with high selectivity to single-stranded (ss) DNA containing the non-template -10 consensus sequence. UV irradiation of holoenzyme-ssDNA complexes efficiently crosslinks sigmaA to DNA and protease mapping supports a primary contact site in or near region 2. Several mutations in sigmaA region 2.3, shown previously to impair promoter melting, affect ssDNA binding: Y184A decreases binding selectivity, while Y189A and W193A decrease the efficiency of photocrosslinking. These results support a model in which these aromatic amino acids are juxtaposed to ssDNA, consistent with their demonstrated role in stabilizing the open complex.
Bacillus subtilis↗
Residue-based control of helix shape in beta-peptide oligomers.
Proteins and RNA are unique among known polymers in their ability to adopt compact and well-defined folding patterns. These two biopolymers can perform complex chemical operations such as catalysis and highly selective recognition, and these functions are linked to folding in that the creation of an active site requires proper juxtaposition of reactive groups. So the development of new types of polymeric backbones with well-defined and predictable folding propensities ('foldamers') might lead to molecules with useful functions. The first step in foldamer development is to identify synthetic oligomers with specific secondary structural preferences. Whereas alpha-amino acids can adopt the well-known alpha-helical motif of proteins, it was shown recently that beta-peptides constructed from carefully chosen beta-amino acids can adopt a different, stable helical conformation defined by interwoven 14-membered-ring hydrogen bonds (a 14-helix; Fig. 1a). Here we report that beta-amino acids can also be used to design beta-peptides with a very different secondary structure, a 12-helix (Fig. 1a). This demonstrates that by altering the nature of beta-peptide residues, one can exert rational control over the secondary structure.
Amino Acids↗
Classification of localized melanoma by the exponential survival trees method.
BACKGROUND: Over the past 2 decades, remarkable progress has been made in the identification of clinical and pathologic factors that affect the survival of patients with melanoma. Through the use of multivariate regression methods, key prognostic factors, such as tumor thickness, tumor ulceration, invasion level, and lesion location, have been identified. Clinical investigators are often interested in developing criteria to classify melanoma patients into different risk groups based on the key prognostic factors identified. However, classical multivariate regression models are generally less efficient in accomplishing this task than newly developed tree-based methods. METHODS: In this study, the authors applied the exponential survival trees method to analyze a combined data set (n = 4568) from the University of Alabama at Birmingham and the Sydney Melanoma Unit in Camperdown, Australia. A survival tree was created according to prognostic factors that classified patients into homogeneous subgroups by survival. Six clinical and pathologic factors were included in the analysis. This tree-based method provided a superior means of prognostic classification and was shown to have greater ability to detect interactions among the variables than regression models. RESULTS: Tumor thickness was found to be the most important prognostic factor, followed by tumor ulceration and primary lesion site. Some important interactions among these prognostic factors were identified. Five distinct risk groups, defined by tumor thickness, ulceration, and primary lesion site, were created. Patients who had tumor thickness less than or equal to 0.75 mm and lesions on their arms or legs had the best prognosis. Patients who had ulcerated tumors with thickness greater than 4.50 mm had the poorest prognosis. CONCLUSIONS: The authors' analysis, based on exponential survival trees, provides a comprehensive, easy-to-use risk grouping system for classifying patients with localized melanoma. This grouping system would be useful in the clinical management of melanoma patients and in designing and analyzing clinical trials.
Decision Trees↗
Cloning and sequencing of ribosomal protein L27a and a gene similar to human GS1 in Drosophila.
Two closely linked genes were identified and characterized in the 24F region on the left arm of chromosome 2 in Drosophila. One cDNA predicts a protein of 231 amino acids, with a molecular mass of 25.7 kDa. The predicted amino-acid sequence of this protein is 47.2% identical to that of the previously reported human GS1 protein, which is encoded by a gene that is of interest because it is one of the few X-linked genes that escapes X-inactivation. We have accordingly named our gene GS1like (GS1l). The second cDNA begins 383 bp proximal to the first. This cDNA encodes a protein of a predicted 149 amino acids and a molecular mass of 17.0 kDa. This protein represents a homolog of ribosomal protein L27a; thus, we have named the gene RpL27a. This gene might be responsible for the Minute mutation located at 24F. An rpL27a gene was previously localized to 87F/88A; thus, this gene might be present in two locations in Drosophila.
Amino Acid Sequence↗
Tumor infarction in mice by antibody-directed targeting of tissue factor to tumor vasculature.
Selective occlusion of tumor vasculature was tested as a therapy for solid tumors in a mouse model. The formation of blood clots (thrombosis) within the tumor vessels was initiated by targeting the cell surface domain of human tissue factor, by means of a bispecific antibody, to an experimentally induced marker on tumor vascular endothelial cells. This truncated form of tissue factor (tTF) had limited ability to initiate thrombosis when free in the circulation, but became an effective and selective thrombogen when targeted to tumor endothelial cells. Intravenous administration of the antibody-tTF complex to mice with large neuroblastomas resulted in complete tumor regressions in 38 percent of the mice.
Animals↗
Nucleotide sequence of a gene encoding the novel Yersinia enterocolitica heat-stable enterotoxin that includes a pro-region-like sequence in its mature toxin molecule.
A novel ST (Y-STc) produced by a pathogenic strain of Yersinia enterocolitica was recently purified and the mature toxin was found to include the pro-region-like sequence (Yoshino et al., FEBS Lett 362: 319-322, 1995). In the present study, we report the nucleotide sequence of the ystC gene. We also present the amino acid sequence of a ystC gene product secreted by a recombinant strain of Escherichia coli. From the nucleotide sequence of ystC gene, the Y-STc precursor protein was deduced to consist of 72 amino acid residues and to be comprised of two regions (pre- and mature toxin regions), while the known ST precursor proteins are comprised of three regions (pre-, pro-, and mature toxin regions). Therefore, we concluded that a long polypeptide corresponding to a pro-toxin of other Sts is secreted as the Y-STc mature toxin. This implies that the proteolytic processing of a pro-form appearing in the periplasm is not essential for the secretion of Yersinia-ST to the extracellular through the outer membrane. The recombinant Y-STc released by E. coli was found to be shorter and composed of C-terminal 24 amino acid residues of the native Y-STc. On the basis of these results, we propose that the cleavage site between the pro- and mature toxin regions of ST depends on both the amino acid sequence of the pro-toxin and on the bacterial protease system responsible for the maturation.
Amino Acid Sequence↗
The novel heat-stable enterotoxin subtype gene (ystB) of Yersinia enterocolitica: nucleotide sequence and distribution of the yst genes.
The gene (ystB) encoding the novel subtype of the heat-stable enterotoxin (Y-STb) was cloned from the chromosome of a clinical isolate of Yersinia enterocolitica 84-50 (serotype O:5, biotype 1A) and the nucleotide sequence was determined. The ystB contained 216 base pairs that encoded a protein of 71 amino acid residues. The C-terminal 30 residues of the precursor protein exactly corresponded to the amino acid sequence of the Y-STb toxin, purified from the culture supernatant of the wild strain. Homology search revealed that there are 76.9% nucleotide sequence similarity between ystB and the Yersinia kristensenii ST gene, and 73.5% with the Y. enterocolitica prototype sequence of yst (ystA). When tested with the PCR generated ystB specific probe, 36 of 304 Y. enterocolitica strains from 18 countries hybridized with the probe. All the ystB probe positive strains belonged to biotype 1A and mostly to the so-called non-pathogenic serotype O:5, O:6, O:7,8 O:7,13 and O:10, while ystA was predominantly found among the pathogenic serotypes (78.5%). Out of 36 ystB gene positive strains, 18 were clinical origin from six countries, which were also positive in the suckling mice assay suggesting that ystB may play an important role in the pathogenesis, and the so-called non-pathogenic serotypes could be virulent for human.
Amino Acid Sequence↗