Biomedical subjects
Publications and source records attributed to Y Cui.
We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 A.
We use molecular dynamics methods to simulate chaperonin-mediated refolding of barnase. A "chaperonin" term is added to the force field in order to simulate the hydrophobic environment in the central cavity of the chaperonins. Two aspects of our simulation results are consistent with experiments: (1) The hydrophobic environment of the central cavity of the chaperonin is an advantageous condition for the refolding of the misfolded intermediates. (2) One cycle of binding and release is not enough for the successful folding. Chaperonin-assisted protein folding maybe a procedure of multiple cycles of binding and release from the chaperonin.
The enterobacterium Erwinia carotovora ssp. carotovora strain 71 (hereafter Ecc71) produces extracellular enzymes such as pectate lyase isozymes (Pels), cellulase (Cel), polygalacturonase (Peh) and protease (Prt). These enzymes degrade plant cell wall components and are largely responsible for the elicitation of soft-rot diseases in plants and plant products. Ecc71 also produces HarpinEcc, the elicitor of hypersensitive reaction (HR) and the quorum-sensing signal, N-(3-oxohexanoyl)-L-homoserine lactone (OHL). OHL controls extracellular enzyme and HarpinEcc production. The levels of these enzymes, as well as the expression of hrpNEcc, the structural gene for HarpinEcc, and ohll, the gene specifying OHL synthesis, are negatively regulated by RsmaA. rsmB, formerly aepH, on the other hand, positively regulates extracellular enzyme production. 6His-RsmA recombinant protein purified from E. coli binds rsmB RNA as indicated by gel mobility shift assays. rsmB comprises 547 bp DNA, which is transcribed from a single start site immediately after a sigma70-like promoter. In Ecc71, two rsmB RNA species are detected: a full-length 479 base rsmB RNA and a 259 base rsmB' RNA. rsmB' DNA hybridizes with the 259 base and the 479 base transcripts. A 3' RNase protection assay revealed that the 259 base and the 479 base RNA species end at the same position immediately after the putative rho-independent terminator. The expression of rsmB-lacZ transcriptional fusions established that the rsmB' RNA is not produced because of the activation of an internal promoter. These data strongly suggest that the 259 base rsmB' RNA is derived by processing of the primary rsmB RNA. In Ecc71, rsmB' expression driven by the lac promoter causes overproduction of Pel, Peh, Cel and Prt, and accumulation of pel-1, peh-1, hrpNEcc and ohll transcripts. By contrast, a plasmid with the rsmB' DNA sequence deleted fails to cause overproduction of the extracellular enzymes in Ecc71. The rsmB' effect also occurs in Escherichia coli as glycogen accumulation is stimulated in the presence of rsmB'. In vivo and in vitro translation as well as mutational analysis of rsmB' have established that rsmB' RNA does not yield a translational product. Therefore, we concluded that the rsmB' RNA itself functions as the regulator. Indeed, the expression rsmB' DNA leads to neutralization of the negative effects of the RNA-binding protein, RsmA, in Ecc71 and Serratia marcescens strain SM274. We propose a model that explains how RsmA and rsmB control the expression of genes for extracellular enzymes.
BACKGROUND: The chemokine receptor, CCR5, has been identified as an essential co-receptor with CD4, which permits entry of human immunodeficiency virus (HIV) into mammalian cells. This receptor may also mediate leukocyte and parenchymal responses to injury by virtue of its binding to locally released chemokines such as RANTES, MIP-1 alpha and MIP-1 beta during inflammation. The localization of CCR5 in human or primate kidney is unknown. In this study we sought to identify sites of CCR5 synthesis through localization of mRNA coding for this peptide. METHODS: CCR5 cDNA cloned into an expression vector was transcribed into a 1.1 Kb antisense riboprobe that was utilized for in situ hybridization (ISH) and Northern blotting studies. RESULTS: Northern analysis demonstrated positive hybridization for CCR5 mRNA in total RNA isolated from allograft nephrectomy tissue with features of severe transplant rejection as well as in kidney tissue with focal interstitial nephritis. No comparable hybridization signal was achieved with human kidney tissue uninvolved by disease. CCR5 mRNA was not identified in intrinsic renal cell types by ISH in normal human (N = 6), normal macaque kidney (N = 5), in kidneys from macaques with established infection by HIV-2 (N = 9), kidneys from macaques infected with HIV-1 (N = 4), nor in kidneys from SIV-infected macaques (N = 5). CCR5 was identified by ISH in human kidneys with features of interstitial nephritis (N = 3) and in rejected human allograft kidneys (N = 14). The expression of CCR5 was restricted to infiltrating mononuclear leukocytes at sites of chronic tubulointerstitial injury and at sites of vascular and interestitial rejection, respectively. CONCLUSIONS: Understanding the localization of CCR5 as well as other chemokine receptors may help us understand how specificity in leukocyte trafficking is achieved in renal inflammatory processes such as allograft rejection and interstitial nephritis. They provide additional evidence that chemokines may be critical mediators of leukocyte trafficking in renal allograft rejection. These findings may account in part for the difficulty in demonstrating HIV infection of renal cells in human HIV infection, since these cells appear to lack constitutive expression of an essential co-receptor needed for viral entry.
Interleukin-12 (IL-12) is one of the important cytokines for promoting the differentiation and maturation of type 1 T helper cells and facilitating the initiation of cell-mediated immune responses. Because of its multi-functional roles in anti-tumor and anti-viral immunity, IL-12 is considered a promising therapeutic cytokine in immunotherapy against cancer and infectious diseases. To evaluate the therapeutic efficacy, an easy and reliable quantitative assay for functional IL-12 is essential. Presently, IL-12 concentration is often determined by ELISA or RIA, which may or may not correlate with IL-12 biological function. Established IL-12 bioassays are based on a time-consuming lymphocyte proliferation assay and require freshly isolated peripheral blood lymphocytes.
We describe a method for making natural, physical movements in a chained polymer by sequentially adjusting a few neighboring torsion angles in the polymer backbone. In addition to being very fast and easy to implement, the method is also very general. It applies equally well to proteins and nucleic acids. This method is then used to design a local refinement procedure. We test the refinement procedure on the minimization of a simple energy function for proteins. The energy function has a simplified potential for hydrophobic interaction, a hydrogen-bond term, and a term for van der Waals interaction. There is considerable current interest in such simple energy functions for protein folding. When applied to refine structures found by a global search method, the refinement is able to produce large reduction in the hydrogen-bond term and the van der Waal term of the energy. We conclude that the method is particularly effective in finding good "packing" of residues in an initially compact conformation.
Mammalian embryos can only survive if they attach to the uterus (implantation) and establish proper maternal-fetal interactions. To understand this complex implantation pathway, we have initiated genomic analysis with a systematic study of the cohort of genes expressed in extraembryonic cells that are derived from the conceptus and play a major role in this process. A total of 2103 cDNAs from the extraembryonic portion of 7.5-day post-conception mouse embryos yielded 3186 expressed sequence tags, approximately 40% of which were novel to the sequence databases. Furthermore, when 155 of the cDNA clones with no homology to previously detected genes were genetically mapped, apparent clustering of these expressed genes was detected in subregions of chromosomes 2, 7, 9 and 17, with 6.5% of the observed genes localized in the t-complex region of chromosome 17, which represents only approximately 1.5% of the mouse genome. In contrast, X-linked genes were under-represented. Semi-quantitative RT-PCR analyses of the mapped genes demonstrated that one third of the genes were expressed solely in extraembryonic tissue and an additional one third of the genes were expressed predominantly in the extraembryonic tissues. The over-representation of extraembryonic-expressed genes in dosage-sensitive autosomal imprinted regions and under-representation on the dosage-compensated X chromosome may reflect a need for tight quantitative control of expression during development.
RpoS (sigma-S or sigma-38) controls a large array of genes that are expressed during stationary phase and under various stress conditions in Escherichia coli and other bacteria. We document here that plant pathogenic and epiphytic Erwinia species, such as E. amylovora; E. carotovora subsp. atroseptica, betavasculorum, and carotovora; E. chrysanthemi; E. herbicola; E. rhapontici; and E. stewartii, possess rpoS genes and produce the alternate sigma factor. We show that rpoS transcription in E. carotovora subsp. carotovora is driven from a major promoter which resides within the nlpD gene located upstream of rpoS as in E. coli. RpoS- E. carotovora subsp. carotovoa strain AC5061, constructed by marker exchange, is more sensitive to hydrogen peroxide, carbon starvation, and acidic pH than its RpoS+ parent strain, AC5006. The basal levels of extracellular pectate lyase, polygalacturonase, and cellulase as well as those of transcripts of E. carotovora subsp. carotovora hrpN (hrpNEcc), the gene for the elicitor of the hypersensitive reaction, are higher in the RpoS- strain than in the RpoS+ parent. Likewise, compared to AC5006, AC5061 causes more extensive maceration of celery petioles. Our findings with the RpoS- mutant and strains carrying multiple copies rpoS+ DNA reveal that rpoS positively controls rsmA expression. We also present evidence that supports the hypothesis that the RpoS effect on extracellular enzyme levels, hrpNEcc expression, and virulence manifests itself by the modulation of rsmA expression.
Although it is essential for protein synthesis to be highly accurate, a number of cases of directed ribosomal frameshifting have been reported in RNA viruses, as well as in procaryotic and eucaryotic genes. Changes in the efficiency of ribosomal frameshifting can have major effects on the ability of cells to propagate viruses which use this mechanism. Furthermore, studies of this process can illuminate the mechanisms involved in the maintenance of the normal translation reading frame. The yeast Saccharomyces cerevisiae killer virus system uses programmed -1 ribosomal frameshifting to synthesize its gene products. Strains harboring the mof2-1 allele demonstrated a fivefold increase in frameshifting and prevented killer virus propagation. In this report, we present the results of the cloning and characterization of the wild-type MOF2 gene. mof2-1 is a novel allele of SUI1, a gene previously shown to play a role in translation initiation start site selection. Strains harboring the mof2-1 allele demonstrated a mutant start site selection phenotype and increased efficiency of programmed -1 ribosomal frameshifting and conferred paromomycin sensitivity. The increased frameshifting observed in vivo was reproduced in extracts prepared from mof2-1 cells. Addition of purified wild-type Mof2p/Sui1p reduced frameshifting efficiencies to wild-type levels. Expression of the human SUI1 homolog in yeast corrects all of the mof2-1 phenotypes, demonstrating that the function of this protein is conserved throughout evolution. Taken together, these results suggest that Mof2p/Sui1p functions as a general modulator of accuracy at both the initiation and elongation phases of translation.
Five children with neuroblastoma (NB) stage IV and five children with rhabdomyosarcoma (RMS) stage III were treated with myeloablative chemotherapy and autologous peripheral blood stem cell transplantation (MCT/PBSCT) in the state of complete remission (CR) achieved by conventional therapy. PBSCs were collected in CR status using a cell separator with blood access through a double-lumen central venous catheter. PBSCs with 1.9+/-0.8x10(5) of CFU-GM per patient weights (kg) were infused following MCT after a period of conventional therapy for 11.1+/-2.1 or 9.7+/-0.9 months in NB or RMS patients, respectively. Regimen-related toxicity of MCT was tolerable and peripheral white blood cell count recovered beyond 1.0x10(3)/microl 10-12 days after infusion of PBSCs in all patients. All of RMS patients and three of five NB patients survived for an average of 31.6 months (ranged 10.8-58.1). The survival rate of these patients was improved as compared with our historical controls, and presumably, with that of conventional chemotherapy previously reported. Despite a limited number of patients, it appears that MCT/PBSCT may be effective in improving survival by preventing relapse which may occur thereafter if treated with conventional therapy alone. Furthermore, MCT/PBSCT reduced the duration of treatment, as compared with that of conventional chemo-therapy. Therefore, this study may suggest the feasibility and promise of the therapy including MCT/PBSCT for children with advanced stages of NB and RMS.
To clarify mortality risks of oesophageal cancer associated with hot tea, alcohol, tobacco and diet, further analyses on the data from a large prospective cohort study in Japan were conducted. The subjects for analysis were 220,272 men and women aged 40 to 69 at the baseline of 1965. There were 440 oesophageal cancer deaths during the period from January 1966 to December 1981. Person-years at risk were 3,065,182 in total. Rate ratio and 95% confidence interval adjusted for attained age, prefecture, occupation and sex were (RR (95% CI)): 1.6 (1.2-2.0) for hot tea (drinking green tea at high temperatures) in comparison with not-hot tea (drinking green tea at moderate temperatures); 2.4 (1.8-3.1) for daily (4 times/week or more) alcohol drinking in comparison with non-drinking; and 2.3 (1.7-3.1) for heavy smoking (15 cigarettes/day or more) in comparison with non-smoking. Dose-response relationships were found in alcohol drinking and smoking among men and women (p for trend; p < 0.001). The rate ratios were not significantly associated with the dietary factors except for green-yellow vegetables (1-3 times/month or less in comparison with daily; RR = 2.0, 95% CI: 1.2-3.1), where a no dose-response trend was observed (p = 0.45). In comparison based on the binary variables, the RR for the subjects with daily alcohol drinking and current smoking was 3.9 with 95% CI of 2.7 to 5.4, relative to those exposed to neither habit. The joint effect of alcohol drinking (A) and smoking (S) was more than additive (A*S > A + S: 3.9 > 1 + (1.0-1) + (1.6-1)). Further sub-analysis showed that the RR for the subjects with daily alcohol drinking, current smoking and hot tea was 5.7 with 95% CI of 3.7 to 8.9, when the reference was the subjects with not-daily alcohol drinking, non-smoking and not-hot tea. Similar results were obtained from further adjustment of green-yellow vegetables. It is concluded that mortality risks of oesophageal cancer in the present cohort were substantially associated with thermal effect of hot tea, alcohol drinking, smoking and lower consumption of green-yellow vegetables. This finding suggests that life-style modification for smoking and dietary habits is essential to reduce the risks of oesophageal cancer in Japan.
OBJECTIVE: To evaluate the accuracy of CT-guided stereotactic biopsy in making correct pathological diagnosis and choosing corresponding management of brain tumors. METHODS: From 1991 to 1995, CT-guided stereotactic biopsy was performed in 310 patients with intracerebral lesions which were deep-seated or located in certain main functional areas. The patients were 198 men and 112 women. Their ages ranged from 4.5 to 70 years (average: 39.3 years). The lesions were located in the deep cerebrum (74 patients), the sellar area (62), the basal ganglion (51), the posterior part of the third ventricle (38), other intraventricleular area (21), the cerebellum (17) and the brain stem (9), and intracranial multiple lesions were found in 38 patients. RESULTS: Brain tumors were diagnosed pathologically in 266 patients (85.8%); inflammatory process in 25 (8.1%), other lesions in 8 (2.6%) and uncertain cases were 11 (3.6%). The overall positive rate of biopsy was 96.4% and the positive rate for brain tumor was 85.8%. Intracranial hematomas after biopsy were found in 5 patients (1.6%). There were no deaths induced by the biopsy or other serious complications. CONCLUSIONS: The results suggest that CT-guided stereotactic biopsy is a reliable method for histopathological diagnosis of brain tumors and it is also of great help in selecting appropriate management.
OBJECTIVE: To determine the epidemiological characteristics and clinical significance of HGV infection, and to compare with HBV and HCV infections. METHODS: Anti-HGV, HBsAg, anti-HBs, anti-HBc and anti-HCV were detected by enzyme-linked immunoassays (EIA). Anti-HGV positive sera were further tested for HGV RNA by a nested reverse transcription polymerase chain reaction (RT-nPCR). RESULTS: The anti-HGV prevalence rate was 12.9%. It was relatively low in children under 10 years, and then increased with age and peaked in the group of 50-60 years of age (29.2%). The positive rate of HBsAg was 12.6%, and it quickly reached the highest (16.2%) in the 5-year old group. The prevalence rate of HBV infection was 64.9%, and increased to a high level in the group of 10 years of age, and maintained high up to 79.2% in the 50 years old group. The HCV infection rate was 15.3%. No anti-HCV positive cases were found in the group under 10 years of age. It was particularly high in the 20-40 years age group, and reached the peak in the group of 30 years old. No significant differences were found in the infection rates of HBV, HCV and HGV between male and female. HGV infection was associated with the history of blood donation, and the sexual transmission between couples. The anti-HGV positive rate of wives with anti-HGV positive husbands was 53.3%, significantly higher than that of those with anti-HGV negative husbands (7.8%). HGV coinfection with HBV or HCV had no influence on serum alanine aminotransferase (ALT). NO ALT elevation was found in the group with HGV infection alone. CONCLUSIONS: The epidemiological characteristics of HGV infection are different from those of HBV and HCV. HGV is transmitted by blood and sex, and does not seem to cause liver damage.
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Treating two cases of vascular palsative tinnitus with digital subtraction angiographic and superselective embolization was reported in this paper. The etiology pathogenesis, clinical sign and its treatment were also discussed.
We applied coronal CT scanning of paranasal sinus to 260 patients with chronic sinusitis before they were performed endoscopy sinus surgery. The correct diagnostic rate was 99.2% in our study. The positive findings of CT were compared with that from normal person. By analyzing, we consider that coronal CT scanning can clearly reveal various anatomic variation for all sinuses, also, it is valuable in evaluating the difficulties of endoscopic sinus surgery and preventing dangerous operative complications.
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The unilateral mucosal samples were taken from 42 patients and were cultured for bacteria. Meanwhile, the antimicrobial susceptibility was determined for 11 antibiotics and the beta-lactamase-producing bacteria(beta LPB) were examined. In 85.71% of all samples, bacterial growth was present. Anaerobic bacteria were present in 21.43% of cases. Predominant aerobic bacteria were alpha-hemolytic streptococci and coagulase-negative staphylococci. Predominant anaerobic bacteria were peptostreptococcus species and bacteroides species. The beta LPB were isolated from 40% patients, which were responsible for the resistance to some antibiotics. The antimicrobial susceptibility testing showed that the antibiotics containing beta-lactamase inhibitor, third-generation cephalosporins and third-generation quinolones had good efficacy. Our findings indicated the bacterial infection may not play the key role in the development of chronic sinusitis and the bacterial infection may not play the key role in the development of chronic sinusitis and the resistance to some antibiotics due to the high prevalence of beta-lactamase production must be considered when the antibiotics therapy is taken.