Biomedical subjects

Z Sun

Publications and source records attributed to Z Sun.

At least 37 records · Page 2Linked to original sources

PubMed2004

Study design considerations in clinical outcome research of lung cancer using microarray analysis.

BACKGROUND: Prognosis following a diagnosis of primary lung cancer is very poor and varies significantly even after adjusting for known predictors. Inherent and acquired gene alterations could cause failure in lung cancer treatment and patient survival. To search for potential molecular markers with significant and independent predictive value in lung cancer survival, we applied oligo-nucleotide microarray analysis, along with patients' phenotypic profile, in a case-control study. The focus of this report is on the methodology used in the identification of potential genes as prognostic factors. METHODS: Selected from 304 patients at Mayo Clinic, 18 stage I squamous cell lung cancer patients who died within 2 years (high-aggressive) or lived beyond 5 years (low-aggressive) were included in this study. Both a one-to-one matched design (paired) and a two-group design (grouped) were utilized. Matching variables were age, gender, tumor size and grade, smoking status, and treatment. Two-GeneChip-array sets from Affymetrix (HG-U133) were used. We applied multiple analytic approaches including Dchip (Harvard University), SAM (Stanford University), ArrayTools (US National Cancer Institute), and MAS5 (Affymetrix); and integrated multiple results to generate the final candidate genes for further investigation. We evaluated the consistency across the methods and the effects of matched versus grouped design on the results. RESULTS: Using the same pre-processed data under the same criteria for type I error and fold-change in expression intensity, results are 94-100% concordant in the list of significant genes by Dchip and by ArrayTools, and 53% concordant between the paired and the grouped analysis. If using differently pre-processed data, the concordance rate is under 6% even by the same analytic tool. Combining results from all analyses, we found 23 potentially important genes that may distinguish the high- versus low-aggressive squamous cell tumors of the lung. CONCLUSION: Given the generally low consistency of results across analytic algorithms and study design, poor agreement is expected from different investigators reporting candidate genes for the same endpoint. A well-designed study with a carefully planned analytic strategy is critical. We are in the process of validating the 23 preliminary candidate genes found from this study among independent yet comparable cases.

Adult↗

PubMed2003

Enkephalinergic striatal projection neurons become less affected by quinolinic acid than substance P-containing striatal projection neurons as rats age.

While the excitotoxic vulnerability of striatal neurons is known to be greater in juvenile than adult animals, it is uncertain if striatal neuron types decline differentially in their vulnerability with age. To examine this issue, we unilaterally injected quinolinic acid (QA), an N-methyl-d-aspartate (NMDA) receptor agonist, into the striatum of juvenile and adult rats, and used in situ hybridization histochemistry with oligonucleotide probes for preproenkephalin and preprotachykinin mRNA to label surviving enkephalinergic (ENK) and substance P-containing (SP) neurons in adjacent sections through the injection center. The results confirmed that the region of severe damage is greater in young than adult animals, but revealed that at the very center of the QA injection, labeled neuron abundance was lower in adult than juvenile striatum. In juvenile rats, the vulnerability of the ENK neurons at all distances from the injection center was the same as that of the SP neurons. By contrast, in adult rats, the ENK neuron survival was greater than the SP neuron survival at all distances beyond the lesion center. The SP neuron survival outside the injection center in the adult rats was similar to that in juvenile rats, while the ENK neuron survival beyond the injection center was better in adult than juvenile rats. These data indicate that there is an age-dependent decrease in the vulnerability of ENK but not SP striatal projection neurons to QA-mediated injury in rats. The results also raise the possibility that, if an excitotoxic process is involved in HD pathogenesis, a differential age-related decline in the sensitivity of striatal projection neuron types to this process may contribute to the more uniform striatal neuron loss in juvenile-onset Huntington's disease (HD) and the more differential loss in adult-onset HD.

Aging↗

PubMed2002

The differential vulnerability of striatal projection neurons in 3-nitropropionic acid-treated rats does not match that typical of adult-onset Huntington's disease.

In adult-onset Huntington's disease (HD), striatal projection neurons are much more vulnerable than striatal interneurons, but even striatal projection neurons show differences in their vulnerability, with the striatal projection neurons projecting to the internal segment of the globus pallidus being the least vulnerable. Previous studies have shown that systemic chronic treatment with 3-nitropropionic acid (3NP), an inhibitor of succinate dehydrogenase, induces the preferential loss of striatal projection neurons over striatal interneurons that is characteristic of HD, which has been taken to support the hypothesis that the pathogenic defect in HD may involve impaired energy metabolism. We sought to determine whether the patterns of survival for striatal projection neurons in 4-month-old rats after chronic systemic 3NP treatment also resemble those in adult-onset HD. We assessed the projection neuron survival using neuropeptide immunolabeling of striatal efferent fibers in striatal target areas and quantified the degree of fiber loss in the striatal target areas using computer-assisted image analysis. We found that 3NP produced relatively equal loss of striatal fibers and terminals in the globus pallidus, substantia nigra, and entopeduncular nucleus, indicating a nondifferential vulnerability of striatal projection neurons to 3NP-induced impairment in energy metabolism. The results suggest that the 3NP rat model does not fully mimic adult-onset HD pathogenesis.

Animals↗

PubMed2002

Differential changes in striatal projection neurons in R6/2 transgenic mice for Huntington's disease.

In early adult-onset Huntington's disease (HD), enkephalinergic striatopallidal projection neurons show preferential loss, reduced preproenkephalin (PPE) expression in surviving striatopallidal neurons, and loss of fibers in their projection target area. We examined PPE and PPT (preprotachykinin) gene expression in striatal projection neurons and in striatal projection fibers immunoreactive for the PPE product enkephalin (ENK) and the PPT product substance P (SP) in a transgenic HD model, the R6/2 mouse, to see if changes occur in these neuron types similar to those seen in early adult-onset HD. The results show that PPE mRNA level, the number of striatal neurons expressing PPE, and the staining intensity of fibers immunoreactive for ENK in the pallidum were all decreased. By contrast, the SP-containing striatal projection systems to the pallidum and substantia nigra were relatively normal in R6/2 mice. The selective reduction in striatal PPE in R6/2 mice is reminiscent of adult-onset HD, but the preservation of the striatonigral projection system is not. Thus, R6/2 mice do not strictly mimic adult-onset HD in their striatal pathology.

Age Factors↗

PubMed2002

Gut barrier permeability, reticuloendothelial system function and protease inhibitor levels following intestinal ischaemia and reperfusion--effects of pretreatment with N-acetyl-L-cysteine and indomethacin.

BACKGROUND: Pathophysiological mechanisms and ways to intervene on intestinal barrier dysfunction following small intestinal ischaemia and prolonged reperfusion are still not fully clarified. AIMS: To evaluate the effect of oxygen free radical and prostaglandin inhibition on intestinal barrier injury following intestinal ischaemia/reperfusion. METHODS: Endothelial and epithelial barrier permeability was evaluated by clearance of radiolabelled albumin. Parameters included 125I-Escherichia coli uptake rate index, host reticuloendothelial system function and organ distribution, as well as protease inhibitor and proenzyme activities in rats subjected to small intestinal ischaemia for 40 minutes followed by 12 hours reperfusion (ischaemia/reperfusion), pretreated with N-acetyl-L-cysteine or indomethacin. RESULTS: Following ischaemia/reperfusion, endothelial and epithelial permeability increased, reticuloendothelial system activation occurred and plasma protease inhibitors were consumed. N-acetyl-L-cysteine pretreatment resulted in improved endothelial and epithelial barrier integrity, a decrease in protease inhibitor consumption and less pronounced reticuloendothelial system activation. Pretreatment with indomethacin was not effective. CONCLUSION: Oxygen free radicals seem to play an important role in the development of intestinal barrier impairment following ischaemia/reperfusion. N-acetyl-L-cystine may be a potential agent for preventing ischaemia/reperfusion damage.

Acetylcysteine↗

PubMed2002

Early treatment with lexipafant, a platelet-activating factor-receptor antagonist, is not sufficient to prevent pulmonary endothelial damage after intestinal ischaemia and reperfusion in rats.

BACKGROUND: Intestinal ischaemia-reperfusion can lead to pulmonary injury characterised by increased macromolecular leakage and leukocyte sequestration. Important mediators of ischaemia-reperfusion-associated injury include polymorphonuclear granulocytes and platelet-activating factor. AIM: To investigate the potential therapeutic inhibition of platelet-activating factor in intestinal ischaemia-reperfusion associated pulmonary injury, by use of a potent platelet-activating factor-receptor antagonist, lexipafant. METHODS: Rats were subjected to 30 minutes of intestinal ischaemia followed by 3 or 12 hours reperfusion. Lexipafant or saline was given intraperitoneally after 30 minutes reperfusion. RESULTS: Increased leakage of radiolabelled human serum albumin was found in the lungs after intestinal ischaemia followed by 3 or 12 hours reperfusion. Administration of lexipafant did not significantly prevent the increased leakage. Pulmonary myeloperoxidase content increased after intestinal ischaemia-reperfusion, indicating polymorphonuclear granulocyte sequestration through the pulmonary endothelium. The increase in interleukin-1beta seen after 3 hours reperfusion was partly reversed by lexipafant. CONCLUSIONS: Pulmonary injury occurred following intestinal ischaemia-reperfusion, characterised by increased leakage of radiolabelled albumin over the endothelial barrier; correlating with increased pulmonary myeloperoxidase-content, implying involvement of polymorphonuclear granulocytes in the pathogenesis of remote organ injury after intestinal ischaemia-reperfusion. Lexipafant did not significantly decrease severity of pulmonary damage.

Animals↗

PubMed2002

Effects of apolipoprotein A-IV genotype on glucose and plasma lipoprotein levels.

The effects of apolipoprotein (apo) A-IV genotype on serum glucose, total cholesterol, low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, triglyceride and glucose concentrations were ascertained in a population of 373 men and 361 women with a mean age of about 57 years. Subjects were evaluated at entry into a lifestyle intervention program. Apolipoprotein A-IV genotype variations at residues 347 and 360 were examined, as these mutations affect the sequence of apo A-IV, a major protein constituent of intestinal triglyceride-rich lipoprotein and HDL. With regard to the apo A-IV 360 mutation, 16.4% of the females and 13.4% of the males carried the apo A-IV 2-allele, almost entirely in the heterozygous state. No effect of the apo A-IV 1/2 genotype was observed in either men or women on total cholesterol, LDL cholesterol, HDL cholesterol, triglyceride, the total cholesterol (TC)/HDL ratio, or on A-I, A-IV and apo B levels. This was also the case for the apo A-IV 347 mutation. However, women with the apo A-IV 360 1/2 genotype had significantly (p < 0.005) higher glucose levels (105.5 mg/dl) compared with the 1/1 wild-type (94.0 mg/dl). All analyses were also adjusted for age, body mass index, medications, alcohol use and cigarette smoking. The prevalence of the 347 mutation was somewhat higher than the 360 mutation, with 29% of the females and 32.0% of the males being heterozygous for this mutation, and 3.9% of the females and 5.4% of the males being homozygous for this mutation. These data are consistent with the concept that the apo A-IV 360 and 347 genotypes have no significant effect on apo A-IV levels and other lipid parameters in either gender. However, apo A-IV 360 1/2 genotype did have a significant effect on serum glucose levels in women.

Apolipoproteins↗

PubMed2001

vhnf1, the MODY5 and familial GCKD-associated gene, regulates regional specification of the zebrafish gut, pronephros, and hindbrain.

Mutations in the homeobox gene vHnf1 are associated with human diseases MODY5 (maturity-onset diabetes of the young, type V) and familial GCKD (glomerulocystic kidney disease). In an insertional mutagenesis screen in zebrafish, we isolated mutant alleles of vhnf1. Phenotypes of these mutants include formation of kidney cysts, underdevelopment of the pancreas and the liver, and reduction in size of the otic vesicles. We show that these abnormalities arise from patterning defects during development. We further provide evidence that vhnf1 regulates the expression of key patterning genes for these organs. vhnf1 is required for the proper expression of pdx1 and shh (sonic hedgehog) in the gut endoderm, pax2 and wt1 in the pronephric primordial, and valentino (val) in the hindbrain. Complementary to the loss-of-function phenotypes, overexpression of vhnf1 induces expansion of the val expression domain in the hindbrain. We propose that vhnf1 controls development of multiple organs through regulating regional specification of organ primordia. The similarity between vhnf1-associated fish phenotypes and human symptoms suggests a correlation between developmental functions of vhnf1 and the molecular etiology of MODY5 and GCKD.

Amino Acid Sequence↗

PubMed2001

[Clinical study on treatment of secondary epilepsy caused by intracranial inflammatory granuloma by removing the lesion and bipolar coagulation].

OBJECTIVE: To study the clinical effects of treatment of secondary epilepsy caused by intracranial inflammatory granuloma by resection of the local focus and resection of local focus combined with bipolar coagulation. METHODS: Twenty-five cases of secondary epilepsy caused by intracranial inflammatory granuloma that were treated from January 1992 to June 1996 (the first group) underwent operation of resection of intracranial granuloma. Pathological examination of the specimens resected during operation was made. Twenty-three cases treated from July 1996 to December 1999 (the second group) underwent operation of the same style and low power thermal cauterization of the surface of multiple cerebral cortex. Specific antibiotic treatment lasted one month after operation for both groups. Antiepileptics were used at least for two years. RESULTS: In the first group, eighteen cases had been followed up, five cases of which showed unsatisfying control of symptoms of epilepsy; and 7 cases were lost to follow-up. In the second group, twenty cases had been followed up and their symptoms of epilepsy were controlled satisfying except in one case. CONCLUSION: Low power thermal cauterization of the horizontal fibers among the neurons in cerebral cortex under pia mater is one of the essential measures for treatment of secondary epilepsy caused by intracerebral inflammatory granuloma. It is of equal importance as resection of local lesion.

Adolescent↗

PubMed2001

Dynamic flexibility in the Escherichia coli genome.

Empirical rules based on tetranucleotide parameters were presented to predict the structural parameters twist (Omega), roll (rho), tilt (tau) and slide (D(y)). A statistical mechanical model was used to analyze the flexibility of the Escherichia coli genome. The replication terminus region displayed a low level of flexibility. A strong correlation can be seen between G+C content and flexibility. Average flexibilities in the coding regions were found to be significantly larger than those in non-coding regions. The flexible characteristics in the 5'-neighborhood of the coding regions and in three class sigma promoter sequences in the E. coli genome were also analyzed.

Escherichia coli↗

PubMed2001

[Persistent ectopic pregnancy, report of seven cases].

OBJECTIVE: To investigate and evaluate the occurrence, diagnosis and treatment of persistent ectopic pregnancy. METHODS: 411 patients with ectopic pregnancy treated via laparoscopy or laparotomy between July 1995 and June 2000 were reviewed. The clinic manifestations of patients who were successfully treated by laparoscopic surgery and those with persistent ectopic pregnancy were analyzed by multivariate stepwise logistic regression. RESULTS: Seven cases with persistent ectopic pregnancy occurred after laparoscopic surgery with an incidence rate of 3.5%. Six cases had been treated by conservative approach and one case by tubectomy. Persistent ectopic pregnancy was diagnosed in two cases because of abdominal pain and intra-abdominal hemorrhage and in five cases because of plateauing beta-hCG titers. Two of the seven cases underwent a second time laparoscopic surgery and five were treated with methotrexate. The size of ectopic mass and the absence of villi by pathologic finding were relevant factors of persistent ectopic pregnancy. CONCLUSION: Small mass of ectopic pregnancy, short amenorrhea time, and biopsy specimens in which no villi are found are all warning indicators of persistent ectopic pregnancy. Close postoperative beta-hCG surveillance is critical for diagnosis and treatment.

Chorionic Gonadotropin, beta Subunit, Human↗

PubMed2001

Salicylate uniquely induces a 27-kDa protein in tubercle bacillus.

Salicylate was found to uniquely induce a 27-kDa protein in Mycobacterium tuberculosis complex organisms but not in Mycobacterium smegmatis or Escherichia coli. The structural analogue antitubercular para-amino-salicylate also induced the 27-kDa protein but to a somewhat lower level than salicylate. Other structural analogues such as benzoic acid and acetyl salicylic acid (aspirin) did not induce the 27-kDa protein. Western blot analysis indicated that the 27-kDa protein was localized mainly in the cytoplasm. The 27-kDa protein was not expressed at different growth phases in the absence of salicylate. The 27-kDa protein was identified as a putative benzoquinone methyltransferase (Rv0560c), which has several homologues in the M. tuberculosis genome. The cloned 27-kDa gene was found to express constitutively in E. coli, M. smegmatis and BCG with or without salicylate.

Aminosalicylic Acid↗

PubMed2001

High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are the foundation of powerful complex trait and pharmacogenomic analyses. The availability of large SNP databases, however, has emphasized a need for inexpensive SNP genotyping methods of commensurate simplicity, robustness, and scalability. We describe a solution-based, microtiter plate method for SNP genotyping of human genomic DNA. The method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification of the signal using fluorescent primers. Only the probe with a 3' base complementary to the SNP is circularized by ligation. RESULTS: SNP scoring by ligation was optimized to a 100,000 fold discrimination against probe mismatched to the SNP. The assay was used to genotype 10 SNPs from a set of 192 genomic DNA samples in a high-throughput format. Assay directly from genomic DNA eliminates the need to preamplify the target as done for many other genotyping methods. The sensitivity of the assay was demonstrated by genotyping from 1 ng of genomic DNA. We demonstrate that the assay can detect a single molecule of the circularized probe. CONCLUSIONS: Compatibility with homogeneous formats and the ability to assay small amounts of genomic DNA meets the exacting requirements of automated, high-throughput SNP scoring.

Journal Article↗

PubMed2001

First experimental observation on different ionic states of the tert-butoxy [(CH3)3CO*] radical.

A continuous tert-butoxy (CH3)+CO* radical beam is produced in situ by respective pyrolysis of both (CH3)3CONO at 115(+/-0.5) degrees C and (CH3)3COOC(CH3)3 at 87(+/- 0.5) degrees C. By combining the HeI photoelectron (PE) spectrum with the improved density function theory (DFT) calculations, we have concluded that the (CH3)3CO* radical has C3V symmetry and X2E ground state. The study does not only provide the ionization energies of different ionic states of the (CH3)3CO* radical for the first time, but also the first example in which there have been similar vibrational structures in different ionic states caused by removal of the electron on an orbital. It is also pointed out that (CH3)3CONO is a good source for obtaining the (CH3)3CO* radical beam, and that NO is a stable regent for the active radical. The results will promote the studies in electron spin resonance (ESR) research on the mechanisms of both the initiation of the formation of a new radical and the radical-chain polymerization in which the (CH3)3CO* radical participates.

Journal Article↗

PubMed2001

Ligand-dependent interaction of estrogen receptor-alpha with members of the forkhead transcription factor family.

Estrogen acting through the estrogen receptor (ER) is able to regulate cell growth and differentiation of a variety of normal tissues and hormone-responsive tumors. Ligand-activated ER binds DNA and transactivates the promoters of estrogen target genes. In addition, ligand-activated ER can interact with other factors to alter the physiology and growth of cells. Using a yeast two-hybrid screen, we have identified an interaction between ER alpha and the proapoptotic forkhead transcription factor FKHR. The ER alpha-FKHR interaction depends on beta-estradiol and is reduced significantly in the absence of hormone or the presence of Tamoxifen. A glutathione S-transferase pull-down assay was used to confirm the interaction and localized two interaction sites, one in the forkhead domain and a second in the carboxyl terminus. The FKHR interaction was specific to ER alpha and was not detected with other ligand-activated steroid receptors. The related family members, FKHRL1 and AFX, also bound to ER alpha in the presence of beta-estradiol. FKHR augmented ER alpha transactivation through an estrogen response element. Conversely, ER alpha repressed FKHR-mediated transactivation through an insulin response sequence, and cell cycle arrest induced by FKHRL1 in MCF7 cells was abrogated by estradiol. These results suggest a novel mechanism of estrogen action that involves regulation of the proapoptotic forkhead transcription factors.

Amino Acid Sequence↗

PubMed2001

Resuscitation of dormant Mycobacterium tuberculosis by phospholipids or specific peptides.

The presence of dormant tubercle bacilli presents a major problem for tuberculosis treatment. The culture supernatant of Mycobacterium tuberculosis was previously shown to resuscitate dormant bacilli in vitro. Here we report identification of active components as phospholipids and a tuberculosis protein Rv1174c. Remarkably, dormant bacilli from a one year old culture which failed to form any colonies could be resuscitated with peptides derived from Rv1174c and formed 10(5-7) colonies/ml. This finding represents the first unambiguous demonstration of resuscitation of dormant tubercle bacilli in vitro and may have implication for the study of mycobacterial dormancy and the design of novel strategies for improved treatment of tuberculosis.

Adaptation, Biological↗

PubMed2001

CaM kinase II-dependent suppression of nicotinic acetylcholine receptor delta-subunit promoter activity.

Nerve-induced muscle activity suppresses nicotinic acetylcholine receptor (nAChR) gene expression by increasing intracellular calcium levels. This suppression is mediated by nAChR promoter sequences harboring at least 1 E-box (CANNTG) that bind myogenic helix-loop-helix transcription factors. How muscle depolarization or increased calcium mediates changes in nAChR promoter activity is not well understood. In chick muscle, protein kinase C (PKC) activation is necessary for activity-dependent nAChR gene suppression. Similar effects of PKC activation have not been found in mammalian skeletal muscle. Therefore, we used rat primary muscle cultures to screen for other calcium-regulated enzymatic activities that may mediate the effects of muscle activity and calcium on nAChR promoter activity. We report here that calcium/calmodulin-dependent protein kinase II (CaM kinase II) can specifically suppress nAChR promoter activity in mammalian muscle. This regulation was mediated by a single E-box sequence residing in the previously characterized nAChR delta-subunit genes 47-base pair activity-dependent enhancer. In vitro protein/DNA interaction studies suggest that CaM kinase II inhibits binding of the myogenic factor, myogenin, to the delta-promoter 47-base pair activity-dependent enhancer. CaM kinase activity is increased in active muscle and inhibition of this enzymatic activity results in increased nAChR delta-promoter activity. Therefore, CaM kinase II may represent a previously unappreciated activity that participates in coupling muscle depolarization to nAChR gene expression.

Animals↗

PubMed2001

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach.

We have introduced a new method of protein secondary structure prediction which is based on the theory of support vector machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than that of traditional machine learning approaches, including neural networks.The first use of the SVM approach to predict protein secondary structure is described here. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of segment overlap accuracy SOV=76.2 % through sevenfold cross validation on a database of 513 non-homologous protein chains with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q(3) achieved 73.5 %, which is at least comparable to existing single prediction methods. Furthermore a useful "reliability index" for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.

Computer Simulation↗