Biomedical subjects

J S Liu

Publications and source records attributed to J S Liu.

At least 19 recordsLinked to original sources

PubMed1999

Human papillomavirus DNA replication. Interactions between the viral E1 protein and two subunits of human dna polymerase alpha/primase.

Papovaviruses are valuable models for the study of DNA replication in higher eukaryotic organisms, as they depend on host factors for replication of their DNA. In this study we investigate the interactions between the human papillomavirus type 11 (HPV-11) origin recognition and initiator protein E1 and human polymerase alpha/primase (pol alpha/primase) subunits. By using a variety of physical assays, we show that both 180- (p180) and 70-kDa (p70) subunits of pol alpha/primase interact with HPV-11 E1. The interactions of E1 with p180 and p70 are functionally different in cell-free replication of an HPV-11 origin-containing plasmid. Exogenously added p180 inhibits both E2-dependent and E2-independent cell-free replication of HPV-11, whereas p70 inhibits E2-dependent but stimulates E2-independent replication. Our experiments indicate that p70 does not physically interact with E2 and suggest that it may compete with E2 for binding to E1. A model of how E2 and p70 sequentially interact with E1 during initiation of viral DNA replication is proposed.

Animals↗

PubMed1999

Detection of cancerous masses for screening mammography using discrete wavelet transform-based multiresolution Markov random field.

When cancerous masses are embedded in and camouflaged by varying densities of parenchymal tissue structures, they are difficult to visually detect on mammograms. We present a novel algorithm based on the discrete wavelet transform (DWT) and multiresolution markov random field (MMRF) that will single out the suspicious masses to assist the attending radiologist in making decisions.

Algorithms↗

PubMed1999

Dual role for nitric oxide in dynorphin spinal neurotoxicity.

The pharmacological effects of nitric oxide synthase (NOS) inhibitors, NO donor, and NOS substrate on dynorphin(Dyn) A(1-17) spinal neurotoxicity were studied. Intrathecal (i.t.) pretreatment with both 7-nitroindazole 1 micromol, a selective neuronal constitutive NOS (ncNOS) inhibitor, and aminoguanidine 1 micromol, a selective inducible NOS (iNOS) inhibitor, 10 min prior to i.t. Dyn A(1-17) 20 nmol significantly ameliorated Dyn-induced neurological outcome. Both 7-nitroindazole and aminoguanidine significantly antagonized the increases of cNOS and iNOS activities measured by conversion of 3H-L-arginine to 3H-L-citrulline in the ventral spinal cord, and blocked the Dyn-induced increases of ncNOS-immunoreactivity in the ventral horn cells 4 h after i.t. Dyn A(1-17) 20 nmol. Pretreatment with Nomega-nitro-L-arginine methyl ester (L-NAME) 1 micromol, a cNOS inhibitor nonselective to both ncNOS and endothelial NOS (ecNOS), did not antagonize Dyn A(1-17) 20 nmol-induced permanent paraplegia but aggravated Dyn A(1-17) 10 nmol-induced transient paralysis and caused permanent paraplegia. Pretreatment with L-NAME 1 micromol 10 min before i.t. Dyn A(1-17) 1.25 and 2.5 nmol, which produced no significant motor dysfunction alone, induced transient paralysis in seven out of 12 and five out of seven rats, respectively. L-NAME 1 micromol plus Dyn A(1-17) 10 nmol induced ncNOS-immunoreactivity expression in ventral horn cells. Both low and high doses of aminoguanidine (0.2-30 micromol) did not affect spinal motor function, but high doses of L-NAME (5-20 micromol) induced dose-dependent hindlimb and tail paralysis associated with spinal cord injury in normal rats. Pretreatment with low-dose Spermine NONOate, a controlled NO releaser, 0.1 and 0.5 micromol 10 min before i.t. Dyn A(1-17) 20 nmol, significantly prevented Dyn spinal neurotoxicity, and high-dose Spermine NONOate 2 micromol i.t. per se induced transient and incomplete paraplegia. But pretreatment with L-Arg 10 micromol 10 min before Dyn A(1-17) 20 nmol produced only partial blockade of Dyn-induced paraplegia. These results demonstrated that relatively specific inhibition of ncNOS and iNOS block Dyn-induced increases in cNOS and iNOS activities and ncNOS-immunoreactivity in ventral spinal cord, but nonspecific inhibition of ncNOS and ecNOS aggravated Dyn spinal neurotoxicity. It suggested that both ncNOS and iNOS play an important role, but ecNOS might be beneficial in Dyn spinal neurotoxicity. Moderate production of NO (at vascular level) has an apparently neuroprotective effect, and overproduction of NO (at cellular level) induces neurotoxicity.

Animals↗

PubMed1999

Bayesian inference on biopolymer models.

MOTIVATION: Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics. RESULTS: The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described. AVAILABILITY: Software and a set of transparencies for a tutorial describing these ideas are available at http://www.wadsworth.org/res&res/bioinfo/

Bayes Theorem↗

PubMed1999

Components of human papillomavirus that activate transcription and support plasmid replication in human airway cells.

Human papillomaviruses (HPVs) such as types 6 and 11 can establish lifelong infections in airway epithelial cells in patients, and long-term infection can lead to pulmonary involvement and death. The mechanisms underlying this persistence depend on both the transcriptional activity of the viral enhancers and promoters and the ability of this virus to maintain its double-stranded circular DNA genome in infected tissues. We investigated the transcription and replication properties of HPV sequence elements and protein products in a human airway cell line. We showed that incorporation of the upstream regulatory region and cotransfection with expression vectors of two virus-encoded proteins, E1 and E2, conferred approximately 5,000-fold stimulation of reporter gene expression. Transient plasmid replication in transfected human airway cells and lungs of FVB/N-C57BL/6 mice was demonstrated by a modified transient replication assay. These results have important implications for viral pathogenesis in airway cells and the potential of HPV-based replicons for gene transfer into airway epithelium.

Animals↗

PubMed1999

The presentation of serum lipids and uric acid in cerebral ischemia.

In this study, we examine the relationship between serum lipids and uric acid in nonembolic cerebral ischemia (NECI) patients. The serum level of total cholesterol (TC) and uric acid increased significantly in male, while TC and triglyceride in female patients. The increase of TC was more significance in female patients. There was no correlation between serum lipids and uric acid in NECI patients or controls, but a significant correlation between triglyceride and uric acid was present in diabetic patient. These findings suggest that lipids and uric acid are essential risk factors for cerebral ischemia in our population. Although there is no association of their metabolism, their parallellic abnormality in diabetic NECI individuals indicates that some possible factors changing in diabetics can influence the metabolic pathway of both lipid and uric acid, which may promote each other for atherogenesis in diabetics.

Aged↗

PubMed1999

Rapid progression of parkinsonism associated with an increase of blood manganese.

In this paper, we report a 72-year-old man whose parkinsonian pictures accelerated rapidly after an ingestion of unknown herb pills. His serum manganese and aluminum level increased 2-fold and 5-fold over physiological level respectively. A reverse of his parkinsonian deterioration was accompanied with a normalization of these metals. Exclusive heavy metals have been widely mentioned in parkinsonism. While industrial source of these metals has extensively been sought, pharmacology is rarely mentioned in this aspect, especially of herb medicine origin. We suggest that an acceleration of parkinsonian pictures should raise the need to re-evaluate the possibility of heavy metal intoxication in parkinsonism. Besides of industrial contamination, we should be alert for the nonindustrial source in our population.

Aged↗

PubMed1998

Inducible nitric oxide synthase expression is selectively induced in astrocytes isolated from adult human brain.

Inducible nitric oxide synthase (iNOS) expression has been shown to be differentially regulated among different cell types and species. In cultures of primary human fetal glial cells, we have shown that astrocytes rather than microglia express iNOS. In the present study, we extended these findings to primary cultures of astrocytes and microglia derived from adult human brains. Mixed cultures of adult brain tissue were stimulated with IL-1beta and IFNgamma, a combination known to induce iNOS maximally in human fetal cells, and the expression of iNOS was determined by immunocytochemistry. Cell types were determined by morphology as well as immunocytochemistry for GFAP (astrocytes) and CD68 (microglia). The results showed that in cultures of adult human glia, iNOS was expressed following stimulation with cytokines, and the expression was restricted to astrocytes. Astrocyte iNOS immunoreactivity was detected both in the cytosol and in a discrete paranuclear region, a pattern noted in human fetal astrocytes. These results demonstrate that the ability to express iNOS is common to both fetal and adult human astrocytes.

Adult↗

PubMed1998

Human Hsp70 and Hsp40 chaperone proteins facilitate human papillomavirus-11 E1 protein binding to the origin and stimulate cell-free DNA replication.

Human papillomavirus replication initiator, the E1 helicase, binds weakly to the origin of DNA replication. Purified human chaperone proteins Hsp70 and Hsp40 (HDJ-1 and HDJ-2) independently and additively enhanced E1 binding to the origin. The interaction between E1 and Hsp70 was transient and required ATP hydrolysis, whereas Hsp40 bound to E1 directly and remained in the complex. A peptide of 20 residues spanning the HPD loop and helix II of the J domain of YDJ-1 also stimulated E1 binding to the origin, alone or in combination with Hsp70 or Hsp40. A mutated peptide (H34Q) had a reduced activity, while an adjacent or an overlapping peptide had no effect. Neither Hsp70 nor the J peptide altered the E1/DNA ratio in the complex. Electron microscopy showed that E1 mainly bound to DNA as a hexamer. In the presence of Hsp40, E1 primarily bound to DNA as a dihexamer. Preincubation of chaperones with viral E1 and template shortened the lag time and increased replication in a cell-free system. Since two helicases are essential for bidirectional replication of human papillomavirus DNA, these results demonstrate that, as in prokaryotes, chaperones play an important role in the assembly of preinitiation complexes on the origin.

Carrier Proteins↗

PubMed1998

IFNs are critical regulators of IL-1 receptor antagonist and IL-1 expression in human microglia.

Because IL-1 is implicated in the pathogenesis of multiple sclerosis, and IFNs are known to alter disease course, we sought to determine whether IFNs can regulate the expression of IL-1 and IL-1R antagonist (IL-1Ra) in primary cultures of human microglia and astrocytes. We found that IL-1 and IL-1Ra are products of microglia but not astrocytes, and IFN-beta and IFN-gamma differentially modulate LPS- and cytokine-induced IL-1 and IL-1Ra. IFN-beta induces IL-1Ra and augments LPS- and IL-4-induced IL-1Ra, but suppresses LPS- and IL-1-induced IL-1, shifting the balance toward the expression of the IL-1Ra. Like IFN-beta, IFN-gamma suppresses the expression of both LPS and IL-1-induced IL-1beta. However, IFN-gamma also suppresses the expression of IFN-beta- and IL-4-induced IL-1Ra so that IFN-gamma may enhance or suppress IL-1 activity depending on the other cytokines present. IL-4 has similar effects to IFN-beta; however, other anti-inflammatory cytokines, did not regulate IL-1 or IL-1Ra in human microglia. Our data demonstrate a novel suppressive effect of IFN-beta and IL-4 on IL-1 activity in human microglia, suggesting that IFN-beta, a therapeutic agent used for multiple sclerosis, could have wider applications in the treatment of other central nervous system disorders in which IL-1 activity has been implicated in the pathogenesis.

Astrocytes↗

PubMed1998

Disassociation of sigma subunit from RNA polymerase of Xanthomonas oryzae pv. oryzae by phage Xp10 infection.

The sigma subunit of Xanthomonas oryzae pv. oryzae is disassociated from host RNA polymerase after phage Xp10 infection. To clarify the possible mechanism for this observation, sigma subunit was purified and an antiserum against sigma subunit was prepared. Immunoprecipitation of RNA polymerase by the anti-core RNA polymerase antiserum, followed by immunoblotting with anti-sigma subunit antibody, revealed that sigma subunit was lost from RNA polymerase within 10 minutes after Xp10 infection. Loss of sigma subunit was not observed under other stress conditions including heat and cold stress, starvation and growth to stationary phase. Two-dimensional immunoblotting analysis did not reveal any covalent modification of either sigma subunit or RNA polymerase after Xp10 infection. These results suggest that separation of th subunit from RNA polymerase may be due to competition with other binding factors.

Antibodies, Bacterial↗

PubMed1998

Identification of neutral and acidic sphingomyelinases in Helicobacter pylori.

We demonstrated for the first time the presence of sphingomyelinase (SMase) in Helicobacter pylori. Activation of SMase has been implicated as the cause of elevation of cellular ceramide levels and consequently of apoptosis. The data indicate that there are two classes of SMase, defined by their optimal pHs and cellular locations, existing in H. pylori. One is an Mg(2+)-dependent membrane-bound enzyme with an optimal activity at pH 7, and the other is an Mg(2+)-independent cytosolic enzyme with an optimal activity at pH 5. Bisalumin, a bismuth salt, was found to inhibit the activities of both forms of SMase regardless of the presence of Mg2+. By Western blot analysis, the membrane-bound SMases of H. pylori and Bacillus cereus were shown to be antigenically related and to have a similar denatured molecular mass of 28 kDa.

Bismuth↗

PubMed1998

Selective inhibition of human glial inducible nitric oxide synthase by interferon-beta: implications for multiple sclerosis.

Nitric oxide generated from the inducible nitric oxide synthase (iNOS) has been implicated in the pathogenesis of multiple sclerosis. Because significant species- and cell-specific differences exist in the expression of iNOS, we used primary human glial cell cultures to screen for an inhibitor of iNOS expression. Remarkably, among numerous soluble factors tested, interferon-beta (IFN-beta) alone showed a selective and potent inhibition of interleukin-1beta/interferon-gamma (IL-1beta/IFN-gamma)-induced iNOS expression in astrocytes. Inhibition of iNOS may provide a mechanism by which IFN-beta can ameliorate inflammation and cytotoxicity in the central nervous system of patients with multiple sclerosis.

Astrocytes↗

PubMed1998

The use of 2 ipsilateral ureteral stents for relief of ureteral obstruction from extrinsic compression.

PURPOSE: We present our early experience with the novel approach of placing 2 parallel stents simultaneously in extrinsically obstructed ureters in which single stents had failed. The increased stiffness of 2 stents reduces kinking and luminal compression, and the potential space between the stents likely preserves flow around as well as through them. MATERIALS AND METHODS: Four patients recently presented with ureteral obstruction secondary to nonurinary tract malignancies. Previous stenting with a single 6F Double-J* stent had failed in all cases. Three patients experienced flank pain and 1 had persistent azotemia within 3 days of initial stent placement. All patients had significant residual sonographic hydronephrosis despite good stent position. In all cases cystoscopy/stent exchange was performed under local anesthesia with intravenous sedation. Parallel 4.7F Double-J stents were placed simultaneously over 2, 0.035 hydrophilic coated glide wires under fluoroscopic guidance after removal of the malfunctioning 6F stent. RESULTS: Stent placement was uneventful in all 4 patients with prompt drainage of contrast material seen after parallel ipsilateral stent placement. Patients tolerated the double 4.7F parallel stents with no discernible difference in irritative symptoms compared to single 6F stents. Flank pain and azotemia resolved in 3 patients, and hydronephrosis improved in all 4 after placement of parallel Double-J stents. All patients remain alive with a mean followup of 5.8 months (range 4 to 8). Except for 1 patient who later underwent ureterolysis, each has subsequently had the stent changed every 3 months. No patient has required proximal urinary diversion (that is percutaneous nephrostomy tube). CONCLUSIONS: Placement of 2 ipsilateral parallel ureteral stents simultaneously is an easy technique. It may obviate percutaneous nephrostomy tube placement in patients in whom drainage with a single stent failed, especially in cases of extrinsic ureteral compression.

Adult↗

PubMed1998

Bayesian adaptive sequence alignment algorithms.

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.

Adenylate Kinase↗

PubMed1998

The carboxyl-terminal region of the human papillomavirus type 16 E1 protein determines E2 protein specificity during DNA replication.

The mechanism of DNA replication is conserved among papillomaviruses. The virus-encoded E1 and E2 proteins collaborate to target the origin and recruit host DNA replication proteins. Expression vectors of E1 and E2 proteins support homologous and heterologous papillomaviral origin replication in transiently transfected cells. Viral proteins from different genotypes can also collaborate, albeit with different efficiencies, indicating a certain degree of specificity in E1-E2 interactions. We report that, in the assays of our study, the human papillomavirus type 11 (HPV-11) E1 protein functioned with the HPV-16 E2 protein, whereas the HPV-16 E1 protein exhibited no detectable activity with the HPV-11 E2 protein. Taking advantage of this distinction, we used chimeric E1 proteins to delineate the E1 protein domains responsible for this specificity. Hybrids containing HPV-16 E1 amino-terminal residues up to residue 365 efficiently replicated either viral origin in the presence of either E2 protein. The reciprocal hybrids containing amino-terminal HPV-11 sequences exhibited a high activity with HPV-16 E2 but no activity with HPV-11 E2. Reciprocal hybrid proteins with the carboxyl-terminal 44 residues from either E1 had an intermediate property, but both collaborated more efficiently with HPV-16 E2 than with HPV-11 E2. In contrast, chimeras with a junction in the putative ATPase domain showed little or no activity with either E2 protein. We conclude that the E1 protein consists of distinct structural and functional domains, with the carboxyl-terminal 284 residues of the HPV-16 E1 protein being the primary determinant for E2 specificity during replication, and that chimeric exchanges in or bordering the ATPase domain inactivate the protein.

Adenosine Triphosphatases↗

PubMed1998

Construction of an inducible nitric-oxide synthase gene transferring vector mediated by retrovirus.

AIM: To construct an inducible nitric-oxide synthase (iNOS) gene transferring vector mediated by retrovirus. METHODS: Recombinant DNA and polymerase chain reaction (PCR) amplification techniques were used. RESULTS: With 2 steps of molecular cloning, the full-length cDNA encoding macrophage iNOS was isolated from plasmid pKSiNOS and subcloned into intermediate vector pSP72, adjusting the restriction enzyme sites in both 5'- and 3'-flanking ends of insert fragment. The retroviral vector pLNCXiNOS which contains iNOS coding region, cytomegalovirus promoter and neomycin resistance (neor) gene was further constructed. The authenticity of insertion size and orientation of iNOS sequence was verified by restriction mapping and PCR analysis with iNOS gene-specific primers. CONCLUSION: Retroviral expression vector carrying iNOS fragment is obtained, which provides a material to establish a model of iNOS gene-modified neurons.

Cloning, Molecular↗

PubMed1997

Extracting protein alignment models from the sequence database.

Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called Probe fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, Probe found on average about four times as many relationships as a pairwise search and yielded many new discoveries. These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences. Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.

Algorithms↗