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S Zhao

Publications and source records attributed to S Zhao.

At least 73 records · Page 4Linked to original sources

Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation.

We compiled and analyzed a data set of paired protein structures containing proteins for which multiple high-quality uncomplexed atomic structures were available in the Protein Data Bank. Side-chain flexibility was quantified, yielding a set of residue- and environment-specific confidence levels describing the range of motion around chi1 and chi2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side-chain motion and estimating the extent of side-chain motion in protein structure prediction. We compare the performance of a simple 40 degrees threshold with these quantitative confidence levels in a critical evaluation of side-chain prediction with the program SCWRL.

Databases, Factual↗

Cloning and characterization of human and mouse mitochondrial elongation factor G, GFM and Gfm, and mapping of GFM to human chromosome 3q25.1-q26.2.

Similar to the translational system in the cell cytoplasm, the initiation, elongation, and termination of protein synthesis in the mitochondria of eukaryotes are catalyzed by several protein factors. These factors, from the viewpoint of evolution, are more closely related to the corresponding prokaryotic factors than to those in the eukaryotic cytoplasm. In this paper, we isolated two cDNAs coding for human and mouse mitochondrial elongation factor G (GFM and Gfm, respectively). The GFM cDNA, which is 3481 bp in length, predicts a protein of 751 amino acids sharing 84 and 42% identity and 88 and 62% similarity to rat EF-G(mt) and Escherichia coli EF-G, respectively, and 24% identity and 39% similarity to human EF-2, the equivalent of EF-G in the cytoplasm. The mouse Gfm cDNA is 2564 bp and contains an intact open reading frame that encodes 751 amino acids showing 89% sequence identity and 94% similarity to human GFM. Northern blot analysis of human GFM revealed three transcripts of 3.8, 3.4, and 2.9 kb. The first two were expressed at high levels in heart, skeletal muscle, and testis, at moderate levels in liver and kidney, and at low levels in other tissues including brain, placenta, and lung, while the last transcript was expressed only in testis. The relative abundance of GFM was consistent with the observations for human EF-Tu(mt) and EF-Ts(mt), the other two mitochondrial elongation factors, indicating that the three factors were expressed at corresponding levels. The expression pattern of mouse Gfm was also determined, which showed that Gfm was expressed as a 3.0-kb transcript, abundantly in heart, skeletal muscle, kidney, and testis. In addition, GFM was assigned to human chromosome 3q25.1-q26.2 by the radiation hybrid mapping method. The genomic organization of GFM was also analyzed by comparing this cDNA with a genomic DNA sequence (Accession No. AC010936), which showed that GFM contained 18 exons and spanned at least 40 kb.

Amino Acid Sequence↗

[Expression of telomerase subunits and its relationship with telomerase activity in nasopharyngeal carcinoma].

OBJECTIVE: To study the expression of telomerase subunits and its relationship with telomerase activity in nasopharyngeal carcinoma. METHODS: The expression of telomerase subunits and the telomerase activity were examined in the same sample from nasopharyngeal carcinoma (NPC) as well as from chronic inflammation of nasopharyngeal epithelium (CINE) with RT-PCR and PCR-ELISA respectively. RESULTS: (1) hTERT mRNA was expressed in 38 of 43 cases of NPC (88%), and in none of the 16 cases of CINE (0%) (P < 0.05). (2) hTR was expressed in 39 of the 43 cases of NPC (90.7%),and in 14 of the 16 cases of CINE (87.5%) (P < 0.05). TP1 mRNA was expressed in 38 of the 43 cases of NPC (88%), and in 14 of the 16 cases of CINE (87.5%). There was no statistically significant difference between the expression of hTR and TP1 mRNA in NPC and their expression in CINE (P > 0.05). (3) Telomerase activity was detected in 37 of the 43 cases of NPC (86%) and in none of the 16 cases of CINE (0%) (P < 0.05). There was a significant correlation between the expression of hTERT mRNA in NPC and CINE (P < 0.05). No correlation was observed between telomerase activity and the expression of hTR and TP1 mRNA (P > 0.05). (5) No correlation was observed between the clinicopathological features of NPC and CINE (such as clinical stage and lymph node metastasis) and the expression of any of the telomerase subunits (P > 0.05). CONCLUSION: The expression of hTERT may play a critical role in regulation of telomerase activity, and detection of hTERT mRNA might be useful for clinical diagnosis of NPC.

Carcinoma, Squamous Cell↗

[Predictive value of combined application of umbilical artery color Doppler velocimetry, nonstress testing and ultrasonography in monitoring umbilical cord entanglement].

OBJECTIVE: To explore the predictive value of combined application of umbilical artery color Doppler flow monitoring (CDFI), nonstress testing (NST) and ultrasonography in monitoring umbilical cord entanglement. METHODS: 1 860 cases of pregnant women between gestational ages of 37 approximately 42 weeks were studied 1 approximately 2 weeks before delivery by CDFI, nonstress testing (NST) and ultrasonography to monitor umbilical cord entanglement. RESULTS: The prevalence rate of umbilical cord entanglement was 23.23% (432/1 860). Positive predictive value and negative predictive value were 95.4 % (412/432) and 98.6% (1 408/1 428) respectively. The rate of accuracy was 97.8% (1 820/1 860). The rate of fetal distress among the fetuses with umbilical cord round the body or four limbs was 85.29% (23/34) and the incidence of cesarean section in this group was 88.28% (30/34). The rate of fetal distress among the fetuses with umbilical cord round the neck was 13.06% (52/398) and the incidence of cesarean section in this group was 44.94% (178/398). The rates of fetal distress and cesarean section were significantly higher in the group with umbilical cord around the body or four limbs than in the group with umbilical cord around the neck (chi(2) = 107.27 and 23.76 respectively, P < 0.001). The systolic/diastolic (S/D) ratio was basically in normal ranges in the group with the umbilical cord round the neck. In cardiotopography (CTG), umbilical cord entanglement mainly showed variable deceleration (VD), early deceleration (ED), nonreaction on NST, and late deceleration (LD) on oxytocin challenge test (OCT). Prolonged fetal heart rate deceleration (PD) could be seen in the group with umbilical cord around the body or four limbs. CONCLUSION: The combined application of umbilical artery color Doppler velocimetry, nonstress testing and ultrasonography have an important auxiliary value in monitoring umbilical cord entanglement. It remarkably increases the positive predictive rate as a valuable reference for the choice of delivery form.

Adult↗

[Relation between BDNF and synaptic reorganization of hippocampal mossy fibers].

OBJECTIVE: To investigate the relation between brain-derived neurotrophic factor (BDNF) and synaptic reorganization of hippocampal fibers (MF). METHODS: Antisense or sense oligomucleotides to BDNF and/or PBS buffer were injected into the cerebal ventricles of rats of epileptic model induced by kainic acid (KA) and control rats respectively. Immunohistochemical staining and Timm's silver sulfide staining were used to examine the effect of antisense oligonucleotides to BDNF upon the MF sprouting in the KA model and control rats. RESULTS: Timm's staining showed that multiple aberrant Timm's granules were found in the inner molecular layer (IML) of the dentate gyrus of hippocampus of the KA model rats intracerebroventricularly injected with sense oligonucleotides to BDNF or PBS, less aberrant Timm's granules were found in the hippocampal IML of KA model rats intracerebroventricularly injected with antisense oligonucleotides to BDNF, and no aberrant Timm's granule was found in the hippocampal IML of non-KA model rats intracerebroventricular injected with antisense oligonucleotides to BDNF. Immunohistochemical staining showed multiple BDNF immunologically labeled neurons in the hilus and CA3 region of hippocampus of KA model rats intracerebroventricularly injected with sense oligonucleotides to BDNF and PBS, less in the KA model rats intracerebroventricularly injected with antisense oligonucleotides to BDNF, and only a few in the non-KA model rats. The A value in both Timm's and immunohistochemical sections of KA model rats was higher than that of non-KA model rats. The A value in both Timm's and immunohistochemical sections of KA model rats was significantly lower in the groups injected with antisense oligonucleotides to BDNF than in the group injected with sense oligonucleotides. CONCLUSION: BDNF may play an important role in promoting the MF sprouting caused by repeated epileptic convulsion in the course of MF synaptic reorganization. The expression of BDNF protein can be upregulated by subcutaneous injection of KA and be decreased by intracerebroventricular injection of antisense oligonucleotides to BDNF.

Animals↗

Mouse phosphoglycerate mutase M and B isozymes: cDNA cloning, enzyme activity assay and mapping.

Two mouse cDNAs encoding the non-muscle-specific or brain isoform (type B, Pgam1) and the muscle-specific isoform (type M, Pgam2) of phosphoglycerate mutase (PGAM) were isolated and characterized. Pgam1 contains a 765 bp open reading frame (ORF) coding for a 254-residue protein while Pgam2 contains a 762 bp ORF coding for a 253-residue protein. The deduced proteins of mouse Pgam1 and Pgam2 are highly similar to those of human and rat (> or = 93% similarity). Northern blot analysis showed that the expression patterns of Pgam1 and Pgam2 were distinct. Pgam1 was expressed as a 2.1-kb transcript highly in brain and kidney and moderately in liver, thyroid, stomach and heart, whereas Pgam2 was expressed as a 1.0-kb transcript highly in muscle, testis and moderately in heart and lung, but was not detectable in the other six tissues examined. Transfecting the cDNA fragments containing the entire ORFs of these two cDNAs into COS7 cells for transient expression, respectively, the enzyme activities of mouse Pgam1 and Pgam2 were detected to be 2.2-2.5 times of those of COS7 cells and COS7 cells transfected with vector, proving the validity of mouse Pgam1 and Pgam2 cDNAs we report here. Pgam1 and Pgam2 were assigned to 116.16 cR from D19Mit52 and 29.57 cR from D11Mit129, respectively, by radiation hybrid method. The partial genomic sequence of Pgam2 was determined, which showed that mouse Pgam2 consisted at least three exons and two introns. In addition, a pseudogene of Pgam1, Pgam1-ps1, was identified from mouse genomic sequence.

Amino Acid Sequence↗

A high-resolution radiation hybrid map of the human genome draft sequence.

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.

Algorithms↗

Integration of cytogenetic landmarks into the draft sequence of the human genome.

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

Chromosome Aberrations↗

Cloning and characterization of a novel human leptin receptor overlapping transcript-like 1 gene (LEPROTL1).

A new full-length cDNA encoding a novel protein was isolated from our human fetal brain cDNA library. The cDNA consists of 2701 bp and has a putative open reading frame encoding 131 amino acids which possesses a JAK binding site (Pro(46)-Ile-Pro(48) which is preceded by a cluster of hydrophobic residues) and is highly homologous to the leptin receptor gene-related protein (OB-RGRP). Northern blot analysis showed that this new gene is widely expressed in human tissues and radiation hybrid mapping placed the gene to human chromosome 8p21.1-8p21.2.

Amino Acid Sequence↗

The influence of ATP on the association and unfolding of the tyrosine repressor ligand response domain of Haemophilus influenzae.

The secondary structure of the ligand response domain of the Haemophilus influenzae tyrosine repressor, TyrR(lrd), was investigated using CD spectroscopy which revealed 42.5% alpha-helix, 17.6% beta-sheet, and 39.9% loops. Quaternary structure analysis by fluorescence anisotropy showed that TyrR(lrd) is monomeric at a concentration of 100 nM to 2 microM but that the protein readily dimerizes in the presence of its natural ligand ATP. Equilibrium unfolding studies of TyrR(lrd) using guanidinium hydrochloride suggested a two-state model with no detectable stable intermediates. The unfolding transition monitored by CD spectroscopy was responsive to tyrosine and ATP resulting in a shift to higher denaturant concentrations in the presence of these ligands. Differential scanning calorimetry yielded melting temperatures, T(m), of 51.15 and 58.07 degrees C for the unliganded and for the ATP-liganded protein, respectively. ATP is thus proposed to be a major structural cofactor for the molecular architecture of TyrR(lrd).

Adenosine Triphosphate↗

A comprehensive BAC resource.

The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to minimize the redundant work for the research community, The Institute for Genomic Research (TIGR) comprehensive BAC resource (cBACr) (http://www.tigr.org/tdb/BacResource/BAC_resourc e_intro. html) was built as an expansion of the TIGR human BAC ends database. This resource collects, integrates and reports the information on library, maps, sequence, annotation and functions for each human and mouse BAC. The current database contains 635 016 human BACs and 265 617 mouse BACs that were characterized by various approaches, among which 22 705 human clones and 1000 mouse clones have sequence and annotation data.

Animals↗

Electrophoretic separation of tryptophan enantiomers in biological samples.

A method for the determination of D- and L-tryptophan (Trp) in biological samples is described. The amino acid enantiomers were precolumn-derivatized with a fluorescence tagging reagent, naphthalene-2,3-dialdehyde (NDA). In the presence of hydroxypropyl-gamma-cyclodextrin (HP-gamma-CD) as the chiral selector, NDA-tagged Trp enantiomers were well resolved by micellar electrokinetic chromatography (MEKC). Using laser induced fluorescence (LIF) detection, a detection limit of 3.3 x 10(-8) M Trp was obtained. The method was applied to the determination of Trp enantiomers in biological samples including human urine and cerebrospinal fluid (CSF), rat brain tissue, and Aplysia ganglia. No interference from other amino acids or the endogenous compounds in the sample matrices was observed. D-Trp was found at the sub-microM level in human urine samples collected from several healthy subjects. Further, the determination of DL-Trp residues in small quantities (10 microg) of peptides after acid hydrolysis is demonstrated.

Chromatography, Micellar Electrokinetic Capillary↗

Quantification of D/L-aspartic acids in Aplysia californica central nervous system by beta-cyclodextrin modified micellar electrokinetic chromatography.

In presence of an organic modifier (e.g. methanol), separation of amino acid enantiomers tagged with naphthalene-2,3-dicarboxaldehyde by beta-cyclodextrin modified micellar electrokinetic chromatography was dramatically improved. Coupled with laser-induced fluorescence detection, the method was well suited for analysis of D/L-amino acid enantiomers present in mass/volume-limited biological samples such as cell clusters. The five major ganglia dissected from the central nervous system of Aplysia californica, a widely used neuronal model, were analyzed to determine D- and L-aspartic acid enantiomers both free and bound in proteins/tissue matrix. The analyses revealed high levels of free D-aspartic acid ranging from 0.13 to 0.82 micromol/g wet tissue (or 6.0-21.2% of the total free aspartic acid) in all of the five ganglia. However, no D-aspartic acid was detected bound in protein/tissue matrix. The content of free D-aspartic acid in the liver tissue was also found below the detection limit of the method, which was 1 x 10(-8) M.

Animals↗

Flow cytometric enumeration of micronucleated reticulocytes: high transferability among 14 laboratories.

This laboratory previously described a single-laser flow cytometric method, which effectively resolves micronucleated erythrocyte populations in rodent peripheral blood samples. Even so, the rarity and variable size of micronuclei make it difficult to configure instrument settings consistently and define analysis regions rationally to enumerate the cell populations of interest. Murine erythrocytes from animals infected with the malaria parasite Plasmodium berghei contain a high prevalence of erythrocytes with a uniform DNA content. This biological model for micronucleated erythrocytes offers a means by which the micronucleus analysis regions can be rationally defined, and a means for controlling interexperimental variation. The experiments described herein were performed to extend these studies by testing whether malaria-infected erythrocytes could also be used to enhance the transferability of the method, as well as control intra- and interlaboratory variation. For these studies, blood samples from mice infected with malaria, or treated with vehicle or the clastogen methyl methanesulfonate, were fixed and shipped to collaborating laboratories for analysis. After configuring instrumentation parameters and guiding the position of analysis regions with the malaria-infected blood samples, micronucleated reticulocyte frequencies were measured (20,000 reticulocytes per sample). To evaluate both intra- and interlaboratory variation, five replicates were analyzed per day, and these analyses were repeated on up to five separate days. The data of 14 laboratories presented herein indicate that transferability of this flow cytometric technique is high when instrumentation is guided by the biological standard Plasmodium berghei.

Animals↗

Determination of enterostatin in human cerebrospinal fluid by capillary electrophoresis with laser induced fluorescence detection.

A capillary electrophoresis (CE) method with laser induced fluorescence (LIF) detection is described for quantification of enterostatin (Val-Pro-Asp-Pro-Arg), a pentapeptide involved in appetite regulation and insulin secretion. Enterostatin and two other pentapeptides belonging to the enterostatin family (i.e. Ala-Pro-Gly-Pro-Arg and Val-Pro-Gly-Pro-Arg) were well separated from each other. The peptides were fluorescently tagged with naphthalene-2,3- dicarboxaldehyde (NDA) and separated by micellar electrokinetic chromatography (MEKC) in the presence of methanol as an organic modifier. Coupled with LIF detection, the method had a detection limit of 4.8 x 10(-6) M for enterostatin. The relative standard deviation was to be 4.0% from five determinations of enterostatin at 37.2 microM in a human cerebrospinal fluid (CSF) sample. Twenty-three human CSF samples were analyzed. The level of enterostatin ranged from 24 microM to 51 microM with a mean (+/- SEM) value of 41.7 +/- 2.0 microM.

Amino Acid Sequence↗

Effects of insulin and glucose loading on FDG uptake in experimental malignant tumours and inflammatory lesions.

Fluorine-18 2-deoxy-2-fluoro-D-glucose (FDG) accumulation in tumours has been well investigated, but much less is known regarding FDG accumulation in inflammatory lesions. In this study, we determined the effects of hypo- and hyperglycaemia on FDG uptake in inflammatory lesions of infectious and non-infectious origin and compared them with those in malignant tumours in rats, to provide a biological basis for differentiating malignant lesions from benign lesions by means of FDG-PET. Rats were inoculated with a suspension of allogenic hepatoma cells (KDH-8) or Staphylococcus aureus, or with turpentine oil into the left calf muscle. Two weeks after KDH-8 inoculation and 1 week after S. aureus and turpentine oil inoculations, the rats were divided into three subgroups: insulin-loaded (2 U/kg body weight, i.p.), glucose-loaded (1.2 g/kg body weight, p.o.) and control groups. Radioactivity in tissues was determined 1 h after i.v. injection of FDG. Intraperitoneal injection of insulin and oral administration of glucose induced hypoglycaemia and hyperglycaemia, respectively. In the control animals, tumours showed a level of FDG uptake which was 2.2 and 3.0 times higher than the levels in the inflammatory lesions induced by S. aureus and turpentine oil, respectively (P<0.0001). There was no significant difference in the level of FDG uptake between the two inflammatory lesions of infectious and non-infectious origin. Insulin loading significantly decreased the level of FDG uptake in tumours and in both types of inflammatory lesion to approximately one-half of the control values (P=0.001 in the tumour group and P<0.0001 in the two inflammatory lesion groups). In the glucose-loaded group, the level of FDG uptake in both types of inflammatory lesion decreased significantly to 50%-61% of the control value (P=0.0002 in the S. aureus group and P<0.0001 in the turpetine group), while the tumour uptake did not decrease significantly (86% of the control value) (P=NS). It is concluded that FDG uptake in both types of inflammatory lesion was significantly impaired in rats with hyperglycaemia induced by glucose loading, while tumour uptake of FDG was not significantly affected. These results indicate that glucose loading has greater effects on FDG uptake in inflammatory lesions than in tumours, providing a biological basis for differentiation of malignant lesions from benign lesions by FDG-PET in a clinical setting.

Animals↗

Diverse effects of chronic treatment with losartan, fosinopril, and amlodipine on apoptosis, angiotensin II in the left ventricle of hypertensive rats.

This study was designed to investigate diverse effects of angiotensin II (AngII) type I receptor antagonists, losartan, angiotensin converting enzyme (ACE) inhibitors, fosinopril, and calcium channel blockade, amlodipine on cardiomyocyte apoptosis and AngII in the left ventricle of spontaneously hypertensive rats (SHR). The SHRs were randomized to four groups: SHR-L (treated with losartan, 30 mg x kg(-1) x d(-1)), SHR-F (with fosinopril, 10 mg x kg(-1) x d(-1)), SHR-A (with amlodipine, 10 mg x kg(-1) x d(-1)) and SHR-C (with placebo). The cardiomyocyte apoptosis was examined by in situ TDT-mediated dUTP nick end labeling, AngII concentrations of plasma and myocardium were measured by radio immunoassay at 8 and 16 weeks of the study respectively. The results showed that: (1) compared with SHR-C at 8 and 16 weeks respectively; the systolic blood pressure was decreased similarly in the three treatment groups. Left ventricular weight and mass indexes were reduced in the three treatment groups. The latter parameter at 16 weeks was lower in SHR-F than that in the other two treatment groups. (2) Compared with SHR-C, the cardiomyocyte apoptotic index (APOI) was reduced significantly at 8 weeks only in SHR-F, and at 16 weeks in all three treatment groups. The APOI of SHR-F was lowest among the three treatment groups examined at latter endpoint. (3) Compared with SHR-C at both endpoints of this study, plasma and myocardium AngII levels were increased in SHR-L. However, plasma AngII concentrations were not altered in SHR-F and SHR-A, myocardium AngII concentrations were reduced significantly at 8 weeks only in SHR-F, and at 16 weeks in SHR-F and SHR-A. Meanwhile, myocardium AngII in SHR-F at 16 weeks was lower than that in SHR-A. The results of this study indicate that losartan, fosinopril, and amlodipine each effectively reverses heart hypertrophy and inhibits cardiomyocyte apoptosis, and fosinopril may be most effective in these cardioprotective effects. These findings suggest that the effects of the three blockers on myocardiocyte apoptosis and left ventricular hypertrophy were related to inhibition of the myocardium rennin-angiotensin-aldsterone system.

Amlodipine↗

Sexual behaviour and contraceptive use among unmarried, young women migrant workers in five cities in China.

This paper reports the results of exploratory research on reproductive and sexual health knowledge and sexual behaviour of young, unmarried women who migrate to cities from rural areas for work, and their access to and needs in relation to family planning in Beijing, Guangzhou, Shanghai, Guiyang and Taiyuan, in China. Focus group discussions were conducted with 146 young women aged 16-25 and 58 in-depth interviews with key informants. Some of the young female migrant workers were sexually active and living with their boyfriends, most of whom expected to marry each other. Most of the women lacked basic information about reproduction and contraception, and did not know where or how to obtain contraception. There were social, psychological and economic barriers to accessing services. Only a small proportion of those who were unmarried were using contraception, so induced abortion was often the outcome of unprotected premarital sex. Pleasing male partners also played an important role in unprotected sex. The training, attitudes and approach of the entire family planning service system in relation to unmarried and young people in China, including this migrant population, needs to be reorientated so as to provide them with appropriate and adequate services.

Abortion, Induced↗