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Biomedical subjects

S Liu

Publications and source records attributed to S Liu.

At least 19 recordsLinked to original sources

Population Genomics of Almond (Prunus dulcis) Reveals Region-Specific Selection and a Complex History of Domestication.

The domestication of perennial crops in the Mediterranean Basin remains unclear, particularly regarding the genomic consequences of human-mediated demographic shifts and selection. We analysed 8.1 million single nucleotide polymorphisms from 96 cultivated almond (Prunus dulcis) accessions from Europe, North America, Central Asia, and New Zealand, alongside four wild relatives. Population structure analyses revealed four geographically differentiated cultivated groups (Central Asian, North American, and two European) and three wild populations (P. spinosissima, P. orientalis, and P. fenzliana). Cultivated almonds retained high genetic diversity, consistent with weak domestication bottlenecks typical of outcrossing perennials. Elevated diversity and private allele counts in Central Asian cultivars, together with limited evidence of crop-wild gene flow, support Central Asia as an important reservoir of ancestral cultivated diversity that may have played a major role during the early stages of almond domestication. In contrast, allele sharing consistent with historical wild-to-crop introgression-especially involving P. orientalis-has contributed to the genomic composition of European and North American almonds. Genome-wide scans for selective sweeps showed most genes overlapping candidate sweep regions were population-specific, though often associated with similar biological functions, including stress responses and agronomic traits. This suggests repeated targeting of comparable pathways during and post-domestication, despite distinct selection histories. Notably, a subset of candidate genes detected in cultivated populations also occurs in wild relatives, particularly P. orientalis. This overlap is consistent with shared ancestral variation, introgression/gene flow between wild and cultivated lineages, and/or parallel adaptation. Altogether, our results support a complex domestication and diversification history for almonds, shaped by geographic expansion, gene flow with wild relatives, and recurrent selection acting in different regions. This study highlights wild relatives as important reservoirs of genetic diversity and emphasises the need for broader geographic sampling to clarify their contributions to almond domestication and adaptation.

Prunus dulcis

102T/C polymorphism of serotonin receptor type 2A gene is not associated with schizophrenia in either Chinese or British populations.

Several pieces of evidence implicate serotonin receptors in the aetiology of schizophrenia, and recently a number of studies have reported a genetic association between the 102T/C polymorphism of serotonin receptor type 2A gene and schizophrenia. Unfortunately a number of failures to replicate these positive associations in both Caucasian and Chinese populations have also been reported. We have examined the 102T/C polymorphism by PCR amplification and restriction analysis of DNA from: 202 schizophrenics and 202 controls from Shanghai; 112 schizophrenics and 224 parents from Chengdu, Cina; and 253 schizophrenics and 244 controls from the the UK. We find no evidence of association or transmission disequilibrium between the 102T/C polymorphism and schizophrenia in any of the groups we have examined. We conclude that either the original positive reports occurred by chance or any effect must be minimal, and urge caution in interpreting small positive results derived using data from different centres.

Carrier Proteins

Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels.

DNA sequencing separations have been performed in microfabricated electrophoresis channels with the goal of determining whether high-quality sequencing is feasible with these microdevices. The separation matrix, separation temperature, channel length and depth, injector size, and injection parameters were optimized. DNA fragment sizing separations demonstrated that 50-micron-deep channels provide the best sensitivity for our detection configuration. One-color sequencing separations of single-stranded M13mp18 DNA on 3% linear polyacrylamide (LPA) were used to optimize the twin-T injector size, injection conditions, and temperature. The best one-color separations were observed with a 250-micron twin-T injector, an injection time of 60 s, and a temperature of 35 degrees C. The first 500 bases appeared in 9.2 min with a resolution of > 0.5, and the separation extended to 700 bases. The best four-color sequencing separations were performed using 4% LPA, a temperature of 40 degrees C, and a 100-micron twin-T injector. These four-color runs were complete in only 20 min, could be automatically base-called using BaseFinder to over 600 bp after the primer, and were 99.4% accurate to 500 bp. These results significantly advance the quality of microchip-based electrophoretic sequencing and indicate the feasibility of performing high-speed genomic sequencing with microfabricated electrophoretic devices.

Base Sequence

Hypoglycemia and impaired hepatic glucose production in mice with a deletion of the C/EBPbeta gene.

The transcription factor CCAAT/enhancer-binding protein beta (C/EBPbeta) is enriched in liver and adipose tissue and controls the expression of a wide variety of genes coding for important metabolic pathways, including gluconeogenesis and lipid synthesis. To investigate the role of C/EBPbeta on glucose homeostasis, we studied mice with a targeted deletion of the gene for C/EBPbeta-/- mice. Adult C/EBPbeta-/- mice have hypoglycemia after an 18-hour fast, accompanied by lower hepatic glucose production (40% of that of wild-type mice), with no change in plasma insulin and a lower concentration of plasma free fatty acids (FFA). Glucagon infusion during a pancreatic clamp acutely stimulated hepatic glucose production by 38% in wild-type animals, with no change detected in C/EBPbeta-/- mice. Unexpectedly, both the basal and glucagon-stimulated hepatic cyclic adenosine monophosphate (cAMP) levels were lower in C/EBPbeta-/- mice, indicating an essential role for C/EBPbeta in controlling proximal signal transduction. Fasting hypoglycemia was associated with normal levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) gene expression, however net liver glycogenolysis was impaired in C/EBPbeta-/- mice. FFA release from isolated adipose tissue in response to epinephrine was 68% lower in C/EBPbeta-/- mice than in control animals; however, N6,O2'-dibutyryladenosine (Bt2) cAMP stimulated a twofold increase in FFA release in C/EBPbeta-/- compared with no further increase in wild-type mice. Because a deletion in the gene for C/EBPbeta reduces blood glucose and circulating FFA, it could be an important therapeutic target for the treatment of non-insulin-dependent diabetes and possibly obesity, based on designing antagonists that decrease C/EBPbeta activity.

Animals

Mechanisms of antihyperglycemic effects of moxonidine in the obese spontaneously hypertensive Koletsky rat (SHROB).

Increased activity of the sympathetic nervous system may be a critical factor in the development of impaired insulin secretion and insulin resistance. We studied the chronic effects of sympathetic inhibition with moxonidine on glucose metabolism in the spontaneously hypertensive genetically obese rat (SHROB). This unique animal model closely resembles human syndrome X, expressing insulin resistance, genetic obesity, spontaneous hypertension, and hyperlipoproteinemia. Moxonidine, a selective imidazoline receptor agonist, was administered to lean spontaneous hypertensive rats (SHR) and SHROBs for 90 days in food at 8 mg/kg/day and significantly reduced mean blood pressure. Moxonidine treatment reduced fasting insulin levels by 71% in SHROB and lowered plasma free fatty acids by 25%. In SHR, moxonidine treatment decreased free fatty acids by 17% compared with controls. During an oral glucose tolerance test, blood glucose levels in moxonidine-treated SHROB were reduced relative to untreated controls from 60 min onwards. Insulin secretion was facilitated at 30 min (83% greater) and 60 min (67% greater) postchallenge compared with control SHROB. In skeletal muscle, moxonidine treatment increased the expression of the insulin receptor beta subunit by 19% in SHROB but was without effect in SHR. The level of insulin receptor substrate-1 (IRS-1) protein was decreased by 60% in control SHROB compared with lean SHR. Moxonidine treatment enhanced the expression and insulin-stimulated phosphorylation of IRS-1 protein in skeletal muscle in SHROB by 74 and 27%, respectively, and in SHR by 40 and 56%, respectively. Moxonidine increased the levels of expression of IRS-1 protein in liver in SHR by 275% and in SHROB by 260%. These findings indicate that chronic inhibition of sympathetic activity with moxonidine therapy can lower free fatty acids and significantly improve insulin secretion, glucose disposal, and expression of key insulin signaling intermediates in an animal model of obese hypertension.

Animals

Connexins regulate calcium signaling by controlling ATP release.

Forced expression of gap junction proteins, connexins, enables gap junction-deficient cell lines to propagate intercellular calcium waves. Here, we show that ATP secretion from the poorly coupled cell lines, C6 glioma, HeLa, and U373 glioblastoma, is potentiated 5- to 15-fold by connexin expression. ATP release required purinergic receptor-activated intracellular Ca2+ mobilization and was inhibited by Cl- channel blockers. Calcium wave propagation also was reduced by purinergic receptor antagonists and by Cl- channel blockers but insensitive to gap junction inhibitors. These observations suggest that cell-to-cell signaling associated with connexin expression results from enhanced ATP release and not, as previously believed, from an increase in intercellular coupling.

Adenosine Triphosphatases

Nonpeptide somatostatin agonists with sst4 selectivity: synthesis and structure-activity relationships of thioureas.

Utilizing NNC 26-9100 (11) as a structural lead, a variety of nonpeptide derivatives of somatostatin were synthesized and evaluated for sst2 and sst4 receptor binding affinity. A novel thiourea scaffold was utilized to attach (1) a heteroaromatic nucleus to mimic the Trp8 residue, (2) a nonheteroaromatic nucleus to mimic Phe7, and (3) a primary amine or other basic group to mimic the Lys9 residue of somatostatin. Displacement studies were carried out using membranes from cell lines expressing ssts [BHK cells (sst4) and HEK 293 cells (sst2)] utilizing [125I]Tyr11-SRIF as the radioligand. Several thioureas (11, 38, 39, 41, and 42) and the urea 66 exhibited Ki values of less than 100 nM. The thioureas 11 (Ki = 6 nM) and 41 (Ki = 16 nM) and the urea 66 (Ki = 14 nM) are believed to be the most potent nonpeptide sst4 agonists known. Since the thiourea 11 and the urea 66 exhibit high sst4 selectivity, these novel nonpeptide derivatives may be useful tools for studying the sst4 receptor. Studies are currently in progress to evaluate the therapeutic potential of NNC 26-9100 (11) in the treatment of glaucoma.

Aminopyridines

Structure of human methionine aminopeptidase-2 complexed with fumagillin.

The fungal metabolite fumagillin suppresses the formation of new blood vessels, and a fumagillin analog is currently in clinical trials as an anticancer agent. The molecular target of fumagillin is methionine aminopeptidase-2 (MetAP-2). A 1.8 A resolution crystal structure of free and inhibited human MetAP-2 shows a covalent bond formed between a reactive epoxide of fumagillin and histidine-231 in the active site of MetAP-2. Extensive hydrophobic and water-mediated polar interactions with other parts of fumagillin provide additional affinity. Fumagillin-based drugs inhibit MetAP-2 but not MetAP-1, and the three-dimensional structure also indicates the likely determinants of this specificity. The structural basis for fumagillin's potency and specificity forms the starting point for structure-based drug design.

Amino Acid Sequence

Crystal structures of acutolysin A, a three-disulfide hemorrhagic zinc metalloproteinase from the snake venom of Agkistrodon acutus.

Acutolysin A alias AaHI, a 22 kDa hemorrhagic toxin isolated from the snake venom of Agkistrodon acutus, is a member of the adamalysin subfamily of the metzincin family and is a snake venom zinc metalloproteinase possessing only one catalytic domain. Acutolysin A was found to have a high-activity and a low-activity under weakly alkaline and acidic conditions, respectively. With the adamalysin II structure as the initial trial-and-error model, the crystal structures were solved to the final crystallographic R-factors of 0. 168 and 0.171, against the diffraction data of crystals grown under pH 5.0 and pH 7.5 conditions to 1.9 A and 1.95 A resolution, respectively. One zinc ion, binding in the active-site, one structural calcium ion and some water molecules were localized in both of the structures. The catalytic zinc ion is coordinated in a tetrahedral manner with one catalytic water molecule anchoring to an intermediate glutamic acid residue (Glu143) and three imidazole Nepsilon2 atoms of His142, His146 and His152 in the highly conserved sequence H142E143XXH146XXGXXH152. There are two new disulfide bridges (Cys157-Cys181 and Cys159-Cys164) in acutolysin A in addition to the highly conserved disulfide bridge Cys117-Cys197. The calcium ion occurs on the molecular surface. The superposition showed that there was no significant conformational changes between the two structures except for a few slight changes of some flexible residue side-chains on the molecular surface, terminal residues and the active-site cleft. The average contact distance between the catalytic water molecule and oxygen atoms of the Glu143 carboxylate group in the weakly alkaline structure was also found to be closer than that in the weakly acidic structure. By comparing the available structural information of the members of the adamalysin subfamily, it seems that, when lowering the pH value, the polarization capability of the Glu143 carboxylate group to the catalytic water molecule become weaker, which might be the structural reason why the snake venom metalloproteinases are inactive or have a low activity under acidic conditions.

Acids

Synthesis and characterization of heteroarotinoids demonstrate structure specificity relationships.

Heteroarotinoids are synthetic retinoids derived from trans-retinoic acid and the arotinoid structures and include a heteroatom in a five- or six-membered cyclic ring. This is the first systematic study of influences of the heteroatom, ring size, number of aryl groups, and terminal side chain on retinoid receptor specificity. Two new heteroarotinoids were synthesized and characterized. Although all heteroarotinoids activated RAR receptors, two dominant associations between structure and specificity were identified across all compounds. The six-membered ring conferred increased RARbeta specificity over the five-membered ring. The sulfur atom conferred greater specificity for RARgamma than the oxygen atom. RARalpha specificity was attenuated by a combination of influences from the heteroatom and aryl groups. In summary, the heteroatom and cyclic ring size exerted dominant effects, while the number of aryl rings and terminal side chain had attenuating effects on retinoid receptor specificity of heteroarotinoids.

Animals

Cloning and functional characterization of the 5'-flanking region of human methionine adenosyltransferase 2A gene.

Methionine adenosyltransferase (MAT) is a critical cellular enzyme which catalyzes the formation of S-adenosylmethionine, the principal methyl donor. In mammals, two different genes, MAT1A and MAT2A, encode for liver-specific and non-liver-specific MAT, respectively. We have cloned and characterized a 1.4-kb 5'-flanking region of the human MAT2A (GenBank Accession No. AF039088). Two major transcriptional start sites were identified by primer extension and S1 nuclease protection analysis; one was within 10 nucleotides downstream and the other was located at 158 nucleotides upstream from the consensus TATA box, respectively. The promoter is highly GC rich (75%) in the first 300 base pairs and contains several Sp-1 binding sites, a C/EBP, a HSF2, a STATx, a c-Myb, several v-Myb, and numerous GATA consensus binding sites. The human MAT2A promoter was able to efficiently drive luciferase expression in both Jurkat and 293 cells, but sequential deletion analysis of the promoter revealed that different regions of the promoter are important for cell-specific MAT2A expression.

Base Sequence

[Detection of minimal residual disease in acute lymphoblastic leukemia using PCR-molecule hybridization of RNA transcripts].

OBJECTIVE: To detect acute lymphoblastic leukemia's(ALL's) minimal residual disease(MRD) rapidly and effectively. METHODS: In this assay, the gamma T-cell receptor gene rearrangements serve as marker genes. The gene rearrangements are amplified from the diagnostic specimens using a consensus V segment primer and a consensus J segment primer to which the promoter T7 RNA polymerase has been appended. The PCR product from this amplification is transcribed into a radiolabeled RNA probe. The opposite DNA strand is transcribed into test RNA from the PCR product of different staged specimens. The test RNA is hybridized with the probe, and later the digestion with RNase A, Polyacrylamide gel electrophoresis and autoradiography are in progress. RESULTS: According to the mechanism, the perfectly matched RNA duplex can prevent the digestion of RNase A, and the presence of the leukemia cells in the test specimen can be determined. Logarithmical dilution experiments with DNA of a cell line from ALL have shown that this assay's sensitivity is at the 10(-5) level. Minimal residual disease was successfully detected in a case of ALL during its complete remission stage. But if the probe and test RNA are not from the same individual, the results of this kind of cross hybridization are negative. CONCLUSION: The above results suggest that this assay can become an effective measure in the detection of ALL-MRD clinically.

Child

Inactivation of voltage-gated cardiac K+ channels.

Inactivation is the process by which an open channel enters a stable nonconducting conformation after a depolarizing change in membrane potential. Inactivation is a widespread property of many different types of voltage-gated ion channels. Recent advances in the molecular biology of K+ channels have elucidated two mechanistically distinct types of inactivation, N-type and C-type. N-type inactivation involves occlusion of the intracellular mouth of the pore through binding of a short segment of residues at the extreme N-terminal. In contrast to this "tethered ball" mechanism of N-type inactivation, C-type inactivation involves movement of conserved core domain residues that result in closure of the external mouth of the pore. Although C-type inactivation can show rapid kinetics that approach those observed for N-type inactivation, it is often thought of as a slowly developing and slowly recovering process. Current models of C-type inactivation also suggest that this process involves a relatively localized change in conformation of residues near the external mouth of the permeation pathway. The rate of C-type inactivation and recovery can be strongly influenced by other factors, such as N-type inactivation, drug binding, and changes in [K+]o. These interactions make C-type inactivation an important biophysical process in determining such physiologically important properties as refractoriness and drug binding. C-type inactivation is currently viewed as arising from small-scale rearrangements at the external mouth of the pore. This review will examine the multiplicity of interactions of C-type inactivation with N-terminal-mediated inactivation and drug binding that suggest that our current view of C-type inactivation is incomplete. This review will suggest that C-type inactivation must involve larger-scale movements of transmembrane-spanning domains and that such movements contribute to the diversity of kinetic properties observed for C-type inactivation.

Allosteric Regulation

A peptide sequence of heparin/heparan sulfate (HP/HS)-interacting protein supports selective, high affinity binding of HP/HS and cell attachment.

We previously have identified a novel cell surface heparan sulfate/heparin (HS/HP)-interacting protein (HIP) found in human uterine epithelia and a variety of other human epithelial and endothelial cells and cell lines (Liu, S., Smith, S. E., Julian, J., Rohde, L. H., Karin, N. J., and Carson, D. D. (1996) J. Biol. Chem. 271, 11817-11823; Rohde, L. H., Julian, J., Babaknia, A., and Carson, D. D. (1996) J. Biol. Chem. 271, 11824-11830). The amino acid sequence predicted for HIP revealed a potential HS/HP-binding motif. In the present studies, a synthetic peptide corresponding to this putative HS/HP-binding motif, HIP peptide, was synthesized and examined with regard to its HS/HP binding and cell attachment promoting activity. Results using solid phase binding assays demonstrate that HIP peptide binds HS/HP with high selectivity and has high affinity for bulk HP (50% saturation congruent with 300 nM) and even higher affinity for a subset of polysaccharides found in commercial [3H]HP (half-saturation congruent with 10 nM). Moreover, HIP peptide binds subsets of cell and extracellular matrix-associated HS and dermatan sulfate expressed by RL95 cells, a human uterine adenocarcinoma cell line. HIP peptide also binds a similar fraction of HS as well as dermatan sulfate expressed by JAR cells, a human choriocarcinoma cell line. In contrast to binding of cell- or extracellular matrix-associated HS, HIP peptide does not bind secreted or released forms of HS or DS from either RL95 or JAR cells to a significant extent. HS species that bind to HIP peptide are generally larger, have a higher negative charge density, and have a larger proportion of di- and trisulfated disaccharide units than HS species that do not bind to HIP peptide, demonstrating structural differences among these polysaccharides. This same peptide supports HS-dependent JAR cell attachment. Collectively, these data demonstrate that a linear peptide sequence found within HIP can account, at least in part, for the HS/HP binding and cell adhesion promoting activities of this protein.

Amino Acid Sequence

Identification of a novel human glutathione S-transferase using bioinformatics.

In searching the expressed sequence tag (EST) data-base of GenBank with coding sequences of 11 known human glutathione S-transferases in conjunction with bioinformatic analysis, we have identified five ESTs that encode a new human glutathione S-transferase (GST) designated GST A4. The cDNA clone (I.M.A.G.E. Consortium cDNA Clone ID 515157) had an insert length of 1279 bp and contains an open reading frame of 666 bp, which encodes a protein of 222 amino acid residues. The GST A4 protein is identical in length to human GST A1 and A2 and is 54% identical to human GST A1 and A2. Sequence comparison with other human GSTs suggests that it is a new GST belonging to the alpha class GSTs. Northern blot analysis and EST database searches have demonstrated that the GST A4 mRNA is expressed at a high level in brain, placenta, and skeletal muscle and much lower in lung and liver. Analysis of the sequence tagged site (STS) database indicated that the GST A4 gene is located on chromosome 6. This STS represents a previously unidentified transcript further confirming the novelty of the new sequence.

Amino Acid Sequence

Adenosine 5'-tetraphosphate phosphohydrolase activity is an inherent property of soluble exopolyphosphatase from yeast Saccharomyces cerevisiae.

Homogeneous soluble exopolyphosphatase (EC 3.6.1.11) from yeast Saccharomyces cerevisiae, (scPPX1) behaves as an adenosine 5'-tetraphosphate phosphohydrolase (EC 3.6.1.14). The hydrolysis of adenosine 5'-tetraphosphate (p4A) to ATP and orthophosphate absolutely depends on one of the following cations: Co2+>Mn2+>Mg2+>Ni2+. Optimum pH is around 4.75 and the Km for p4A estimated at that pH in 50 mM sodium acetate and at 5 mM CoCl2 is 80+/-10 microM. Adenosine 5'-pentaphosphate (p5A) is degraded under these conditions 18-fold more slowly than p4A. Assuming that the mass of scPPX1 is 45 kDa, the calculated kcat values for p4A and for p5A are 723 and 40 s-1, respectively. Two other nucleoside 5'-tetraphosphates (p4N), guanosine tetraphosphate (p4G) and inosine tetraphosphate (p4I), were hydrolyzed to Pi and either GTP or ITP, respectively, at the same rate as that observed for the hydrolysis of p4A. Ammonium molybdate, sodium o-vanadate and zinc chloride inhibit the hydrolysis of p4A (I50 values are 0.08, 0.3 and 0.4 mM, respectively). This newly recognized 'acidic' adenosine tetraphosphatase activity from yeast is compared with two 'pH 8' adenosine tetraphosphatases described earlier in rabbit and yellow lupin.

Acid Anhydride Hydrolases

Trends and variations in length of hospital stay for childbirth in Canada.

BACKGROUND: Early discharge after childbirth is widely reported. In this study the authors examined trends in maternal length of hospital stay in Canada from fiscal year 1984-85 through fiscal year 1994-95. They also examined variations in length of stay in 1994-95 in most of the Canadian provinces and the territories. METHODS: Epidemiologic analyses of the temporal and geographic variations in maternal length of hospital stay in Canada from 1984-85 to 1994-95 (even years only), based on hospital discharge data collected by the Canadian Institute for Health Information, with a total of 1,456,800 women for the 6 study years. RESULTS: Mean length of hospital stay decreased during the decade, from 5.3 days in 1984-85 to 3.0 days in 1994-95, with similar trends for both cesarean and vaginal delivery. The decrease resulted from both increasing rates of short stay (less than 2 days) and decreasing rates of long stay (more than 4 days). Substantial temporal and interprovincial variations in several medical and obstetric complications were also observed but did not explain the corresponding variations in length of stay. The reduction in length of hospital stay was not restricted to uncomplicated cases: there was an equivalent decrease in cases with complications. In 1994-95 the average length of hospital stay in Alberta was 2.6 days, 0.3 to 1.7 days shorter than in the other provinces and the territories. INTERPRETATION: Length of hospital stay for childbirth has decreased substantially in Canada in recent years, but there remain important interprovincial variations. These trends and variations are not likely due to changes or differences in patient-specific factors.

Canada

Genotoxicity of nitric oxide produced from sodium nitroprusside.

Induction of mutation and micronucleus (MN) formation by nitric oxide (NO) was investigated in mammalian cells using sodium nitroprusside (SNP) as a drug donor of NO. Results showed that the concentration of NO2- in the tested solution rose according to time- and concentration-exposure to SNP. The treatment of SNP (0.5-8 micromol/ml with S9 or 2-8 micromol/ml without S9) induced a concentration-dependent increase in the mutation frequency at the gpt gene locus in g12 cells and caused a 13- (-S9) to 25- (+S9) fold increase above the background level at the highest concentration. A statistically significant increase in the number of micronucleated binucleated cells (MNBN) was also observed in treated groups. MNBN per thousand, MN per thousand and the proportion of the multiple micronuleated cells increased in a concentration-dependent manner in the concentration range of SNP (0.5-4 micromol/ml with S9 or 2-8 micromol/ml without S9). Our results indicate that SNP, an NO releasing drug, is genotoxic in g12 cells.

Cell Line