Biomedical subjects

Ming Xiao

Publications and source records attributed to Ming Xiao.

At least 37 records · Page 2Linked to original sources

PubMed2004

Influence of a 12-nt insertion present in the 3' untranslated region of classical swine fever virus HCLV strain genome on RNA synthesis.

The function of a 12-nt insertion 'CTTTTTTCTTTT' in the 3' untranslated region (3'UTR) of the HCLV strain, a vaccine strain derived from the Shimen strain of classical swine fever virus (CSFV), was examined in vitro. RNA synthesis increased when the 12-nt insertion was deleted from the 3'UTR of the HCLV strain. RNA synthesis also decreased when the 12-nt insertion was introduced into the 3'UTR of the CSFV Shimen, virulent strain. Therefore, the 12-nt insertion present in the 3'UTR of the HCLV strain may be a marker for avirulence. It was also found that the predicted secondary structure of the 3'UTR of the HCLV strain was more stable when the 12-nt insertion was deleted, and that the 3'UTR of Shimen strain was more unstable when the 12-nt insertion was introduced. Replacement of the 12-nt insertion 'CTTTTTTCTTTT' by another 12-nt fragment 'ATTATTATTTAT' in the 3'UTR of HCLV strain facilitated RNA synthesis and stabilized the predicted secondary structure, which was also observed in the 3'UTR of the Shimen strain.

3' Untranslated Regions↗

PubMed2004

Preparation of ZnS/CdS composite nanoparticles by coprecipitation from reverse micelles using CO2 as antisolvent.

The possibility of simultaneously recovering ZnS and CdS particles from reverse micelles by dissolving antisolvent CO2 into the micellar solution was investigated by high-pressure UV-Vis spectra. It was found that all the ZnS and CdS particles in the reverse micelles could be precipitated by compressed CO2 at suitable pressures. The phase structures and morphologies of the obtained composites were characterized by X-ray diffraction and transmission electronic micrographs. The results illustrate that the smaller molar ratio of water to surfactant of the reverse micelles and higher pressure of CO2 are favorable for producing smaller particles. This method has many potential advantages for the production of composite nanoparticles.

Journal Article↗

PubMed2004

Single-molecule analysis for molecular haplotyping.

In the genome era, there is great hope that genetic approaches such as linkage equilibrium mapping can be used to study common human disorders using a case-control population association study design. Ideally, the parental chromosomes are marked so that chromosomal regions in the form of haplotypes are compared in these studies to increase the power of association. Determining the haplotypes in a diploid individual is a major technical challenge in genetic studies of complex traits. A molecular approach to haplotyping is therefore highly desirable. Recent advances in DNA preparation, separation, labeling, and image analysis provide hope that a strategy of using a three-dye system coupled with DNA distance measurements between alleles will yield haplotype information of sufficiently high quality for genetic studies. In this work, we present the outline of the major challenges one must meet in developing a robust strategy for SNP detection and molecular haplotyping using single molecule analysis.

Alleles↗

PubMed2004

Diagnostic value of 16 slices spiral-CT for portal vein disorders.

The diagnostic value of 16-slices spiral computed tomography (CT) for portal vein disorders was evaluated. Forty-one patients were scanned by the 16-slices spiral-CT. The celiac trunk, portal vein and their branches were reconstructed by volume rendering (VR), multiplanar volume reconstruction (MPVR) and maximum intensity projection (MIP) technique, and the results were compared with digital subtraction angiography (DSA). VR, MPVR and MIP could display celiac trunk, portal vein, inferior vena cava and their branches and extent of portal vein-vena cava shunt, portal vein emboli and the fistula of hepatic artery-portal vein. The results from 16-slices CT were better than DSA and identical with pathologic ones. The vessel three-dimension reconstruction technique of 16-slices spiral CT is valuable for evaluating the portal systemic disorders.

Adult↗

PubMed2004

The role of opsin expression and apoptosis in determination of cone types in human retina.

In primates, short wavelength sensitive cones (S cones) and medium- or long-wavelength-sensitive cones (L/M cones) are two separate populations. Each cone type has a different developmental timecourse, contributes to different intra-retinal circuits, and transmits different types of information to the brain. However, in fetal human retina a significant population of cones express both S and L/M opsin (S+L/M cones), raising questions about whether S+L/M cones die or change opsin expression during development. We have utilized fetal, postnatal and adult human retinae to study the immunohistochemical distribution and morphology of S+L/M cones during development. Because S cones appear to be at higher density in fetal compared to adult retinae, we used antibodies to S opsin and alpha-transducin to estimate the proportion of S-cones, and TUNEL labelling to detect apoptotic death in the L/M, S or S+L/M population during development. S cones were present in central retina from fetal week (Fwk)11 and covered the retina by Fwk20. L/M cones appeared in the foveal cone mosaic 3-4 weeks after S-opsin was first detected, and covered the retina by birth. S+L/M cones were detected in all retinae older than Fwk14. They were most numerous at the retinal eccentricity where L/M opsin was just appearing; i.e. at the 'front' of L/M opsin expression. In this region, five morphological types of cones were present. (1) Heavily labelled S cones had thick cell bodies, a thick basal axon and pedicle, and a nucleus at any level of the outer nuclear layer (ONL). (2) Heavily labelled L/M cones were wine goblet shaped with a small round cell body, a large nucleus at the outer ONL edge, and a thin axon with a prominent synaptic pedicle. (3) Goblet-shaped S+L/M cones. (4) Goblet-shaped cones lightly labelled for S-opsin. (5) Cones that were not immunoreactive to either opsin. Only type 1 S cones were present peripheral to the L/M expression front, and their labelling intensity, morphology and distribution indicates that these are the 'true blue' cones of the adult mosaic. Only type 2 L/M cones were present in the foveal cone mosaic. Types 3 and 4 were most numerous within 500-750 microm of the L/M expression front, but type 3 S+L/M cones were also scattered throughout more central regions in fetal, infant and adult retinae. S+L/M cones comprised 5-10% of opsin immunoreactive cones at the L/M front in fetal and early postnatal retinas but 0.01-0.03% throughout P8mo and adult retinae. We found no evidence of significant levels of apoptosis in L/M cones at the expression front, suggesting that this decrease was not due to cell death. The findings suggest that goblet-shaped cones destined to express L or M opsin may initially and transiently express S opsin. Near the optic disc, at Fwk17 S cone density was around 2000 cells mm(-2), which dropped 50% by Fwk20 and stabilized at around 500 cells mm(-2) by birth. Double labelling with alpha-transducin showed that throughout this period 8-10% of all cones expressed S opsin. TUNEL labelling found no significant apoptosis in the S cone population. The decrease in S cone density near the optic disc occurs in the absence of apoptosis, and is likely due to other developmental events acting on the photoreceptor layer, including displacement of cones towards the fovea.

Adult↗

PubMed2004

Pharmacogenomic assessment of carboxylesterases 1 and 2.

Human carboxylesterases 1 and 2 (CES1 and CES2) catalyze the hydrolysis of many exogenous compounds. Alterations in carboxylesterase sequences could lead to variability in both the inactivation of drugs and the activation of prodrugs. We resequenced CES1 and CES2 in multiple populations (n = 120) to identify single-nucleotide polymorphisms and confirmed the novel SNPs in healthy European and African individuals (n = 190). Sixteen SNPs were found in CES1 (1 per 300 bp) and 11 in CES2 (1 per 630 bp) in at least one population. Allele frequencies and estimated haplotype frequencies varied significantly between African and European populations. No association between SNPs in CES1 or CES2 was found with respect to RNA expression in normal colonic mucosa; however, an intronic SNP (IVS10-88) in CES2 was associated with reduced CES2 mRNA expression in colorectal tumors. Functional analysis of the novel polymorphisms described in this study is now warranted to identify putative roles in drug metabolism.

Adult↗

PubMed2004

Effects of citral on Aspergillus flavus spores by quasi-elastic light scattering and multiplex microanalysis techniques.

Citral refined from Litsea cubeba oil has been found to have a strong influence on fungi, especially Aspergillus flavus. Multiplex microanalysis and quasi-elastic light scattering techniques were applied to study the effects of citral on Aspergillus flavus spores from the levels of membrane, organelle and intracellular macromolecule. It was found that citral injured the wall and the membrane of A. flavus spore, resulting in decrease of its elasticity. After entering the cell, citral not only influenced the genetic expression of mitochondrion reduplication and its morphology, but also changed the aggregation of protein-like macromolecules. As a result, cells, organelles and macromolecules lost their normal structures and functions, eventually leading to the loss of germination ability of A. flavus spores. Since Litsea cubeba oil as food additive and antifungal agent is safe and less poisonous, it is important to elucidate the inhibitory mechanisms of Litsea cubeba oil on the germination ability of A. flavus spore.

Absorption↗

PubMed2004

Specific interaction between the classical swine fever virus NS5B protein and the viral genome.

The NS5B protein of the classical swine fever virus (CSFV) is the RNA-dependent RNA polymerase of the virus and is able to catalyze the viral genome replication. The 3' untranslated region is most likely involved in regulation of the Pestivirus genome replication. However, little is known about the interaction between the CSFV NS5B protein and the viral genome. We used different RNA templates derived from the plus-strand viral genome, or the minus-strand viral genome and the CSFV NS5B protein obtained from the Escherichia coli expression system to address this problem. We first showed that the viral NS5B protein formed a complex with the plus-strand genome through the genomic 3' UTR and that the NS5B protein was also able to bind the minus-strand 3' UTR. Moreover, it was found that viral NS5B protein bound the minus-strand 3' UTR more efficiently than the plus-strand 3' UTR. Further, we observed that the plus-strand 3' UTR with deletion of CCCGG or 21 continuous nucleotides at its 3' terminal had no binding activity and also lost the activity for initiation of minus-strand RNA synthesis, which similarly occurred in the minus-strand 3' UTR with CATATGCTC or the 21 nucleotide fragment deleted from the 3' terminal. Therefore, it is indicated that the 3' CCCGG sequence of the plus-strand 3' UTR, and the 3' CATATGCTC fragment of the minus-strand are essential to in vitro synthesis of the minus-strand RNA and the plus-strand RNA, respectively. The same conclusion is also appropriate for the 3' 21 nucleotide terminal site of both the 3' UTRs.

3' Untranslated Regions↗

PubMed2003

Light stimulates a transducin-independent increase of cytoplasmic Ca2+ and suppression of current in cones from the zebrafish mutant nof.

Transducins couple visual pigments to cGMP hydrolysis, the only recognized phototransduction pathway in vertebrate photoreceptors. Here we describe a zebrafish mutant, no optokinetic response f(w21) (nof), with a nonsense mutation in the gene encoding the alpha subunit of cone transducin. Retinal morphology and levels of phototransduction enzymes are normal in nof retinas, but cone transducin is undetectable. Dark current in nof cones is also normal, but it is insensitive to moderate intensity light. The nof cones do respond, however, to bright light. These responses are produced by a light-stimulated, but transducin-independent, release of Ca2+ into the cone cytoplasm. Thus, in addition to stimulating transducin, light also independently induces release of Ca2+ into the photoreceptor cytoplasm.

Adaptation, Ocular↗

PubMed2003

Identification of a frequent variant in ALG6, the cause of Congenital Disorder of Glycosylation-Ic.

Congenital Disorder of Glycosylation (CDG) type Ic is caused by mutations in ALG6. This gene encodes an alpha1,3 glucosyltransferase used for synthesis of the lipid linked oligosaccharide (LLO) precursor of the protein N-glycosylation pathway. CDG-Ic patients have moderate to severe psychomotor retardation, seizures, hypotonia, strabismus, and feeding difficulties. We previously identified a typical patient with a heterozygous point mutation, c.391T>C (p.Tyr131His) in ALG6. Using complementation analysis of ALG6-deficient yeast, we show that this alteration is as severe as the most common disease-causing mutation, c998C>T (p. Ala333Val), which occurs in over half of all known CDG-Ic patients. The frequency of c.391T>C (p.Tyr131His) in the US population, is 0.0214, suggesting that homozygotes would occur at a rate of& tilde;1:2,200. We identified one patient with typical CDG-Ic symptoms and a homozygous p.Tyr131His alteration in ALG6. However, in contrast to most CDG patients, her LLO and plasma transferrin glycosylation appeared normal. Thus, it is unclear whether c.391T>C causes CDG-Ic or contributes to the symptoms. Genotyping additional patients with CDG-like symptoms will be required to resolve this issue.

Apoptosis Regulatory Proteins↗

PubMed2003

Characterization of RNA-dependent RNA polymerase activity of CSFV NS5B proteins expressed in Escherichia coli.

The full-length NS5B protein, and the truncated NS5B proteins of classical swine fever virus (CSFV) resulted from deletion of 24, 36, 65 or 82, amino acid residues at the C terminal were expressed in Escherichia coli cells and purified with a C-terminal hexahistidine tag. In addition to the full-length NS5B protein, those truncated NS5B proteins with deletion of 24, 36, or 65 amino acid residues were demonstrated to have RNA-dependent RNA polymerase (RdRp) activity, which was not found in the truncated NS5B proteins with deletion of 82 amino acid residues. Analysis of the template specificity of CSFV RdRp was done containing the different NS5B proteins with RdRp activity. It was shown that the template specificity of the enzyme was not strict with NS5B proteins truncated, suggesting that the C terminal of CSFV NS5B protein was involved in the template specificity of the enzyme. Site-directed mutagenesis of and prediction of the secondary structure of 3' terminal sequence of the template indicated that the cytidines at 3' terminus and the correct secondary structure of the template were essential to initiation of RNA synthesis by RdRp. Oxidation of the hydroxyl groups of the RNA template revealed that both the de novo initiation mechanism and the template-priming mechanism preference might be employed by the CSFV RdRp.

Base Sequence↗

PubMed2003

An actin-dependent conformational change in myosin.

Conformational changes within myosin lead to its movement relative to an actin filament. Several crystal structures exist for myosin bound to various nucleotides, but none with bound actin. Therefore, the effect of actin on the structure of myosin is poorly understood. Here we show that the swing of smooth muscle myosin lever arm requires both ADP and actin. This is the first direct observation that a conformation of myosin is dependent on actin. Conformational changes within myosin were monitored using fluorescence resonance energy transfer techniques. A cysteine-reactive probe is site-specifically labeled on a 'cysteine-light' myosin variant, in which the native reactive cysteines were removed and a cysteine engineered at a desired position. Using this construct, we show that the actin-dependent ADP swing causes an 18 A change in distance between a probe on the 25/50 kDa loop on the catalytic domain and a probe on the regulatory light chain, corresponding to a 23 degrees swing of the light-chain domain.

Actins↗

PubMed2003

DNA analysis by fluorescence quenching detection.

The analysis of human genetic variations such as single nucleotide polymorphisms (SNPs) has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching as the detection. The template-directed dye-terminator incorporation with fluorescence quenching detection (FQ-TDI) assay is based on the observation that the intensity of fluorescent dye R110- and R6G-labeled acycloterminators is universally quenched once they are incorporated onto a DNA oligonucleotide primer. By comparing the rate of fluorescence quenching of the two allelic dyes in real time, we have extended this method for allele frequency estimation of SNPs in pooled DNA samples. The kinetic FQ-TDI assay is highly accurate and reproducible both in genotyping and in allele frequency estimation. Allele frequencies estimated by the kinetic FQ-TDI assay correlated well with known allele frequencies, with an r(2) value of 0.993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations.

Alleles↗

PubMed2003

Kinetic FP-TDI assay for SNP allele frequency determination.

Strategies for identifying genetic risk factors in complex diseases by association studies require the comparison of allele frequencies of numerous SNPs between affected and control populations. Theoretically, hundreds of thousands of SNP markers across the genome will have to be genotyped in these studies. Genotyping SNPs one sample at a time is extremely costly and time consuming. To streamline whole genome association studies, some have proposed to screen SNPs by pooling the DNA samples initially for allele frequency determination and perform individual genotyping only when there is a significant discrepancy in allele frequencies between the affected and control populations. Here we describe a new method for determining the allele frequency of SNPs in pooled DNA samples using a two-color primer extension assay with real-time monitoring of fluorescence polarization (named kinetic FP-TDI assay). By comparing the ratio of the rate of incorporation of the two allele-specific dye-terminators, one can calculate the relative amounts of each allele in the pooled sample. The accuracy of allele frequency determination with pooled samples is within 3.3 +/- 0.8% of that determined by genotyping individual samples that make up the pool.

Algorithms↗

PubMed2002

Holding two heads together: stability of the myosin II rod measured by resonance energy transfer between the heads.

Myosin, similar to many molecular motors, is a two-headed dimer held together by a coiled-coiled rod. The stability of the coiled coil has implications for head-head interactions, force generation, and possibly regulation. Here we used two different resonance energy transfer techniques to measure the distances between probes placed in the regulatory light chain of each head of a skeletal heavy meromyosin, near the head-rod junction (positions 2, 73, and 94). Our results indicate that the rod largely does not uncoil when myosin is free in solution, and at least beyond the first heptad, the subfragment 2 rod remains relatively intact even under the relatively large strain of two-headed myosin (rigor) binding to actin. We infer that uncoiling of the rod likely does not play a role in myosin II motility. To keep the head-rod junction intact, a distortion must occur within the myosin heads. This distortion may lead to different orientations of the light-chain domains within the myosin dimer when both heads are attached to actin, which would explain previously puzzling observations and require reinterpretation of others. In addition, by comparing resonance energy transfer techniques sensitive to different dynamical time scales, we find that the N terminus of the regulatory light chain is highly flexible, with possible implications for regulation. An intact rod may be a general property of molecular motors, because a similar conclusion has been reached recently for kinesin, although whether the rod remains intact will depend on the relative stiffness of the coiled coil and the head in different motors.

Actins↗

PubMed2002

A new method based on entropy theory for genomic sequence analysis.

We have refined entropy theory to explore the meaning of the increasing sequence data on nucleic acids and proteins more conveniently. The concept of selection constraint was not introduced, only the analyzed sequences themselves were considered. The refined theory serves as a basis for deriving a method to analyze non-coding regions (NCRs) as well as coding regions. Positions with maximal entropy might play the most important role in genome functions as opposed to positions with minimal entropy. This method was tested in the well-characterized coding regions of 12 strains of Classical Swine Fever Virus (CSFV) and non-coding regions of 20 strains of CSFV. It is suitable to analyze nucleic acid sequences of a complete genome and to detect sensitive positions for mutagenesis. As such, the method serves to formulate the basis for elucidating the functional mechanism.

Algorithms↗

PubMedDate not supplied

Discontinuous pore fluid distribution under microgravity--KC-135 flight investigations.

Designing a reliable plant growth system for crop production in space requires the understanding of pore fluid distribution in porous media under microgravity. The objective of this experimental investigation, which was conducted aboard NASA KC-135 reduced gravity flight, is to study possible particle separation and the distribution of discontinuous wetting fluid in porous media under microgravity. KC-135 aircraft provided gravity conditions of 1, 1.8, and 10(-2) g. Glass beads of a known size distribution were used as porous media; and Hexadecane, a petroleum compound immiscible with and lighter than water, was used as wetting fluid at residual saturation. Nitrogen freezer was used to solidify the discontinuous Hexadecane ganglia in glass beads to preserve the ganglia size changes during different gravity conditions, so that the blob-size distributions (BSDs) could be measured after flight. It was concluded from this study that microgravity has little effect on the size distribution of pore fluid blobs corresponding to residual saturation of wetting fluids in porous media. The blobs showed no noticeable breakup or coalescence during microgravity. However, based on the increase in bulk volume of samples due to particle separation under microgravity, groups of particles, within which pore fluid blobs were encapsulated, appeared to have rearranged themselves under microgravity.

Alkanes↗

PubMedDate not supplied

[Prediction of recognition sites for genomic replication of classical swine fever virus with information analysis].

In order to explore the mechanism for the genomic replication of classical swine fever virus (CSFV), so as to make a basis for investigating its pathogenicity, an introduction of the information theory is presented in connection with the statistical mechanics, whence small-sample statistics appears naturally as a consequence of the Bayesian approach. Furthermore, a selection rule for identifying the pattern of a recognition site for an RNA-binding protein is proposed by means of the maximum entropy principle. Based on those, the information contents of 3'-untranslated regions (3'UTRs) of genomes of 20 CSFV strains and 5'-untranslated regions (5'UTRs) of genomes of 58 CSFV strains are analyzed with a computational algorithm in a reduction mode, and the 3'UTR sites of 20 strains and 5'UTR sites of 58 strains containing important motifs are extracted from the unaligned RNA sequences of unequal lengths. These sites, which have the patterns of sequence and structure similar to the putative cis elements related to the regulation of genomic replication, would be identified as the potential recognition sites in 3'UTRs and 5'UTRs for CSFV replicase responsible for classical swine fever virus genomic replication, and to some extent, this identification is supported by experimental evidence. Finally, information analysis allows a presumption to be made about the CSFV RNA replication initiation mechanism.

3' Untranslated Regions↗