Biomedical subjects

Jianzhong Wu

Publications and source records attributed to Jianzhong Wu.

At least 19 recordsLinked to original sources

PubMed2026

Pan-genome based on chromosome sequences of wild and cultivated Agaricus bisporus.

Agaricus bisporus, one of the most widely cultivated mushrooms around the world, plays an important role in economy and agriculture. In this study, by employing long-reads generated by PacBio and Nanopore sequencing, we assembled six novel high-quality genomes (of which three are telomere-to-telomere assemblies) with sizes 29.6 ~ 30.8 Mb and N50 lengths of 2.5 ~ 2.6 Mb. Combined with public genome data of nine strains, we successfully established a pan-genome of A. bisporus, comprising a total of 14,626 clusters of protein coding genes, of which 50.70%, 7.45%, 24.74% and 17.01% are defined as core, soft core, dispensable, and private clusters, respectively. A total of 5,646 non- redundant structural variants (SVs) were identified among wild and cultivated strains and the genes associated with SV were mapped. This work provides valuable whole-genome sequences and genomic resources across wild and cultivated strains of the most widely cultivated mushroom species for functional analyses of genomes.

Agaricus↗

PubMed2007

Density-functional theory for complex fluids.

Density-functional theory (DFT) and its variations provide a fruitful approach to the computational modeling of the microscopic structures and phase behavior of soft-condensed matter. The methodology takes deep root in quantum mechanics but shares a mathematical similarity with a number of classical approaches in statistical mechanics. This review discusses different strategies commonly used to formulate the free-energy functional of complex fluids for either phenomena-oriented applications or as a generic description of the thermodynamic nonideality owing to various components of intermolecular forces. We emphasize the connections among different schemes of DFT approximations, their underlying assumptions, and inherent limitations. We also address extensions of equilibrium DFT to phenomenological theories for the dynamic properties of complex fluids and for the kinetics of phase transitions. In addition, we highlight the recent literature concerning applications of DFT to diverse static and time-dependent phenomena in complex fluids.

Journal Article↗

PubMed2006

Germline mutations and polymorphic variants in MMR, E-cadherin and MYH genes associated with familial gastric cancer in Jiangsu of China.

Germline mutations in MSH2, MLH1, E-cadherin and MutY (MYH) genes have been implicated in the occurrence of gastric cancer (GC). Epidemiological investigation was performed by recruiting patients with GC onset during 2002 in Jiangsu province, China. We identified suspected hereditary GC patients based on either the GC family history or GC onset at early ages. We have screened germline variations in 101 suspected hereditary GC patients at the coding sequences of MSH2, MLH1, E-cadherin and MYH genes with polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC) analysis and DNA sequencing. The result showed that about 40% of patients carried germline variations, predominantly with missense mutations. Of the variations detected are 2 base pair substitutions, c.53C > T and c.74G > A, which is predicted to generate missense mutations of p.Pro18Leu and p.Gly25Asp, respectively, and occurred at the same allele of MYH gene. The frequency of variant haplotype T/A in patients was higher than that in the control group (p = 0.021, odds ratio [OR] = 4.43, 95% confidence interval [95% CI] = 1.33-14.72). Difference in the frequency of the silent mutation p.Asn751Asn in E-cadherin gene was also found between patients and controls (p = 0.009, OR = 2.54, 95% CI = 1.30-4.95). Moreover, 6 types of variations were detected in MSH2 and MLH1 genes in 14 of 101 patients. Most of them occurred at exon7 of MSH2, frequently c.1168C > T, resulting in mutation of p.Leu390Phe. In summary, germline mutation at MSH2, MLH1, E-cadherin and MYH genes is a frequent event in the familial GC. They may form a genetic basis for the familial GC susceptibility in Chinese population.

Adaptor Proteins, Signal Transducing↗

PubMed2006

Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their flanking regions.

Rice (Oryza sativa ssp. japonica cv. Nipponbare) harbors a ribosomal RNA gene (rDNA) cluster in the nucleolar-organizing region at the telomeric end of the short arm of chromosome 9. We isolated and sequenced two genomic clones carrying rice rDNA fragments from this region. The rice rDNA repeat units could be classified into three types based on length, which ranged from 7,928 to 8,934 bp. This variation was due to polymorphism in the number of 254-bp subrepeats in the intergenic spacer (IGS). Polymerase chain reaction (PCR) analysis suggested that the rDNA units in rice vary widely in length and that the copy number of the subrepeats in the IGS ranges from 1 to 12 in the rice genome. PCR and Southern blot analyses showed that most rDNA units have three intact and one truncated copies of the subrepeats in the IGS, and distal (telomere-side) rDNA units have more subrepeats than do proximal (centromere-side) ones. Both genomic clones we studied contained rDNA-flanking DNA sequences of either telomeric repeats (5'-TTTAGGG-3') or a chromosome-specific region, suggesting that they were derived from the distal or proximal end, respectively, of the rDNA cluster. A similarity search indicated that retrotransposons appeared more frequently in a 500-kb portion of the proximal rDNA-flanking region than in other subtelomeric regions or sequenced regions of the genome. This study reveals the repetitive nature of the telomeric end of the short arm of chromosome 9, which consists of telomeric repeats, an rDNA array, and a retrotransposon-rich chromosomal region.

Base Sequence↗

PubMed2006

A hybrid method for predicting the microstructure of polymers with complex architecture: combination of single-chain simulation with density functional theory.

A hybrid method is proposed to investigate the microstructure of various polymeric fluids confined between two parallel surfaces. The hybrid method combines a single-chain Monte Carlo (MC) simulation for the ideal-gas part of the Helmholtz energy and a density functional theory (DFT) for the excess part that arises from nonbonded intersegment interactions. The latter consists of a modified fundamental measure theory for excluded-volume effect, the first-order thermodynamics perturbation theory for chain connectivity, and a mean-field approximation for the van der Waals attraction. In comparison with a conventional DFT, the hybrid method avoids calculation of the time-consuming recursive functions and is directly applicable to polymers with arbitrary molecular architecture. Its numerical performance has been validated by extensive comparisons with MC data for the density distributions of totally flexible, semiflexible, or rigid polymers and those with starlike architecture. Special attention is also given to the formation of a nematic monolayer by rigid molecules laying perpendicular to a planar surface. The hybrid method predicts the surface pressure versus surface coverage in good agreement with experiment.

Journal Article↗

PubMed2006

Density functional theory for planar electric double layers: closing the gap between simple and polyelectrolytes.

We report a nonlocal density functional theory (NLDFT) for polyelectrolyte solutions within the primitive model; i.e., the solvent is represented by a continuous dielectric medium, and the small ions and polyions by single and tangentially connected charged hard spheres, respectively. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for hard-sphere repulsion, an extended first-order thermodynamic perturbation theory for chain connectivity, and a quadratic functional Taylor expansion for electrostatic correlations. With the direct and cavity correlation functions of the corresponding monomeric systems as inputs, the NLDFT predicts the segment-level microscopic structures and adsorption isotherms of polyelectrolytes at oppositely charged surfaces in good agreement with molecular simulations. In particular, it faithfully reproduces the layering structures of polyions, charge inversion, and overcharging that cannot be captured by alternative methods including the polyelectrolyte Poisson-Boltzmann equation and an earlier version of DFT. The NLDFT has also been used to investigate the influences of the small ion valence, polyion chain length, and size disparity between polyion segments and counterions on the microscopic structure, mean electrostatic potential, and overcharging in planar electric double layers containing polyelectrolytes.

Journal Article↗

PubMed2006

Surface forces between telechelic brushes revisited: the origin of a weak attraction.

Telechelic polymers are useful for surface protection and stabilization of colloidal dispersions by the formation of polymer brushes. A number of theoretical investigations have been reported on a weak attraction between two telechelic brushes when they are at the classical contact, i.e., when the surface separation is approximately equal to the summation of the brush thicknesses. While recent experiments have confirmed the weak attraction between telechelic brushes, its origin remains elusive because of conflicting approximations used in the previous theoretical calculations. In this paper, we have investigated the telechelic polymer-mediated surface forces by using a polymer density functional theory (PDFT) that accounts for both the surface-adhesive energy and segment-level interactions specifically. Within a single theoretical framework, the PDFT is able to capture both the depletion-induced attraction in the presence of weakly adhesive polymers and the steric repulsion between compressed polymer brushes. In comparison of the solvation forces between telechelic brushes with those between brushes formed by surfactant-like polymers and with those between two asymmetric surfaces mediated by telechelic polymers, we conclude that the weak attraction between telechelic brushes is primarily caused by the bridging effect. Although both the surfactant-like and telechelic polymers exhibit a similar scaling behavior for the brush thickness, a significant difference has been observed in terms of the brush microstructures, in particular, the segment densities near the edges of the polymer brushes.

Journal Article↗

PubMed2006

Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.

Proteins fold in a confined space not only in vivo, i.e., folding assisted by molecular chaperons and chaperonins in a crowded cellular medium, but also in vitro as in production of recombinant proteins. Despite extensive work on protein folding in bulk, little is known about how and to what extent the thermodynamics and kinetics of protein folding are altered by confinement. In this work, we use a Gō-like off-lattice model to investigate the folding and stability of an all beta-sheet protein in spherical cages of different sizes and surface hydrophobicity. We find whereas extreme confinement inhibits correct folding, a hydrophilic cage stabilizes the protein due to restriction of the unfolded configurations. In a hydrophobic cage, however, strong attraction from the cage surface destabilizes the confined protein because of competition between self-aggregation and adsorption of hydrophobic residues. We show that the kinetics of protein collapse and folding is strongly correlated with both the cage size and the surface hydrophobicity. It is demonstrated that a cage of moderate size and hydrophobicity optimizes both the folding yield and kinetics of structural transitions. To support the simulation results, we have also investigated the refolding of hen-egg lysozyme in the presence of cetyltrimethylammoniumbromide (CTAB) surfactants that provide an effective confinement of the proteins by micellization. The influence of the surfactant hydrophobicity on the structural and biological activity of the protein is determined with circular dichroism spectrum, fluorescence emission spectrum, and biological activity assay. It is shown that, as predicted by coarse-grained simulations, CTAB micelles facilitate the collapse of denatured lysozyme, whereas the addition of beta-cyclodextrin-grafted-PNIPAAm, a weakly hydrophobic stripper, dissociates CTAB micelles and promotes the conformational rearrangement and thereby gives an improved recovery of lysozyme activity.

Acrylic Resins↗

PubMed2006

Density functional theory for polyelectrolytes near oppositely charged surfaces.

We report a nonlocal density functional theory of polyelectrolyte solutions that faithfully accounts for both short- and long-range correlations neglected in a typical mean-field method. It is shown that for systems with strong electrostatic interactions, the long-range correlations are subdued by direct Coulomb attractions, thereby manifesting strong local excluded-volume effects. The theory has also been used to describe the influence of the polyion chain length and small ion valence on charge inversion due to the adsorption of polyelectrolytes at an oppositely charged surface.

Electrolytes↗

PubMed2006

Premature mortality in people with epilepsy in rural China: a prospective study.

BACKGROUND: In China, few studies have described annual mortality associated with epilepsy in a general population and these have provided a range of 3.0-7.9 deaths per 100,000 people. We calculated the case fatality rate (CFR), proportional mortality rate (PMR), and standardised mortality ratio (SMR) to assess mortality in people with epilepsy in rural China. METHODS: The target population was people with epilepsy who participated in an assessment of epilepsy management at primary health level in rural China. Neurologists confirmed the diagnosis using strict criteria in all participants who were then treated with phenobarbital. Demographic data and putative cause of death were recorded for each person whose death was reported. PMRs for each cause of death and SMRs were estimated on the basis of the 2004 Chinese population. FINDINGS: Case fatality rate was 1.4% (35 deaths) among 2455 people with epilepsy. The age-adjusted PMRs for injury, stroke, neoplasm, myocardial infarction, and pneumonia were 30%, 30%, 15%, 6%, and 5%, respectively. The SMR was 3.9 (95% CI 3.8-3.9). Patients aged 15-29 years had higher mortality ratios than did those in other age-groups, with SMRs exceeding 23. INTERPRETATION: Risk for premature death is three to four times higher in people with epilepsy than in the general Chinese population. Furthermore, the risk in young people with epilepsy in China is much higher than previously reported. Injury, stroke, myocardial infarction, and pneumonia are among the leading putative causes of death in patients with epilepsy in rural China.

Adolescent↗

PubMed2006

Simultaneous determination of trilobolide-6-O-isobutyrates A and B in Wedelia trilobata by gas chromatography.

A simple, sensitive, and specific gas chromatographic (GC) method was developed to determine the main bioactive sesquiterpene lactones, trilobolide-6-O-isobutyrates A and B (TBO-A and TBO-B), in Wedelia trilobata, a useful folk herb. A commercially available HP-5 capillary column (30 m x 0.25 mm i.d. x 0.25 microm) was utilized for the direct determination of TBO-A and TBO-B in W. trilobata. Calibration curves were obtained by spiking authentic compounds and the internal standard (ferulic acid) into W. trilobata samples before extraction. Extraction was carried out by refluxing the dried herb (0.5 g) for 1 h in methanol (25 mL). All calibration curves showed good linear regressions (r2 > 0.992) within test ranges. The assay was reproducible and accurate with the overall intraday and interday relative standard deviations and accuracies of less than 10% and more than 90%, respectively. The developed GC method was successfully utilized to analyze the TBO-A and TBO-B in aerial parts and flowers of W. trilobata, indicating that it was suitable for the quality control of this commonly used herb and related traditional Chinese medicines.

Butyrates↗

PubMed2006

Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S.

Telomeres, which are important for chromosome maintenance, are composed of long, repetitive DNA sequences associated with a variety of telomere-binding proteins. We characterized the organization and structure of rice telomeres and adjacent subtelomere regions on the basis of cytogenetic and sequence analyses. The length of the rice telomeres ranged from 5.1 to 10.8 kb, as revealed by both fibre-fluorescent in situ hybridization and terminal restriction-fragment assay. Physical maps of the chromosomal ends were constructed from a fosmid library. This facilitated sequencing of the telomere regions of chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. The resulting sequences contained conserved TTTAGGG telomere repeats, which indicates that the physical maps partly covered the telomere regions of the respective chromosome arms. These repeats were organized in the order of 5'-TTTAGGG-3' from the chromosome-specific region, except in chromosome 7S, in which seven inverted copies also existed in tandem array. Analysis of the telomere-flanking regions revealed the occurrence of deletions, insertions, or chromosome-specific substitutions of single nucleotides within the repeat sequences at the junction between the telomere and subtelomere. The sequences of the 500-kb regions of the seven chromosome ends were analysed in detail. A total of 598 genes were predicted in the telomeric regions. In addition, repetitive sequences derived from various kinds of retrotransposon were identified. No significant evidence for segmental duplication could be detected within or among the subtelomere regions. These results indicate that the rice chromosome ends are heterogeneous in both sequence and characterization.

Base Sequence↗

PubMed2005

Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome.

The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly 95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps, it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some 5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes 1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome.

Base Sequence↗

PubMed2005

A fine physical map of the rice chromosome 5.

A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.

Centromere↗

PubMed2005

Theoretical study of cooperativity in multivalent polymers for colloidal stabilization.

Multivalent polymers, i.e., copolymers with multiple binding sites, have been proposed recently for stabilization of fusogentic liposomes and other liposomal colloids useful for drug delivery. The performance of such polymers critically depends on their molecular architecture, in particular the strength and frequency of surface anchoring sites along the backbone of a highly soluble polymer. In this work, we investigate the adsorption and surface forces due to multivalent polymers based on coarse-grained polymer models. We find that for W-type polymers that form dangling tails when all anchoring segments are attached to a surface, increasing the chain length at fixed polymer composition leads to a stronger repulsive barrier in the polymer-mediated surface forces thereby increasing the ability of the polymer to stabilize colloidal particles. This prediction conforms to an earlier experiment indicating that increasing the number of hydrophobic anchors along poly(ethylene glycol) polymers results in the cooperative behavior for both surface adsorption and steric stabilization. For M-type multivalent polymers that have weakly anchoring sites placed at the ends, however, addition of binding sites at fixed polymer composition could lead to negative cooperativity, i.e., the more binding sites, the less the amount of adsorption or the weaker the ability of surface protection. The theory also predicts that polymers with two anchoring sites (e.g., telechelic copolymers) are most efficient for colloidal stabilization.

Journal Article↗

PubMed2005

Layering, condensation, and evaporation of short chains in narrow slit pores.

The phase behavior of short-chain fluids in slit pores is investigated by using a nonlocal-density-functional theory that takes into account the effects of segment size, chain connectivity, and van der Waals attractions explicitly. The layering and capillary condensation/evaporation transitions are examined at different chain length, temperature, pore width, and surface energy. It is found that longer chains are more likely to show hysteresis loops and multilayer adsorptions along with the capillary condensation and evaporation. Decreasing temperature favors the inclusion of layering transitions into the condensation/evaporation hysteresis loops. For large pores, the surface energy has relatively small effect on the pressures of the capillary condensation and evaporation but affects significantly on the layering pressures. It is also observed that all phase transitions within the pore take place at pressures lower than the corresponding bulk saturation pressure. The critical temperature of condensation/evaporation is always smaller than that of the bulk fluid. All coexistence curves for confined phase transitions are contained within the corresponding bulk vapor-liquid coexistence curve. As in the bulk phase, the longer the chain length, the higher are the critical temperatures of phase transitions in the pore.

Journal Article↗

PubMed2005

Surface-induced phase transitions in ultrathin films of block copolymers.

We study theoretically the lamellar-disorder-lamellar phase transitions of AB diblock and tetrablock copolymers confined in symmetric slitlike pores where the planar surface discriminatingly adsorbs A segments but repels B segments, mimicking the hydrophobic/hydrophilic effects that have been recently utilized for the fabrication of environmentally responsive "smart" materials. The effects of film thickness, polymer volume fraction, and backbone structure on the surface morphology have been investigated using a polymer density-functional theory. The surface-induced phase transition is manifested itself in a discontinuous switch of microdomains or a jump in the surface density dictated by the competition of surface adsorption and self-aggregation of the block copolymers. The surface-induced first-order phase transition is starkly different from the thickness-induced symmetric-asymmetric or horizontal-vertical transitions in thin films of copolymer melts reported earlier.

Journal Article↗

PubMed2005

Density-functional theory and Monte Carlo simulation for the surface structure and correlation functions of freely jointed Lennard-Jones polymeric fluids.

We present a nonlocal density-functional theory of polymeric fluids consisting of freely jointed Lennard-Jones chains with explicit consideration of the segment size, van der Waals attraction, and structural correlations due to chain connectivity. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the short-ranged repulsion and the first-order thermodynamic perturbation theory for chain connectivity. The contribution of the long-ranged attraction to the Helmholtz energy functional is taken into account using a quadratic density expansion with the direct correlation function obtained from the first-order mean-spherical approximation. The numerical performance of the density-functional theory is compared well with the simulation results from this work as well as those from the literature for the segment-level density profiles and correlation functions of Lennard-Jones chains in slit pores, near isolated nanoparticles, or in bulk.

Journal Article↗