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Biomedical subjects

Yang Zhong

Publications and source records attributed to Yang Zhong.

At least 37 records · Page 2Linked to original sources
PubMed2004

Molecular genetic variation in Chinese populations of three subspecies of Hippophae rhamnoides.

To provide a population-level genetic profile for investigation and conservation of genetic diversity of the sea buckthorn (Hippophae rhamnoides L.), 300 individuals of fifteen natural populations of sea buckthorn in China were analyzed by using ISSR (inter-simple sequence repeats) markers. On the basis of Shannon's index and Nei's genetic diversity, the mean genetic diversity detected in the natural populations of Hippophae rhamnoides ssp. yunnanensis, ssp. sinensis, and ssp. gyantsensis was 0.1944, 0.2169, and 0.1372, respectively. The coefficient of gene differentiation (Gst) of seven ssp. yunnanensis populations is 0.2790, and that of seven ssp. sinensis populations is 0.4184. This means that 28% of the total molecular variance of seven ssp. yunnanensis populations existed among populations, and 42% for seven ssp. sinensis populations, suggesting that the subspecies have different genetic structures. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers.

China↗
PubMed2004

Semantic search among heterogeneous biological databases based on gene ontology.

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

Database Management Systems↗
PubMed2004

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (pisces: cypriniformes) inferred from cytochrome b sequences.

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leucisciriae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

Amino Acid Sequence↗
PubMed2004

[Introduction to the methods of constructing phylogenetic trees with DNA sequences].

Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.

Base Sequence↗
PubMed2003

Urbanization, land use, and water quality in Shanghai. 1947-1996.

The paper undertakes a preliminary investigation into the relationship between water quality and urbanization as well as the changing patterns of land use within Shanghai. Longitudinal changes to water quality at various points along the course of the Huangpu River are analysed and compared to changes in the rates of urbanization and changes in land uses. The results reveal that rapid urbanization corresponds with rapid degradation of water quality. It also shows that urban land uses are positively correlated with the decline in water quality. A regression model shows that close to 94% of the variability in water quality classifications is explained by industrial land area. The paper concludes with the need for comprehensive land use planning as a way of protecting valuable water resources.

China↗
PubMed2003

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences.

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.

Animals↗
PubMed2003

Genetic diversity in Primula obconica (Primulaceae) from central and south-west China as revealed by ISSR markers.

Genetic diversity was investigated in 60 individuals of Primula obconica from four natural populations (from Hubei, central China, and Sichuan, south-west China) and from cultivated material. Inter-simple sequence repeat (ISSR) techniques produced 249 polymorphic bands and identified 60 ISSR genotypes. Based on Shannon's index and Nei's genetic diversity, the genetic diversity detected in all natural populations of P. obconica was much higher than that in the cultivated plants, and that in the three Dalaoling (Hubei) populations was higher than that in the Wawushan (Sichuan) population. UPGMA cluster analysis showed that there was no distinct genetic differentiation between populations from the Mt Dalaoling area and the Mt Wawushan area. This study provides a population-level genetic profile of P. obconica, which was previously poorly known but which is important for Primula breeding and cultivation.

China↗
PubMed2003

Genetic diversity of Hibiscus tiliaceus (Malvaceae) in China assessed using AFLP markers.

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88.5%) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84.8%), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on phiST was moderate (Nm=1.395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species.

China↗
PubMed2003

Putative hAPN receptor binding sites in SARS_CoV spike protein.

AIM: To obtain the information of ligand-receptor binding between the S protein of SARS-CoV and CD13, identify the possible interacting domains or motifs related to binding sites, and provide clues for studying the functions of SARS proteins and designing anti-SARS drugs and vaccines. METHODS: On the basis of comparative genomics, the homology search, phylogenetic analyses, and multi-sequence alignment were used to predict CD13 related interacting domains and binding sites in the S protein of SARS-CoV. Molecular modeling and docking simulation methods were employed to address the interaction feature between CD13 and S protein of SARS-CoV in validating the bioinformatics predictions. RESULTS: Possible binding sites in the SARS-CoV S protein to CD13 have been mapped out by using bioinformatics analysis tools. The binding for one protein-protein interaction pair (D757-R761 motif of the SARS-CoV S protein to P585-A653 domain of CD13) has been simulated by molecular modeling and docking simulation methods. CONCLUSION: CD13 may be a possible receptor of the SARS-CoV S protein, which may be associated with the SARS infection. This study also provides a possible strategy for mapping the possible binding receptors of the proteins in a genome.

Amino Acid Sequence↗
PubMed2003

Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.

AIM: To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS. METHODS: Based on the studies about the genomic packaging signals of MHV and BCoV, especially the information about primary and secondary structures, the putative genomic packaging signal of SARS-CoV were analyzed by using bioinformatic tools. Multi-alignment for the genomic sequences was performed among SARS-CoV, MHV, BCoV, PEDV and HCoV 229E. Secondary structures of RNA sequences were also predicted for the identification of the possible genomic packaging signals. Meanwhile, the N and M proteins of all five viruses were analyzed to study the evolutionary relationship with genomic packaging signals. RESULTS: The putative genomic packaging signal of SARS-CoV locates at the 3' end of ORF1b near that of MHV and BCoV, where is the most variable region of this gene. The RNA secondary structure of SARS-CoV genomic packaging signal is very similar to that of MHV and BCoV. The same result was also obtained in studying the genomic packaging signals of PEDV and HCoV 229E. Further more, the genomic sequence multi-alignment indicated that the locations of packaging signals of SARS-CoV, PEDV, and HCoV overlaped each other. It seems that the mutation rate of packaging signal sequences is much higher than the N protein, while only subtle variations for the M protein. CONCLUSIONS: The probable genomic packaging signal of SARS-CoV is analogous to that of MHV and BCoV, with the corresponding secondary RNA structure locating at the similar region of ORF1b. The positions where genomic packaging signals exist have suffered rounds of mutations, which may influence the primary structures of the N and M proteins consequently.

Amino Acid Sequence↗
PubMed2003

[Phylogenetic diversity of microbes and its perspectives in conservation biology].

Molecular phylogenetic analysis plays a very important role in the study of microbial diversity. For both cultivated and uncultivated microbes, the comparative sequence analysis of 16S rRNA enabled the investigation of phylogenetic relationships among microorganisms in a manner that was not feasible through traditional microbiological methods. As a result, there are drastic revisions in our understanding of microbiology. The phylogenetic diversity based on the comparative sequence analysis of 16S rRNA produced new insights into the biodiversity conservation. It provides a method for biodiversity judgment and a guideline for biodiversity conservation. Also, it produces the aim of conservation, which is to keep the phylogenetic information as much as possible. In this review, some characters of microbial phylogenetic diversity and the perspectives in conservation biology are outlined.

Conservation of Natural Resources↗
PubMed2002

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid, nuclear gene and spacer sequences.

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretumand Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretumis strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminaliaas it forms a polytomy with Anogeissus. This clade is sister to Conocarpus.

Journal Article↗
PubMed2002

Composition of volatile oil of Primula obconica in Central China.

Primula obconica was introduced to Europe from Hubei, China in 1880, and has been cultivated worldwide as one of popular ornamental plants. The volatile oil of wild P. obconica collected from its original place, Yichang, Hubei was first investigated. A total of 43 compounds constituting 93.49% of the oil were identified by using GC and GC-MS. The major compounds were methyl 2,4-dihydroxy-5-methyl benzoate (30.41%), methyl 2,6-dihydroxy-4-methyl benzoate (29.27%), and hypnone (8.92%) etc. In comparison with the published data of some European cultivars, the native P. obconica seems to be allergen-free due to absence of primin and miconidin.

China↗
PubMed2002

Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae).

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids, which are important for the pigmentation of flowers and act as attractants to the pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. Plants of the Dendranthema genus have white, yellow, and pink flowers, exhibiting considerable variation in flower color. In this article, 18 CHS genes from six Dendranthema species were sequenced. Two of them were found to be pseudogenes. The functional Dendranthema CHS genes formed three well-supported subfamilies: SF1, SF2, and SF3. The inferred phylogeny of the CHS genes of Dendranthema and Gerbera suggests that those genes originated as a result of duplications before divergence of these two genera, and the function of Dendranthema CHS genes have diverged in a similar fashion to the Gerbera CHS genes; i.e., the genes of SF1 and SF3 code for typical CHS enzymes expressed during different stages of development, whereas the genes of SF2 code for another enzyme that is different from CHS in substrate specificity and reaction. Relative rate tests revealed that the Dendranthema CHS genes significantly deviated from clocklike evolution at nonsynonymous sites. Maximum likelihood analysis showed that the nonsynonymous-synonymous (omega = d(N)/d(S)) rate ratio for the lineage ancestral to SF2 was much higher than for other lineages, with some sites having a ratio well above one. Positive selective pressure appears to have driven the divergence of SF2 from SF1 and SF3.

Acyltransferases↗
PubMedDate not supplied

Genetic diversity and population structure of Lamiophlomis rotata (Lamiaceae), an endemic species of Qinghai-Tibet Plateau.

Lamiophlomis rotata (Lamiaceae), a perennial medicinal herb, is endemic to the Qinghai-Tibet Plateau. A total of 188 individuals from eight natural populations of L. rotata in Qinghai-Tibet Plateau (four from Tibet, two from Yunnan, and two from Qinghai) were analyzed using intersimple sequence repeats (ISSR) and randomly amplified polymorphic DNA (RAPD) techniques. Our results revealed that the level of genetic variation in L. rotata was relatively high (P = 94.85%, I = 0.440 +/- 0.220, H(T) = 0.289 +/- 0.028). Three genetic groups corresponding to the three geographic regions were detected, suggesting significant geographic structure. Our results suggest that the highly structured geographic pattern found in L. rotata might represent diverging evolutionary processes associated with the uplifting of the Qinghai-Tibet Plateau and Quaternary climatic oscillations. These findings imply that as many populations as possible should be preserved in situ for the conservation of this species. Given their genetic variability and peripheral distribution, Qinghai and Yunnan populations should be assigned priority for conservation. Optimal harvesting strategies, domestication and tissue culture of L. rotata should be developed as soon as possible to guarantee its sustainable use.

China↗
PubMedDate not supplied

Polypeptide multilayer films.

Research on polypeptide multilayer films, coatings, and microcapsules is located at the intersection of several disciplines: synthetic polymer chemistry and physics, biomaterials science, and nanoscale engineering. The past few years have witnessed considerable growth in each of these areas. Unexplored territory has been found at the borders, and new possibilities for technology development are taking form from technological advances in polypeptide production, sequencing of the human genome, and the nature of peptides themselves. Most envisioned applications of polypeptide multilayers have a biomedical bent. Prospects seem no less positive, however, in fields ranging from food technology to environmental science. This review of the present state of polypeptide multilayer film research covers key points of polypeptides as materials, means of polymer production and film preparation, film characterization methods, focal points of current research in basic science, and the outlook for a few specific applications. In addition, it discusses how the study of polypeptide multilayer films could help to clarify the physical basis of assembly and stability of polyelectrolyte multilayers, and mention is made of similarities to protein folding studies.

Absorbable Implants↗
PubMedDate not supplied

Fine tuning of physical properties of designed polypeptide multilayer films by control of pH.

Adjustment of pH can alter the ensemble of three-dimensional structures of a polypeptide in solution by changing the distribution of charge and Coulombic interactions. The role of pH in layer-by-layer self-assembly (LbL) of designed 32mer peptides containing the amino acid cysteine has been investigated using a combination of physical methods. Results show that pH can have a substantial influence on the mass of adsorbed peptide, surface roughness, and film density over a range of 1.5 pH units. Peptide film thickness depends on the number of layers, as with "conventional" polyelectrolytes. Film density and morphology, however, vary more with pH than does thickness, translating into a change in density on the order of 70% over the pH range 7.4-8.9. Results of this work provide insight on the physical basis of LbL and suggest that peptides are a promising class of polyelectrolytes for the creation of designer thin films for applications in biotechnology and other areas.

Amino Acid Sequence↗