Biomedical subjects

Ren Zhang

Publications and source records attributed to Ren Zhang.

32 records · Page 2Linked to original sources

PubMed2004

[Accidents in acupuncture treatment: history and current state].

Acupuncture is widely used as an alternative therapy with few side effects because of its simple manipulation and low cost. However, accidents may occur if the practitioner uses it improperly. Early in the Qin dynasty, the Canon of Medicine mentioned that improper use of acupuncture could cause injury to the body and even death, and it systematically described the occurrence and prevention of acupuncture accidents. Physicians in the successive dynasties frequently reported it, and realized that the manipulation skills were significantly important in preventing the occurrence of acupuncture accidents. Since the 1950s, acupuncture accidents had been effectively prevented because of the improving of acupuncture instruments, enhancing of the quality of the practitioners, popularizing of sterilization and disseminating of anatomic knowledge. Nevertheless, with the renovating of acupuncture techniques, new accidents may occur constantly. The prevention of acupuncture accidents still should be an arduous task for acupuncturists. Nowadays, acupuncture therapy is being used in more than 140 countries, and acupuncture accidents due to improper application are increasing. Prevention of acupuncture accidents has become a global issue deserving of great attention.

Acupuncture↗

PubMed2004

[History and current state of moxibustion].

Moxibustion is an important invention of the Chinese nation, which originated as early as in the clan commune period of the primitive society. The literature records on moxibustion can be traced back to the Warring States Period (475 B.C. to 221 B.C.). Doctors through the ages made considerable progress and published a great number of books on moxibustion. Moxibustion has been applied in treating a great range of diseases. Since the 1950s, the treatment scope of moxibustion has been expanded, and the therapeutic methods of moxibustion are becoming increasingly rich and varied, and great progress in research on the mechanism of moxibustion has been made. Moxibustion was once popular in Europe after its dissemination to the West in the seventeenth century, and the practitioners invented some new methods of moxibustion. Japan is the country in the West where fruitful efforts have been made in research on moxibustion. In modern times, moxibustion has been used for health protection, and the scientists are paying great attention to the experimental research on moxibustion.

China↗

PubMed2003

Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis.

Horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. The availability of both complete genome sequences of Bacillus cereus and B. anthracis provides the possibility to perform comparative analysis based on their genomes. By using a windowless method to display the distribution of the genomic GC content of B. cereus and B. anthracis, we have found three genomic islands in the genome of B. cereus, i.e., BCGI-1, BCGI-2, and BCGI-3, respectively, which are absent in the genome of B. anthracis. All the genomic islands have abrupt changes in GC content compared with that of surrounding regions. BCGI-1 has many conserved features of genomic islands, e.g., a Val-tRNA gene is utilized as the integration site, and a site-specific recombinase gene is located at the 3' end. BCGI-2 has a large percentage of phage protein, suggesting a phage-related recombination is involved. BCGI-3 contains a ferric anguibactin transport system, which is likely to be involved in the iron transport that enables the bacterium to overcome the iron limitation in the host. In addition, BCGI-3 also contains a cluster of genes related to lantibiotics, which may play a role during the evolution of the genome. Furthermore, the integrations of the genomic islands, BCGI-1 and BCGI-3, result in deletions of DNA sequence fragments; therefore, such integrations lead to both gene gain and gene loss simultaneously.

Bacillus anthracis↗

PubMed2003

An isochore map of the human genome based on the Z curve method.

The distribution of the G+C content in the human genome has been studied by using a windowless technique derived from the Z curve method. The most important findings presented in this paper are twofold. First, abrupt variations of the G+C content along human chromosome sequences are the main variation patterns of G+C content. It is found that at some sites, the G+C content undergoes abrupt changes from a G+C-rich region to a G+C-poor region alternatively and vice versa. Second, it is shown that long domains with relatively homogeneous G+C content along each chromosome do exist. These domains are thought to be isochores, which usually have sharp boundaries. Consequently, 56 isochores longer than 3 Mb have been identified in chromosomes 1-22, X and Y. Boundaries, size and G+C content of each isochore identified are listed in detail. As an example to demonstrate the power of the method, the boundary between the Classes III and II isochores of the MHC sequence has been determined and found to be at 2,477,936, which is in good agreement with the experimental evidence. A homogeneity index is introduced to measure the homogeneity of G+C content in isochores. We emphasize that the homogeneity of G+C content is relative. The isochores in which the G+C content keeps absolutely constant do not exist. Isochore structures appear to be a basic organization of the human genome. Due to the relevance to many important biological functions, the clarification of isochore structures will provide much insight into the understanding of the human genome.

Algorithms↗

PubMed2003

ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes.

A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5-6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (http://tubic.tju.edu.cn/sars/). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.

Algorithms↗

PubMed2003

The Z curve database: a graphic representation of genome sequences.

MOTIVATION: Genome projects for many prokaryotic and eukaryotic species have been completed and more new genome projects are being underway currently. The availability of a large number of genomic sequences for researchers creates a need to find graphic tools to study genomes in a perceivable form. The Z curve is one of such tools available for visualizing genomes. The Z curve is a unique three-dimensional curve representation for a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z curve database for more than 1000 genomes have been established here. RESULTS: The database contains the Z curves for archaea, bacteria, eukaryota, organelles, phages, plasmids, viroids and viruses, whose genomic sequences are currently available. All the 3-dimensional Z curves and their three component curves are stored in the database. The applications of the Z curve database on comparative genomics, gene prediction, computation of G+C content with a windowless technique, prediction of replication origins and terminations of bacterial and archaeal genomes and study of local deviations from the Chargaff Parity Rule 2 etc. are presented in detail. The Z curve database reported here is a treasure trove in which biologists could find useful biological knowledge.

Animals↗

PubMed2003

Multiple replication origins of the archaeon Halobacterium species NRC-1.

The genomic sequence of the halophilic archaeon Halobacterium NRC-1 has been analyzed by the Z curve method. The Z curve is a three-dimensional curve that uniquely represents a given DNA sequence. Based on the known behaviors of the Z curves for the archaea whose replication origins have been identified, the analysis of the Z curve for the genome of Halobacterium NRC-1 strongly suggests that the large genome has two replication origins, oriC1 (921,863-922,014) and oriC2 (1,806,444-1,807,229), which are located at two sharp peaks of the Z curve. These two regions are next to the cdc6 genes and contain multiple copies of stretches of G and C, i.e., ggggtgggg and ccccacccc, which may also be regarded as direct and inverted repeats. Based on the above analysis, a model of replication of Halobacterium NRC-1 with two replication origins and two termini has been proposed. The experimental confirmation of this model would constitute the first example of multiple replication origins of archaea, which will finally provide much insight into the understanding of replication mechanisms of eukaryotic organisms, including human. In addition, the potential multiple replication origins of the archaeon Sulfolobus solfataricus are suggested by the analysis based on the Z curve method.

Base Sequence↗

PubMed2003

Q9, a content-balancing accuracy index to evaluate algorithms of protein secondary structure prediction.

A content-balancing accuracy index, called Q(9), has been proposed to evaluate algorithms of protein secondary structure prediction. Here the content-balancing means that the evaluation is independent of the contents of helix, strand and coil in the protein being predicted. It is shown that Q(9) is much superior to the widely used index Q(3). Therefore, algorithms are more objectively evaluated by Q(9) than Q(3). Based on 396 non-homologous proteins, five algorithms of secondary structure prediction were evaluated and compared by the new index Q(9). Of the five algorithms, PHD turned out to be the unique algorithm with an average Q(9) better than 60%. Based on the new index, it is shown that the performance of the consensus method based on a jury-decision from several algorithms is even worse than that of the best individual method. Rather than Q(3), we believe that Q(9) should be used to evaluate algorithms of protein secondary structure prediction in future studies in order to improve prediction quality.

Algorithms↗

PubMed2003

[Cloning and sequencing of cathepsin L1 (FheCL1) gene cDNA of Fasciola hepatica].

OBJECTIVE: To search for a candidate DNA vaccine of Fasciola hepatica. METHODS: Using RT-PCR and digestion with Hind III and BamHI, Fasciola hepatica secreted cathepsin L1 (FheCL1) cDNA was cloned into the expression vector pcDNA3.1. RESULTS: The cloning was successful, the cDNA sequence and its deduced amino acid sequence were analyzed. There was much difference between the cloned FheCL1 and the published one. But the first 20 residues of their amino acid sequences were the same. CONCLUSION: The recombinant plasmid pcDNA3.1-FheCL1 may be a new type of candidate DNA vaccine candidate for Fasciola hepatica. It is possible that Fasciola hepatica presents different sub-species but their amino acid residues (1 to 20) encoded by FheCL1 might build up membrane spanning helix.

Amino Acid Sequence↗

PubMed2002

Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method.

The genomic sequence of the archaeon Methanosarcina mazei has been analyzed by the Z curve method. The Z curve is a three-dimensional curve that uniquely represents the given DNA sequence. The three-dimensional Z curve and its x and y components for the genome of M. mazei show a sharp peak and relatively broad peak, respectively. The cdc6 gene is located exactly at the position of the sharp peak. Based on the known behavior of the Z curves for the archaea whose replication origins have been identified, we hypothesize that the replication origin and termination sites correspond to the positions of the sharp peak and broad peak, respectively. We have located an intergenic region that is between the cdc6 gene (MM1314) and the gene for an adjacent protein (MM1315), which shows strong characteristics of the known replication origins. This region is highly rich in AT and contains multiple copies of consecutive repeats. Our results strongly suggest that the single replication origin of M. mazei is situated at the intergenic region between the cdc6 gene and the gene for the adjacent protein, from 1,564,657 to 1,566,241 bp of the genome.

Base Sequence↗

PubMed2002

Movement to bark and metabolism of xylem cytokinins in stems of Lupinus angustifolius.

Following uptake of [(3)H]zeatin riboside and [(3)H]dihydrozeatin riboside by girdled lupin (Lupinus angustifolius L.) stems via the transpiration stream, rapid lateral movement of the radioactivity from xylem to bark was observed. Short-term studies with intact stems, and other studies with excised stem tissues, revealed that the ribosides and/or the corresponding nucleotides were the cytokinin forms which actually moved into the bark tissues. Relative to cytokinin metabolism in xylem plus pith, metabolism in bark was both more rapid and more complex. Riboside cleavage and formation of the O-acetylzeatin and O-acetyldihydrozeatin ribosides and nucleotides were almost completely confined to bark tissues. Exogenous (3)H-labelled O-acetylzeatin riboside was converted to zeatin riboside in bark tissue, but the presence of the acetyl group suppressed degradation to adenine metabolites. The sequestration and modification of xylem cytokinins by stem tissues probably contributes significantly to the cytokinin status of the shoot. New cytokinins identified by mass spectrometry in lupin were: O-acetyldihydrozeatin 9-riboside, a metabolite of exogenous dihydrozeatin riboside in stem bark; O-methylzeatin nucleotide and O-methyldihydrozeatin 9-riboside, metabolites of endogenous cytokinins in stem bark; O-methylzeatin nucleotide and O-methylzeatin 9-riboside, metabolites of exogenous zeatin riboside in excised pod walls.

Adenosine↗

PubMed2002

Using a Euclid distance discriminant method to find protein coding genes in the yeast genome.

The Euclid distance discriminant method is used to find protein coding genes in the yeast genome, based on the single nucleotide frequencies at three codon positions in the ORFs. The method is extremely simple and may be extended to find genes in prokaryotic genomes or eukaryotic genomes with less introns. Six-fold cross-validation tests have demonstrated that the accuracy of the algorithm is better than 93%. Based on this, it is found that the total number of protein coding genes in the yeast genome is less than or equal to 5579 only, about 3.8-7.0% less than 5800-6000, which is currently widely accepted. The base compositions at three codon positions are analyzed in details using a graphic method. The result shows that the preference codons adopted by yeast genes are of the RGW type, where R, G and W indicate the bases of purine, non-G and A/T, whereas the 'codons' in the intergenic sequences are of the form NNN, where N denotes any base. This fact constitutes the basis of the algorithm to distinguish between coding and non-coding ORFs in the yeast genome. The names of putative non-coding ORFs are listed here in detail.

Algorithms↗

PubMed2002

Evaluation of gene-finding algorithms by a content-balancing accuracy index.

A content-balancing accuracy index, called q(9), to evaluate gene-finding algorithms has been proposed. Here the concept of content-balancing means that the evaluation by this index is independent of the coding and non-coding composition of the sequence being evaluated. Since the coding and non-coding compositions are severely unbalanced in eukaryotic genomes, the performance of gene-finding algorithms is either over- or under-evaluated by the widely used accuracy indices, e.g., the correlation coefficient, due to the lack of content-balancing ability. Using the new accuracy index q(9), seven gene-finding algorithms, FGENES; Gene-Mark.hmm; Genie; Genescan; HMMgene; Morgan and MZEF, were compared and evaluated. It is shown that Genescan is still the best one, but with q(9)= 89%, averaged over the prediction for 195 sequences. In addition to the content-balancing ability, q(9) has the merit of having definition in all possible cases. It is also shown that the traditional specificity s(p) carries important information on the performance of the algorithm being evaluated. The set of sensitivity s(n), specificity s(p) and the accuracy q(9) constitutes a complete kit to evaluate gene-finding algorithms at nucleotide level. In addition, a graphic method to compare and evaluate gene-finding algorithms has been proposed, too. Its major advantage is that the overall performance of algorithms can be grasped quickly in a perceivable form. Additionally, the new accuracy index q(9) may be applied to evaluate the performance of weather forecast, clinical diagnosis, psychological examination and protein secondary structure prediction etc.

Algorithms↗

PubMed2002

A plant gene up-regulated at rust infection sites.

Expression of the fis1 gene from flax (Linum usitatissimum) is induced by a compatible rust (Melampsora lini) infection. Infection of transgenic plants containing a beta-glucuronidase (GUS) reporter gene under the control of the fis1 promoter showed that induction is highly localized to those leaf mesophyll cells within and immediately surrounding rust infection sites. The level of induction reflects the extent of fungal growth. In a strong resistance reaction, such as the hypersensitive fleck mediated by the L6 resistance gene, there is very little fungal growth and a microscopic level of GUS expression. Partially resistant flax leaves show levels of GUS expression that were intermediate to the level observed in the fully susceptible infection. Sequence and deletion analysis using both transient Agrobacterium tumefaciens expression and stable transformation assays have shown that the rust-inducible fis1 promoter is contained within a 580-bp fragment. Homologs of fis1 were identified in expressed sequence tag databases of a range of plant species including dicots, monocots, and a gymnosperm. Homologous genes isolated from maize (Zea mays; mis1), barley (Hordeum vulgare; bis1), wheat (Triticum aestivum; wis1), and Arabidopsis encode proteins that are highly similar (76%-82%) to the FIS1 protein. The Arabidopsis homologue has been reported to encode a delta1-pyrroline-5-carboxylate dehydrogenase that is involved in the catabolism of proline to glutamate. RNA-blot analysis showed that mis1 in maize and the bis1 homolog in barley are both up-regulated by a compatible infection with the corresponding species-specific rust. The rust-induced genes homologous to fis1 are present in many plants. The promoters of these genes have potential roles for the engineering of synthetic rust resistance genes by targeting transgene expression to the sites of rust infection.

1-Pyrroline-5-Carboxylate Dehydrogenase↗