Biomedical subjects

Lin Fang

Publications and source records attributed to Lin Fang.

11 recordsLinked to original sources

PubMed2006

WEGO: a web tool for plotting GO annotations.

Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn.

Genes↗

PubMed2006

The varying microsporidian genome: existence of long-terminal repeat retrotransposon in domesticated silkworm parasite Nosema bombycis.

Microsporidia are a group of intracellular parasites with an extremely compact genome and there is no confirmed evidence that retroelements are parasitised in these organisms. Using the dataset of 200,000 genomic shotgun reads of the silkworm pebrine Nosema bombycis, we have identified the eight complete N. bombycis long-terminal repeat retrotransposon (Nbr) elements. All of the Nbr elements are Ty3/gypsy members and have close relationships to Saccharomycetes long-terminal repeat retrotransposons identified previously, providing further evidence of their relationship to fungi. To explore the effect of retrotransposons in microsporidian genome evolution, their distribution was characterised by comparisons between two N. bombycis contigs containing the Nbr elements with the completed genome of the human parasite Encephalitozoon cuniculi, which is closely related to N. bombycis. The Nbr elements locate between or beside syntenic blocks, which are often clustered with other transposable-like sequences, indicating that they are associated with genome size variation and syntenic discontinuities. The ratios of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site of the open reading frames among members of each of the eight Nbr families were estimated, which reveal the purifying selection acted on the N. bombycis long-terminal repeat retrotransposons. These results strongly suggest that retrotransposons play a major role in reorganization of the microsporidian genome and they might be active. The present study presents an initial characterization of some transposable elements in the N. bombycis genome and provides some insight into the evolutionary mechanism of microsporidian genomes.

Amino Acid Sequence↗

PubMed2005

Determination of ibuprofen in dog plasma by liquid chromatography and application in pharmacokinetic studies of an ibuprofen prodrug in dogs.

A liquid chromatography (LC) method for the determination of ibuprofen in dog plasma is described. Chromatographic separation was performed on a Diamonsil C18 column with a C18 guard column using a binary mixture of acetonitrile and 0.02 mol/l phosphate buffer (pH 6.5) (35:65, v/v) delivered at a flow rate of 1.2 ml/min. The linear range for ibuprofen was from 1.0 to 40.0 microg/ml with a limit of quantitation of 1.0 microg/ml. Within-run accuracy and precision ranged from -0.1% to 4.0% and from 1.1% to 5.5% and between-run accuracy and precision ranged from -1.1% to 4.7% and from 1.3% to 7.0%, respectively. The mean extraction recoveries of ibuprofen determined over the concentrations of 1.0, 10.0, and 40.0 microg/ml were (100.5+/-1.8)%, (99.8+/-1.0)%, and (99.2+/-2.3)%. The developed LC method greatly simplified the sample preparation and adopted mild conditions to prevent the possible hydrolysis of the prodrug and was successfully applied to the pharmacokinetic studies of an ibuprofen prodrug in dogs.

Animals↗

PubMed2005

The Genomes of Oryza sativa: a history of duplications.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Base Sequence↗

PubMed2005

ChickVD: a sequence variation database for the chicken genome.

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the 'Chicken Variation Database' (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn.

Animals↗

PubMed2004

Liquid chromatography-mass spectrometry method for determination of tetramethylpyrazine and its metabolite in dog plasma.

A liquid chromatography-mass spectrometry method is described for the determination of tetramethylpyrazine (TMP) and its active metabolite, 2-hydroxymethyl-3,5,6-trimethylpyrazine (HTMP) in dog plasma. This method involves a plasma clean-up step using protein precipitation procedure followed by LC separation and positive electrospray ionization mass spectrometry detection (ESI-MS). Chromatographic separation of the analytes was achieved on a C18 column using a mobile phase of methanol, water and acetic acid (50:50:0.6, v/v/v) at a flow rate of 1.0 ml/min. Selected ion monitoring (SIM) mode was used for analyte quantitation at m/z 137.2 for TMP, m/z 153.2 for HTMP and m/z 195.2 for caffeine. The linearity was obtained over the concentration ranges of 20-6000 ng/ml for TMP and 20-4000 ng/ml for HTMP and the lower limit of quantitation was 20 ng/ml for both analytes. For each level of QC samples, both inter- and intra-day precisions (R.S.D.) were <or=7.4% for TMP and <or=6.0% for HTMP, and accuracy (R.E.) was +/-6.0% for TMP and <or=3.5% for HTMP. The proposed LC-MS method was successfully applied to the pharmacokinetic studies of a TMP formulation preparation after oral administration to beagle dogs.

Animals↗

PubMed2004

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

Algorithms↗

PubMed2004

Genetic enhancement of ventricular contractility protects against pressure-overload-induced cardiac dysfunction.

In response to pressure-overload, cardiac function deteriorates and may even progress to fulminant heart failure and death. Here we questioned if genetic enhancement of left ventricular (LV) contractility protects against pressure-overload. Transgenic (TG) mice with cardiac-restricted overexpression (66-fold) of the alpha(1A)-adrenergic receptor (alpha(1A)-AR) and their non-TG (NTG) littermates, were subjected to transverse aorta constriction (TAC)-induced pressure-overload for 12 weeks. TAC-induced hypertrophy was similar in the NTG and TG mice but the TG mice were less likely to die of heart failure compared to the non-TG animals (P <0.05). The hypercontractile phenotype of the TG mice was maintained over the 12-week period following TAC with LV fractional shortening being significantly greater than in the NTG mice (42+/-2 vs 29+/-1%, P <0.01). In the TG animals, 11-week beta-AR-blockade with atenolol neither induced hypertrophy nor suppressed the hypercontractile phenotype. The hypertrophic response to pressure-overload was not altered by cardiac alpha(1A)-AR overexpression. Moreover, the inotropic phenotype of alpha(1A)-AR overexpression was well maintained under conditions of pressure overload. Although the functional decline in contractility with pressure overload was similar in the TG and NTG animals, given that contractility was higher before TAC in the TG mice, their LV function was better preserved and heart failure deaths were fewer after induction of pressure overload.

Actins↗

PubMed2003

A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China.

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.

Base Sequence↗

PubMed2003

The emotional distress in a community after the terrorist attack on the World Trade Center.

OBJECTIVES: To examine psychological impact of the September 11th disaster on the immediate neighborhood of the New York World Trade Center. METHODS: 555 residents from the local Chinatown community participated in the study. They were surveyed retrospectively on their emotional-distress immediately after the tragedy and five months later. RESULTS: Prevalent anxiety was found in general community residents and additional depression in those who lost family members or friends. The mental health condition of the community improved tremendously five months later, with the initial 59% of general residents having 4 or more emotional symptoms dropping to 17%. However, more than half of the community residents had persistently shown one or more symptoms of emotional distress. Those who had lost a family member or friend in the disaster showed significantly higher distress, with 90% of them had four or more major psychiatric symptoms during the first few weeks right after the disaster, and the rate dropped to 35% five months later. Overall, those in their 40s and 50s seemed to have had relatively higher emotional distress than both younger and older groups. DISCUSSION: Methodological limitations were discussed concerning retrospective reporting and sample characteristics.

Adolescent↗

PubMed2003

[Study of multi-factor cognition evoked by binocular disparity].

It is the aim of studies in cognitive process to understand how the impressive cognitive capacity of the human mind is uninterruptedly developed and how the process is controlled. We have been focusing attention on the central question with stereoscopic research. A multi-channel EEG data acquisition system is constructed for cognition studies which not only works perfectly in the EEG collection and signal processing of stereoscopic visual evoked potentials(VEP) but also is suitable for investigative and clinical use. We have identified the fact that the processing of stereoscopic depth information is done in the cortical advance functional areas with labeled characteristic signaling of the depth related VEP and the results were shown to be of no difference when compared with the ones of other investigations. We believe, the stereoscopic depth cognition is both a dynamic multi-factor processing process and a consequence of depth perception in advanced cortical areas through biological feedback to the whole process of visual signal processing. It is our novel and significant supposition in the psychophysical study, and the experimental results of the VEP are presented in this article.

Adult↗