Biomedical subjects

Xin Hu

Publications and source records attributed to Xin Hu.

45 records · Page 3Linked to original sources

PubMed2004

[The structural, transcriptional and homology analysis of two frr genes in rice].

Two rice (Oryza sativa subsp. japonica cv. Nipponbare) ribosome recycling factor genes--OsfrrA and OsfrrB had been identified and characterized in this study. The gene OsfrrA is located on chromosome 4 while OsfrrB on chromosome 7. No other homologue is found in rice organelle genomes. Both genes are unique in rice genome and constitutively expressed. The N-terminal character of their encoded protein products suggests that the proteins are transferred to mitochondrion and chloroplast respectively and carry out their functions. The sequence conservation and the constitutive expression profile of the two genes strongly imply their indispensable role in plant growth. In addition, these sequences share phylogenetic homology to some extent with other prokaryotic and eukaryotic RRFs, providing further evidence for the endosymbiotic theory, and implying the potential value of RRFs in molecular evolution research.

Amino Acid Sequence↗

PubMed2003

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction.

Docking of metalloproteinase inhibitors remains a challenge due to the zinc multiple coordination geometries and the lack of appropriate force field parameters to model the metal/ligand interactions. In this study, we explore the docking accuracy and scoring reliability for the docking of matrix metalloproteinase (MMP) inhibitors using AutoDock 3.0. Potential problems associated with zinc ion were investigated by docking 16 matrix metalloproteinase ligands to their crystal structures. A good coordination between the zinc binding group (ZBG) and the zinc was shown to be a prerequisite for the ligand to fit the binding site. A simplex optimization of zinc parameters, including zinc radius, well depth, and zinc charges, was performed utilizing the 14 MMP complexes with good docking. The use of optimized zinc parameters (zinc radius: 0.87 A; well depth: 0.35 kcal/mol; and zinc charges: +0.95 e) shows improvement in both docking accuracy at the zinc binding site and the prediction of binding free energies. Although further improvement in the docking procedure, particularly the scoring function is needed, optimization of zinc parameters provides an efficient way to improve the performance of AutoDock as a drug discovery tool.

Binding Sites↗

PubMed2003

[Morphologic features of the acetabulum bone joint area].

The research on the morphology features of the acetabulum bone joint surface area would be helpful to establishing the acetabulum 3D model for the purpose of the biomechanical analysis of hip joint, and therefore might have its important clinical significance. However, in former studies, the acetabulum was simply considered as a semi sphere. In this study, based on the acetabulum 3D-point data acquired by the 3D laser surface scanner and the reverse engineering technology together with the optimal fit algorithm, two kinds of best-fit model were achieved by a sphere surface and a rotating elliptical surface respectively approaching to the acetabulum bone joint surface. Both fitting errors were then compared and analyzed. The results showed that the fitting error of the rotating elliptical surface was significantly less than that of the sphere surface (P < 0.001). The average radius of fitting sphere was 24.37 +/- 2.22 mm and the average long axis of fitting rotating elliptical surface was 26.02 +/- 2.76 mm while its short axis was 24.17 +/- 2.16 mm. These findings would be helpful to our new recognition of the acetabulum since they were results of the first quantitative analyses for the acetabulum bone surface and also might serve as an important reference base in its further studies and application.

Acetabulum↗

PubMed2002

Sequence and analysis of rice chromosome 4.

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Arabidopsis↗

PubMed2002

Leptin--a growth factor in normal and malignant breast cells and for normal mammary gland development.

BACKGROUND: Obesity is a risk factor for breast cancer in postmenopausal women. As body weight and fat mass increase, circulating leptin increases. Leptin is an adipocyte-derived cytokine that acts through the long form of its receptor, termed OB-Rb. To investigate whether leptin is associated with breast cancer, we determined the expression of OB-Rb in human breast epithelial HBL100 cells and human breast carcinoma-derived T-47D cells, determined whether leptin influenced the proliferation of these cells, and evaluated the structure of mammary tissue in genetically obese leptin-deficient Lep(ob)Lep(ob) and leptin receptor-deficient Lepr(db)Lepr(db) mice. METHODS: Cell numbers and cell colony formation by HBL100 and T-47D cells were determined by anchorage-dependent and anchorage-independent growth assays. OB-Rb expression was examined by reverse transcription-polymerase chain reaction and immunoblot analyses. Expression of leptin signaling pathway components was evaluated with immunoblot and electrophoretic mobility shift assays. Mammary gland development in lean and obese mice was investigated in whole-mount studies. All statistical tests were two-sided. RESULTS: Leptin enhanced anchorage-dependent proliferation by 138% (95% confidence interval [CI] = 108% to 169%) in T-47D cells and 50% (95% CI = 38% to 60%) in HBL100 cells. In both cell lines, OB-Rb was expressed, and leptin increased the expression of phosphorylated signal transducers and activators of transcription 3 (STAT3), phosphorylated extracellular signal-regulated kinase (ERK), and transcript activator protein 1 (AP-1). However, leptin increased anchorage-independent cell growth only in the breast cancer cell line (by 81% [95% CI = 62% to 101%] compared with untreated cells). Obese Lep(ob)Lep(ob) and Lepr(db)Lepr(db) mice had minimal epithelial development in the mature mammary gland compared with their lean counterparts. CONCLUSIONS: Leptin appears to be able to control the proliferation of both normal and malignant breast epithelial cells. Consequently, the leptin pathway should be further studied as a target for interventions to treat or prevent breast cancer.

Animals↗

PubMed2002

[Effects of soil pH value on the bioavailability and fractionation of rare earth elements in wheat seedling (Triticum aestivum L.)].

The effect of soil pH value on the bioavailability and fractionation of rare earth elements (REEs) in wheat seedling (Triticum aestivum L.) were investigated. The results showed that the concentration of REEs in wheat decreased with increasing pH value, and their inter-relationship was best expressed as quadratic equation, with correlation coefficients from 0.6003 to 0.9572. The response of individual elements to pH value change tended to be Ce > La > Nd > Sm > Gd > Yb > Eu, with Ce most sensitive to changing pH conditions and Eu lest. Chemical fractionation indicated that the order of REEs concentration in three fractions could be as follows: B2(NH2OH.HCl extraction) > B3(H2O2-NH4Ac extract) > B1(HAc extract). The increase of pH value resulted in transformation from B1 to B2 and B3. Multiple regression analysis was utilized to obtain the regression equations for prediction plant uptake of REEs. B1 fraction was most available to wheat. Meanwhile, it was found that the fractionation factors of REEs in wheat were negatively correlated with the soil pH value.

Biological Availability↗

PubMed2002

Bioaccumulation of lanthanum and cerium and their effects on the growth of wheat (Triticum aestivum L.) seedlings.

Through short-term exposure (7-d exposure), long-term exposure (16-d exposure) and exposure-recovery (7-d exposure + 9-d recovery), the bioaccumulation and distribution of La and Ce and their effects on growth of wheat seedlings were studied. Addition of La (0.5-25 mg/l) and Ce (0.5-25 mg/l) to the culture medium individually and in combination inhibited primary root elongation, reduced the dry weight of roots and shoots and the content of mineral elements (Ca, Mg, K, Cu, Zn). The damage increased with an increase in the concentrations of La and Ce in culture medium. Relative damage ratio increased with an increase in concentrations of La and Ce in the culture medium and with exposure time. Comparing exposure-recovery groups with long-term exposure groups, primary root lengths, dry weight of roots and shoots and the content of five mineral elements were higher. The accumulation of La and Ce in the seedlings was positively correlated with the concentrations of La and Ce in the culture medium and with exposure time. Bioaccumulation factors of La and Ce in roots were much higher than those of shoots. The uptake rates of La and Ce by the plants were much higher than the translocation rates from roots to shoots. The accumulation and distribution of La and Ce in the seedlings in exposure-recovery groups showed that there was very little excretion through metabolism during the recovery period, but redistribution occurred throughout the whole plant. No apparent selective uptake was found between La and Ce by the plants when they were applied in combination.

Cerium↗

PubMed2002

A fine physical map of the rice chromosome 4.

As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies.

Chromosomes↗

PubMed1997

The Discovery of Streptomycin-binding IgG and Its Distribution in the Population.

It was found by using several immunochemistry methods that a kind of immunoglobulin G (IgG) which accounted for 0.5%-1% of the total IgG in human, rabbit or mice with no history of taking any streptomycin could bind specifically with the antibiotic. Although the IgG-binding action has not relation with the specificity of the antibody, the streptomycin-binding area was found to be on the antigen-binding region of Fab fragment of the antibody. This kind of IgG was termed streptomycin-binding IgG (SMBIgG) which may be capable of catalyzing the metabolism of streptomycin. The average content of SMBIgG in human and rabbit sera is about 0.1 mg/ml, with no samples with a lower level than the mean value, but in a few cases levels two or three times higher than the mean were detected. Further study indicated that the ratio of SMBIgG to total IgG is nearly constant in the population. The discovery of SMBIgG in the normal body and its catalytic characteristic may be very helpful for understanding some of the special physiological functions of the antibody in the organism.

Journal Article↗