Search PubMed⌕ Search

Biomedical subjects

Xiao Sun

Publications and source records attributed to Xiao Sun.

At least 19 recordsLinked to original sources
PubMed2025

G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm.

G-quadruplexes (G4s) are nucleic acid secondary structures with important regulatory functions. Single-nucleotide variants (SNVs), one of the most common forms of genetic variation, can potentially impact the formation of G4 structures if they occur within G4 regions. However, there is currently a lack of software tools specifically designed to assess such effects. Here, we present an R/Bioconductor package named G4SNVHunter, which enables rapid detection of variants that may disrupt G4 structures. This tool, based on the core principles of the G4Hunter algorithm, can provide precise quantitative assessment of the propensity for G4 formation within genomic sequences. Specialized experimental methods can then be designed based on the results provided by G4SNVHunter to further verify the specific functions of the affected G4 structures, facilitating deeper insights into the biological impacts of genetic variants from the perspective of G4 structures. To showcase the functionality of the G4SNVHunter package, we analyzed the Neandertal and Denisovan archaic introgressed variants detected by the Sprime software, and identified approximately 5,800 variants located within G4 regions, among which around 230 may impair G4 structure formation propensity. The source code for the G4SNVHunter package has been publicly released under the MIT license at https://github.com/rongxinzh/G4SNVHunter and https://bioconductor.org/packages/devel/bioc/html/G4SNVHunter.html.

G-Quadruplexes↗
PubMed2007

From trifluoroacetate complex precursors to monodisperse rare-earth fluoride and oxyfluoride nanocrystals with diverse shapes through controlled fluorination in solution phase.

We report the first systematic synthesis of monodisperse rare-earth (RE=La to Lu, Y) fluoride and oxyfluoride nanocrystals with diverse shapes (trigonal REF3 triangular, truncated-triangular, hexagonal, and polygonal nanoplates; orthorhombic REF3 quadrilateral and zigzag-shaped nanoplates; cubic REOF nanopolyhedra and nanorods) from single-source precursors (SSP) of [RE(CF(3)COO)(3)] through controlled fluorination in oleic acid (OA)/oleylamine (OM)/1-octadecene (ODE). To selectively obtain REF3 or REOF nanocrystals, the fluorination of the RE-O bond to the RE-F bond at the nucleation stage was controlled by finely tuning the ratio of OA/ODE or OA/OM, and the reaction temperature. For phase-pure REF3 or REOF naocrystals, their shape-selective syntheses could be realized by further modifying the reaction conditions. The two-dimensional growth of the REF3 nanoplates and the one-dimensional growth of the REOF nanorods were likely due to the selective adsorption of the capping ligands on specific crystal planes of the nanocrystals. Those well-shaped nanocrystals with diverse geometric symmetries (such as D(3h), D(6h), C(2h), O(h), and D(nh)) displayed a remarkable capability to form self-assembled superlattices. By manipulating the solvent-substrate combination, the plate-shaped REF3 nanocrystals could form highly ordered nanoarrays by means of either the face-to-face formation or the edge-to-edge formation. By using this SSP strategy, we also obtained high-quality LaF3:Eu and LaF3:Eu/LaF3 triangular nanoplates that showed photoluminescent red emissions of Eu3+ ions sensitive to the surface effect.

Crystallization↗
PubMed2006

Evaluating the correlation and prediction of trunk fat mass with five anthropometric indices in Chinese females aged 20-40 years.

BACKGROUND AND AIMS: Obesity is a worldwide problem, and excess trunk fat mass (FM(trunk)) has been associated with an increased risk of diseases. The early measurement of FM(trunk) has potential importance to evaluate trunk obesity. We sought to evaluate the correlation and predication of FM(trunk) with five anthropometric indices in Chinese females. METHODS AND RESULTS: A sample of 850 China females aged 20-40 years were recruited and divided into four age groups with a 5-year range in each group. Five anthropometric indices were measured or calculated. FM(trunk) in kg was measured using a dual-energy X-ray absorptiometry scanner. Principal component analysis (PCA) and multiple regression analysis were performed to develop prediction equations. There was an increasing trend of FM(trunk) and five anthropometric indices in successively older age groups. Four formed principal components (PCs) interpreted over 99% of the total variation of five relative anthropometric indices in all age groups. Regression analyses showed that four PCs combined explained a greater variance (R(2)=45.2-81.6%) in FM(trunk) than did each of the five indices alone (R(2)=2.4-72.2%). CONCLUSIONS: Our results suggested that there is an increasing trend of FM(trunk) and five anthropometric indices with aging; that age obviously influences the relationship of FM(trunk) and the anthropometric indices studied; and that the accuracy of predicting the FM(trunk) using five anthropometric indices combined is greater than using the five indices alone.

Absorptiometry, Photon↗
PubMed2006

Receiver-operating characteristic analyses of body mass index, waist circumference and waist-to-hip ratio for obesity: Screening in young adults in central south of China.

BACKGROUND & AIMS: Recent data suggest that current obesity diagnostic criterion based on body mass index (BMI) above 30 in Caucasians may not be appropriate for Asian populations. Our aim was to identify the usefulness of BMI, waist circumference (WC) and waist-to-hip ratio (WHR) in screening for obesity in an Asian population. METHODS: A cross-sectional sample of 1109 males and 879 females aged 20-45-yr were recruited. Height, weight, WC, hip circumference and percentage body fat (PBF) were measured in all subjects. Then receiver-operating characteristic analyses were used to evaluate the performances of the three anthropometric indices. RESULTS: BMI, WC and WHR showed strong positive correlation with PBF (r=0.47-0.75) in both males and females within both age groups. True-positive rates ranged from 82.4% to 94.1% and 68.8% to 86.3% in males and females, respectively. True-negative rates ranged from 64.1% to 84.7% and from 56.9% to 79.0%, respectively. The areas under the curves (AUCs) for WC and BMI were high (0.76-0.92) in both sexes and divided age groups (20-30-yr and 31-45-yr), and those for WHR were a little lower (0.74-0.88). CONCLUSIONS: BMI and WC are two important predictors for obesity in Chinese, and WHR is an alternative.

Adipose Tissue↗
PubMed2006

Genetic and environmental correlations between bone geometric parameters and body compositions.

The purpose of this study was to determine the genetic and environmental correlations between weight, lean mass and bone geometric parameters (sub-periosteal diameter, W; cross-sectional area, CSA; cortical thickness, CT; section modulus, Z; and buckling ratio, BR) of femoral neck. The sample was composed of 512 Caucasian pedigrees, including 2667 females and 1822 males. Bivariate quantitative genetic analyses were performed to evaluate the genetic (rho(G)), environmental (rho(E)) and phenotypic (rho(P)) correlations between the study traits. Univariate genetic analyses showed that the heritabilities (h(2)) for bone geometric parameters were significant (P < 0.001) ranging from 0.50 to 0.60. The significant common household effects indicated the common environment shared by household members for W, CSA, CT, Z and BR (P < 0.05), but the magnitude was small compared with heritabilities. rho(E), rho(G) and rho(P) between bone geometric parameters and weight, lean mass were generally significant. Interestingly, lean mass showed both stronger genetic and environmental correlations with the bone geometric parameters than weight. In addition, according to the magnitude of correlation coefficients, the rho(G) between body compositions and bone geometric parameters were generally stronger than rho(E) (except for that between BR and body compositions). These data suggested that the geometric parameters of femoral neck are under strong genetic control. Furthermore, some common genetic and environmental factors are shared by bone geometric parameters and weight, lean mass. The results may help understand the intertwined relationships between bone metabolisms, mechanical loading and body compositions.

Absorptiometry, Photon↗
PubMed2006

Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition.

BACKGROUND: Meiotic double-strand breaks occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Hotspots and coldspots are receiving increasing attention in research into the mechanism of meiotic recombination. However, predicting hotspots and coldspots from DNA sequence information is still a challenging task. RESULTS: We present a novel method for classification of hot and cold ORFs located in hotspots and coldspots respectively in Saccharomyces cerevisiae, using support vector machine (SVM), which relies on codon composition differences. This method has achieved a high classification accuracy of 85.0%. Since codon composition is a fusion of codon usage bias and amino acid composition signals, the ability of these two kinds of sequence attributes to discriminate hot ORFs from cold ORFs was also investigated separately. Our results indicate that neither codon usage bias nor amino acid composition taken separately performed as well as codon composition. Moreover, our SVM based method was applied to the full genome: We predicted the hot/cold ORFs from the yeast genome by using cutoffs of recombination rate. We found that the performance of our method for predicting cold ORFs is not as good as that for predicting hot ORFs. Besides, we also observed a considerable correlation between meiotic recombination rate and amino acid composition of certain residues, which probably reflects the structural and functional dissimilarity between the hot and cold groups. CONCLUSION: We have introduced a SVM-based novel method to discriminate hot ORFs from cold ones. Applying codon composition as sequence attributes, we have achieved a high classification accuracy, which suggests that codon composition has strong potential to be used as sequence attributes in the prediction of hot and cold ORFs.

Algorithms↗
PubMed2006

Correlation and prediction of trunk fat mass with four anthropometric indices in Chinese males.

To increase our understanding of the relationships of trunk fat mass (FMtrunk) and four anthropometric indices in Chinese males, 1090 males aged 20-40 years were randomly recruited from the city of Changsha, China. Waist circumference (WC) and hip circumference (HC) were measured using standardized equipment, and three other anthropometric indices of BMI, waist:hip ratio (WHR) and conicity index (CoI) were calculated using weight, height, HC and WC. FMtrunk (in kg) was measured using a Hologic QDR 4500 W dual-energy X-ray absorptiometry scanner. There was an increasing trend of FMtrunk, %FMtrunk (percentage of FMtrunk) and BMI, WC, WHR, CoI in successively older age groups (e.g. the mean FMtrunk values were 4.63 (SD 2.58), 5.39 (SD 2.74), 5.93 (SD 2.82), 6.57 (SD 2.94) in four 5-year age groups, respectively). FMtrunk and %FMtrunk were significantly correlated with four anthropometric indices with the Pearson's correlation coefficients ranging from 0.25 to 0.86. Principal component analysis was performed to form three principal components that interpreted over 99.5% of the total variation of four related anthropometric indices in all age groups, with over 65% of the total variation accounted by principal component 1. Multiple regression analyses showed that three principal components explained a greater variance (R(2) 70.0-80.1%) in FMtrunk than did BMI or WC alone (R(2) 57.8-74.1%). The present results suggest that there is an increasing trend of FMtrunk and four anthropometric indices in successively older age groups; that age has important effects on the relationships of FMtrunk and studied anthropometric indices; and that the accuracy of predicting FMtrunk using four anthropometric indices is higher than using BMI or WC alone.

Adipose Tissue↗
PubMed2006

Copper catalyzing growth of single-walled carbon nanotubes on substrates.

Metallic copper, which is normally considered as a contaminant in the growth of single-walled carbon nanotubes (SWNTs), was found to be an efficient catalyst to grow SWNTs under suitable conditions. It showed very high catalytic activity for the growth of both random SWNT networks and horizontally aligned SWNT arrays. Especially, high-quality SWNT arrays were obtained when monodispersed copper nanoparticles were used. The catalytic behavior of copper for the growth of SWNTs was discussed. The weaker interaction between the copper and silica surfaces plays an important role in the growth of high-quality horizontally aligned SWNT arrays. This new synthesis process of SWNTs with a non-ferromagnetic catalyst brings more convenience to the study of magnetic properties of SWNTs and gives more insight in structure-controlled synthesis of SWNTs.

Journal Article↗
PubMed2005

Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae.

Publication of the complete genome sequence for the Acanthamoeba sp. endosymbiont UWE25 has illuminated the evolution history of chlamydiae. In this study, the codon usage bias in UWE25 and five other species of pathogenic chlamydiae was calculated. It was found that genomic composition constraints are the major source of codon usage variation in UWE25. This result is different from the former observation in pathogenic chlamydiae, whose genomic base composition is more unbiased. Four other factors, such as strand-specific mutational bias, natural selection acting at the level of translation, hydropathy level of each protein and the conservation level of amino acids also have influence in shaping the codon usage in these six species to some extent. Further analysis suggests that the high stability of the UWE25 genome partially account for the difference in codon usage pattern between environmental and pathogenic chlamydiae. Moreover, our results imply that the replicational selection pressure in pathogenic chlamydiae is stronger than that in UWE25. Analyzing the codon usage pattern in the environmental chlamydia and comparing it with that of the pathogenic chlamydiae may provide clues how the chlamydiae have evolved from their common ancestor.

Amino Acids↗
PubMed2005

Linkage exclusion analysis of two important chromosomal regions for height.

Adult height (stature), as an important parameter of human physical development, has been studied in many populations. Recently, we reported a whole genome scan of height on a sample of 630 Caucasian subjects from 53 human pedigrees. Two chromosome regions, 6q24-25 and 7q31.3-36, achieved low linkage signals (multipoint LOD score 0.5), but gained significant results in the linkage studies of height by other groups. In addition, the region 6q24-25 harbors the ER-alpha gene, an important candidate gene for linear growth. To resolve the controversies over these two regions for height, linkage exclusion analyses were performed in an extended sample of 79 pedigrees with 1816 subjects, which include the 53 pedigrees containing 630 subjects for our previous whole genome study and additional 128 new subjects, and 26 new pedigrees containing 1058 subjects. The two regions, 6q24-25 and 7q31.3-36, were excluded at a relative effect size of 10% or greater (p value < 0.0005) and 5% or greater (p value < 0.0018), respectively. Our results suggest that the two regions may not contribute substantially to height variation in our Caucasian population.

Adult↗
PubMed2005

Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses.

We isolated and screened two tumor cell clones DD1 and DG6 with different capacity of metastasis from the same parent cell line, a mouse dendritic cell (DC) sarcoma, using limited dilution method. The genome-wide expressions of DD1 and DG6 cells were detected by Affymetrix's MOE-430A microarray. The expression profiles related with mouse DC development were downloaded from GEO at NCBI and ArrayExpress at EBI database. In order to compare the expression of DC sarcoma and DC developmental arrays which was performed by MG-U74av2, we had screened the best matched probesets between MOE-430A and MG-U74av2 according to the probe identities from Affymetrix technical annotation. After the normalization of 11 housekeeping genes across the 34 arrays (2 DC sarcoma and 32 DC developmental arrays), all these expression profiles were analyzed by the methods of hierarchical clustering, principal component analysis, nearest-neighborhood, and self-organizing maps. The results indicate that expression profiles of DC sarcoma are closer to those of the DC progenitors and hematopoietic stem cells from bone marrow compared with the sorted DCs from spleen. The results support the hypothesis that cancers (tumors or sarcomas) arise from stem cells. It is suggested that the DC sarcomas are more similar to the DC progenitors and hematopoietic stem cells than the relative mature DCs in gene expressions on the large-scale.

Animals↗
PubMed2005

The (CA)n polymorphism of the TNFR2 gene is associated with peak bone density in Chinese nuclear families.

Low peak bone density (PBD) in adulthood is an important determinant of osteoporotic fracture (OF) in the elderly. The tumor necrosis factor receptor 2 (TNFR2) gene has been considered as an important candidate gene for PBD due to its important role in bone turnover. In this study, we recruited a total of 1,263 subjects from 402 Chinese nuclear families composed of both parents and at least one daughter, and tested the association of the (CA)(n) polymorphism in intron 4 of the TNFR2 gene with PBD using a more contemporary quantitative transmission disequilibrium test (QTDT). Significant within-family association was detected between the CA16 allele and bone mineral density (BMD) at the lumbar spine with the P-value of 0.005 after permutations, which is still significant after correction for multiple testing. Some evidence of total-family association between the CA16 allele and lumbar spine BMD was found (P=0.021), although the significant level did not reach the empirical threshold (P< or =0.007). About 3.14% of lumbar spine BMD variation can be explained by the CA16 allele. In summary, our results suggest that the TNFR2 gene may play an important role in determining lumbar spine BMD variation in Chinese women.

Bone Density↗
PubMed2005

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses.

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Base Composition↗
PubMed2005

Single-crystalline and monodisperse LaF3 triangular nanoplates from a single-source precursor.

Single-crystalline and monodisperse LaF3 triangular nanoplates (2.0 x 16.0 nm) in trigonal tysonite structure were synthesized by the thermolysis of a single-source precursor (SSP), La(CF3COO)3, in a hot oleic acid/octadecene solution. The combined use of SSP and coordinating and noncoordinating solvents was demonstrated to have played key roles in the formation of such high-quality nanoplates, which could spontaneously organize into two types of superlattices (edge-to-edge and face-to-face) on a large area. This SSP approach has advantages of one-step, mass production, and easy operation, and may represent a rather general route toward metal fluoride nanocrystals.

Journal Article↗
PubMed2005

Synthesis, structure, texture, and CO sensing behavior of nanocrystalline tin oxide doped with scandia.

Weakly agglomerated nanocrystalline scandia doped tin oxide powders with high surface area (170-220 m(2)/g) and uniform size (3-4 nm) were synthesized for the first time by a two-step hydrothermal process in the presence of urea, followed by the calcination between 500 and 1200 degrees C. The structure and texture of the binary oxide system were characterized by thermogravimetry and differential thermal analysis, Brunauer-Emmett-Teller-specific surface area analysis, transmission electron microscopy, X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy. A metastable scandium tin oxide solid solution in tetragonal structure was formed for the scandia content lower than 6 mol % as the samples were calcined at 800 degrees C, and the excess Sc atoms were dispersed at the surface of the crystallites above this limit. The solid solution was metastable, so scandium migrated toward the surface region of the crystallites and produced a second phase of Sc(4)Sn(3)O(12) during calcining at high temperatures over 1000-1200 degrees C. In the case of the samples with higher dopant concentration (>15 mol %), the calcination at the temperature between 500 and 800 degrees C caused the precipitation of Sc(2)O(3), and the calcination over 1000-1200 degrees C led to the formation of more Sc(4)Sn(3)O(12). Textural analysis showed that doping an appropriate amount of Sc(2)O(3) into nanosized SnO(2) could effectively inhibit the grain growth and stabilize the surface area against high-temperature calcinations below 1000 degrees C. CO gas-sensing property measurements revealed that the dispersion of Sc at the surfaces of the SnO(2) nanocrystallites could improve the CO sensitivity significantly, and the pellet sample with scandia content of 10 mol % sintered at 800 degrees C showed the best CO gas-sensing property in the operation temperature range of 300-400 degrees C. On the basis of the structural and textural analysis, the correlation between the structure/texture and the sensitivity to CO for the as-calcined (SnO(2))(1-x)(Sc(2)O(3))(x) nanocrystallites has been established and explained.

Journal Article↗
PubMed2005

Classifying genomic sequences by sequence feature analysis.

Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream, exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

Algorithms↗
PubMed2005

[A gene-chip image grid localization method based on profiles of image].

Automatic gene-chip image grid localization is an essential task for gene-chip image analysis. Now an method based on profiles of gene-chip image is proposed. Using the differences between two profiles after filtration by arithmetic mean method, we can easily find the local grayscale minimum between two probe spots, then the probe spots are automatically located. The experiments show that the new approach correctly locates the probes while giving protection against noise affection robustly. Grid location

Algorithms↗