A whole genome linkage scan for QTLs underlying peak bone mineral density

We conducted a whole genome linkage scan for quantitative trait loci (QTLs) underlying peak bone mineral density (PBMD). Our efforts identified several potential genomic regions for PBMD and highlighted the importance of epistatic interaction and sex-specific analyses in identifying genetic regions underlying PBMD variation.

INTRODUCTION

Peak bone mineral density (PBMD) is an important clinical risk predictor of osteoporosis and explains a large part of bone mineral density (BMD) variation.

METHODS

To detect susceptive quantitative trait loci (QTLs) for PBMD variation including consideration of epistatic and sex-specific effects, we conducted a whole genome linkage scan (WGLS) for PBMD using 2,200 Caucasians from 207 pedigrees, aged 20-50 years. All the individuals were genotyped with 410 microsatellite markers. In addition to WGLS in the total combined sample of males and females, we conducted epistatic interaction analyses, and sex-specific subgroup linkage analyses.

RESULTS

We identified several potential genomic regions that met the criteria for suggestive linkage. The most impressing region is 12p12 for hip PBMD (LOD = 2.79) in the total sample. Epistatic interaction analyses found a significant epistatic interaction between 12p12 and 22q13 (p = 0.0021) for hip PBMD. Additionally, we detected suggestive linkage evidence at 15q26 (LOD = 2.93), 2p13 (LOD = 2.64), and Xq27 (LOD = 2.64). Sex-specific analyses suggested the presence of sex-specific QTLs for PBMD variation.

CONCLUSIONS

Our efforts identified several potential regions for PBMD and highlighted the importance of epistatic interaction and sex-specific analyses in identifying genetic regions underlying PBMD variation.

Association analysis of vitamin D-binding protein gene polymorphisms with variations of obesity-related traits in Caucasian nuclear families

BACKGROUND

Vitamin D-binding protein (DBP) gene is well known for its function on glucose and vitamin D metabolism in human populations. Previous studies suggested that the in vivo DBP level may play a role in the etiology of obesity. However, few studies explored the contribution of DBP gene to the variance of obesity phenotypes.

OBJECTIVE

To investigate the relationship of DBP polymorphisms and obesity in Caucasian nuclear families.

DESIGN

We genotyped 14 single-nucleotide polymorphisms (SNPs) located in and around the DBP gene in 1873 Caucasian subjects from 405 nuclear families. Three obesity-related quantitative phenotypes were investigated, including body mass index (BMI), fat mass and percentage of fat mass (PFM). Single SNPs and haplotypes (three blocks) were tested by family-based association using the FBAT software.

RESULTS

SNP2 (rs17467825) and its corresponding haplotype GAA (frequency 0.270) in block 1 showed strongest associations with PFM (P=0.0011 and 0.0023, respectively). In multivariate test significant association was also observed for SNP2 with fat mass&BMI&PFM (P=0.0098). Subsequent sex-stratified analyses demonstrated nominal association for SNP2 and haplotype GAA with PFM in the female subgroup.

CONCLUSION

Polymorphisms of DBP gene were significantly association with human PFM, especially in female, suggesting the importance of DBP gene in the pathogenesis of human obesity.

Theoretical and experimental studies on filtering tumor cells from blood cell mixtures with dam structure in microfluidic devices

Here, a filter with series of pools and dams structures was designed and fabricated, utilizing size difference between tumor and blood cells. The cell mixtures were successfully filtrated out by the filter, and separation efficiency was up to 99.9%. To evaluate the filter, physical models were made to describe the behaviors of different cells in microfluidic systems. As the ability of cell deformation depends on both cells' size and excess surface index (ESI), we measured the excess membrane area of different cells, and got tumor cell's ESI is 61.7% ~ 81% comparing with red blood cell (RBC) (44%) and white blood cell (WBC) (84%~137%). Then from the formulas we deduced, we get the filtering limitations of RBC, WBC, and tumor cell are respectively, around 1.8μm, 1.0-1.6μm and 3.7-4.4μm for dam structure; and 1.3μm, 0.9-1.3μm and 3-3.4μm radius for pipes, which actually show conditions for separation. The accuracy and high flux of the filter provide possibilities to isolate cancer cells directly from the blood in real-time, which could become a potential therapy to cancers.

Post-hybridisation by Electrophoresis for Reinforcing the Hybridization Result

In this paper, we developed an electrophoresis method for reinforcing hybridization efficiency, and distinguishing the perfectly matched sequences from the mismatched ones. The non-specific binding labeled targets in the hybridization were effectively removed by electrophoresis instead of the conventional washing procedure in the post-hybridisation process. During electrophoresis, the hybrids (the dual-spiral structures formed in hybridization) would be unchained when targets were continuously removed. In this case, not only the non-specific binding labeled targets, but also the targets participating in hybridization would be removed. Therefore, only the perfectly matched sequences had the distinct hybridization signals, the perfectly matched probes from the single-base mismatched ones could more easily be distinguished, and the single nucleotide polymorphisms (SNP) genotypes were also easily determined by dual-color fluorescence targets.

Method for efficient storage and transportation of sputum specimens for molecular testing of tuberculosis

SETTING

The polymerase chain reaction (PCR) is a highly sensitive method for the detection of Mycobacterium tuberculosis and is available in most countries, though to a lesser extent in rural areas.

OBJECTIVE

To amplify M. tuberculosis DNA sequences of sputum spotted on FTA cards and compare them with the results of microscopic examination among culture-positive samples.

DESIGN

A total of 102 sputum specimens of TB patients in treatment were spotted on FTA cards and stored at room temperature until DNA analysis. We assessed the IS6110 region of M. tuberculosis. The efficacy of the PCR assay for the direct detection of M. tuberculosis was evaluated and compared with the results of cultures (Middlebrook 7H9 broth) and smears of fresh sputum specimens.

RESULTS

We were able to detect 10 fg/microl of mycobacterial DNA even after 6 months in storage. The PCR sensitivity and specificity using the FTA card system were 82% and 96%, while microscopic examination showed 41% and 95%, respectively.

CONCLUSION

The FTA card system for the storage of bacterial DNA from sputum samples should be considered for the molecular diagnosis of tuberculosis. Samples can easily be obtained from geographically isolated populations and shipped by mail for accurate molecular diagnosis.

A genomewide scan for quantitative trait loci underlying areal bone size variation in 451 Caucasian families

BACKGROUND

Bone size is an important determinant of bone strength and is under strong genetic control.

OBJECTIVE

To identify quantitative trait loci (QTL) for areal bone size variation, a large-scale genomewide linkage scan was carried out in 451 Caucasian families.

PARTICIPANTS AND METHODS

Of 4124 people with phenotypes, 3899 were genotyped with 410 microsatellite markers. Multipoint linkage analyses were carried out in the entire sample, as well as in men and women separately. Potential epistatic interactions between identified genomic regions were also assessed.

RESULTS

Several potentially important genomic regions were identified, such as 8q24 for hip bone size (logarithm of the ratio of the odds that two loci are linked (LOD) 3.27) and 2p24 (LOD 2.04) for spine bone size. 8q24 may also interact with 19p13 to affect hip bone size. Several sex-specific QTL were also detected, such as 14q21 (LOD 2.94) for wrist bone size in women and 16q12 (LOD 2.19) for hip bone size in men.

CONCLUSIONS

Together with previous findings, this study has further delineated the genetic basis of bone size and laid a foundation for future studies to eventually elucidate the mechanisms of bone size regulation and associated fracture risks.

A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases

BACKGROUND

The haplotype based association method offers a powerful approach to complex disease gene mapping. In this method, a few common haplotypes that account for the vast majority of chromosomes in the populations are usually examined for association with disease phenotypes. This brings us to a critical question of whether rare haplotypes play an important role in influencing disease susceptibility and thus should not be ignored in the design and execution of association studies.

METHODS

To address this question we surveyed, in a large sample of 1873 white subjects, six candidate genes for osteoporosis (a common late onset bone disorder), which had 29 SNPs, an average marker density of 13 kb, and covered a total of 377 kb of the DNA sequence.

RESULTS

Our empirical data demonstrated that two rare haplotypes of the parathyroid hormone (PTH)/PTH related peptide receptor type 1 and vitamin D receptor genes (PTHR1 and VDR) with frequencies of 1.1% and 2.9%, respectively, had significant effects on osteoporosis phenotypes (p = 4.2 x 10(-6) and p = 1.6 x 10(-4), respectively). Large phenotypic differences (4.0 approximately 5.0%) were observed between carriers of these rare haplotypes and non-carriers. Carriers of the two rare haplotypes showed quantitatively continuous variation in the population and were derived from a wide spectrum rather than from one extreme tail of the population phenotype distribution.

CONCLUSIONS

These findings indicate that rare haplotypes/variants are important for disease susceptibility and cannot be ignored in genetics studies of complex diseases. The study has profound implications for association studies and applications of the HapMap project.

A genome-wide linkage scan for bone mineral density in an extended sample: evidence for linkage on 11q23 and Xq27

BACKGROUND

Osteoporosis is a major public health problem, mainly quantified by low bone mineral density (BMD). The majority of BMD variation is determined by genetic effects. A pilot whole genome linkage scan (WGS) was previously reported in 53 white pedigrees with 630 subjects. Several genomic regions were suggested to be linked to BMD variation.

OBJECTIVE

To substantiate these previous findings and detect new genomic regions.

METHODS

A WGS was conducted on an extended sample where the size was almost tripled (1816 subjects from 79 pedigrees). All the subjects were genotyped with 451 microsatellite markers spaced approximately 8.1 cM apart across the human genome. Two point and multipoint linkage analyses were carried out using the variance component method.

RESULTS

The strongest linkage signal was obtained on Xq27 with two point LOD scores of 4.30 for wrist BMD, and 2.57 for hip BMD, respectively. Another important region was 11q23, which achieved a maximum LOD score of 3.13 for spine BMD in multipoint analyses, confirming the results on this region in two earlier independent studies. Suggestive linkage evidence was also found on 7p14 and 20p12.

CONCLUSIONS

Together with the findings from other studies, the current study has further delineated the genetic basis of bone mass and highlights the importance of increasing sample size to confirm linkage findings and to identify new regions of linkage.

New diterpene from Hedychium villosum

The stems of Hedychium villosum yielded the new diterpenoid 1, named villosin, along with coronarin E and beta-sitosterol. Their structures were elucidated by spectroscopic methods including mono- and bi-dimensional NMR.

[The effect of lactate-buffered peritoneal dialysis fluid in human peritoneal mesothelial cells function]

OBJECTIVE

To investigate the effect of lactate-buffered peritoneal dialysis fluid (L-PDF) on human peritoneal mesothelial cells (HPMC) function.

METHODS

Mesothelial cells from human omentum were isolated and cultured in vitro. Proliferation of HPMC was detected by MTT assay. The quantity of interleukin-8 (IL-8) and fibronectin (FN) in culture supernatants was determined by ELISA. Reverse transcription and polymerase chain reaction amplification were used to detect the expression of IL-8 mRNA in HPMC. Total cellular protein in these supernatants was estimated by using Lowry method.

RESULTS

L-PDF inhibited proliferation of HPMC in a time-dependent manner. The levels of IL-8 and FN in the supernatants were remarkably high, and expression of IL-8 mRNA was up-regulated in HPMC exposure to L-PDF. During a subsequent recovery period of 48 hours in culture medium containing lipopolysaccharide (LPS, 10 mg/L), enterotoxin of staphylococcus aureus (10 mg/L) or TNFalpha(10 x 10(6) U/L), the levels of FN in the supernatants increased (P < 0.05). The levels of IL-8 also increased in HPMC stimulated with TNFalpha(P < 0.01).

CONCLUSION

L-PDF inhibited proliferation of HPMC and increased levels of IL-8 and FN in the HPMC.

Antifungal activity of octyl gallate: structural criteria and mode of action

Octyl gallate (3,4,5-trihydroxybenzoate) was found to possess antifungal activity against Saccharomyces cerevisiae and Zygosaccharomyces bailii, in addition to its potent antioxidant activity. Catechol moiety is essential to elicit this activity. The primary fungicidal activity of octyl gallate comes from its ability to act as a nonionic surface-active agent (surfactant). The length of the alkyl chain is not a major contributor but plays an important role in eliciting the activity.

Effects of intrahippocampal aniracetam treatment on Y-maze avoidance learning performance and behavioral long-term potentiation in dentate gyrus in rat

Effects of intrahippocampal treatment of aniracetam, a selective agonist for DL-alpha-amino-3-hydroxy-5-methyl-4-isoxazoleproionic acid (AMPA) receptors, on Y-maze avoidance learning task and behavioral long-term potentiation (LTP) in perforant path-dentate gyrus were studied in freely moving rats by using in vivo electrophysiology combined with behavioral tests. The results were as follows: (1) intrahippocampal treatment of aniracetam reversibly enhanced basal synaptic transmission in perforant path to dentate gyrus in a dosage dependent manner; (2) aniracetam produced improvement in Y-maze learning performance when administration occurred 5 min prior to maze learning; (3) aniracetam administration significantly facilitated behavioral LTP in dentate gyrus, while the maximal amplitude of LTP has no significant difference when compared to saline group. The present results indicate that hippocampal AMPA receptors are involved in learning and memory.

[Arsenic trioxide induces human tumor cell apoptosis and G2 + M arrest whereas causes HPV16 DNA immortalized cervical epithelial cells G1 block]

OBJECTIVE

To investigate whether As2O3 induces tumor cell apoptosis and cell cycle arrest.

METHODS

DNA agarose gel electrophoresis, flowcytometry analysis, RT-PCR, and Western blot.

RESULTS

As2O3 induced G2 + M arrest of tumor cells such as GLC-82, MGC-803, SGC-7901, Eca109 and HeLa cells before inducing apoptosis and decreased c-myc gene expression, whereas caused G1 block of HPV16 DNA immortalized cervical epithelial HCE16/3 cells and did not affect c-myc expression.

CONCLUSIONS

As2O3 caused apoptosis was related with cell cycle arrest. However, the phase of arrest of tumor cells was different from the pre-tumor cell HCE16/3 cells, which could be related to the change of c-myc gene expression.

[Arsenic trioxide induced human esophageal cancer Ec109 cell apoptosis with downregulation of c-myc gene expression]

OBJECTIVE

To study effect of downregulation of c-myc gene expression with As2O3 on inducing Ec109 cell apoptosis.

METHODS

MTT reduction assay, flowcytometric analysis, DNA gel electrophoresis, Western blot and in situ cell death detection (TUNEL).

RESULTS

The viability of the cells treated with As2O3 was decreased. The cells treated with As2O3 showed a typical apoptotic morphology and hypodiploid peak before G1 phase. DNA of treated Ec109 cells appeared a ladder pattern characteristic of apoptosis. TUNEL detection analysis also revealed the DNA fragmentation and As2O3 decreased c-myc gene expression was observed.

CONCLUSIONS

As2O3 can induce Ec109 cell apoptosis with downregulation of c-myc gene expression.

[Detection of DNA variation after space flight in Datura innoxia by random amplified polymorphic DNA markers]

OBJECTIVE

To substantiate the effect of space environment on medicinal plants, the seeds of Datura innoxia were set up in retrievable satellites.

METHODS

After returning to earth, the DNA variation of different groups was detected by random amplified polymorphic DNA (RAPD) markers.

RESULTS

From a pre-screening of 65 primers with 20 oligonucleotide lengths, 15 primers that produced distinct profiles for each DNA sample were selected. In contrast with the earth controlled group, 39 polymorphic bands were produced in weightless group, and its degree of gene polymorphism was 23.1%; 45 polymophic bands were produced in hit group, and its degree of gene polymorphism was 24.4%. The polymorphic bands ranged approximately from 200 to 1990 bp.

CONCLUSIONS

These results indicate that weightlessness induce DNA variation to some extents in Datura innoxia, while the compound effect of weightlessness and high energy heavy ions is more notable than the effect of single weightlessness.

Overexpression of Bcl-2 partly inhibits apoptosis of human cervical cancer SiHa cells induced by arsenic trioxide

OBJECTIVE

To study the biological effect of arsenic trioxide (As2O3) on human cervical cancer SiHa cells and SiHa cells overexpressing bcl-2 gene.

METHODS

SiHa cells with overexpression of Bcl-2 (SiHa-Bcl2 cells) were established by transfecting SiHa cells with Bcl-2 expression vector. The sensitivities of SiHa and SiHa-Bcl2 cells to As2O3 were determined using MTT (Thiazolyl blue) reduction and colony forming ability assay, morphological analysis, flow cytometric analysis, DNA agarose gel electrophoresis, in situ cell death detection (TUNEL), Northern blot, RT-PCR and Western blot.

RESULTS

As2O3 inhibited the growth of SiHa cells and induced G2/M arrest and apoptosis of the cells. RT-PCR and Western blot analysis revealed that As2O3 induced SiHa cell apoptosis possibly via inhibiting the expression of HPV16 E7 and decreasing the expression of c-myc. However, we found that SiHa-Bcl2 cells partly resisted As2O3 induced apoptosis, which might be related to the prevention of the down-regulation of HPV16 E7 and c-myc gene expression. Nevertheless, As2O3 at a high concentration could still induce apoptosis of SiHa-Bcl2 cells mainly via decreasing Bcl-2 expression and slightly inhibiting viral gene expression.

CONCLUSION

As2O3 is an inducer of the apoptosis of human cervical carcinoma cells and the cells overexpressing Bcl-2 can partly resist As2O3 induced apoptosis, but the exact mechanism is unclear.

[Studies on the plant hormones produced by 5 species of endophytic fungi isolated from medicinal plants (Orchidacea)]

OBJECTIVE

To study the plant hormones produced by 5 species of endophytic fungi isolated from medicinal plants and to illustrate the mechanism on endophytic fungi stimulating the growth of plants.

METHODS

Extracting plant hormones from mycelia and its culture solution with organic solvent, and detecting them by HPLC.

RESULTS

One or more plant hormones [GA3 (Gibberellin), IAA (Indoleacetic acid), ABA (Abscisic acid), Z (Zeatin), ZR (Zeatin riboside)] were detected from the mycelia and its culture solution.

CONCLUSIONS

The plant hormones produced by the endophytic fungi are important materials that may be used to reveal the mechanism of endophytic fungi stimulating the growth of medicinal plants (Orchidacea).