The effect of Qing Huan Ling combined risperidone on the open field behavior of schizophrenic mice model

Objective

To observe the effect of Qing Huan Ling and (or) risperidone on locomotor activity and explorative behavior of schizophrenia mice model by open field test.

Methods

Seventy kunming mice were randomly divided into 5 groups, one group as blank group. The rest groups ip MK-801 continuously 14 day, then randomly numbered: model group, risperidone group, Qing Huan Ling group and risperidone combined Qing Huan Ling group. Ig give corresponding drugs for each group 4 weeks, observe the change of locomotor activity and explorative behavior by open field test.

Results

After Ig 4 weeks, compared with the blank group, there were no obvious difference in locomotor activity and explorative behavior between risperidone group, Qing Huan Ling group and the combined group. Compared with the model group, risperidone had statistics meaning in the repression of explorative behavior (P < 0.05),the combined group has statistics meaning in the repression of locomotor activity and explorative behavior (78.92 ± 36.18 m vs. 186.92 ± 41.08 m, P < 0.01).

Conclusion

Qing Huan Ling regulate the central nervous system of schizophrenia mice model; when combined with risperidone, it restrain the central nervous system of schizophrenia mice model and the effect is stronger than risperidone alone.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

CCSI: a database providing chromatin-chromatin spatial interaction information

Distal regulatory elements have been shown to regulate gene transcription through spatial interactions, and single nucleotide polymorphisms (SNPs) are linked with distal gene expression by spatial proximity, which helps to explain the causal role of disease-associated SNPs in non-coding region. Therefore, studies on spatial interactions between chromatin have created a new avenue for elucidating the mechanism of transcriptional regulation in disease pathogenesis. Recently, a growing number of chromatin interactions have been revealed by means of 3C, 4C, 5C, ChIA-PET and Hi-C technologies. To interpret and utilize these interactions, we constructed chromatin–chromatin spatial interaction (CCSI) database by integrating and annotating 91 sets of chromatin interaction data derived from published literature, UCSC database and NCBI GEO database, resulting in a total of 3 017 962 pairwise interactions (false discovery rate < 0.05), covering human, mouse and yeast. A web interface has been designed to provide access to the chromatin interactions. The main features of CCSI are (i) showing chromatin interactions and corresponding genes, enhancers and SNPs within the regions in the search page; (ii) offering complete interaction datasets, enhancer and SNP information in the download page; and (iii) providing analysis pipeline for the annotation of interaction data. In conclusion, CCSI will facilitate exploring transcriptional regulatory mechanism in disease pathogenesis associated with spatial interactions among genes, regulatory regions and SNPs.

Database URL: http://120.79.23.67/ccsi/search.php

Fludarabine and busulfan as a reduced-toxicity myeloablative conditioning regimen in allogeneic hematopoietic stem cell transplantation for acute leukemia patients

The optimal conditioning regimen for allogeneic hematopoietic stem cell transplantation (allo-HSCT) in acute leukemia remains undefined. We evaluated the outcomes in 30 patients with acute leukemia who underwent allo-HSCT from human leukocyte antigen-matched donors after conditioning with busulfan and fludarabine (BuFlu). The regimen comprised injection of busulfan 3.2 mg/kg daily on 4 consecutive days and fludarabine 30 mg/m² daily for 4 doses. All 30 patients achieved hematopoiesis reconstitution with full donor chimerism confirmed by short tandem repeat DNA analysis. The most common regimen-related toxicity was mucositis (86.7%), followed by cytomegalovirus infection (80%). Serious regimen-related toxicities were rare. Acute graft vs. host disease (aGVHD) was detected in 46.7% of the patients; 33.4% had grade I-II aGVHD and 13.3% had grade III-IV aGVHD. Chronic GVHD (cGVHD) was noted in 20% of the patients. The overall survival and disease-free survival rates were 66.7 and 53%, respectively, with a median follow-up of 25 months for surviving patients. Therefore, BuFlu was an effective conditioning regimen with a low rate of transplant-related adverse effects and increased antileukemic effects in patients with acute leukemia undergoing allo-HSCT.

Dimedone Derivative {2-[(4-Hydroxy-phenylamino)- methylene]-5,5-dimethyl-cyclohexane-1,3-dione} Plays an Important Role in Breast Cancer Treatment

Purpose: To investigate the effect of 2-[(4-hydroxy-phenylamino)-methylene]-5,5-dimethyl-cyclohex (HPDH) on mammary carcinogenesis induced by 7,12-dimethylbenz(a)anthracene in female Sprague Dawley rats.Methods: Among three groups of rats (50 each) used in the study, the control group was fed standard diet alone, ibuprofen group received standard diet containing 1200 mg/kg ibuprofen while HPDH group was administered standard diet containing 1200 mg/kg HPDH. The treatment was for 10 days for all the groups. All the animals received 20 mg of DMBA intragastrically by gavage. Clinical parameters for the rats were recorded weekly. Micrometer caliper was used to measure the diameter of all the tumors at the end of the experiment and tumor volume calculated. Histological evaluation was performed using  hematoxylin and eosin (H&E) staining. High performance liquid chromatography (HPLC) was used to determine the level of HPDH and ibuprofen in the serum of the animals.Results: The data revealed a significant decrease in the number of rats with mammary tumor, number of tumors/rat and tumor volume by 54, 72 and 75 %, respectively, in HPDH group compared to control group. The ibuprofen- treated rats also showed significant decrease in the number of rats with tumor, number of tumors/rat and tumor volume by 43, 55, and 59 %, respectively. Treatment of rats with HPDH increased the latency period of tumor induction significantly (p < 0.005). Median detection period (50 % of tumors) was 92, 83 and 56 days, respectively, in HPDH, ibuprofen and control groups, respectively, after DMBA induction.Conclusion: These results demonstrate that HPDH possesses strong chemopreventive activity against mammary carcinogenesis.Keywords: Carcinogenesis, Mammary tumor, Median detection period, Tumor, Latency period, Chemopreventive activity, Ibuprofen

Gray matter correlates of migraine and gender effect: A meta-analysis of voxel-based morphometry studies

BACKGROUND

An increasing number of neuroimaging studies have revealed gray matter (GM) anomalies of several brain regions by voxel-based morphometry (VBM) studies in migraineurs. However, not all the studies reported entirely consistent findings. Our aim is to investigate concurrence across VBM studies to help clarify the structural anomalies underpinning this condition.

METHODS

A systematic search of VBM studies of patients with migraine and healthy controls (HC) published in PubMed and Embase databases from January 2000 to March 2014 was conducted. A quantitative meta-analysis of whole-brain VBM studies in patients with migraine compared with HC was performed by means of anisotropic effect size version of signed differential mapping (AES-SDM) software package.

RESULTS

Nine studies comprising 222 patients with migraine and 230 HC subjects were included in the present study. Compared to HC subjects, the patients group showed consistent decreased GM in the posterior insular-opercular regions, the prefrontal cortex, and the anterior cingulate cortex. Results remained largely unchanged in the following jackknife sensitivity analyses. Meta-regression analysis showed that a higher percentage of females in the patient sample was associated with decreased GM in the right dorsolateral prefrontal cortex.

CONCLUSIONS

This is the first quantitative whole-brain VBM meta-analysis in migraine showing strong evidence of brain GM anomalies within the pain-processing neural network. Further longitudinal investigations are needed to determine whether these structural anomalies are reversible with effective treatment on migraine.

Kaempferol Promotes Transplant Tolerance by Sustaining CD4+FoxP3+ Regulatory T Cells in the Presence of Calcineurin Inhibitor

Calcineurin inhibitor cyclosporine is widely used as an immunosuppressant in clinic. However, mounting evidence has shown that cyclosporine hinders tolerance induction by dampening Tregs. Therefore, it is of paramount importance to overcome this pitfall. Kaempferol was reported to inhibit DC function. Here, we found that kaempferol delayed islet allograft rejection. Combination of kaempferol and low-dose, but not high-dose, of cyclosporine induced allograft tolerance in majority of recipient mice. Although kaempferol plus either dose of cyclosporine largely abrogated proliferation of graft-infiltrating T cells and their CTL activity, both proliferation and CTL activity in mice treated with kaempferol plus low-dose, but not high-dose, cyclosporine reemerged rapidly upon treatment withdrawal. Kaempferol increased CD4+FoxP3+ Tregs both in transplanted mice and in vitro, likely by suppressing DC maturation and their IL-6 expression. Reduction in Tregs by low dose of cyclosporine was reversed by kaempferol. Kaempferol-induced Tregs exhibited both allospecific and non-allospecific suppression. Administering IL-6 abrogated allograft tolerance induced by kaempferol and cyclosporine via diminishing CD4+FoxP3+ Tregs. Thus, for the first time, we demonstrated that kaempferol promotes transplant tolerance in the presence of low dose of cyclosporine, which allows for sufficient Treg generation while minimizing side effects, resulting in much-needed synergy between kaempferol and cyclosporine.

Association between change in body weight after midlife and risk of hip fracture-the Singapore Chinese Health Study

The relationship between change in body weight and risk of fractures is inconsistent in epidemiologic studies. In this cohort of middle-aged to elderly Chinese in Singapore, compared to stable weight, weight loss ≥10 % over an average of 6 years is associated with nearly 40 % increase in risk of hip fracture.

INTRODUCTION

Findings on the relationship between change in body weight and risk of hip fracture are inconsistent. In this study, we examined this association among middle-aged and elderly Chinese in Singapore.

METHODS

We used prospective data from the Singapore Chinese Health Study, a population-based cohort of 63,257 Chinese men and women aged 45-74 years at recruitment in 1993-1998. Body weight and height were self-reported at recruitment and reassessed during follow-up interview in 1999-2004. Percent in weight change was computed based on the weight difference over an average of 6 years, and categorized as loss ≥10 %, loss 5 to <10 %, loss or gain <5 % (stable weight), gain 5 to <10 %, and gain ≥10 %. Multivariable Cox proportional hazards regression model was applied with adjustment for risk factors for hip fracture and body mass index (BMI) reported at follow-up interview.

RESULTS

About 12 % experienced weight loss ≥10 %, and another 12 % had weight gain ≥10 %. After a mean follow-up of 9.0 years, we identified 775 incident hip fractures among 42,149 eligible participants. Compared to stable weight, weight loss ≥10 % was associated with 39 % increased risk (hazard ratio 1.39; 95 % confidence interval 1.14, 1.69). Such elevated risk with weight loss ≥10 % was observed in both genders and age groups at follow-up (≤65 and >65 years) and in those with baseline BMI ≥20 kg/m(2).There was no significant association with weight gain.

CONCLUSIONS

Our findings provide evidence that substantial weight loss is an important risk factor for osteoporotic hip fractures among the middle-aged to elderly Chinese.

Effect of daily short-duration weight-bearing on disuse-induced deterioration of musculoskeletal system

OBJECTIVES

To investigate deterioration of musculoskeletal system due to prolonged disuse and the potential of daily short-duration weight-bearing as countermeasures.

METHODS

Twenty-four adult male Sprague-Dawley rats were divided into Control Group (CG, no intervention), Tail-suspension Group (TG, tail-suspension without treatment), and Weight-Bearing Group (WBG, tail-suspension with 20 min/day, 5 days/week body weight loading). After four weeks of treatment, femur and tibia, soleus and extensor digitorum longus were evaluated for bone and muscle quality respectively. Tensile properties of bone-tendon insertion (BTI) were evaluated using patella-patellar tendon complex.

RESULTS

Disuse induced deterioration on bone, muscle, and BTI after four weeks. Compared with CG, TG and WBG showed significant decrease in bone mineral density (BMD) of trabecular bone in distal femur (4.3-15.2%), muscle mass (31.3-52.3%), muscle cross-sectional area (29.1-35%), and failure strength of BTI (23.9-29.4%). Tensile test showed that the failure mode was avulsion of bone at the BTI. No significant difference was detected between TG and WBG for all assessments on bone, muscle, and BTI.

CONCLUSIONS

Disuse caused deterioration of bone, muscle, and BTI while daily short-duration of weight-bearing did not prevent this deterioration. Mechanical stimulation with higher intensity and longer duration may be necessary to prevent musculoskeletal deterioration resulted from prolonged disuse.

Gene expression of OCT4, SOX2, KLF4 and MYC (OSKM) induced pluripotent stem cells: identification for potential mechanisms

Background

Somatic cells could be reprogrammed to induced pluripotent stem cells (iPS) by ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM). We aimed to gain insights into the early mechanisms underlying the induction of pluripotency.

Methods

GSE28688 containing 14 gene expression profiles were downloaded from GEO, including untreated human neonatal foreskin fibroblasts (HFF1) as control, OSKM-induced HFF1 (at 24, 48, 72 h post-transduction of OSKM encoding viruses), two iPS cell lines, and two embryonic stem (ES) cell lines. Differentially expressed genes (DEGs) were screened between different cell lines and the control by Limma package in Bioconductor. KEGG pathway enrichment analysis was performed by DAVID. The STRING database was used to construct protein-protein interaction (PPI) network. Activities and regulatory networks of transcription factors (TFs) were calculated and constructed by Fast Network Component Analysis (FastNCA).

Results

Compared with untreated HFF1, 117, 347, 557, 2263 and 2307 DEGs were obtained from three point post-transduction HFF1, iPS and ES cells. Meanwhile, up-regulated DEGs in first two days of HFF1 were mainly enriched in RIG-I-like receptor (RLR) and Toll-like receptor (TLR) signaling pathways. Down-regulated DEGs at 72 h were significantly enriched in focal adhesion pathway which was similar to iPS cells. Moreover, ISG15, IRF7, STAT1 and DDX58 were with higher degree in PPI networks during time series. Furthermore, the targets of six selected TFs were mainly enriched in screened DEGs.

Conclusion

In this study, screened DEGs including ISG15, IRF7 and CCL5 participated in OSKM-induced pluripotency might attenuate immune response post-transduction through RLR and TLR signaling pathways.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2503890341543007.

Expression and significance of SATB1 in the development of breast cancer

Special AT-rich sequence binding protein 1 (SATB1) is a recently discovered gene regulator that can promote the growth and metastasis of breast cancer. However, its expression in different stages of breast cancer development have not been examined. We explored the role of SATB1 in the development of breast cancer by detecting SATB1 expression levels in different stages of breast cancer. SATB1 expression was determined using an immunohistochemical streptavidin peroxidase method; the relationship between clinicopathological features of breast cancer and SATB1 expression was analyzed using the X(2) test. Positive rates of SATB1 protein in normal breast tissue, normal breast ductal hyperplasia tissue, precancerous lesions of breast cancer, non-invasive cancer, early invasive carcinoma, and invasive breast cancer tissue were, respectively, 6.25 (2/32), 6.4 (3/47), 20.4 (10/49), 45.0 (9/20), 52.9 (9/17), and 76.6% (72/94). SATB1 in the latter 3 groups was significantly higher than in the first 3 groups (P < 0.05). The positive rate of SATB1 protein in invasive non-special types of breast cancer (88.5%, 54/61) was significantly higher than in the special type of invasive breast cancer (54.5%, 18/33) and early invasive breast cancer (52.9%, 9/17) (P < 0.05). SATB1 protein expression in breast cancer with lymph node metastasis was generally increased, and the difference was statistically significant (P < 0.05). SATB1 protein expression showed an increasing trend in different stages of breast cancer development. Overexpression indicated poor prognosis.

TeloPIN: a database of telomeric proteins interaction network in mammalian cells

Interaction network surrounding telomeres has been intensively studied during the past two decades. However, no specific resource by integrating telomere interaction information data is currently available. To facilitate the understanding of the molecular interaction network by which telomeres are associated with biological process and diseases, we have developed TeloPIN (Telomeric Proteins Interaction Network) database (http://songyanglab.sysu.edu.cn/telopin/), a novel database that points to provide comprehensive information on protein–protein, protein–DNA and protein–RNA interaction of telomeres. TeloPIN database contains four types of interaction data, including (i) protein–protein interaction (PPI) data, (ii) telomeric proteins ChIP-seq data, (iii) telomere-associated proteins data and (iv) telomeric repeat-containing RNAs (TERRA)-interacting proteins data. By analyzing these four types of interaction data, we found that 358 and 199 proteins have more than one type of interaction information in human and mouse cells, respectively. We also developed table browser and TeloChIP genome browser to help researchers with better integrated visualization of interaction data from different studies. The current release of TeloPIN database includes 1111 PPI, eight telomeric protein ChIP-seq data sets, 1391 telomere-associated proteins and 183 TERRA-interacting proteins from 92 independent studies in mammalian cells. The interaction information provided by TeloPIN database will greatly expand our knowledge of telomeric proteins interaction network.

Database URL: TeloPIN database address is http://songyanglab.sysu.edu.cn/telopin. TeloPIN database is freely available to non-commercial use.

Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures

Background

Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated.

Results

In this paper, we have developed a computational method to generate a genome-wide landscape of TFs and their characteristic binding DNA structures in Saccharomyces cerevisiae. We revealed DNA structural features for different TFs. The structural conservation shows positional preference in TFBSs. Structural levels of DNA sequences are correlated with TF-DNA binding affinities.

Conclusions

We provided the genome-wide correspondences of TFs to DNA structures. Our findings will have implications in understanding TF regulatory mechanisms.

Hybrid monitor for both beam position and tilt of pulsed high-current beams

A Hybrid beam monitor, integrated with both azimuthal and axial B-dot probes, was designed for simultaneous measurement of both beam position and beam angle for pulsed high-current beams at the same location in beam pipe. The output signals of axial B-dot probes were found to be mixed with signals caused by transverse position deviation. In order to eliminate the unwanted signals, an elimination method was developed and its feasibility tested on a 50-Ω coaxial line test stand. By this method, a waveform, shape-like to that of input current and proportional to the tilt angle, was simulated and processed by following integration step to achieve the tilt angle. The tests showed that the measurement error of displacement and tilt angle less than 0.3 mm and 1.5 mrad, respectively. The latter error could be reduced with improved probes by reducing the inductance of the axial B-dot probe, but the improvement reached a limit due to some unknown systemic mechanism.

Gpr177-mediated Wnt Signaling is Required for Fungiform Placode Initiation

Fungiform papillae are formed as patterned rows on the surface of the anterior tongue at early organogenesis and contain one taste bud in each papilla to form one of the important sensory organs. Despite the essential role of Wnt/β-catenin signaling in controlling the development of fungiform taste papillae, the universal function of Wnt ligands in the initiation of the fungiform placode has not been completely elucidated. Here, by Shh (Cre) -mediated oral epithelial deletion of Wntless (Gpr177), a regulator essential for intracellular Wnt trafficking, we demonstrate that an overall function of Wnts is required for initiation of the fungiform placode. Multiple Wnts are expressed in the tongue epithelium at E11.5 before initiation of the fungiform placodes. Epithelial Gpr177 loss-of-function, associated with reduction of canonical Wnt signaling in lingual epithelium as exhibited by a loss of TopGal activity and Axin2 expression, results in the failure of fungiform placode initiation, as assessed by diminished expression of several taste placode molecular markers. Moreover, LiCl treatment of Gpr177 epithelial-deficient tongue explants at E11.5, but not at E12.5, restores tongue placode formation, demonstrating that Wnt ligands in the tongue surface prior to but not after fungiform placode initiation are responsible for fungiform papilla initiation. Epithelium-specific expression of an active β-catenin in the Gpr177-deficient tongue leads to fungiform papillae generation, suggesting that an intra-epithelial response to Wnts is required for placode initiation. Together, these results suggest that Gpr177 controls epithelial initiation of the fungiform placode through signaling via epithelial Wnt ligands.

Neighboring genes show interchromosomal colocalization after their separation

The order of genes on eukaryotic chromosomes is nonrandom. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution. Here, we investigated whether neighboring genes show interactions after their separation. We found that neighboring gene pairs tend to show interchromosomal colocalization (i.e., nuclear colocalization) in the species in which they separate. These nuclear colocalized separated neighboring gene pairs 1) show neighborhood conservation in more species, 2) tend to be regulated by the same transcription factor, and 3) tend to be regulated by the same histone modification. These results suggest a mechanism by which neighboring genes could retain nuclear proximity after their separation.

Natural CD8+CD122+ T cells are more potent in suppression of allograft rejection than CD4+CD25+ regulatory T cells

Despite extensive studies on CD4+CD25+ regulatory T cells (Tregs), their application in adoptive transfer therapies is still not optimal in immune-competent wild-type (WT) animal models. Therefore, it is compelling to search for more potent Tregs for potential clinical application. Mounting evidence has shown that naturally occurring CD8+CD122+ T cells are also Tregs. However, their suppression in allograft rejection, efficiency in suppression and underlying mechanisms remain unclear. Using a murine allotransplantation model, we reported here that CD8+CD122+ Tregs were actually more potent in suppression of allograft rejection and underwent more rapid homeostatic proliferation than their CD4+CD25+ counterparts. Moreover, they produced more IL-10 and were more potent in suppressing T cell proliferation in vitro. Deficiency in IL-10 in CD4+CD25+ and CD8+CD122+ Tregs resulted in their reduced but equal suppression in vivo and in vitro, suggesting that IL-10 is responsible for more effective suppression by CD8+CD122+ than CD4+CD25+ Tregs. Importantly, transfer of CD8+CD122+ Tregs together with the administration of recombinant IL-15 significantly prolonged allograft survival in WT mice. Thus, for the first time, we demonstrate that naturally arising CD8+CD122+ Tregs not only inhibit allograft rejection but also exert this suppression more potently than their CD4+CD25+ counterparts. This novel finding may have important implications for tolerance induction.

Effects on tumor development and metastatic dissemination by the NKG2D lymphocyte receptor expressed on cancer cells

The stimulatory NKG2D lymphocyte receptor together with its tumor-associated ligands enable the immune system to recognize and destroy cancer cells. However, with dynamic changes unfolding, cancers exploit NKG2D and its ligands for immune evasion and suppression. Recent findings have added yet another functional dimension wherein cancer cells themselves coopt NKG2D for their own benefit to complement the presence of its ligands for self stimulation of parameters of tumorigenesis. Those findings are here extended to in vivo tumorigenicity testing by employing orthotopic xenotransplant breast cancer models in mice. Using human cancer lines with ectopic NKG2D expression and RNAi-mediated protein depletion among other controls, we show that NKG2D self-stimulation has tumor promoting capacity. NKG2D signals had no notable effects on cancer cell proliferation and survival but acted at the level of angiogenesis, thus promoting tumor growth, tumor cell intravasation and dissemination. NKG2D-mediated effects on tumor initiation may represent another factor in the observed overall enhancement of tumor development. Altogether, these results may impact immunotherapy approaches, which currently do not account for such NKG2D effects in cancer patients and thus could be misdirected as underlying assumptions are incomplete.

The pattern and evolution of looped gene bendability

Gene looping, defined as the physical interaction between the promoter and terminator regions of a RNA polymerase II-transcribed gene, is widespread in yeast and mammalian cells. Gene looping has been shown to play important roles in transcription. Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB. However, whether other factors contribute to gene looping remains to be elucidated. Here, we investigated the contribution of intrinsic DNA and chromatin structures to gene looping. We found that Saccharomyces cerevisiae looped genes show high DNA bendability around middle and 3/4 regions in open reading frames (ORFs). This bendability pattern is conserved between yeast species, whereas the position of bendability peak varies substantially among species. Looped genes in human cells also show high DNA bendability. Nucleosome positioning around looped ORF middle regions is unstable. We also present evidence indicating that this unstable nucleosome positioning is involved in gene looping. These results suggest a mechanism by which DNA bendability and unstable nucleosome positioning could assist in the formation of gene loops.

BGDB: a database of bivalent genes

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions.

Database URL:http://dailab.sysu.edu.cn/bgdb/

Dietary B vitamin intake and risk of hip fracture: the Singapore Chinese Health Study

This prospective cohort study that comprehensively examined effects of different B vitamins in an Asian population showed an inverse relationship between dietary intake of pyridoxine and hip fracture risk in elderly women. These findings suggest that maintaining sufficient pyridoxine intake may be beneficial in preserving bone health in postmenopausal women.

INTRODUCTION

B vitamins have recently been investigated for their possible roles in maintaining bone health. Incidence of osteoporotic hip fracture has been rising in Asia, but epidemiological data on dietary B vitamins and risk of osteoporotic fractures are sparse. We aimed to examine the association between dietary intakes of B vitamins (thiamin, riboflavin, niacin, pyridoxine, folate, and cobalamin) and hip fracture risk among elderly Chinese in Singapore.

METHODS

The current study was conducted in the Singapore Chinese Health Study, which is a population-based cohort prospective study that enrolled a total of 63,257 men and women aged 45-74 years between 1993 and 1998. Dietary intakes of B vitamins were derived from a validated food frequency questionnaire and the Singapore Food Composition Database.

RESULTS

After a mean follow-up period of 13.8 years, 1,630 hip fracture incident cases were identified. A statistically significant inverse relationship between dietary pyridoxine intake and hip fracture risk was observed among women (p for trend = 0.002) but not among men. Compared to women in the lowest quartile intake (0.37-0.61 mg/1,000 kcal/day), women in the highest quartile intake (0.78-1.76 mg/1,000 kcal/day) had a 22 % reduction in hip fracture risk (hazard ratio 0.78, 95 % confidence interval 0.66-0.93). Dietary intakes of the other B vitamins of interest were not related to hip fracture risk.

CONCLUSIONS

Our findings suggest that maintaining adequate intake of pyridoxine may prevent osteoporotic fractures among elderly women.

Hypophosphatemic osteomalacia and renal Fanconi syndrome induced by low-dose adefovir dipivoxil: a case report and literature review suggesting ethnic predisposition

WHAT IS KNOWN AND OBJECTIVE

Adefovir dipivoxil (ADV) is one of the commonly used antiviral agents in the treatment of chronic hepatitis B (CHB) infection. Safety of a daily dose of 10 mg ADV is advocated by the registration trials. We report a case of severe hypophosphatemic osteomalacia and renal Fanconi syndrome induced by low-dose ADV in a CHB-related cirrhosis patient, and discuss the case through a thorough review of other cases reported in the literature.

CASE SUMMARY

A 48-yr-old Chinese man with CHB-related cirrhosis developed severe progressive generalized bone pain and muscle weakness after receiving ADV 10 mg daily for 54 months. The laboratory results showed severe hypophosphatemia and features of proximal renal tubule dysfunction. Imaging studies were consistent with osteomalacia. After discontinuation of ADV, his symptoms resolved, laboratory abnormalities normalized and imaging studies showed improvement. In addition to our case, 12 other patients have been reported to have developed hypophosphatemic osteomalacia induced by low-dose ADV. Most of the reported cases were of subjects of East-Asian ethnicity. After discontinuation or reduction of ADV, serum phosphate level increased and clinical symptoms significantly improved in all cases.

WHAT IS NEW AND CONCLUSION

Hypophosphatemic osteomalacia and renal Fanconi syndrome can be associated with low-dose ADV. Clinicians treating CHB patients with ADV 10 mg daily over long periods of time should be aware of this infrequent but serious complication.

RIP140 is associated with subclinical inflammation in type 2 diabetic patients

AIMS

To evaluate the expression level of RIP140 (receptor interaction protein 140) and its correlation with inflammatory cytokine production and free fatty acids (FFAs) in type 2 diabetes.

METHODS

Plasma and peripheral blood mononuclear cells (PBMCs) were collected from 24 diabetic and 30 healthy individuals. The levels of FFAs, TC, TG, HDL-C, LDL-C, FIN, and FBG were measured. The insulin resistance index was calculated using the homeostasis model assessment (HOMA). Additionally, PBMCs from control group were cultured alone or with 500 μmol/L palmitic acid (PA). Levels of RIP140 TNF-α, and IL-6 in PBMCs were analyzed using real-time RT-PCR, Western blots and ELISA. The relationship between RIP140 and other variables was performed using SPSS 11.5 software.

RESULTS

TG, LDL-C, FIN, FBG, HOMA, and HDL-C were significantly different between diabetic patients and the control group. Levels of RIP140, TNF-α, and IL-6 were higher in the diabetic group compared to control. RIP140 expression was positively correlated with FFAs, HDL-c, TNF-α, IL-6, FIN, FBG, and HOMA. Finally, 500 μmol/L PA treatment increased RIP140 expression and the secretion of inflammatory cytokines in cultured control PBMCs.

CONCLUSIONS

Increased RIP140 level may be closely associated with inflammation and disorder of lipid and glucose metabolism in diabetic patients.

Cigarette smoke exposure hinders long-term allograft survival by suppressing indoleamine 2, 3-dioxygenase expression

Cigarette smoke causes cancer and increases the vulnerability of smokers to infections. Epidemiologic studies have shown that smoking is one of major risk factors for late allograft rejection. Despite statistical data that associate smoking with allograft rejection, no any study has been conducted to prove that cigarette smoke directly causes allograft rejection in a cause-effect manner. In particular, investigation into immunologic mechanisms underlying smoke-related allograft rejection is lacking. Here we found that second hand smoke (SHS) hindered long-term islet allograft survival induced by CD154 costimulatory blockade plus donor-specific splenocyte transfusion (DST), although it failed to alter acute islet allograft rejection. SHS did not directly interfere with vigorously alloreactive T-cell proliferation in vivo and in vitro. Neither naturally occurring nor induced CD4+CD25+ Treg cell numbers were significantly reduced by SHS. However, SHS suppressed mRNA and protein expression of indoleamine 2, 3-dioxygenase (IDO) and its activity upon transplantation while IDO overexpression in islet allografts restored their long-term survival induced by CD154 blockade. Therefore, SHS prevents long-term allograft survival by inhibiting IDO expression and activity. Thus, our study for the first time demonstrates that SHS shortens allograft survival in a cause-effect manner and unveils a novel immunologic mechanism underlying smoking-related allograft rejection.

Tacrolimus enhances the invasion potential of hepatocellular carcinoma cells and promotes lymphatic metastasis in a rat model of hepatocellular carcinoma: involvement of vascular endothelial growth factor-C

PURPOSE

The purpose of this study was to elucidate the effect of tacrolimus treatment on tumor growth and metastasis of hepatocellular carcinoma (HCC).

METHODS

The effect of tacrolimus was investigated on tumor growth and lymph node metastasis in a rat model of HCC. Angiogenesis and lymphangiogenesis were assessed by CD31 and vascular endothelial growth factor receptor 3 (VEGFR-3) immunostaining. Cell proliferation and invasion were monitored in vitro using the Cell Counting Kit-8 (CCK8) and Matrigel Invasion Chambers, respectively. Levels of vascular endothelial growth factor-C (VEGF-C) expression were measured using quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemisty and Western blots.

RESULTS

Tacrolimus had no effect on the proliferation of HCC in vitro or in vivo. Treatment with tacrolimus resulted in a dose-dependent increase in the invasive potential of HCC cells in vitro, in the density of peritumoral lymphatic vessels, and in the number and volume of metastatic lymph nodes in August Copenhagen Irish (ACI) rats. qRT-PCR, immunohistochemisty, and Western blot revealed that tacrolimus increased the levels of expression of VEGF-C in HCC.

CONCLUSIONS

Tacrolimus enhanced the invasive potential of HCC cells, facilitating HCC lymphangiogenesis and promoting lymphatic metastasis in a rat model of HCC. This influence may be the result of an increase in VEGF-C expression by HCC cells. Targeting the VEGF-C/Fms-related tyrosine kinase 4 axis may be a novel treatment for HCC patients after liver transplantation.

Gene expression divergence is coupled to evolution of DNA structure in coding regions

Sequence changes in coding region and regulatory region of the gene itself (cis) determine most of gene expression divergence between closely related species. But gene expression divergence between yeast species is not correlated with evolution of primary nucleotide sequence. This indicates that other factors in cis direct gene expression divergence. Here, we studied the contribution of DNA three-dimensional structural evolution as cis to gene expression divergence. We found that the evolution of DNA structure in coding regions and gene expression divergence are correlated in yeast. Similar result was also observed between Drosophila species. DNA structure is associated with the binding of chromatin remodelers and histone modifiers to DNA sequences in coding regions, which influence RNA polymerase II occupancy that controls gene expression level. We also found that genes with similar DNA structures are involved in the same biological process and function. These results reveal the previously unappreciated roles of DNA structure as cis-effects in gene expression.

The unique phenotype of each organism is partly determined by gene expression. Changes in gene expression are an important source of phenotypic variation, and can be caused by changes in regulatory and coding sequences of the gene itself (cis) and changes in regulatory factors (trans). The contribution of cis regulation to gene expression divergence between closely related species is much greater than that of trans regulation. However, evolution of primary nucleotide sequences is not correlated with gene expression divergence in yeast, suggesting that other factors in cis drive gene expression divergence. Here, we found that evolution of DNA structure in coding regions is coupled to gene expression divergence in yeast. We also found that DNA structure is associated with specific gene characteristics. Genes with similar DNA structures are involved in the same biological process and function. These results demonstrate the important roles of DNA structure in directing gene expression.

Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast

Eukaryotic chromosomes are not randomly distributed in the interphase nucleus, but instead occupy distinct territories. Nonetheless, the genome-wide relationships of gene regulation to gene nuclear location remain poorly understood in yeast. In the three-dimensional view of gene regulation, we found that a considerable number of transcription factors (TFs) regulate genes that are colocalized in the nucleus. Colocalized TF target genes are more strongly coregulated compared with the other TF target genes. Target genes of chromatin regulators are also colocalized. These results demonstrate that colocalization of coregulated genes is a common process, and three-dimensional gene positioning is an important part of gene regulation. Our findings will have implications in understanding nuclear architecture and function.

Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast

MOTIVATION

The intrinsic DNA sequence is an important determinant of nucleosome positioning. Some DNA sequence patterns can facilitate nucleosome formation, while others can inhibit nucleosome formation. Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood.

RESULTS

Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA show distinct polymorphism patterns to maintain adequate nucleosome architecture on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal DNA tend to facilitate nucleosome formation, whereas polymorphisms in nucleosome-depleted DNA tend to inhibit nucleosome formation, which is especially evident at nucleosome-disfavored sequences in nucleosome-free regions at both ends of genes. Sequence polymorphisms facilitating nucleosome positioning correspond to stable nucleosome positioning. These results reveal that sequence polymorphisms are under selective constraints to maintain nucleosome positioning.

CONTACT

zhimdai@gmail.com; issdxh@mail.sysu.edu.cn

Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae

Background

Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear.

Results

We investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions.

Conclusions

The results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.

Identifying the combinatorial effects of histone modifications by association rule mining in yeast

Eukaryotic genomes are packaged into chromatin by histone proteins whose chemical modification can profoundly influence gene expression. The histone modifications often act in combinations, which exert different effects on gene expression. Although a number of experimental techniques and data analysis methods have been developed to study histone modifications, it is still very difficult to identify the relationships among histone modifications on a genome-wide scale.We proposed a method to identify the combinatorial effects of histone modifications by association rule mining. The method first identified Functional Modification Transactions (FMTs) and then employed association rule mining algorithm and statistics methods to identify histone modification patterns. We applied the proposed methodology to Pokholok et al's data with eight sets of histone modifications and Kurdistani et al's data with eleven histone acetylation sites. Our method succeeds in revealing two different global views of histone modification landscapes on two datasets and identifying a number of modification patterns some of which are supported by previous studies.We concentrate on combinatorial effects of histone modifications which significantly affect gene expression. Our method succeeds in identifying known interactions among histone modifications and uncovering many previously unknown patterns. After in-depth analysis of possible mechanism by which histone modification patterns can alter transcriptional states, we infer three possible modification pattern reading mechanism ('redundant', 'trivial', 'dominative'). Our results demonstrate several histone modification patterns which show significant correspondence between yeast and human cells.

Nucleosomal context of binding sites influences transcription factor binding affinity and gene regulation

Transcription factor (TF) binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites (TFBSs) also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

Insights into distinct regulatory modes of nucleosome positioning

BACKGROUND

The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown.

RESULTS

We found that transcription factor binding sites (TFBSs) with particular nucleosomal contexts show a preference to reside on specific chromosomes. We identified four typical gene classes associated with distinct regulatory modes of nucleosome positioning, and further showed that they are distinguished by transcriptional regulation patterns. The first mode involves the cooperativity between chromatin remodeling and stable transcription factor (TF)-DNA binding that is linked to high intrinsic DNA binding affinities, evicting nucleosomes from favorable DNA sequences. The second is the DNA-encoded low nucleosome occupancy that is associated with high gene activity. The third is through chromatin remodeling and histone acetylation, sliding nucleosomes along DNA. This mode is linked to more cryptic sites for TF binding. The last consists of the nucleosome-enriched organization driven by other factors that overrides nucleosome sequence preferences. In addition, we showed that high polymerase II (Pol II) occupancy is associated with high nucleosome occupancy around the transcription start site (TSS).

CONCLUSIONS

We identified four different regulatory modes of nucleosome positioning and gave insights into mechanisms that specify promoter nucleosome location. We suggest two distinct modes of recruitment of Pol II, which are selectively employed by different genes.

Robustness of transcriptional regulatory program influences gene expression variability

Background

Most genes are not affected when any transcription factor (TF) is knocked out, indicating that they have robust transcriptional regulatory program. Yet the mechanism underlying robust transcriptional regulatory program is less clear.

Results

Here, we studied the cause and effect of robust transcriptional regulatory program. We found that cooperative TFs in the robust transcriptional regulatory program regulate their common target genes in an activity-redundant fashion, and they are able to compensate for each other's loss. As a result, their target genes are insensitive to their single perturbation. We next revealed that the degree of robustness of transcriptional regulatory program influences gene expression variability. Genes with fragile (unrobust) transcriptional regulatory program under normal growth condition could be readily reprogrammed to significantly modulate gene expression upon changing conditions. They also have high evolutionary rates of gene expression. We further showed that the fragile transcriptional regulatory program is a major source of expression variability.

Conclusion

We showed that activity-redundant TFs guarantee the robustness of transcriptional regulatory programs, and the fragility of transcriptional regulatory program plays a major role in gene expression variability. These findings reveal the mechanisms underlying robust transcription and expression variability.

A 100 nanometer scale resistive heater-thermometer on a silicon cantilever

This paper reports a method for fabricating a 100 nm scale heater-thermometer into a silicon microcantilever based on contact photolithography and a controlled annealing process. The heater is formed during a photolithography process that can achieve a minimum feature size of about 1 microm, while careful control of doping and annealing parameters allows the heater size to be further decreased, to a width of 100 nm. The heater is fabricated onto the free end of a silicon cantilever suitable for scanning probe microscopy, and can be integrated into cantilevers with or without sharp tips. The fabricated heater has a maximum temperature of over 700 degrees C, and a heating time of 56 micros to reach 500 degrees C.

Transcriptional interaction-assisted identification of dynamic nucleosome positioning

Background

Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo.

Results

Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we developed a novel computational approach to identify dynamic nucleosome positions at promoters by combining transcriptional interaction and genomic sequence information. Our approach successfully identified experimentally determined nucleosome positioning dynamics available in three cellular conditions, and significantly improved the prediction accuracy which is based on sequence information alone. We then applied our approach to various cellular conditions and established a comprehensive landscape of dynamic nucleosome positioning in yeast.

Conclusion

Analysis of this landscape revealed that the majority of nucleosome positions are maintained during most conditions. However, nucleosome occupancy at most promoters fluctuates with the corresponding gene expression level and is reduced specifically at the phase of peak expression. Further investigation into properties of nucleosome occupancy identified two gene groups associated with distinct modes of nucleosome modulation. Our results suggest that both the intrinsic sequence and regulatory proteins modulate nucleosomes in an altered manner.

Knockdown of Abl interactor 1 expression impairs invadopodia formation, tumor angiogenesis, and markedly slows tumor growth of breast cancer cells

Abstract #2054

Background: Abl interactor 1 (Abi1) is a key regulator of actin polymerization/depolymerization. Previous studies have revealed that Abi1 interacts with Wiskott–Aldrich syndrome protein (Wasp) family proteins, and regulates the nucleation promoting activity of Wasp proteins. In addition to Wasp family proteins, Abi1 also binds to a variety of other signaling molecules, including those involved in the signal transductions of small GTP-binding protein Rac and PI3 kinase. The ability to interact with diverse signaling pathways places Abi1 at a central position in the signaling network that regulates cell motility and proliferation. The involvement of Abi1 in the development of abnormal cytoskeletal functions of cancer cells has recently been reported. It remains unclear, however, how Abi1 exerts its effects in tumor cells and whether it contributes to tumor progression in vivo.&#x2028; Material and Methods: The short hairpin RNA (shRNA)-mediated gene silencing was used, in conjunction with murine tumor xenograft models, to examine the effects of Abi1 knockdown on cytoskeleton remodeling, cell migration, invasion, as well as tumor growth and angiogenesis of MDA-MB231 breast cancer cells.&#x2028; Results: We report here a novel function for Abi1 in the regulation of invadopodia formation as well as in the tumor angiogenesis and invasion of breast cancer cells, possibly through the modulation of Src and matrix metalloproteinase 9 (MMP-9) activities. Abi1 co-localizes with invadopodia, the specialized adhesive/invasive structures believed to control the invasion of tumor cells, in MDA-MB231 breast cancer cells. Epigenetic silencing of the Abi1 gene by shRNA in MDA-MB231 cells impaired the formation of invadopodia and decreased the activity of c-Src and MMP-9. The decreased invadopodia formation and MMP-9 activity correlated with a reduction in the ability of these cells to degrade extracellular matrix (ECM). Remarkably, the knockdown of Abi1 expression inhibited tumor invasion and angiogenesis and markedly slowed tumor growth in xenograft mouse models. Taken together, these results indicate that the Abi1 signaling plays a critical role in breast cancer progression and suggest that this pathway may serve as a therapeutic target for the treatment of human breast cancer.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2054.

Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence

BACKGROUND

The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning plays a central role in diverse cellular processes that rely on access to genomic DNA. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Yet it is less clear whether the role of the underlying DNA sequence in nucleosome positioning varies across different promoters. Whether different determinants of nucleosome positioning have characteristic influences on nucleosome modulation also remains to be elucidated.

RESULTS

We identified two typical promoter classes in yeast associated with high or low dependence of nucleosome positioning on the underlying DNA sequence, respectively. Importantly, the two classes have low or high intrinsic sequence preferences for nucleosomes, respectively. The two classes are further distinguished by multiple promoter features, including nucleosome occupancy, nucleosome fuzziness, H2A.Z occupancy, changes in nucleosome positions before and after transcriptional perturbation, and gene activity. Both classes have significantly high turnover rates of histone H3, but employ distinct modes of nucleosome modulation: The first class is characterized by hyperacetylation, whereas the second class is highly regulated by ATP-dependent chromatin remodelling.

CONCLUSION

Our results, coupled with the known features of nucleosome modulation, suggest that the two distinct modes of nucleosome modulation selectively employed by different genes are linked with the intrinsic sequence preferences for nucleosomes. The difference in modes of nucleosome modulation can account for the difference in the contribution of DNA sequence to nucleosome positioning between both promoter classes.

Missing value imputation for microarray gene expression data using histone acetylation information

Background

It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages.

Results

The paper explores the feasibility of doing missing value imputation with the help of gene regulatory mechanism. An imputation framework called histone acetylation information aided imputation method (HAIimpute method) is presented. It incorporates the histone acetylation information into the conventional KNN(k-nearest neighbor) and LLS(local least square) imputation algorithms for final prediction of the missing values. The experimental results indicated that the use of acetylation information can provide significant improvements in microarray imputation accuracy. The HAIimpute methods consistently improve the widely used methods such as KNN and LLS in terms of normalized root mean squared error (NRMSE). Meanwhile, the genes imputed by HAIimpute methods are more correlated with the original complete genes in terms of Pearson correlation coefficients. Furthermore, the proposed methods also outperform GOimpute, which is one of the existing related methods that use the functional similarity as the external information.

Conclusion

We demonstrated that the using of histone acetylation information could greatly improve the performance of the imputation especially at high missing percentages. This idea can be generalized to various imputation methods to facilitate the performance. Moreover, with more knowledge accumulated on gene regulatory mechanism in addition to histone acetylation, the performance of our approach can be further improved and verified.

DH1, a LOB domain-like protein required for glume formation in rice

T-DNA tagging is a high throughput strategy for identifying and cloning functional genes in plants. In this study, we screened 4416 lab-created T(1) rice T-DNA tagged lines and identified a mutant, designated dh1 (degenerated hull1), with phenotype of degenerated hull and naked pistils and stamens. Approximately 60% florets on the dh1 panicle defected in forming normal palea and lemma. Instead, they formed degenerative velum-like or filamentous organs accompanying with the lack of lodicules, stamens and pistils at different degree. A 361 bp of genomic sequence flanking the T-DNA isolated using TAIL-PCR (Thermal asymmetric interlaced PCR) co-segregated with the mutation phenotype. Results of blastn and gene prediction revealed the T-DNA inserted into the promoter region of a function-predicted gene at 283 bp upstream of its transcription start site (TSS). The predicted gene encoded a LOB (Lateral Organ Boundaries) domain-like protein. RT-PCR analyses indicated the transcription level of target candidate gene, DH1, decreased significantly in dh1 mutant. RNAi aimed at DH1 in wild type plants could partially result in the mutation phenotype of dh1. DH1 could also rescue the mutation phenotype in the complement experiment. The result of transformation by a fused expression vector, pDH1::GFP, revealed that DH1 had the keen spatial and temporal characteristics of expressing at axillary bud, young panicle and floral organs but not at root, leaf, node and culm, and strongly expressing at young tissues but weakly at mature organs. The dh1 presented severer mutation phenotype under relatively longer daylight than under shorter daylight implied that shorter daylight induced the expression of gene(s) redundant to DH1 in function and partially compensated for the loss-of-function. It is the first time to report the LOB-domain gene participating in the development of floral organs in rice.

Resveratrol enhances proliferation and osteoblastic differentiation in human mesenchymal stem cells via ER-dependent ERK1/2 activation

In the present study, we investigated the in vitro effect of resveratrol (RSVL), a polyphenolic phytoestrogen, on cell proliferation and osteoblastic maturation in human bone marrow-derived mesenchymal stem cell (HBMSC) cultures. RSVL (10(-8)-10(-5) M) increased cell growth dose-dependently, as measured by [(3)H]-thymidine incorporation, and stimulated osteoblastic maturation as assessed by alkaline phosphatase (ALP) activity, calcium deposition into the extracellular matrix, and the expression of osteoblastic markers such as RUNX2/CBFA1, Osterix and Osteocalcin in HBMSCs cell cultures. Further studies found that RSVL (10(-6)M) resulted in a rapid activation of both extracellular signal-regulated kinase 1/2 (ERK1/2) and p38 mitogen-activated protein kinase (MAPK) signaling in HBMSCs cultures. The effects of RSVL were mimicked by 17beta-estrodial (10(-8) M) and were abolished by estrogen receptor (ER) antagonist ICI182780. An ERK1/2 pathway inhibitor, PD98059, significantly attenuated RSVL-induced ERK1/2 phosphorylation, consistent with the reduction of cell proliferation and osteoblastic differentiation as well as expression of osteoblastic markers. In contrast, SB203580, a p38 MAPK pathway blocker, blocked RSVL-induced p38 phosphorylation, but resulted in an increase of cell proliferation and a more osteoblastic maturation. These data suggest that RSVL stimulates HBMSCs proliferation and osteoblastic differentiation through an ER-dependent mechanism and coupling to ERK1/2 activation.

Neutralizing IL-7 promotes long-term allograft survival induced by CD40/CD40L costimulatory blockade

Memory T cells are somewhat resistant to immunosuppresion. They therefore pose a threat to inducing long-term allograft survival. IL-7 is essential for memory T-cell generation. Here, we investigated whether neutralizing IL-7 promotes allograft survival. We found that neutralizing IL-7 alone did not significantly prolong allograft survival. However, blocking both IL-7 and CD154 signaling synergistically prolonged allograft survival. In contrast, neutralizing IL-2 failed to further prolong allograft survival induced by CD40/CD154 costimulatory blockade. Allospecific memory CD8+ T-cell generation was severely impaired under the treatment of anti-IL-7 plus anti-CD154 Ab while administering recombinant IL-7 enhanced CD8+ memory generation even under donor-specific transfusion plus anti-CD154 Ab treatment. Neutralizing IL-7, but not IL-2, together with blocking CD154 synergistically suppressed the proliferation of naïve/effector CD8+ T cells infiltrating grafts. Nevertheless, neutralizing IL-7 did not alter regulatory T-cell generation while neutralizing IL-2 suppressed their generation. Hence, targeting IL-7 represents a new strategy to prolong allograft survival by acting on both naïve and memory T cells. Long-term allograft survival may be achieved by neutralizing IL-7 plus CD40/CD154 blockade, since CD40/CD154 costimulatory blockade prevents acute rejection while neutralizing IL-7 suppresses the generation of memory T cells that persist and mediate late or chronic rejection.

A new glucoside from Selaginella sinensis

A new glucoside, selaginoside (1), together with two known compounds, hinokiflavone (2) and 2,3-dihydroamentoflavone (3), were isolated from the whole plants of Selaginella sinensis. Their structures were elucidated by means of spectroscopic methods.