Chlorate-induced molecular floral transition revealed by transcriptomes.

Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.

Functions of lysine 2-hydroxyisobutyrylation and future perspectives on plants.

Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein post-translational modifications (PTMs) observed in both eukaryotes and prokaryotes. Recent studies suggested that this novel PTM has the potential to regulate different proteins in various pathways. Khib is regulated by lysine acyltransferases and deacylases. This novel PTM reveals interesting connections between modifications and protein physiological functions, including gene transcription, glycolysis and cell growth, enzymic activity, sperm motility, and aging. Here, we review the discovery and the current understanding of this PTM. Then, we outline the networks of complexity of interactions among PTMs in plants, and raise possible directions of this novel PTM for future investigations in plants.

Global crotonylatome and GWAS revealed a TaSRT1-TaPGK model regulating wheat cold tolerance through mediating pyruvate.

Here, we reported the complete profiling of the crotonylation proteome in common wheat. Through a combination of crotonylation and multi-omics analysis, we identified a TaPGK associated with wheat cold stress. Then, we confirmed the positive role of TaPGK-modulating wheat cold tolerance. Meanwhile, we found that cold stress induced lysine crotonylation of TaPGK. Moreover, we screened a lysine decrotonylase TaSRT1 interacting with TaPGK and found that TaSRT1 negatively regulated wheat cold tolerance. We subsequently demonstrated TaSRT1 inhibiting the accumulation of TaPGK protein, and this inhibition was possibly resulted from decrotonylation of TaPGK by TaSRT1. Transcriptome sequencing indicated that overexpression of TaPGK activated glycolytic key genes and thereby increased pyruvate content. Moreover, we found that exogenous application of pyruvate sharply enhanced wheat cold tolerance. These findings suggest that the TaSRT1-TaPGK model regulating wheat cold tolerance is possibly through mediating pyruvate. This study provided two valuable cold tolerance genes and dissected diverse mechanism of glycolytic pathway involving in wheat cold stress.

De novo assembly of a haplotype-resolved human genome.

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

[Relationship between mesenchymal stem cells and liver cancer recurrence after liver transplantation in mice].

OBJECTIVE: To explore the relationship between mesenchymal stem cells (MSCs) and liver cancer recurrence after liver transplantation in mice. METHODS: The recurrent murine model of hepatocellular carcinoma (HCC) after liver transplantation was established by transplanting tumor cells of hind paw pads. MSCs labeled with green fluorescent protein (GFP) were injected into the marrow cavity of 615 mice after successful modeling. And the proliferation of MSCs in marrow cavity was observed under stereoscopic fluorescence microscope. MSCs labeled with red fluorescent protein (RFP) were injected into tail vein of mice during tumor dissection. The migration of GFP and RFP- labeled MSCs were tracked before and after tumor recurrence. After recurrence, the mice were sacrificed and the recurrent lesions harvested for conforming pathological type by biopsy. RESULTS: The rate of success modeling was 37.5%. Both gross morphology and pathological examination corresponded to typical HCC manifestations. Thirty mice were detected by GFP/RFP fluorescence for a recurrence of HCC. The outcomes were GFP+RFP (n = 4), GFP (n = 1) and neither (n = 25). CONCLUSIONS: The presence of MSCs in host may be one of important reasons for recurrent HCC after liver transplantation.It helps to support the traditional view of residual tumor cells mediating the relapse and metastasis of HCC.

Investigation of thermo-sensitive amphiphilic micelles as drug carriers for chemotherapy in cholangiocarcinoma in vitro and in vivo.

Cholangiocarcinoma is an epithelial cancer of the bile ducts with poor prognosis and, in recent years, a rapidly increasing incidence. In this study, nano-sized thermo-sensitive micelles were investigated as drug carriers to improve chemotherapy in cholangiocarcinoma. Thermo-sensitive amphiphilic block copolymer, P-(N,N-isopropylacrylamide-co-N-hydroxymethylacrylamide)-b-caprolactone [P-(NIPAAm-co-NHMAAm)-b-PCL] with lower critical solution temperature (LCST) at about 38°C was synthesized. Doxorubicin (DOX)-loaded micelles were prepared by dialysis method. The micelles exhibited a sustained and temperature-dependent DOX release. Toxicity of the blank micelles for human cholangiocarcinoma (QBC939) cells was minimal both in vitro and in vivo. In contrast, the DOX-loaded micelles effectively inhibited proliferation and induced apoptosis of QBC939 cells in vitro (p<0.05) and inhibited tumor growth in nude mice by 21.49%. These results indicated that thermo-sensitive amphiphilic micelles are a promising and effective drug carrier, and show potential for improving chemotherapy for cholangiocarcinoma.

[The effect of drainage in cavities on preventing from grade B and C of the pancreatic fistula after pancreaticoduodenectomy].

OBJECTIVE: To explore the effect of drainage in cavities on preventing from grade B and C of the pancreatic fistula after pancreaticoduodenectomy (PD). METHODS: From June 2008 to June 2010, the medical team had performed the operations of digestive tract reconstruction by the same way in 68 cases with PD. There were 43 male and 25 female patients, with a mean age of (64 ± 3) years. The patients were simply randomly divided into drainage in cavities group (DC, n = 32) and conventional drainage group (CD, n = 36) according to the different drainage way. The methods of drainage in cavities were composed of three aspects which include drainage in main pancreatic duct, drainage around cholecystojejunostomy anastomosis and peripancreatic drainage. The clinical parameters of the two groups were collected. The characteristics of the drainage juice which include color, volume and amylase value in the two groups were compared. The incidence and severity grading of pancreatic fistula between the two groups were evaluated. RESULTS: The average of amylase value and the peripancreatic drainage flow were (1401 ± 8) U/L and (49 ± 5) ml in the DC group. Their average in the CD group were (2160 ± 13) U/L and (76 ± 4) ml. There was significant statistical difference in the peripancreatic drainage flow between the two groups (t = 2.597, P = 0.031). The amylase values of the drainage juice between the two groups were of no statistical difference (P > 0.05). According to the definition of pancreatic fistula by an international study group, the incidence of pancreatic fistula in the DC group was 25.0% (8/32) and the CD group 30.5% (11/36) (P > 0.05). The proportion of grades B and C of pancreatic fistula in the DC group had statistical difference compared with one of the CD group (χ(2) = 4.797, P = 0.029). CONCLUSION: Drainage in cavities could significantly decrease and the occurring ratio of grade B and C of pancreatic fistula after PD.

HIVID: an efficient method to detect HBV integration using low coverage sequencing.

We reported HIVID (high-throughput Viral Integration Detection), a novel experimental and computational method to detect the location of Hepatitis B Virus (HBV) integration breakpoints in Hepatocellular Carcinoma (HCC) genome. In this method, the fragments with HBV sequence were enriched by a set of HBV probes and then processed to high-throughput sequencing. In order to evaluate the performance of HIVID, we compared the results of HIVID with that of whole genome sequencing method (WGS) in 28 HCC tumors. We detected a total of 246 HBV integration breakpoints in HCC genome, 113 out of which were within 400bp upstream or downstream of 125 breakpoints identified by WGS method, covering 89.3% (125/140) of total breakpoints. The integration was located in the gene TERT, MLL4, and CCNE1. In addition, we discovered 133 novel breakpoints missed by WGS method, with 66.7% (10/15) of validation rate. Our study shows HIVID is a cost-effective methodology with high specificity and sensitivity to identify viral integration in human genome.

A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing.

OBJECTIVE: To report the feasibility of fetal chromosomal deletion/duplication detection using a novel bioinformatic method of low coverage whole genome sequencing of maternal plasma. METHOD: A practical method Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS), integrated with GC-bias correction, binary segmentation algorithm and dynamic threshold strategy, was developed to detect fetal chromosomal deletions/duplications of >10 Mb by low coverage whole genome sequencing (about 0.08-fold). The sensitivity/specificity of the resultant FCAPS algorithm in detecting deletions/duplications was firstly assessed in silico and then tested in 1311 maternal plasma samples from those with known G-banding karyotyping results of the fetus. RESULTS: Deletions/duplications, ranged from 9.01 to 28.46 Mb, were suspected in four of the 1311 samples, of which three were consistent with the results of fetal karyotyping. In one case, the suspected abnormality was not confirmed by karyotyping, representing a false positive case. No false negative case was observed in the remaining 1307 low-risk samples. The sensitivity and specificity for detection of >10-Mb chromosomal deletions/duplications were100% and 99.92%, respectively. CONCLUSION: Our study demonstrated FCAPS has the potential to detect fetal large deletions/duplications (>10 Mb) with low coverage maternal plasma DNA sequencing currently used for fetal aneuploidy detection.

Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing.

BACKGROUND: The applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. However, most previous research based on maternal plasma sequencing has been restricted to fetal aneuploidies. To detect specific parentally inherited mutations, invasive approaches to obtain fetal DNA are the current standard in the clinic because of the experimental complexity and resource consumption of previously reported non-invasive approaches. METHODS: Here, we present a simple and effective non-invasive method for accurate fetal genome recovery-assisted with parental haplotypes. The parental haplotype were firstly inferred using a combination strategy of trio and unrelated individuals. Assisted with the parental haplotype, we then employed a hidden Markov model to non-invasively recover the fetal genome through maternal plasma sequencing. RESULTS: Using a sequence depth of approximately 44X against a an approximate 5.69% cff-DNA concentration, we non-invasively inferred fetal genotype and haplotype under different situations of parental heterozygosity. Our data show that 98.57%, 95.37%, and 98.45% of paternal autosome alleles, maternal autosome alleles, and maternal chromosome X in the fetal haplotypes, respectively, were recovered accurately. Additionally, we obtained efficient coverage or strong linkage of 96.65% of reported Mendelian-disorder genes and 98.90% of complex disease-associated markers. CONCLUSIONS: Our method provides a useful strategy for non-invasive whole fetal genome recovery.

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation.

BACKGROUND: Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees). RESULTS: Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability. CONCLUSIONS: Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against pébrine. The genome data and annotation information of N. bombycis and N.antheraeae were submitted to GenBank (Accession numbers ACJZ01000001 -ACJZ01003558).

A role for p21-activated kinase 7 in the development of gastric cancer.

p21-activated kinase (PAK)7 (also known as PAK5) is a member of the group B PAK family of serine/threonine protein kinases, which are effectors of the small GTPases Rac and CDC42. PAK7 can promote neurite outgrowth, induce microtubule stabilization, and activate cell survival signaling pathways. However, the role of PAK7 in cancer is still poorly understood. Here, we showed that PAK7 expression was upregulated in different gastric cancer cell lines and gastric cancer tissues, as compared with human embryonic kidney 293 cells and adjacent normal tissues, respectively. The results suggested that PAK7 expression was related to gastric cancer progression. Thus, we employed lentivirus-mediated small interfering RNA to inhibit PAK7 expression, to investigate the role of PAK7 in human gastric carcinogenesis. RNA interference efficiently downregulated expression of PAK7 in SGC-7901 and MGC-803 cells at both mRNA and protein levels. Knockdown of PAK7 inhibited human gastric cancer cell proliferation by inducing cell cycle arrest in G(0)/G(1) phase, in concordance with the downregulation of CDK2, CDC25A, and cyclin D1. Our data suggest that PAK7 is a new hallmark of gastric cancer, in which PAK7 might contribute to gain of tumor growth potential, acting by affecting the expression of cell cycle regulators. Therefore, PAK7 may be an attractive candidate as a therapeutic target in gastric cancer.

The Combined effects of hematoporphyrin monomethyl ether-SDT and doxorubicin on the proliferation of QBC939 cell lines.

It is well established that both hematoporphyrin monomethyl ether-sonodynamic therapy (HMME-SDT) and doxorubicin (DOX) can induce cell apoptosis but each alone has its own limitations. To date, the combined effects of HMME-SDT and DOX on inducing cell apoptosis are little known and the mechanism for the combined effects remains poorly understood. In the present study, we reported the synergistic effects of HMME-SDT and DOX on inhibiting the proliferation of human cholangiocarcinoma QBC939 cells and investigated the mechanism of this synergy. The data from MTT assay, flow cytometer, Hoechst staining and cell arrest analysis showed that the combination of HMME-SDT and DOX exhibited higher inhibiting effects on proliferation of QBC939 cells than the sole application of HMME-SDT or DOX. In addition, the synergistic effects were shown to result from the DNA damage as demonstrated by single cell gel electrophoresis and DNA fragmentation. Furthermore, the expression of p53, Fas, Bax and activated caspase-3 protein was significantly upregulated in cells treated with HMME-SDT and DOX, whereas Bcl-2 protein was downregulated. Taken together, our data suggested that the application of HMME-SDT combined with DOX had better inhibiting effects on QBC939 cells and the effects were caused mainly by DNA damage.

Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies.

BACKGROUND: Conventional prenatal screening tests, such as maternal serum tests and ultrasound scan, have limited resolution and accuracy. METHODS: We developed an advanced noninvasive prenatal diagnosis method based on massively parallel sequencing. The Noninvasive Fetal Trisomy (NIFTY) test, combines an optimized Student's t-test with a locally weighted polynomial regression and binary hypotheses. We applied the NIFTY test to 903 pregnancies and compared the diagnostic results with those of full karyotyping. RESULTS: 16 of 16 trisomy 21, 12 of 12 trisomy 18, two of two trisomy 13, three of four 45, X, one of one XYY and two of two XXY abnormalities were correctly identified. But one false positive case of trisomy 18 and one false negative case of 45, X were observed. The test performed with 100% sensitivity and 99.9% specificity for autosomal aneuploidies and 85.7% sensitivity and 99.9% specificity for sex chromosomal aneuploidies. Compared with three previously reported z-score approaches with/without GC-bias removal and with internal control, the NIFTY test was more accurate and robust for the detection of both autosomal and sex chromosomal aneuploidies in fetuses. CONCLUSION: Our study demonstrates a powerful and reliable methodology for noninvasive prenatal diagnosis.

Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors.

OBJECTIVE: To report the performance of massively parallel sequencing (MPS) based prenatal noninvasive fetal trisomy test based on cell-free DNA sequencing from maternal plasma in a routine clinical setting in China. METHOD: The MPS-based test was offered as a prenatal screening test for trisomies 21 and 18 to pregnant women in 49 medical centers over 2 years. A total of 11,263 participants were recruited and the MPS-based test was performed in 11,105 pregnancies. Fetal outcome data were obtained after the expected date of confinement. RESULTS: One hundred ninety cases were classified as positive, including 143 cases of trisomy 21 and 47 cases of trisomy 18. With the karyotyping results and the feedback of fetal outcome data, we observed one false positive case of trisomy 21, one false positive case of trisomy 18 and no false negative cases, indicating 100% sensitivity and 99.96% specificity for the detection of trisomies 21 and 18. CONCLUSION: Our large-scale multicenter study proved that the MPS-based test is of high sensitivity and specificity in detecting fetal trisomies 21 and 18. The introduction of this screening test into a routine clinical setting could avoid about 98% of invasive prenatal diagnostic procedures.

A metagenome-wide association study of gut microbiota in type 2 diabetes.

Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.

[Differential gene expression profiles of gastric cancer].

OBJECTIVE: To explore the different gene expressions of normal versus tumor tissues of gastric cancer at molecular levels. METHODS: Gene chip technology was used to determine the differentially expressed genes between gastric cancer (n = 12) and normal tissues (n = 12) from December 2009 to June 2010 of Xinhua Hospital of Shanghai Jiaotong University School of Medicine. And reverse transcriptase (RT)-PCR was performed to validate the results of gene chip analysis. RESULTS: Sixty-nine up-regulated genes and 80 down-regulated genes were identified by significance analysis of microarrays (SAM). And these genes were correlated with cell adhesion, angiogenesis, cell proliferation and apoptosis, et al. They were also closely correlated with the signaling pathways of Wnt (1/151, 0.66%) and vascular endothelial growth factor (VEGF) (2/76, 2.63%). The differential expressions of ATP4A, CLDN10, OLFM4, SAA1 and PROK2 were confirmed by RT-PCR (0.94 ± 0.19 vs 4.33 ± 0.39, 1.00 ± 0.14 vs 3.04 ± 0.26, 5.37 ± 0.30 vs 1.02 ± 0.14, 4.37 ± 0.30 vs 0.95 ± 0.29, 2.62 ± 0.54 vs 1.35 ± 0.35, all P < 0.05). CONCLUSION: The classifier genes identified in this study may be closely correlated with the carcinogenesis of gastric cancer.

Characteristic gene expression profiles in the progression from normal gastric epithelial cells to moderate gastric epithelial dysplasia and to gastric cancer.

BACKGROUND: Gastric cancer ranks high among the most common causes of cancer-related death worldwide. This study was designed to explore key genes involved in the progression of normal gastric epithelial cells to moderate gastric epithelial dysplasia (mGED) and to gastric cancer. METHODS: Twelve pairs of mGED tissues, gastric cancer tissues, and normal gastric tissues were collected by gastroscopy. Total RNA was then extracted and purified. After the addition of fluorescent tags, hybridization was carried out on a Gene chip microarray slide. Significance analysis of microarrays was performed to determine significant differences in gene expression between the different tissue types. RESULTS: Microarray data analysis revealed totally 34 genes that were expressed differently: 18 highly expressed (fold change > 2; P < 0.01) and 16 down-regulated (fold change > 2; P < 0.01). Of the 34 genes, 24 belonged to several different functional categories such as structural molecule activity, extracellular regions, structural formation, cell death, biological adhesion, developmental processes, locomotion, and biological regulation that were associated with cancer. The remaining 10 genes were not involved in cancer research. Of these genes, the expression levels of Matrix metalloproteinase-12 (MMP12), Caspase-associated recruitment domain 14 (CARD14), and Chitinase 3-like 1 (CHI3L1) were confirmed by semi-quantitative RT-PCR. A two-way clustering algorithm divided the 36 samples into three categories and the overall correct classification efficiency was 80.6% (29/36). Almost all of these genes (31/34) showed constant changes in the process of normal gastric epithelial cells to mGED to gastric cancer. CONCLUSIONS: The results of this study provided global gene expression profiles during the development and progression from normal gastric epithelial cells to mGED to gastric cancer. These data may provide new insights into the molecular pathology of gastric cancer which may be useful for the detection, diagnosis, and treatment.

The sequence and analysis of a Chinese pig genome.

BACKGROUND: The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome. RESULTS: Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes. CONCLUSION: Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

Effects of matrine on proliferation and apoptosis in gallbladder carcinoma cells (GBC-SD).

Although matrine, a primary active component of dried Sophora flavescens root (ku shen), is known to induce apoptosis in a variety of tumor cells in vitro, the molecular mechanism of such apoptosis remains elusive. This analysis of the cell cycle and apoptosis in matrine-treated human gallbladder carcinoma cells (GBC-SD) showed that matrine can indeed inhibit cell proliferation and induce G1 cell cycle arrest and apoptosis in a dose- and time-dependent manner. An additional western blot analysis of matrine-treated cells also showed caspase-3 and Bcl-2 activation, as well as cyclinE down-regulation. Overall, the results indicate that matrine perturbs gallbladder cancer cell progression during the G1 phase by down-regulating cyclinE and induces apoptosis by decreasing the expression of the antiapoptotic protein Bcl-2 and increasing expression of the proapoptotic protein Bax.