Diversity of methanogens in the hindgut of grower and finisher pigs

This study examined the diversity of the methanogens in the hindgut of two different weight groups of pigs and correlated it with the amount of digested organic carbon (OC) and various components of dietary fiber. Five grower (58.9 ± 1.15 kg) and five finisher (89.4 ± 0.85 kg) Duroc × Landrace × Large Yorkshire female pigs were allocated into two groups and individually housed in cages. During the experiment, feed intake and fecal output were recorded for determination of apparent digestibility of OC, crude fiber (CF), neutral detergent fiber (NDF) and acid detergent fiber (ADF). At the end of the digestibility trial, pigs were sacrificed, and the contents of five segments of hindgut were sterilely collected to determine diversity of methanogens. Total microbial DNA of the hindgut contents was used as template for amplification of the methanogen16S rRNA gene, and the PCR products were further subjected to denaturing gradient gel electrophoresis (DGGE) analysis. Results show that the number of DGGE bands and Shannon diversity index for the 90 kg pigs were higher (P<0.05) than those for the 60 kg pigs. Methanogen communities did not alter along the different segments of the hindgut for the two weight groups. In addition, the amount of OC, CF, NDF and ADF digested (g/d) for the 90 kg pigs (1018.77, 23.11, 268.86 and 99.16, respectively) was higher (P<0.05) than the respective values for the 60 kg pigs (669.27, 13.77, 222.31 and 69.07), indicating that the higher diversity of  methanogens in the former group was related to the higher quantity of fiber materials fermented in the hindgut. The positive correlation (p<0.05) between number of DGGE bands and Shannon diversity index with quantity of digested OC and ADF further reaffirmed the above suggestion.Key words: Methanogen, pig, Shannon diversity index, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)

Polymorphisms of two neuroendocrine–correlated genes associated with body weight and reproductive traits in Jinghai yellow chicken

In this study, insulin-like growth factor binding protein 2 (IGFBP-2) and signal transducers activators of transcription 5b (STAT5b) gene were studied as candidate gene associated with body weight and reproductive traits of the Jinghai Yellow chicken. Single nucleotide polymorphisms (SNPs) of the IGFBP-2 and STAT5b genes were examined in both Jinghai Yellow chicken and three reference chicken populations by PCR-SSCP. Two SNPs (T3746TG and CC3753TT) were detected in the IGFBP-2 gene. One SNP (C8066T) was observed in the STAT5b gene. For primer 1, the general linear model analysis showed that Jinghai yellow chickens with FF genotypes had significant effect on hatch weight, egg weight at 300 days and body weight at 300 days than those of the EF genotype and had significant effect on body weight at 8 weeks of age than those of the EE genotype (P < 0.05). For primer 2, Jinghai yellow chickens with CT genotype had significant effect on hatch weight and age at first egg than CC genotype and TT genotype respectively (P < 0.05). SNPs in both IGFBP-2 and STAT5b genes had significant effect on body weight and reproductive traits of the Jinghai yellow chicken than those with either SNP alone. These SNPs may be served as a potential genetic marker for growth and reproduction traits evaluation of the Jinghai yellow chicken.Key words: Jinghai Yellow chicken, IGFBP-2 gene, STAT5b gene, economic traits, polymorphism

Review on an advanced high-temperature measurement technology : the optical fiber thermometry

Author name used in this publication: W. K. Chow2009-2010 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Human foot three-dimensional finite element of modeling and its biomechanical applications

2007-2008 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Intracellular interferons in fish : a unique means to combat viral infection

Peer reviewedPublisher PD

Research on testing the characteristics of hydrogel film by using a long-period fiber grating

Author name used in this publication: Min Zhang2008-2009 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation

BACKGROUND: PUMA is a pro-apoptotic Bcl-2 family member that has been shown to be involved in apoptosis in many cell types. We sought to ascertain whether induction of PUMA plays a crucial role in E2F-1-induced apoptosis in melanoma cells. METHODS: PUMA gene and protein expression levels were detected by real-time PCR and Western blot in SK-MEL-2 and HCT116 cell lines after Ad-E2F-1 infection. Activation of the PUMA promoter by E2F-1 overexpression was detected by dual luciferase reporter assay. E2F-1-induced Bax translocation was shown by immunocytochemistry. The induction of caspase-9 activity was measured by caspase-9 colorimetric assay kit. RESULTS: Up-regulation of the PUMA gene and protein by E2F-1 overexpression was detected by real-time PCR and Western blot analysis in the SK-MEL-2 melanoma cell line. In support of this finding, we found six putative E2F-1 binding sites within the PUMA promoter. Subsequent dual luciferase reporter assay showed that E2F-1 expression could increase the PUMA gene promoter activity 9.3 fold in SK-MEL-2 cells. The role of PUMA in E2F-1-induced apoptosis was further investigated in a PUMA knockout cell line. Cell viability assay showed that the HCT116 PUMA-/- cell line was more resistant to Ad-E2F-1-mediated cell death than the HCT116 PUMA+/+ cell line. Moreover, a 2.2-fold induction of the PUMA promoter was also noted in the HCT116 PUMA+/+ colon cancer cell line after Ad-E2F-1 infection. Overexpression of a truncated E2F-1 protein that lacks the transactivation domain failed to up-regulate PUMA promoter, suggesting that PUMA may be a transcriptional target of E2F-1. E2F-1-induced cancer cell apoptosis was accompanied by Bax translocation from the cytosol to mitochondria and the induction of caspase-9 activity, suggesting that E2F-1-induced apoptosis is mediated by PUMA through the cytochrome C/Apaf-1-dependent pathway. CONCLUSION: Our studies strongly demonstrated that E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation. The signaling pathways provided here will further enhance insights on the mechanisms of E2F-1-induced cancer cell apoptosis as a strategy for cancer therapy

Copy number variation analysis based on AluScan sequences

BACKGROUND: AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing. RESULTS: In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained. CONCLUSIONS: The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.published_or_final_versio

Characterization of Fish IRF3 as an IFN-Inducible Protein Reveals Evolving Regulation of IFN Response in Vertebrates

In mammals, IFN regulatory factor (IRF) 3 is a critical player in modulating transcription of type I IFN and IFN-stimulated genes (ISGs). In this study, we describe the roles of crucian carp (Carassius auratus L.) IRF3 in activating fish IFN and ISGs. Fish IRF3 exhibits a large sequence divergence from mammalian orthologs. Whereas mammalian IRF3 is constitutively expressed, fish IRF3 protein is significantly upregulated by IFN, poly-IC, and other stimuli known as IFN inducers in mammals. The IFN-inducible property of fish IRF3 is consistent with the comparative analysis of 5' flanking regulatory region of vertebrate IRF3 genes, which reveals the presence of typical IFN-stimulated response elements in fish and amphibians, but an absence in tetrapods. Furthermore, either IFN or poly-IC induces phosphorylation and cytoplasmic-to-nuclear translocation of IRF3, which seems essential for its function in that phosphomimic active IRF3 exhibits stronger transactivation than wild type IRF3. Finally, overexpression of fish IRF3 activates production of IFN that in turn triggers ISG transcription through Stat1 pathway, whereas transfection of dominant negative mutant IRF3-DN abrogates poly-IC induction of ISGs, probably owing to blockade of IFN production. Therefore, regulation of IFN response by vertebrate IRF3 is another ancient trait. These data provide evidence of the evolving function of vertebrate IRF3 on regulating IFN response. The Journal of Immunology, 2010, 185: 7573-7582