Differential gene expression in the murine gastric fundus lacking interstitial cells of Cajal

Gene Expressing Difference in Sclerotial Formation of Morchella conica

The difference of gene expression between sclerotia-producing and non-sclerotia-producing single spore isolates from Morchella conica were preliminary analyzed by mRNA differential display reverse transcription-polymerase chain reaction (RT-PCR) technique and 67 differential gene fragments were obtained. Fifty-eight of their second PCR products were cloned and sequenced. Thirteen special differential gene fragments related to sclerotial formation were validated by semi-quantitative RT-PCR. Some gene fragments had certain homologies with lipoprotein, cyclin-dependent kinase C-3, glycerophosphoryl diester phosphodiesterase, Rho GDP-dissociation inhibitor, gamma-aminobutyrate permease, OmpA family protein, Transcript antisense to ribosomal RNA protein, sodium-calcium exchange protein and keratin-associated proteins 5, 6. In addition, the putative protein of some DNA fragments had higher similarity with hypothetical protein-coding gene in NCBI database, as well as some were only putative gene fragments. All these fragments were speculated to be the functional gene associated with sclerotial formation in morel.

Molecular cloning, sequence identification and tissue expression profile of three novel genes Sfxn1, Snai2 and Cno from Black-boned sheep (Ovis aries)

The complete coding sequences of three of Black-boned sheep (Ovis aries) genes Sfxn1, Snai2 and Cno were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) according to the conserved sequence information of the cattle or other mammals and known highly homologous sheep ESTs. Black-boned sheep Sfxn1 gene encodes a protein of 322 amino acids which has high homology with the Sfxn1 proteins of five species--cattle 98%, pig 95%, human 95%, rat 93%, and mouse 93%. Black-boned sheep Snai2 gene encodes a protein of 268 amino acids that has high identity with the Snai2 proteins of six species--cattle 99%, pig 94%, human 93%, dog 93%, rat 91%, and mouse 90%. Black-boned sheep Cno gene encodes a protein of 214 amino acids that has high homology with the Cno proteins of four species--cattle 97%, human 75%, mouse 67%, and rat 65%. The phylogenetic tree analysis demonstrated that Black-boned sheep Sfxn1, Snai2 and Cno proteins have close relationship with cattle Sfxn1, Snai2 and Cno proteins. The tissue expression analysis indicated that Black-boned sheep Sfxn1, Snai2 and Cno genes were expressed in a range of tissues including leg muscle, kidney, skin, longissimus dorsi muscle, spleen, heart and liver. Our experiment is the first to provide the primary foundation for further insight into these three sheep genes.

Molecular characterization and association analysis of FBXO40 with partial hematological indexes in pig

F-box proteins are quite significant ubiquitin-proteasome pathway regulators in eukaryotic cells. FBXO40, a member of this large family, alters its expression pattern in muscle atrophy. Here we isolated most of the verified porcine FBXO40 coding sequence (CDS) (2258 bp) and assigned it to the porcine chromosome 13q4.1-4.6 by using the INRA-Minnesota porcine radiation hybrid panel, and we also explored the tissue expression distributions, which is relatively high in longissimus dorsi muscle, heart, low in kidney, small intestine, brain, hypophysis, lymphonode, thymus, spleen, large intestine, ovary, stomach, and undetectable in testis, liver, uterus and thyroid gland. Inferring phylogenetic tree was constructed to study the evolutionary implications. Moreover, a HindII (HincII)-RFLP (A/C) polymorphism in 3'-untranslated region (3'-UTR) of porcine FBXO40 gene was demonstrated by sequencing and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. Statistical analysis result of this polymorphism showed that the allele A was predominant in all detected indigenous breeds, but C in western introduced commercial breeds. The SNP was further analyzed in our experimental pig population including Tongcheng, Landrace, Large White, and crossbreds of Large White × (Landrace × Tongcheng) and Landrace × (Large White × Tongcheng). The association analysis results indicated that the A/C base substitution was associate with some hematological indexes, the hemoglobin concentration (P < 0.0001), mean corpuscular volume hemoglobin concentration (P = 0.0002) and mean corpuscular volume (P = 0.0138).

Isolation, nucleotide identification and tissue expression of three novel ovine genes-SLC25A4, SLC25A5 and SLC25A6

The complete coding sequences of three of sheep genes SLC25A4, SLC25A5 and SLC25A6 were firstly amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) according to the conserved sequence information of the cattle or other mammals and known highly homologous sheep ESTs. Sheep SLC25A4, SLC25A5 and SLC25A6 genes encode three corresponding proteins of 298 amino acids which contain the identically conserved putative mitochondrial carrier protein domain. Sheep SLC25A4 protein has high homology with the SLC25A4 proteins of six species-cattle (99%), human (95%), rat (95%), mouse (94%), dog (94%) and chicken (89%). Sheep SLC25A5 protein has high identity with the SLC25A5 proteins of five species-cattle (100%), dog (99%), mouse (98%), rat (98%) and human (98%). Sheep SLC25A6 protein also has high homology with the SLC25A6 proteins of four species-cattle (99%), human (97%), pig (97%) and chicken (93%). The phylogenetic tree analysis demonstrated that sheep SLC25A4, SLC25A5 and SLC25A6 proteins share a common ancestor. Moreover, SLC25A4, SLC25A5 and SLC25A6 proteins present stronger interaction each other. The tissue expression analysis indicated that sheep SLC25A4, SLC25A5 and SLC25A6 genes were expressed in a range of tissues including leg muscle, kidney, skin, longissimus dorsi muscle, spleen, heart and liver. Our experiment is the first to provide the primary foundation for further insight into these three sheep genes.

A novel porcine gene--erlin2, differentially expressed in the liver tissues from Meishan and Large White pigs

The messenger RNA differential display technique was performed to investigate the differences of gene expression in the liver tissues from Meishan and Large White pigs. A fragment of one differentially expressed gene was isolated and sequenced. A complete complementary DNA (cDNA) sequence was obtained using the rapid amplification of cDNA end method. Nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 339 amino acids which have high homology with those of the ER lipid-raft-associated 2 isoform 2 (ERLIN2) of eight species--human (97%), rhesus monkey (97%), rat (96%), horse (97%), cattle (97%), mouse (97%), dog (95%), and red jungle fowl (90%)--so that it can be defined as the swine erlin2 gene. The phylogenetic tree analysis revealed that the swine erlin2 gene has a closer genetic relationship with the erlin2 genes of human and rhesus monkey. The tissue expression profile analysis indicated that the swine erlin2 gene is differentially expressed in detected tissues from Meishan and Large White pigs. Our experiment suggested that the swine erlin2 gene might play an important role in the superabundant fat deposition of Chinese pigs.

cDNA cloning and tissue expression analyses of the encoding regions for three novel porcine genes- MJD1, CDC42 and NECD

The cDNAs for Machado-Joseph disease protein 1 homolog (MJD1), cell division control protein 42 homolog precursor(CDC42) and necdin (NECD) genes of pig were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved coding sequence information of the MJD1, CDC42, and NECD genes from mouse and other mammals and the referenced porcine EST sequence information. Tissue expression analysis showed the swine MJD1, CDC42, and NECD genes were obviously differentially expressed in different tissues including muscle, heart, liver, backfat, kidney, lung, small intestine, and large intestine. Our experiment established the primary foundation for further research on these three swine genes.

Isolation, sequence analysis and expression profile of a novel porcine gene, CXCL10, differentially expressed in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display (DD) technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Meishan (MS), Meishan x Large White (ML) cross and Large White (LW) pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its full-length cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 104 amino acids that contains the putative conserved domain of the chemokine CXC which could be designated as chemokine cd00273 subgroup and this protein has high homology with the small inducible cytokine B10 precursor (CXCL10) of five species - dog(87%), human (84%), monkey (84%), mouse (75%) and rat (70%) - so that it can be defined as swine small inducible cytokine B10 precursor. The phylogenetic tree analysis revealed that the swine CXCL10 has a closer genetic relationship with the CXCL10 of dog than with those of human, monkey, mouse and rat. The tissue expression analysis indicated that the swine CXCL10 gene is more highly expressed in muscle and weakly expressed in fat and kidney. The genomic sequence of swine CXCL10 gene was finally amplified and result revealed that the swine CXCL10 gene contains four exons and three introns. Our experiment is the first to establish the primary foundation for further research on the swine CXCL10 gene.

Molecular cloning and expression analyses of a novel swine gene--ARF4

The mRNA differential display technique was performed to investigate the differences of gene expression in the longissimus muscle tissues from Meishan and Large White pigs. One novel gene that was differentially expressed was identified through semi-quantitative RT-PCR and the cDNA complete sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 180 amino acids that contains the putative conserved domain of ADP-ribosylation factor (ARF) which has high homology with the ADP-ribosylation factor 4 (ARF4) of six species-bovine (98%), human and orangutan (96%), African clawed frog (96%), mouse and rat (98%)-so that it can be defined as swine ADP-ribosylation factor 4 (ARF4). This novel porcine gene was finally assigned to GeneID:595108. The phylogenetic tree analysis revealed that the swine ARF4 has a closer genetic relationship with the rat and mouse ARF4 than with those of human and African clawed frog. The tissue expression analysis indicated that the swine ARF4 gene is over expressed in muscle, fat, heart, spleen, liver, and ovary and moderately expressed in lung and kidney but weakly expressed in small intestine. Our experiment is the first to establish the primary foundation for further research on the swine ARF4 gene.

Molecular characterization and expression profile of a novel porcine gene differentially expressed in the muscle tissues from Meishan, Large White and their hybrids

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its full-length cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. Sequence analysis revealed that open reading frame of this gene encoding a protein of 105 amid acids and this protein showed 100% homology to bovine and ovine CYCS, and therefore, this gene can be defined as the swine CYCS gene. The genomic sequence of swine CYCS gene was finally amplified and result revealed that the swine CYCS gene contains no introns. Tissue expression profile analysis revealed that swine CYCS gene was highly expressed in muscle, fat and lung, moderately expressed in ovary, kidney, and liver, and weekly expressed in heart, spleen and small intestine. Our results established the primary foundation for further research into the biological significance of swine CYCS gene.

Molecular characterization of the encoding regions and tissue expression analyses for three novel porcine genes--HNRPA1, YIPF5 and UB2D2

The complete encoding regions of three porcine genes--heterogeneous nuclear ribonucleoprotein A1 (HNRPA1), YIP1 family member 5 (YIPF5) and ubiquitin-conjugating enzyme E2 D2 (UB2D2) were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved encoding region information of the mouse or other mammals and the referenced highly homologous pig ESTs of these conserved encoding regions. These three novel porcine genes were assigned to GeneID: 768103, 768112, and 780418. The phylogenetic tree analysis revealed that the swine HNRPA1 has closer genetic relationships with the HNRPA1 of mouse and rhesus monkey, but the swine YIPF5 has a closer genetic relationship with the YIPF5 of cattle and the swine UB2D2 shows an evolutional model different with the UB2D2 of other five species. The tissue expression analysis indicated that the swine HNRPA1 gene was moderately expressed in fat, spleen and kidney, weakly expressed in muscle and lung, and hardly expressed in small intestine, large intestine and liver. The swine YIPF5 gene was moderately expressed in fat and spleen, and hardly expressed in small intestine, large intestine, liver, lung, muscle and kidney. The swine UB2D2 gene was weakly expressed in lung, and hardly expressed in small intestine, large intestine, liver, muscle, fat, spleen and kidney. Our experiment established the primary foundation for further research on these three swine genes.

Isolation, sequence identification and tissue expression distribution of three novel porcine genes--RAB14, S35A3 and ITM2A

The complete coding sequences of three porcine genes--RAB14, S35A3 and ITM2A were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals. The nucleotide sequence analysis of these three genes revealed that porcine RAB14 gene encodes a protein of 215 amino acids that contains the conserved putative Ras-related protein Rab-14 domain and has high homology with the Ras-related protein Rab-14 (RAB14) of four species--human and mouse (99%) and rat (100%), dictyostelium discoideum (71%). The porcine S35A3 gene encodes a protein of 325 amino acids that contains the conserved putative nucleotide-sugar transporter domain and has high homology with the UDP-N-acetylglucosamine transporter (S35A3) of five species--cattle (98%), dog (97%), human (96%), mouse (95%) and rat (94%). The porcine ITM2A gene encodes a protein of 254 amino acids that contains the conserved putative BRICHOS domain and has high homology with the integral membrane protein 2A (ITM2A) of two species--human (89%), and mouse (88%). The tissue expression analysis indicated that the swine RAB14 gene was over-expressed in fat, lung, spleen, and kidney, moderately in large intestine, weakly in small intestine, and hardly expressed in muscle and liver. The swine S35A3 gene was moderately expressed in large intestine, fat, and spleen, weakly in liver and lung, and almost not expressed in muscle, small intestine, and liver. The swine ITM2A gene was over-expressed in fat and spleen, moderately in lung, weakly in muscle, and hardly expressed in liver, small intestine, large intestine, and kidney. Our experiment established the primary foundation for further research on these three swine genes.

Isolation, sequence analysis and expression profile of a novel porcine gene, NIP7, differentially expressed in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 180 amino acids that contains the conserved putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase (PUA) and has high homology with the 60S ribosome subunit biogenesis protein NIP7 homolog of three species--human (98%), mouse (97%) and rat (96%)--so that it can be defined as swine 60S ribosome subunit biogenesis protein NIP7 homolog (NIP7). The tissue expression analysis indicated that the swine NIP7 gene is over expressed in muscle, heart, liver, fat, kidney, and lung, but weakly expressed in small intestine, ovary, and spleen. The genomic DNA sequence of swine NIP7 gene was finally amplified and result revealed that the swine NIP7 gene contains five exons and four introns. Our experiment is the first to establish the primary foundation for further research on the swine NIP7 gene.

Downregulation of two novel genes in Sl/Sld and W(LacZ)/Wv mouse jejunum

Interstitial cells of Cajal (ICC) are the so-called pacemaker cells of the gut. W(LacZ)/Wv and Sl/Sld mice lack ICC surrounding the myenteric plexus (MP) in the jejunum. We compared the gene expression profile of wild type (WT) and W(LacZ)/Wv and Sl/Sld mice using suppression subtractive hybridization (SSH), generating a cDNA library of 1303 clones from which 48 unique sequences were differentially expressed with Southern blot. Among them, we identified heme oxygenase2, TROY, and phospholamban in ICC using immunohistochemistry. Using RT-qPCR, c-Kit and two new transcripts Dithp and prenylcysteine oxidase1 were significantly lower expressed in Sl/Sld and W(LacZ)/Wv versus WT. Prenylcysteine oxidase1 appeared cytotoxic for COS-7 cells and was highly expressed in liver while Dithp was mainly expressed in small intestine. The combination of SSH, Southern blot, RT-qPCR, and immunohistochemistry turned out to be a useful approach to identify rarely expressed genes and genes with small differences in expression.