Isolation, cloning and sequence analysis of differentially expressed genes in the backfat tissue between hybrids and parents in pigs

2006 ◽  
Vol 3 (1) ◽  
pp. 47-52
Author(s):  
Ren Zhu-Qing ◽  
Xiong Yuan-Zhu ◽  
Deng Chang-Yang ◽  
Lei Ming-Gang ◽  
Zuo Bo ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Annealing Temperature ◽  
Differentially Expressed ◽  
Fat Tissue ◽  
Rt Pcr ◽  
Cloning And Sequencing ◽  
Large White ◽  
Arbitrary Primers ◽  
Polymerase Chain ◽  
Expressed Sequence

AbstractIn order to reveal the molecular basis of heterosis, Large White (LW), an introduced European pig breed, and Meishan (MS), a Chinese indigenous pig breed, were selected to hybridize directly and reciprocally in the present experiment. mRNA differential display (DD) technique was performed to identify genes that were differentially expressed in the backfat tissues of hybrids (LW×MS, MS×LW) and purebred (LW×LW, MS×MS) pigs. The ten anchor primers in combination with ten arbitrary primers (100 sets in total) were used and nearly 1500 reproducible bands were observed in polyacrylamide gels. The 40 differentially displayed bands were selected for cloning and sequencing. Thirty-six out of 40 expressed sequence tags (ESTs) proved to be novel and the sequences were submitted to GenBank (accession No. CV507051-CV507087); the other four showed similarity to known genes published in GenBank. Three among 36 novel ESTs were chosen for further identification with semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR). The result showed that two ESTs were differentially expressed, and the third showed no obvious difference between hybrids and purebreds. In order to reduce the percentage of false-positive DD, RNA pools of four types of pigs were constructed, by mixing samples from six pigs of the same genotype, and subjected to DD. Stringent annealing temperature was applied and only bands that could be repeated in duplicate PCR were used for further study. The results showed that the expression pattern of these 36 ESTs differed among the four genotypes of pigs, suggesting that the genes corresponding to these differentially expressed ESTs might be related to the heterosis occurring in fat tissue.

Isolation, identification and expression profile of fourteen differentially expressed sequence tags in the longissimus dorsi muscle tissues from Meishan, Meishan×Large White cross and Large White pigs

2007 ◽  
Vol 4 (1) ◽  
pp. 9-14
Author(s):  
Liu Yong-Gang ◽  
Xiong Yuan-Zhu ◽  
Zuo Bo ◽  
Jiang Si-Wen ◽  
Deng Chang-Yan ◽  
...  
Keyword(s):  
Expression Profile ◽  
Differential Display ◽  
Expressed Sequence Tags ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Large White ◽  
Longissimus Dorsi Muscle ◽  
Dorsi Muscle ◽  
Muscle Tissues ◽  
Expressed Sequence

AbstractIn order to detect the molecular mechanism of heterosis in pigs, an mRNA differential display (DD) technique was performed to investigate the differences in gene expression in the longissimus dorsi muscle tissues from Meishan, Meishan×Large White cross and Large White pigs. Fourteen expressed sequence tags (ESTs), differentially expressed between the hybrid and purebred pigs, were isolated and identified through semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Nucleotide sequence analysis revealed that the 14 ESTs are not homologous to any of the known genes or ESTs. These novel ESTs were then deposited in the GenBank database. Tissue expression profile analysis showed that the ESTs were expressed in most tissues, including heart, spleen, liver, kidney, small intestine, ovary and lung, and this also implied that these genes must be important for the life process. Our results indicate the diversity of differential display of genes between the hybrids and purebreds in the Meishan×Large White cross combination. Results also suggest that heterosis in pigs might be derived from the differential expression of many indispensable genes in specific life phases.

scholarly journals Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos

Reproduction ◽  
2006 ◽  
Vol 131 (4) ◽  
pp. 651-660 ◽  
Author(s):  
D Corcoran ◽  
T Fair ◽  
S Park ◽  
D Rizos ◽  
O V Patel ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Differentially Expressed ◽  
Bovine Embryos ◽  
Quantitative Real Time Pcr ◽  
Expression Of Genes ◽  
Mrna Transcripts ◽  
Induced Changes ◽  
Expressed Sequence

In vivo-derived bovine embryos are of higher quality than those derivedin vitro. Many of the differences in quality can be related to culture environment-induced changes in mRNA abundance. The aim of this study was to identify a range of mRNA transcripts that are differentially expressed between bovine blastocysts derived fromin vitroversusin vivoculture. Microarray (BOTL5) comparison betweenin vivo- andin vitro-cultured bovine blastocysts identified 384 genes and expressed sequence tags (ESTs) that were differentially expressed; 85% of these were down-regulated inin vitrocultured blastocysts, showing a much reduced overall level of mRNA expression inin vitro- compared within vivo-cultured blastocysts. Relative expression of 16 out of 23 (70%) differentially expressed genes (according toPvalue) were verified in new pools ofin vivo- andin vitro-cultured blastocysts, using quantitative real-time PCR. Most (10 out of 16) are involved in transcription and translation events, suggesting that the reason whyin vitro-derived embryos are of inferior quality compared within vivo-derived embryos is due to a deficiency of the machinery associated with transcription and translation.

Development of an EST-SSR marker in Panax ginseng

2008 ◽  
Vol 5 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Yang Cheng-Jun ◽  
Wang Jun ◽  
Mu Li-Qiang ◽  
Li Shao-Chen ◽  
Liu Guan-Jun ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Expressed Sequence Tags ◽  
Genomic Dna ◽  
Ssr Marker ◽  
Panax Quinquefolius ◽  
Chain Reaction ◽  
Acanthopanax Senticosus ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Expressed Sequence

AbstractA total of 791 microsatellites (SSRs) were isolated from 7055 Panax ginseng expressed sequence tags (ESTs). According to primer design criteria, 68 primer pairs for EST-SSR were designed. Under an appropriate polymerase chain reaction (PCR) system, all EST-SSR primer pairs were screened against genomic DNA of Ji'anchangbo and Fusong'ermaya from Panax ginseng, and 43 EST-SSR primer pairs out of the above 68 resulted in PCR products. Then, all 43 pairs were detected in nine P. ginseng, two Panax quinquefolius and two Acanthopanax senticosus cultivars for polymorphisms, and 26 pairs (60.47%) were found to be polymorphic, accounting for 38.23% of the total number of designed primer pairs. These results demonstrate the possibility of developing EST-SSR markers using P. ginseng ESTs.

The elusive factor Xa receptor: failure to detect transcripts that correspond to the published sequence of EPR-1

Blood ◽  
2000 ◽  
Vol 96 (1) ◽  
pp. 145-148 ◽  
Author(s):  
Guido J. R. Zaman ◽  
Edward M. Conway
Keyword(s):  
Expressed Sequence Tags ◽  
Messenger Rna ◽  
Blot Hybridization ◽  
Factor Xa ◽  
Southern Blot Hybridization ◽  
Cellular Responses ◽  
Cellular Effects ◽  
Strong Homology ◽  
Polymerase Chain ◽  
Expressed Sequence

The coagulation protease factor Xa induces cellular responses implicated in cardiovascular and inflammatory disease. Effector-cell protease receptor 1 (EPR-1) is a functionally characterized receptor of factor Xa, and the EPR-1complementary DNA (cDNA) was published. Remarkably, the cDNA encoding an inhibitor of apoptosis, survivin, is reportedly identical to that ofEPR-1 except for a few nucleotide differences and its orientation opposite to EPR-1. To isolate the EPR-1cDNA and gene, we surveyed gene databases for expressed sequence tags (ESTs) that could be derived from EPR-1. All ESTs with strong homology to EPR-1/survivin were derived from survivinand could not encode EPR-1. By polymerase chain reaction and Southern blot hybridization, EPR-1 was not detectable in the human or murine genome, but survivin was. Our data suggest that EPR-1 is either highly cell-specific or the published EPR-1 cDNA includes sequences from clones derived from survivin messenger RNA. The means by which factor Xa mediates its cellular effects requires further evaluation.

Cloning of differentially expressed sequence tags from nickel-transformed human embryonic lung cells

2000 ◽  
Vol 161 (1) ◽  
pp. 57-62 ◽  
Author(s):  
Xinliang Mao ◽  
Tatsuhiko Kashii ◽  
Ryuji Hayashi ◽  
Kazuhiko Sassa ◽  
Takashi Fujishita ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Differentially Expressed ◽  
Lung Cells ◽  
Embryonic Lung ◽  
Human Embryonic Lung ◽  
Expressed Sequence

scholarly journals IDENTIFICACIÓN DE cDNAs DE Agave tequilana Weber Var. azul SIMILARES A FUROSTANOL GLICÓSIDO 26-O-β-GLUCOSIDASAS

2019 ◽  
Vol 42 (4) ◽  
pp. 439-447
Author(s):  
Zurisadaí Monroy-González ◽  
Aída Martínez-Hernández
Keyword(s):  
Expressed Sequence Tags ◽  
Asparagus Officinalis ◽  
Agave Tequilana ◽  
Rt Pcr ◽  
Expresión Génica ◽  
Expressed Sequence

La furostanol glicósido 26-O-β-glucosidasa (F26G) participa en el último paso de la biosíntesis de saponinas esteroidales, lo que escinde la glucosa unida al hidroxilo del C26 del furostanol glucósido para permitir la formación del espirostano. A pesar de la existencia de numerosos estudios que muestran la diversidad estructural y actividad biológica de las saponinas de plantas, así como su reconocido potencial biotecnológico y farmacológico, pocas enzimas participantes en la ruta de biosíntesis de las saponinas esteroidales han sido estudiadas y sólo una enzima nativa tipo F26G ha sido purificada y caracterizada funcionalmente. En este estudio, mediante búsqueda por BLASTX en una base de datos de Agave tequilana Weber var. azul (Agave DB), se identificaron 46 ESTs (Expressed Sequence Tags) de DNA complementario (cDNAs) similares a la F26G de Asparagus officinalis, la mayoría provienen de cDNAs clonados a partir de tejidos florales (anteras y ovarios) o raíz; ambos órganos son productores de saponinas. Entre ellos, se identificaron seis ESTs cuyo alineamiento indica que representan a tres cDNAs diferentes entre sí. Estos ESTs se registraron en la base de datos dbEST de NCBI (National Center for Biotechnology Information), el cual fue el primer registro de secuencias nativas de cDNAs potencialmente codificantes similares a F26G en Agave. El tamaño de los cDNAs clonados y su alineamiento hacia el lado 5’ de las F26G conocidas sugieren que son cDNAs completos. Se diseñaron iniciadores diferenciales específicos para cada tipo de cDNA y se analizó por RT-PCR su expresión en tejidos vegetativos de A. tequilana. Se establecieron protocolos de PCR cuantitativo (qPCR) para estudios posteriores de regulación de su expresión génica. La información aquí reportada servirá como base para estudiar la función, regulación y actividad enzimática de las enzimas clonadas de Agave similares a F26G.

The elusive factor Xa receptor: failure to detect transcripts that correspond to the published sequence of EPR-1

Blood ◽  
2000 ◽  
Vol 96 (1) ◽  
pp. 145-148 ◽  
Author(s):  
Guido J. R. Zaman ◽  
Edward M. Conway
Keyword(s):  
Expressed Sequence Tags ◽  
Messenger Rna ◽  
Blot Hybridization ◽  
Factor Xa ◽  
Southern Blot Hybridization ◽  
Cellular Responses ◽  
Cellular Effects ◽  
Strong Homology ◽  
Polymerase Chain ◽  
Expressed Sequence

Abstract The coagulation protease factor Xa induces cellular responses implicated in cardiovascular and inflammatory disease. Effector-cell protease receptor 1 (EPR-1) is a functionally characterized receptor of factor Xa, and the EPR-1complementary DNA (cDNA) was published. Remarkably, the cDNA encoding an inhibitor of apoptosis, survivin, is reportedly identical to that ofEPR-1 except for a few nucleotide differences and its orientation opposite to EPR-1. To isolate the EPR-1cDNA and gene, we surveyed gene databases for expressed sequence tags (ESTs) that could be derived from EPR-1. All ESTs with strong homology to EPR-1/survivin were derived from survivinand could not encode EPR-1. By polymerase chain reaction and Southern blot hybridization, EPR-1 was not detectable in the human or murine genome, but survivin was. Our data suggest that EPR-1 is either highly cell-specific or the published EPR-1 cDNA includes sequences from clones derived from survivin messenger RNA. The means by which factor Xa mediates its cellular effects requires further evaluation.

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