Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

<p>Abstract</p> <p>Background</p> <p>The Solanaceae family includes several economically important vegetable crops. The tomato (<it>Solanum lycopersicum</it>) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance.</p> <p>Results</p> <p>To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%.</p> <p>Conclusion</p> <p>The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom <url>http://www.pgb.kazusa.or.jp/kaftom/</url> via the website of the National Bioresource Project Tomato <url>http://tomato.nbrp.jp</url>.</p

Genomic Characterization of Lactobacillus delbrueckii TUA4408L and Evaluation of the Antiviral Activities of its Extracellular Polysaccharides in Porcine Intestinal Epithelial Cells

In lactic acid bacteria, the synthesis of exopolysaccharides (EPS) has been associated with some favorable technological properties as well as health-promoting benefits. Research works have shown the potential of EPS produced by lactobacilli to differentially modulate immune responses. However, most studies were performed in immune cells and few works have concentrated in the immunomodulatory activities of EPS in non-immune cells such as intestinal epithelial cells. In addition, the cellular and molecular mechanisms involved in the immunoregulatory effects of EPS have not been studied in detail. In this work, we have performed a genomic characterization of Lactobacillus delbrueckii subsp. delbrueckii TUA4408L and evaluated the immunomodulatory and antiviral properties of its acidic (APS) and neutral (NPS) EPS in porcine intestinal epithelial (PIE) cells. Whole genome sequencing allowed the analysis of the general features of L. delbrueckii TUA4408L genome as well as the characterization of its EPS genes. A typical EPS gene cluster was found in the TUA4408L genome consisting in five highly conserved genes epsA-E, and a variable region, which includes the genes for the polymerase wzy, the flippase wzx, and seven glycosyltransferases. In addition, we demonstrated here for the first time that L. delbrueckii TUA4408L and its EPS are able to improve the resistance of PIE cells against rotavirus infection by reducing viral replication and regulating inflammatory response. Moreover, studies in PIE cells demonstrated that the TUA4408L strain and its EPS differentially modulate the antiviral innate immune response triggered by the activation of Toll-like receptor 3 (TLR3). L. delbrueckii TUA4408L and its EPS are capable of increasing the activation of interferon regulatory factor (IRF)-3 and nuclear factor κB (NF-κB) signaling pathways leading to an improved expression of the antiviral factors interferon (IFN)-β, Myxovirus resistance gene A (MxA) and RNaseL

Gene expression profiling of HiMAC-irradiated normal human fibroblasts by HiCEP

Gene expression profiling of normal human fibroblasts irradiated with heavy ion particles by a novel analysis methodFujimori, A., Suetomi,K., Kojima, A., Fang, Y-Q., Egusa, A., Takahashi, S., Okayasu, R.HiCEP (High-coverage expression profiling) is a novel comprehensive analysis method which is based on DNA finger printing and PCR amplification. It enables to detect any altered gene expression among 60-70% of all the actually transcribed genes in any eukaryotic cells and tissues. We previously applied HiCEP to a primary culture of normal human fibroblasts and observed gene expression responding to X-ray at the very low dose (10 mGy). As the result of screening approximately 23,000 transcripts, we have identified a set of CXC chemokines (CXCL1, CXCL2, CXCL6 and CXCL8) up-regulated by the 10 mGy X-rays in the normal human fibroblasts (HFLIII) (Cancer Res 2005; 65: 10159-10163). Those genes have hardly been expected from the previous studies using the higher (>100 mGy) doses of radiation. Our observation indicated that different molecular mechanisms are involved in the response to ionizing radiation with different doses /dose rates, suggesting that different cellular responses could be induced by ionizing radiation with different LETs. Accelerated heavy ion particles (at high LET) provide promising effects for radiotherapy of certain types of malignancy, however, the molecular basis of its advantage to gamma rays is not fully understood.This time, we applied HiCEP to normal human fibroblasts (HFL III) irradiated with high-LET radiation generated in our institute. More than 40 genes were found to be up-regulated in the irradiated cells by 3 folds within 4 hrs post-irradiation of carbon ion at 2Gy (70 keV/micro m). Those included the DNA damage-inducible genes (CDKN1A, CyclinG, Gadd45a), and also some unexpected genes, both predicted and unpredicted from the current public databases.53th Annual Meeting of the Radiation Research Societ

Genomic characterization of lactobacillus delbrueckii TUA4408L and evaluation of the antiviral activities of its extracellular polysaccharides in porcine intestinal epithelial cells

In lactic acid bacteria, the synthesis of exopolysaccharides (EPS) has been associated with some favorable technological properties as well as health-promoting benefits. Research works have shown the potential of EPS produced by lactobacilli to differentially modulate immune responses. However, most studies were performed in immune cells and few works have concentrated in the immunomodulatory activities of EPS in non-immune cells such as intestinal epithelial cells. In addition, the cellular and molecular mechanisms involved in the immunoregulatory effects of EPS have not been studied in detail. In this work, we have performed a genomic characterization of Lactobacillus delbrueckii subsp. delbrueckii TUA4408L and evaluated the immunomodulatory and antiviral properties of its acidic (APS) and neutral (NPS) EPS in porcine intestinal epithelial (PIE) cells. Whole genome sequencing allowed the analysis of the general features of L. delbrueckii TUA4408L genome as well as the characterization of its EPS genes. A typical EPS gene cluster was found in the TUA4408L genome consisting in five highly conserved genes epsA-E, and a variable region, which includes the genes for the polymerase wzy, the flippase wzx, and seven glycosyltransferases. In addition, we demonstrated here for the first time that L. delbrueckii TUA4408L and its EPS are able to improve the resistance of PIE cells against rotavirus infection by reducing viral replication and regulating inflammatory response. Moreover, studies in PIE cells demonstrated that the TUA4408L strain and its EPS differentially modulate the antiviral innate immune response triggered by the activation of Toll-like receptor 3 (TLR3). L. delbrueckii TUA4408L and its EPS are capable of increasing the activation of interferon regulatory factor (IRF)-3 and nuclear factor κB (NF-κB) signaling pathways leading to an improved expression of the antiviral factors interferon (IFN)-β, Myxovirus resistance gene A (MxA) and RNaseL.Fil: Kanmani, Paulraj. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; JapónFil: Albarracín, Leonardo Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; JapónFil: Kobayashi, Hisakazu. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; JapónFil: Hebert, Elvira Maria. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; Japón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Saavedra, Maria Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Komatsu, Ryoya. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; JapónFil: Gatica, Brian. University of Concepcion. Departmento de Farmacología; ChileFil: Miyazaki, Ayako. National Institute of Animal Health. Viral Diseases and Epidemiology Research Division; JapónFil: Ikeda-Ohtsubo, Wakako. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; JapónFil: Suda, Yoshihito. Miyagi University. Department of Food, Agriculture, and Environment; JapónFil: Aso, Hisashi. Tohoku University. Graduate School of Agricultural Science. Cell Biology Laboratory; JapónFil: Egusa, Shintaro. Marusan-Ai Co. Research & Development Division; JapónFil: Mishima, Takashi. Mie University. Graduate School of Regional Innovation Studies; JapónFil: Salas-Burgos, Alexis. University of Concepcion. Departmento de Farmacología; ChileFil: Takahashi, Hideki. Tohoku University. Graduate School of Agricultural Science. Laboratory of Plant Pathology; JapónFil: Villena, Julio Cesar. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; Japón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Kitazawa, Haruki. Tohoku University. Graduate School of Agricultural Science. Food and Feed Immunology Group, Laboratory of Animal Products Chemistry; Japó