scholarly journals Suppressive Subtraction Hybridization on Stimulated Primary Horse Macrophages

2006 ◽  
Vol 75 (3) ◽  
pp. 337-341
Author(s):  
J. Matiašovic ◽  
P. Králík ◽  
L. Leva ◽  
M. Faldyna ◽  
P. Hořín
Keyword(s):  
Expressed Sequence Tags ◽  
Sequence Similarity ◽  
Genetic Resistance ◽  
Macrophage Cell ◽  
Cdna Subtraction ◽  
Subtraction Hybridization ◽  
E Coli ◽  
Suppressive Subtraction Hybridization ◽  
Expressed Sequence ◽  
Overnight Culture

To study genes potentially involved in genetic resistance to infectious diseases in the horse, suppressive subtraction hybridization was used to identify genes expressed in primary horse macrophages after their stimulation with E. coli. Overnight culture of blood monocyte-derived macrophage cells was stimulated with E. coli K12 in ratio 40 E. coli cells to one macrophage cell. After 4 hours of incubation, non-phagocyted bacteria were washed away. Following next 20 hour incubation in MEM alpha containing 5 μg of gentamycin in 1 ml of media, mRNA was isolated and used in Clontech PCR-Select cDNA Subtraction Kit. Expression of several known horse genes, as well as some new ESTs (expressed sequence tags) showing sequence similarity with immunity-related genes from other species was identified.

Isolation and analysis of genes induced by rehydration after serious drought in broomcorn millet (Panicum miliaceum L.) by SSH

2006 ◽  
Vol 3 (3) ◽  
pp. 237-242 ◽  
Author(s):  
Lin Fan-Yun ◽  
Hu Yin-Gang ◽  
Song Guo-Qi ◽  
Zhang Hong ◽  
Liu Tian-Ming ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Rattus Norvegicus ◽  
Protein Processing ◽  
Panicum Miliaceum ◽  
Subtraction Hybridization ◽  
Suppressive Subtraction Hybridization ◽  
Broomcorn Millet ◽  
And Function ◽  
Expressed Sequence ◽  
Blast Result

AbstractIn order to investigate the molecular mechanism of rehydration after serious drought in broomcorn millet (Panicum miliaceum L.), a forward subtracted cDNA library was constructed between normal watered leaves and rehydrated leaves after serious drought conditions, using the suppressive subtraction hybridization (SSH) technique. A total of 60 positive clones were picked out at random from the subtracted library and sequenced, and redundancy sequences were removed after sequence alignment. Based on the results of sequence homologous comparison and function querying, 32 expressed sequence tags (EST) were highly homologous with known ESTs. Most of those sequences were related to either abiotic or biotic stress in plants. Of those sequences, 11 ESTs were homologous with ESTs in rat (Rattus norvegicus) liver after partial hepatectomy. The Blast result of proteins revealed that 28 ESTs were similar to known proteins. The functions of these proteins mainly involve signal transduction, transcription and protein processing. This experiment demonstrated that a range of specific genes was induced and expressed in broomcorn millet during the rehydration stage after serious drought.

scholarly journals Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass

2009 ◽  
Vol 63 (1-2) ◽  
pp. 25-28
Author(s):  
Gintaras Brazauskas ◽  
Izolda Pašakinskienė
Keyword(s):  
Differentially Expressed Genes ◽  
Perennial Ryegrass ◽  
Expressed Sequence Tags ◽  
Sequence Similarity ◽  
Differentially Expressed ◽  
Sequence Length ◽  
Auxin Response ◽  
Suppression Subtractive Hybridisation ◽  
Subtractive Hybridisation ◽  
Expressed Sequence

Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass A PCR-based suppression subtractive hybridisation (SSH) technique was used to identify differentially expressed genes in the primary and axillary tillers of a perennial ryegrass (Lolium perenne L.) mutant with enhanced axillary tillering. A total of 310 expressed sequence tags (ESTs) were obtained representing 249 non-redundant sequences. The average EST sequence length was 249 nt and varied from 30 to 508 nt. Putative function was assigned to 152 ESTs by comparing sequences with publicly available databases of NCBI. The remaining 97 ESTs had no sequence similarity matches to any of the known databases. Several ESTs were selected as potential candidates for the control of axillary tiller formation. RUB1 conjugating enzyme and BIG protein were shown to play role in auxin response regulation, SHOOT1 protein was associated with fasciation mutation in soybean (Glycine max L.), and brassinosteroid LRR receptor kinase with brassinosteroid signalling.

scholarly journals PASSIOMA: Exploring Expressed Sequence Tags during Flower Development inPassifloraspp.

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Lucas Cutri ◽  
Marcelo Carnier Dornelas
Keyword(s):  
Expressed Sequence Tags ◽  
Flower Development ◽  
Agronomic Traits ◽  
Sequence Similarity ◽  
Reproductive Development ◽  
Floral Diversity ◽  
Genomic Tools ◽  
Wide Range ◽  
Expressed Sequence

The genusPassifloraprovides a remarkable example of floral complexity and diversity. The extreme variation ofPassifloraflower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs) as an approach for the characterization of genes expressed duringPassiflorareproductive development. Analyzing thePassiflorafloral EST database (named PASSIOMA), we found sequences showing significant sequence similarity to genes known to be involved in reproductive development such as MADS-box genes. Some of these sequences were studied using RT-PCR andin situhybridization confirming their expression duringPassifloraflower development. The detection of these novel sequences can contribute to the development of EST-based markers for important agronomic traits as well as to the establishment of genomic tools to study the naturally occurring floral diversity amongPassifloraspecies.

Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1081-1088 ◽  
Author(s):  
Quang Hien Le ◽  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Caenorhabditis Elegans ◽  
Expressed Sequence Tags ◽  
Large Family ◽  
Insertion Sequences ◽  
Normal Plant ◽  
Nematode Caenorhabditis Elegans ◽  
Plant Genomes ◽  
Plant Genes ◽  
Expressed Sequence ◽  
Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Sign in / Sign up

Export Citation Format

Share Document