scholarly journals Mirror orientation selection (MOS): a method for eliminating false positive clones from libraries generated by suppression subtractive hybridization

2000 ◽  
Vol 28 (20) ◽  
pp. 90e-90 ◽  
Author(s):  
D. V. Rebrikov
Keyword(s):  
Suppression Subtractive Hybridization ◽  
False Positive ◽  
Subtractive Hybridization ◽  
Orientation Selection ◽  
Mirror Orientation Selection

scholarly journals A Suppression Subtractive Hybridization Approach Reveals Niche-Specific Genes That May Be Involved in Predator Avoidance in Marine Synechococcus Isolates

2006 ◽  
Vol 72 (4) ◽  
pp. 2730-2737 ◽  
Author(s):  
H. Jones ◽  
M. Ostrowski ◽  
D. J. Scanlan
Keyword(s):  
Suppression Subtractive Hybridization ◽  
False Positive ◽  
Predator Avoidance ◽  
Subtractive Hybridization ◽  
Bacterial Strains ◽  
Genes Encoding ◽  
Specific Predator ◽  
Export System ◽  
Potential False Positive ◽  
Marine Primary Production

ABSTRACT Picocyanobacteria of the genus Synechococcus are important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains, Synechococcus sp. strain WH8103 (clade III) and Synechococcus sp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.

scholarly journals Suppression Subtractive Hybridization and Differential Screening Reveals Endodormancy-associated Expression of an SVP/AGL24-type MADS-box Gene in Lateral Vegetative Buds of Japanese Apricot

2008 ◽  
Vol 133 (5) ◽  
pp. 708-716 ◽  
Author(s):  
Hisayo Yamane ◽  
Yukinobu Kashiwa ◽  
Tomomi Ooka ◽  
Ryutaro Tao ◽  
Keizo Yonemori
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Subtractive Hybridization ◽  
Differential Screening ◽  
Gene Pools ◽  
Mads Box ◽  
Japanese Apricot ◽  
Cell Wall Modification ◽  
Gibberellin Metabolism ◽  
Lateral Buds ◽  
Mirror Orientation Selection

To understand the molecular basis of the endodormancy of buds of perennial plants, we searched for the genes that are expressed preferentially in endodormant lateral buds of the deciduous fruit tree japanese apricot (Prunus mume Sieb. et Zucc.) using suppression subtractive hybridization with mirror orientation selection (SSH/MOS). We generated two SSH/MOS libraries containing gene pools that are expressed preferentially in endodormant buds in comparison with paradormant or ecodormant buds to search for the genes that are upregulated by endodormancy induction or down-regulated by endodormancy release, respectively. Differential screening and sequencing indicated that genes involved in gibberellin metabolism, stress resistance, cell wall modification, and signal transduction, such as transcription factors, are upregulated in endodormant buds. After a further expression survey and full-length cDNA cloning, we found that a gene similar to the SVP/AGL24-type MADS-box transcription factor showed endodormancy-associated expression. Seasonal expression analysis suggested that the SVP/AGL24 homolog in japanese apricot might be involved in endodormancy regulation of its lateral buds.

scholarly journals Genomic Diversity of Burkholderia pseudomallei Clinical Isolates: Subtractive Hybridization Reveals a Burkholderia mallei-Specific Prophage in B. pseudomallei 1026b

2004 ◽  
Vol 186 (12) ◽  
pp. 3938-3950 ◽  
Author(s):  
David DeShazer
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Burkholderia Pseudomallei ◽  
Genomic Sequence ◽  
Subtractive Hybridization ◽  
Etiologic Agent ◽  
Polyclonal Antiserum ◽  
Genomic Diversity ◽  
Clinical Isolates ◽  
Immunogold Electron Microscopy ◽  
Burkholderia Mallei

ABSTRACT Burkholderia pseudomallei is the etiologic agent of the disease melioidosis and is a category B biological threat agent. The genomic sequence of B. pseudomallei K96243 was recently determined, but little is known about the overall genetic diversity of this species. Suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of B. pseudomallei, 1026b and K96243. Numerous mobile genetic elements, including a temperate bacteriophage designated φ1026b, were identified among the 1026b-specific suppression subtractive hybridization products. Bacteriophage φ1026b was spontaneously produced by 1026b, and it had a restricted host range, infecting only Burkholderia mallei. It possessed a noncontractile tail, an isometric head, and a linear 54,865-bp genome. The mosaic nature of the φ1026b genome was revealed by comparison with bacteriophage φE125, a B. mallei-specific bacteriophage produced by Burkholderia thailandensis. The φ1026b genes for DNA packaging, tail morphogenesis, host lysis, integration, and DNA replication were nearly identical to the corresponding genes in φE125. On the other hand, φ1026b genes involved in head morphogenesis were similar to head morphogenesis genes encoded by Pseudomonas putida and Pseudomonas aeruginosa bacteriophages. Consistent with this observation, immunogold electron microscopy demonstrated that polyclonal antiserum against φE125 reacted with the tail of φ1026b but not with the head. The results presented here suggest that B. pseudomallei strains are genetically heterogeneous and that bacteriophages are major contributors to the genomic diversity of this species. The bacteriophage characterized in this study may be a useful diagnostic tool for differentiating B. pseudomallei and B. mallei, two closely related biological threat agents.

scholarly journals Identification of up-regulated Ras-like GTPase, Rap1b, by suppression subtractive hybridization

2001 ◽  
Vol 60 (6) ◽  
pp. 2129-2141 ◽  
Author(s):  
Sun Lin ◽  
Sumant Chugh ◽  
Xiaomin Pan ◽  
Elisabeth I. Wallner ◽  
Jun Wada ◽  
...  
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Subtractive Hybridization
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