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Journal articles on the topic 'Libraries subtractives'

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Published: 4 June 2021

Last updated: 1 February 2022

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Wu, Gin, Shiawhwa Su, and R. Curtis Bird. "Optimization of subtractive hybridization in construction of subtractive cDNA libraries." Genetic Analysis: Biomolecular Engineering 11, no. 2 (1994): 29–33. http://dx.doi.org/10.1016/1050-3862(94)90057-4.

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Bassett, Carole L., Michael E. Wisniewski, Timothy S. Artlip, John L. Norelli, Jenny Renaut, and Robert E. Farrell. "Global Analysis of Genes Regulated by Low Temperature and Photoperiod in Peach Bark." Journal of the American Society for Horticultural Science 131, no. 4 (2006): 551–63. http://dx.doi.org/10.21273/jashs.131.4.551.

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In response to environmental cues plants undergo changes in gene expression that result in the up- or down-regulation of specific genes. To identify genes in peach [Prunus persica (L.) Batsch.] trees whose transcript levels are specifically affected by low temperature (LT) or short day photoperiod (SD), we have created suppression subtractive hybridization (SSH) libraries from bark tissues sampled from trees kept at 5 °C and 25 °C under short day (SD) photoperiod or exposed to a night break (NB) interruption during the dark period of the SD cycle to simulate a long day (LD) photoperiod. Sequences expressed in forward and reverse subtractions using various subtracted combinations of temperature and photoperiod treatments were cloned, sequenced, and identified by BLAST and ClustalW analysis. Low temperature treatment resulted in the up-regulation of a number of cold-responsive and stress-related genes and suppression of genes involved in “housekeeping” functions (e.g., cell division and photosynthesis). Some stress-related genes not observed to be up-regulated under LT were increased in response to SD photoperiod treatments. Comparison of the patterns of expression as a consequence of different temperature and photoperiod treatments allowed us to determine the qualitative contribution of each treatment to the regulation of specific genes.

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HAN, H. "Construction of Subtractive cDNA Libraries of the Sporogony Stage of Eimeria tenella by Suppression Subtractive Hybridization." Chinese Journal of Biotechnology 23, no. 6 (2007): 1005–10. http://dx.doi.org/10.1016/s1872-2075(07)60060-0.

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Amaral, Daniel Oliveira Jordão do, Marleide Magalhães de Andrade Lima, Luciane Vilela Resende, and Márcia Vanusa da Silva. "Differential gene expression, induced by salicylic acid and Fusarium oxysporum f. sp. lycopersici infection, in tomato." Pesquisa Agropecuária Brasileira 43, no. 8 (2008): 1017–23. http://dx.doi.org/10.1590/s0100-204x2008000800010.

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The objective of this work was to determine the transcript profile of tomato plants (Lycopersicon esculentum Mill.), during Fusarium oxysporum f. sp. lycopersici infection and after foliar application of salicylic acid. The suppression subtractive hybridization (SSH) technique was used to generate a cDNA library enriched for transcripts differentially expressed. A total of 307 clones was identified in two subtractive libraries, which allowed the isolation of several defense-related genes that play roles in different mechanisms of plant resistance to phytopathogens. Genes with unknown roles were also isolated from the two libraries, which indicates the possibility of identifying new genes not yet reported in studies of stress/defense response. The SSH technique is effective for identification of resistance genes activated by salicylic acid and F. oxysporum f. sp. lycopersici infection. Not only the application of this technique enables a cost effective isolation of differentially expressed sequences, but also it allows the identification of novel sequences in tomato from a relative small number of sequences.

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Soule, Marilyn, Kenneth Cain, Stacey LaFrentz, and Douglas R. Call. "Combining Suppression Subtractive Hybridization and Microarrays To Map the Intraspecies Phylogeny of Flavobacteriumpsychrophilum." Infection and Immunity 73, no. 6 (2005): 3799–802. http://dx.doi.org/10.1128/iai.73.6.3799-3802.2005.

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ABSTRACT Reciprocal subtractive libraries were prepared for two strains of Flavobacterium psychrophilum, one virulent and the other avirulent in a trout challenge model. Unique clones were sequenced and their distribution assessed among 34 strains. The analysis showed that F. psychrophilum is composed of two genetic lineages, possibly reflecting host specificity.

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Zaveri, K., A. Krishna Chaitanya, and I. Bhaskar Reddy. "Virtual Screening and Docking Studies of Identified Potential Drug Target: Polysaccharide Deacetylase in Bacillus anthracis." International Letters of Natural Sciences 34 (February 2015): 70–77. http://dx.doi.org/10.18052/www.scipress.com/ilns.34.70.

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In recent years, insilico approaches have been predicting novel drug targets. The present day development in pharmaceutics mainly ponders on target based drugs and this has been aided by structure based drug designing and subtractive genomics. In the present study, the computational genome subtraction methodology was applied for identification of novel, potential drug target against Bacillus anthracis, cause of deadly anthrax. The potential drug target identified through subtractive genomics approach was considered as polysaccharide deacetylase. By virtual screening against NCI database and Drugbank chemical libraries, two potential lead molecules were predicted. Further the potential lead molecules and target protein were subjected for docking studies using Autodock.

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Rowland, Lisa J., Anik L. Dhanaraj, Dhananjay Naik, Nadim Alkharouf, Ben Matthews, and Rajeev Arora. "Study of Cold Tolerance in Blueberry Using EST Libraries, cDNA Microarrays, and Subtractive Hybridization." HortScience 43, no. 7 (2008): 1975–81. http://dx.doi.org/10.21273/hortsci.43.7.1975.

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To gain a better understanding of changes in gene expression associated with cold acclimation in the woody perennial blueberry (Vaccinium corymbosum L.) and ultimately use this information to develop more freeze-tolerant cultivars, a genomics approach based on the analysis of expressed sequence tags (ESTs) and microarrays was undertaken. Initially, two standard cDNA libraries, constructed using RNA from cold-acclimated (CA) and nonacclimated (NA) floral buds of the blueberry cultivar Bluecrop, were used for the generation of ≈2400 ESTs, half from each library. Putative functions were assigned to cDNAs based on homology to other genes/ESTs from GenBank. From contig analyses, 796 and 865 unique transcripts were identified from the CA and NA libraries, respectively. The most highly abundant cDNAs, that were picked many more times from one library than from the other, were identified as representing potentially differentially expressed transcripts. A cDNA microarray was constructed and used to study gene expression under cold-acclimating conditions in the field and cold room. Results indicated that the abundance of transcripts of numerous blueberry genes change during cold acclimation, including genes not found previously to be cold-responsive in Arabidopsis, and, interestingly, more transcripts were found to be upregulated under cold room conditions than under field conditions. Finally, forward and reverse subtracted cDNA libraries were prepared from ‘Bluecrop’ RNA to enrich for transcripts that are expressed at higher levels in floral buds at 400 h and at 0 h of low-temperature exposure, respectively. Many genes encoding putative transcription factors and other proteins related to signal transduction were identified from both libraries.

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Bower, Neil I., and Ian A. Johnston. "Discovery and characterization of nutritionally regulated genes associated with muscle growth in Atlantic salmon." Physiological Genomics 42A, no. 2 (2010): 114–30. http://dx.doi.org/10.1152/physiolgenomics.00065.2010.

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A genomics approach was used to identify nutritionally regulated genes involved in growth of fast skeletal muscle in Atlantic salmon ( Salmo salar L. ). Forward and reverse subtractive cDNA libraries were prepared comparing fish with zero growth rates to fish growing rapidly. We produced 7,420 ESTs and assembled them into nonredundant clusters prior to annotation. Contigs representing 40 potentially unrecognized nutritionally responsive candidate genes were identified. Twenty-three of the subtractive library candidates were also differentially regulated by nutritional state in an independent fasting-refeeding experiment and their expression placed in the context of 26 genes with established roles in muscle growth regulation. The expression of these genes was also determined during the maturation of a primary myocyte culture, identifying 13 candidates from the subtractive cDNA libraries with putative roles in the myogenic program. During early stages of refeeding DNAJA4, HSPA1B, HSP90A, and CHAC1 expression increased, indicating activation of unfolded protein response pathways. Four genes were considered inhibitory to myogenesis based on their in vivo and in vitro expression profiles ( CEBPD, ASB2, HSP30, novel transcript GE623928). Other genes showed increased expression with feeding and highest in vitro expression during the proliferative phase of the culture ( FOXD1, DRG1) or as cells differentiated ( SMYD1, RTN1, MID1IP1, HSP90A, novel transcript GE617747). The genes identified were associated with chromatin modification ( SMYD1, RTN1), microtubule stabilization ( MID1IP1), cell cycle regulation ( FOXD1, CEBPD, DRG1), and negative regulation of signaling ( ASB2) and may play a role in the stimulation of myogenesis during the transition from a catabolic to anabolic state in skeletal muscle.

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Lin, C. T., and D. R. Sargan. "A method for generating subtractive cDNA libraries retaining clones containing repetitive elements." Nucleic Acids Research 25, no. 21 (1997): 4427–28. http://dx.doi.org/10.1093/nar/25.21.4427.

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Triplett, Lindsay R., Youfu Zhao, and George W. Sundin. "Genetic Differences between Blight-Causing Erwinia Species with Differing Host Specificities, Identified by Suppression Subtractive Hybridization." Applied and Environmental Microbiology 72, no. 11 (2006): 7359–64. http://dx.doi.org/10.1128/aem.01159-06.

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ABSTRACT PCR-based subtractive hybridization was used to isolate sequences from Erwinia amylovora strain Ea110, which is pathogenic on apples and pears, that were not present in three closely related strains with differing host specificities: E. amylovora MR1, which is pathogenic only on Rubus spp.; Erwinia pyrifoliae Ep1/96, the causal agent of shoot blight of Asian pears; and Erwinia sp. strain Ejp556, the causal agent of bacterial shoot blight of pear in Japan. In total, six subtractive libraries were constructed and analyzed. Recovered sequences included type III secretion components, hypothetical membrane proteins, and ATP-binding proteins. In addition, we identified an Ea110-specific sequence with homology to a type III secretion apparatus component of the insect endosymbiont Sodalis glossinidius, as well as an Ep1/96-specific sequence with homology to the Yersinia pestis effector protein tyrosine phosphatase YopH.

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Wang, Xiao-Lan, Rui-Feng He, and Guang-Cun He. "Construction of suppression subtractive hybridization libraries and identification of brown planthopper-induced genes." Journal of Plant Physiology 162, no. 11 (2005): 1254–62. http://dx.doi.org/10.1016/j.jplph.2005.01.005.

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Rodrigues, Fabiana Aparecida, Juliana Marcolino-Gomes, Josirlei de Fátima Corrêa Carvalho, et al. "Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit." Genetics and Molecular Biology 35, no. 1 suppl 1 (2012): 304–14. http://dx.doi.org/10.1590/s1415-47572012000200011.

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Chávez-Navarrete, Tatiana Paola, Eduardo Sánchez-Timm, and Efrén Santos-Ordóñez. "Dataset of suppression subtractive hybridization libraries of banana-biostimulant-Pseudocercospora fijiensis molecular interaction." Data in Brief 27 (December 2019): 104557. http://dx.doi.org/10.1016/j.dib.2019.104557.

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Biagiotti, Sara, Michele Menotta, Elisa Giacomini, et al. "Forward subtractive libraries containing genes transactivated by dexamethasone in ataxia-telangiectasia lymphoblastoid cells." Molecular and Cellular Biochemistry 392, no. 1-2 (2014): 13–30. http://dx.doi.org/10.1007/s11010-014-2013-7.

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Berg, Noëlani van den, Bridget G. Crampton, Ingo Hein, Paul R. J. Birch, and Dave K. Berger. "High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis." BioTechniques 37, no. 5 (2004): 818–24. http://dx.doi.org/10.2144/04375rr02.

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Straub, Peter F., Mary L. Higham, Arnaud Tanguy, et al. "Suppression Subtractive Hybridization cDNA Libraries to Identify Differentially Expressed Genes from Contrasting Fish Habitats." Marine Biotechnology 6, no. 4 (2004): 386–99. http://dx.doi.org/10.1007/s10126-004-3146-6.

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Lévesque, V., T. Fayad, K. Ndiaye, M. Nahé Diouf, and J. G. Lussier. "Size-selection of cDNA libraries for the cloning of cDNAs after suppression subtractive hybridization." BioTechniques 35, no. 1 (2003): 72–78. http://dx.doi.org/10.2144/03351st02.

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Johnson, R., A. Khan, C. Voisey, et al. "Analysis of expressed sequence tags derived from the endophytic fungus Neotyphodium lolii grown in vitro and in association with its host plant perennial ryegrass." NZGA: Research and Practice Series 13 (January 1, 2007): 501–4. http://dx.doi.org/10.33584/rps.13.2006.3135.

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As a first step towards a functional genomics approach to gain a greater understanding of this important symbiosis, we have generated, sequenced and analysed two EST libraries from cultures of N. lolii and six in planta subtracted EST libraries enriched for differentially expressed genes. A total of 12871 ESTs were sequenced which, after filtering for quality, clustered into 1066 contigs and 3230 singletons to give a set of 4296 unique sequences or unigenes. BLASTX analysis revealed that 60% of fungal sequences derived from cultures were of unknown function with a sub-set of these corresponding to orphans. For the in planta-derived ESTs, most of the sequences with homologs in the public databases (98%) were of ryegrass origin. Comparisons made against fully sequenced genomes revealed that most fungal ESTs were homologous to genes present in both pathogenic and non-pathogenic ascomycete filamentous fungi, whereas the subtracted libraries comprised mostly plant genes. A range of sequences having significant homology to demonstrated pathogenicity/virulence genes in other fungal pathosystems were also identified, as well as some ESTs with proven roles in endophyte secondary metabolism. Keywords: ESTs, cDNA, Neotyphodium lolii, Lolium perenne, symbiosis, mutualism, suppression subtractive hybridisation

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Harrison, S. M., S. L. Dunwoodie, R. M. Arkell, H. Lehrach, and R. S. Beddington. "Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo." Development 121, no. 8 (1995): 2479–89. http://dx.doi.org/10.1242/dev.121.8.2479.

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A total of 5 conventional, directionally cloned plasmid cDNA libraries have been constructed from the entire embryonic region of the mid-gastrulation mouse embryo and from its four principal tissue constituents (ectoderm, mesoderm, endoderm and primitive streak). These libraries have been validated with respect to the number of independent clones, insert-size and appropriate representation of diagnostic marker genes. Subtractive hybridisation has been used to remove clones common to the Endoderm and Mesoderm cDNA libraries resulting in an Endoderm minus Mesoderm subtracted library. Probe prepared from this subtracted library has been hybridised to a grid containing approximately 18,500 Embryonic Region library clones. Three novel clones have been recovered as well as expected genes already known to be highly expressed in the primitive endoderm lineage at this stage of development. In situ hybridisation to early postimplantation embryos has revealed the expression patterns of these novel genes. One is highly expressed exclusively in visceral endoderm, one is expressed in ectodermal and endodermal tissues, and the third proves to be an early marker of prospective and differentiated surface ectoderm as well as being expressed in endoderm and its derivatives.

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Barraclough, Dong Liu, Susan Sewart, Philip S. Rudland, et al. "Microarray Analysis of Suppression Subtracted Hybridisation Libraries Identifies Genes Associated with Breast Cancer Progression." Analytical Cellular Pathology 32, no. 1-2 (2010): 87–99. http://dx.doi.org/10.1155/2010/582416.

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Background: A major challenge of cancer research is to identify key molecules which are responsible for the development of the malignant metastatic phenotype, the major cause of cancer death.Methods: Four subtracted cDNA libraries were constructed representing mRNAs differentially expressed between benign and malignant human breast tumour cells and between micro-dissected breast carcinoma in situ and invasive carcinoma. Hundreds of differentially expressed cDNAs from the libraries were micro-arrayed and screened with mRNAs from human breast tumor cell lines and clinical specimens. Gene products were further examined by RT-PCR and correlated with clinical data.Results: The combination of subtractive hybridisation and microarray analysis has identified a panel of 15 cDNAs which shows strong correlations with estrogen receptor status, malignancy or relapse. This panel included S100P, which was associated with aneuploidy in cell lines and relapse/death in patients, and AGR2 which was associated with estrogen receptor and with patient relapse. X-box binding protein-1 is also an estrogen-dependent gene and is associated with better survival for breast cancer patients.Conclusions: The combination of subtracted cDNA libraries and microarray analysis has thus identified potential diagnostic/prognostic biomarkers and targets for cancer therapy, which have not been identified from common prognostic gene signatures.

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LI, Liang, Wei-qi WANG, Cun-xiang WU, Tian-fu HAN, and Wen-sheng HOU. "Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean." Journal of Integrative Agriculture 11, no. 7 (2012): 1075–85. http://dx.doi.org/10.1016/s2095-3119(12)60100-2.

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Zheng, Senlin, Xiaoyan Qiu, Bin Chen, et al. "Toxicity evaluation of benzo[a]pyrene on the polychaete Perinereis nuntia using subtractive cDNA libraries." Aquatic Toxicology 105, no. 3-4 (2011): 279–91. http://dx.doi.org/10.1016/j.aquatox.2011.06.018.

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Tarr, Alexander W., Steven P. Boneham, Anna M. Grabowska, and Jonathan K. Ball. "Tagged polymerase chain reaction subtractive hybridization for the enrichment of phage display random peptide libraries." Analytical Biochemistry 339, no. 1 (2005): 61–68. http://dx.doi.org/10.1016/j.ab.2004.12.020.

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Goswami, Rubella S., Jin-Rong Xu, Frances Trail, Karen Hilburn, and H. Corby Kistler. "Genomic analysis of host–pathogen interaction between Fusarium graminearum and wheat during early stages of disease development." Microbiology 152, no. 6 (2006): 1877–90. http://dx.doi.org/10.1099/mic.0.28750-0.

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Fusarium graminearum strains responsible for causing the plant disease Fusarium head blight vary greatly in their ability to cause disease and produce mycotoxins on wheat. With the goal of understanding fungal gene expression related to pathogenicity, three cDNA libraries were created by suppression subtractive hybridization using wheat heads inoculated with a highly aggressive strain and either water or a less aggressive strain of this pathogen. Eighty-four fungal genes expressed during initial disease development were identified. The probable functions of 49 of these genes could be inferred by bioinformatic analysis. Thirty-five ESTs had no known homologues in current databases and were not identified by ab initio gene prediction methods. These ESTs from infected wheat heads probably represent F. graminearum genes that previously were not annotated. Four genes represented in one of these libraries were selected for targeted gene replacement, leading to the characterization of a two-component response regulator homologue involved in pathogenicity of the fungus. The mutants for this gene showed reduced sporulation and delayed spread of Fusarium head blight on wheat.

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Diatchenko, L., Y. F. Lau, A. P. Campbell, et al. "Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries." Proceedings of the National Academy of Sciences 93, no. 12 (1996): 6025–30. http://dx.doi.org/10.1073/pnas.93.12.6025.

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Kubota, Ryo, Chris McGuire, Blair Dierks, and Thomas A. Reh. "Identification of ciliary epithelial-specific genes using subtractive libraries and cDNA arrays in the avian eye." Developmental Dynamics 229, no. 3 (2004): 529–40. http://dx.doi.org/10.1002/dvdy.20000.

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Qu, Xiancheng, Jiaoyun Jiang, Xiaoli Shang, Cui Cheng, Long Feng, and Qigen Liu. "Construction and analysis of gonad suppression subtractive hybridization libraries for the rice field eel, Monopterus albus." Gene 540, no. 1 (2014): 20–25. http://dx.doi.org/10.1016/j.gene.2014.02.044.

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Villányi, Zoltán, István Gyurján, Viktor Stéger, and László Orosz. "Plaque-Based Competitive Hybridization." Journal of Biomolecular Screening 13, no. 1 (2007): 80–84. http://dx.doi.org/10.1177/1087057107310876.

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The authors have developed a simple, cost-saving experimental design, plaque-based competitive hybridization (PBCH), for genome-wide identification of genes differentially expressed in different tissues. PBCH offers advantages in comparison with other methods used in comparative genomics by combining the principles of differential hybridization with the subtractive hybridization. PBCH is particularly advantageous when libraries with few differences are to be analyzed. The authors demonstrate the use of PBCH by identifying 3 genes, up-regulated in the developing velvet antler of red deer ( Cervus elaphus): ApoD, C011A2, and S100a1. The fidelity and sensitivity of PBCH is also shown: 1 specific clone among a library sample of 15,000 can be recognized. Possibilities for further utilizations are discussed. ( Journal of Biomolecular Screening 2008:80-84)

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Wishart, J., M. S. Phillips, A. Paterson, and V. C. Blok. "Comparison of gene expression in Solanum bulbocastanum infected with virulent and avirulent isolates of Meloidogyne chitwoodi." Plant Protection Science 38, SI 2 - 6th Conf EFPP 2002 (2017): 721–22. http://dx.doi.org/10.17221/10599-pps.

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Resistance to root knot nematode M. chitwoodi has been identified in the wild tuber-bearing Solanum species, S. bulbocastanum. Three pathotypes were identified suggesting at least two different genetic factors for virulence and resistance in the pathogen and the host species, respectively. Roots of S. bulbocastanum were infested with two isolates of M. chitwoodi differing in virulence. The infection process was monitored by histological examination of roots allowing time points to be identified. cDNA libraries were constructed from infected root tissue using Suppression Subtractive Hybridisation (SSH) to enrich for transcripts from either compatible or incompatible interactions, at three days and seven days post infection. Both plant and nematode genes, which may be important during the host/parasite interaction, were identified.

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Ghorbel, Mohamed T., Greig Sharman, Charles Hindmarch, Kevin G. Becker, Tanya Barrett, and David Murphy. "Microarray screening of suppression subtractive hybridization-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus." Physiological Genomics 24, no. 2 (2006): 163–72. http://dx.doi.org/10.1152/physiolgenomics.00229.2005.

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The magnocellular neurons (MCNs) of the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus are the principal site of biosynthesis of prepropeptide precursor of the antidiuretic hormone vasopressin (VP). This precursor is processed during anterograde axonal transportation to terminals in the posterior pituitary gland, where biologically active VP is stored until release into the general circulation in response to physiological activation of the SON by osmotic cues. By binding to V2-type receptors located in the kidney, VP decreases the amount of water lost in urine. Osmotic activation of the SON is accompanied by a dramatic morphological and functional remodeling. We have sought to understand the mechanistic basis of this plasticity in terms of the differential expression of genes. To identify such genes, we adopted an unbiased global approach based on suppressive subtractive hybridization-polymerase chain reaction (SSH-PCR) Using this method, we generated libraries of clones putatively differentially expressed in control vs. dehydrated SON. To rapidly screen these libraries, 1,152 clones were subjected to microarray analysis, resulting in the identification of 459 differentially expressed transcripts. cDNA clones corresponding to 56 of these RNAs were sequenced, revealing many of them to be novel expressed sequence tags (ESTs). Four transcripts were shown by in situ hybridization (ISH) to be significantly up- or downregulated in the SON after dehydration. These genes may represent novel effectors or mediators of SON physiological remodeling.

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BOUCHUT, A., C. COUSTAU, B. GOURBAL, and G. MITTA. "Compatibility in the Biomphalaria glabrata/Echinostoma caproni model: new candidate genes evidenced by a suppressive subtractive hybridization approach." Parasitology 134, no. 4 (2006): 575–88. http://dx.doi.org/10.1017/s0031182006001673.

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In order to elucidate mechanisms underlying snail/echinostome compatibility, numerous molecular studies comparing transcripts and proteins of Biomphalaria glabrata susceptible or resistant to Echinostoma caproni were undertaken. These studies focused on plasma and haemocytes of the two strains and revealed that some transcripts and/or proteins were differentially expressed between strains. The aim of the present study was to develop a complementary transcriptomic approach by constructing subtractive libraries. This work revealed some candidate transcripts already identified in previous studies (calcium-binding proteins and glycolytic enzymes) as well as novel candidate transcripts that were differentially represented between strains of B. glabrata. Among these newly identified genes, we revealed several genes potentially involved in immune processes encoding proteases, protease inhibitors, a lectin, an aplysianin-like molecule, and cell adhesion molecules.

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Beitner-Johnson, D., K. Seta, Y. Yuan, et al. "Identification of hypoxia-responsive genes in a dopaminergic cell line by subtractive cDNA libraries and microarray analysis." Parkinsonism & Related Disorders 7, no. 3 (2001): 273–81. http://dx.doi.org/10.1016/s1353-8020(00)00070-5.

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Jia, Ying, James V. Anderson, David P. Horvath, Yong-Qiang Gu, Rodney G. Lym, and Wun S. Chao. "Subtractive cDNA Libraries Identify Differentially Expressed Genes in Dormant and Growing Buds of Leafy Spurge (Euphorbia esula)." Plant Molecular Biology 61, no. 1-2 (2006): 329–44. http://dx.doi.org/10.1007/s11103-006-0015-x.

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Robalino, Javier, Jonas S. Almeida, David McKillen, et al. "Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge." Physiological Genomics 29, no. 1 (2007): 44–56. http://dx.doi.org/10.1152/physiolgenomics.00165.2006.

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Infectious disease constitutes a major obstacle to the sustainability of shrimp aquaculture worldwide and a significant threat to natural populations of shrimp and other crustacea. The study of the shrimp immune system, including the response to viral infection, has been hampered by a relative lack of molecular genetic information and of tools suitable for high-throughput assessment of gene expression. In this report, the generation of a cDNA microarray encompassing 2,469 putative unigenes expressed in gills, circulating hemocytes, and hepatopancreas of Litopenaeus vannamei is described. The unigenes printed on the microarray were derived from the analyses of 7,021 expressed sequence tags obtained from standard cDNA libraries as well as from libraries generated by suppression subtractive hybridization, after challenging shrimp with a variety of immune stimuli. The general utility of the cDNA microarray was demonstrated by interrogating the array with labeled RNA from four different shrimp tissues (gills, hemocytes, hepatopancreas, and muscle) and by analyzing the transcriptomic response of shrimp to a lethal challenge with white spot syndrome virus. Our results indicate that white spot syndrome virus infection upregulates (in the hepatopancreas) genes encoding known and potential antimicrobial effectors, while some genes involved in protection from oxidative stress were found to be downregulated by the virus.

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Nguyen, Binh, Robert M. Bowers, Thomas M. Wahlund, and Betsy A. Read. "Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures of Emiliania huxleyi Strain 1516." Applied and Environmental Microbiology 71, no. 5 (2005): 2564–75. http://dx.doi.org/10.1128/aem.71.5.2564-2575.2005.

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ABSTRACT The marine coccolithophorid Emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization in E. huxleyi is promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.

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Cimerman, Agnï¿½s, Guillaume Arnaud, and Xavier Foissac. "Stolbur Phytoplasma Genome Survey Achieved Using a Suppression Subtractive Hybridization Approach with High Specificity." Applied and Environmental Microbiology 72, no. 5 (2006): 3274–83. http://dx.doi.org/10.1128/aem.72.5.3274-3283.2006.

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ABSTRACT Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, suppression subtractive hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83% were homologous to “Candidatus Phytoplasma asteris” (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase.

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Kang, Jae Soon, Hyoungseok Lee, Il Sung Moon, et al. "Construction and characterization of subtractive stage-specific expressed sequence tag (EST) libraries of the pinewood nematode Bursaphelenchus xylophilus." Genomics 94, no. 1 (2009): 70–77. http://dx.doi.org/10.1016/j.ygeno.2009.03.001.

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Rebrikov, D. V. "Mirror orientation selection (MOS): a method for eliminating false positive clones from libraries generated by suppression subtractive hybridization." Nucleic Acids Research 28, no. 20 (2000): 90e—90. http://dx.doi.org/10.1093/nar/28.20.e90.

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Daldoul, Samia, Michael Hoefer, and Ahmed Mliki. "Osmotic Stress Induces the Expression of VvMAP Kinase Gene in Grapevine (Vitis vinifera L.)." Journal of Botany 2012 (February 6, 2012): 1–4. http://dx.doi.org/10.1155/2012/737035.

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Abiotic stress adversely affects the growth of grapevine plants. In order to study the early expression changes of genes particularly involved in signal transduction upon salt and drought stresses in grapevines, ESTs derived from a suppressive subtractive hybridization approach (SSH) were selected for expression studies. We were particularly interested in the expression behaviour of the MAP kinase cDNA clone identified by differential screening of the salt-stressed SSH libraries. Interestingly, VvMAP kinase transcript showed a differential expression towards salt and drought treatment in the salt tolerant cultivar Razegui. The upregulation of this transcript was confirmed by RNA blot analysis. Our results revealed that the VvMAP kinase gene could be classified as an osmotic stress responsive gene as its expression was induced by salinity and drought. Furthermore, our study provides the basis for future research on the diverse signaling pathways mediated by MAPKs in grapevine.

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Vargas-Sanchez, Karina, Antonios Vekris, and Klaus G. Petry. "DNA Subtraction of In Vivo Selected Phage Repertoires for Efficient Peptide Pathology Biomarker Identification in Neuroinflammation Multiple Sclerosis Model." Biomarker Insights 11 (January 2016): BMI.S32188. http://dx.doi.org/10.4137/bmi.s32188.

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To streamline in vivo biomarker discovery, we developed a suppression subtractive DNA hybridization technique adapted for phage-displayed combinatorial libraries of 12 amino acid peptides (PhiSSH). Physical DNA subtraction is performed in a one-tube-all-reactions format by sequential addition of reagents, producing the enrichment of specific clones of one repertoire. High-complexity phage repertoires produced by in vivo selections in the multiple sclerosis rat model (experimental autoimmune encephalomyelitis, EAE) and matched healthy control rats were used to evaluate the technique. The healthy repertoire served as a physical DNA subtractor from the EAE repertoire to produce the subtraction repertoire. Full next-generation sequencing (NGS) of the three repertoires was performed to evaluate the efficiency of the subtraction technique. More than 96% of the clones common to the EAE and healthy repertoires were absent from the subtraction repertoire, increasing the probability of randomly selecting various specific peptides for EAE pathology to about 70%. Histopathology experiments were performed to confirm the quality of the subtraction repertoire clones, producing distinct labeling of the blood–brain barrier (BBB) affected by inflammation among healthy nervous tissue or the preferential binding to IL1-challenged vs. resting human BBB model. Combining PhiSSH with NGS will be useful for controlled in vivo screening of small peptide combinatorial libraries to discover biomarkers of specific molecular alterations interspersed within healthy tissues.

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Wulf, Anne, Katja Manthey, Jasmin Doll, et al. "Transcriptional Changes in Response to Arbuscular Mycorrhiza Development in the Model Plant Medicago truncatula." Molecular Plant-Microbe Interactions® 16, no. 4 (2003): 306–14. http://dx.doi.org/10.1094/mpmi.2003.16.4.306.

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Significant changes in root morphology and physiology during arbuscular mycorrhiza (AM) development are likely to be controlled by specific gene expression pattern in the host plant. Until now, little was known about transcriptional changes which occur AM-exclusively; that is, they do not occur during other root-microbe associations, nor are they induced by improved phosphate nutrition. In order to identify such AM-exclusive gene inductions of Medicago truncatula, we used a pool of different RNA samples as subtractor population in a suppressive subtractive hybridization (SSH) experiment. This approach resulted in the identification of a number of new AM-regulated genes. None of these genes were expressed in nonmycorrhiza roots or leaves. Electronic data obtained by comparison of the cDNA sequences to expressed sequence tag (EST) sequences from a wide range of cDNA libraries in the M. truncatula EST database (Gene Index, MtGI) support the mycorrhiza specificity of the corresponding genes, because sequences in the MtGI that were found to match the identified SSH-cDNA sequences originated exclusively from AM cDNA libraries. The promoter of one of those genes, MtGst1, showing similarities to plant glutathione-S-transferase (GST) encoding genes, was cloned and used in reporter gene studies. In contrast to studies with the potato GST gene PRP, MtGst 1 promoter activity was detected in all zones of the root cortex colonized by Glomus intraradices, but nowhere else.

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Jacobi, Volker, Josée Dufour, Guillaume F. Bouvet, Mirella Aoun, and Louis Bernier. "Identification of transcripts up-regulated in asexual and sexual fruiting bodies of the Dutch elm disease pathogenOphiostoma novo-ulmi." Canadian Journal of Microbiology 56, no. 8 (2010): 697–705. http://dx.doi.org/10.1139/w10-053.

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Suppression subtractive hybridization cDNA libraries were prepared from asexual synnemata (S-lib) and sexual perithecia (P-lib) fruiting bodies of the Dutch elm disease pathogen Ophiostoma novo-ulmi subsp. novo-ulmi isolate H327 (mating-type MAT1-1) consisting of 630 and 401 cDNA clones, respectively. Both libraries were differentially screened in duplicate with forward and reverse subtracted probes. Up-regulated S-lib transcripts included those with homologies to phosphoenolpyruvate carboxykinase and aquaporin. Up-regulated P-lib transcripts included those with homologies to aspartyl proteinase, DNA lyase 2, and part of a mating-type (MAT) protein containing a DNA-binding domain of the high-mobility group (HMG) type. Phylogenetic analyses of HMG domains present within the putative O. novo-ulmi MAT protein and within MAT1-1-3 and MAT1-2-1 proteins of other ascomycete fungi identified the O. novo-ulmi protein as a homologue of the MAT1-1-3 protein, which represents part of the so far uncharacterized O. novo-ulmi MAT1-1 idiomorph. Reverse transcription – quantitative real-time PCR indicated up-regulation of the MAT1-1-3 homologue in O. novo-ulmi perithecia and synnemata. The present work identifies, for the first time, proteins involved in the formation of asexual and sexual fruiting bodies in O. novo-ulmi and should be of interest to researchers concerned with reproduction, mating type, and sexuality of filamentous ascomycete fungi.

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De Long, Susan K., Kerry A. Kinney, and Mary Jo Kirisits. "Prokaryotic Suppression Subtractive Hybridization PCR cDNA Subtraction, a Targeted Method To Identify Differentially Expressed Genes." Applied and Environmental Microbiology 74, no. 1 (2007): 225–32. http://dx.doi.org/10.1128/aem.01647-07.

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ABSTRACT Molecular biology tools can be used to monitor and optimize biological treatment systems, but the application of nucleic acid-based tools has been hindered by the lack of available sequences for environmentally relevant biodegradation genes. The objective of our work was to extend an existing molecular method for eukaryotes to prokaryotes, allowing us to rapidly identify differentially expressed genes for subsequent sequencing. Suppression subtractive hybridization (SSH) PCR cDNA subtraction is a technique that can be used to identify genes that are expressed under specific conditions (e.g., growth on a given pollutant). While excellent methods for eukaryotic SSH PCR cDNA subtraction are available, to our knowledge, no methods previously existed for prokaryotes. This work describes our methodology for prokaryotic SSH PCR cDNA subtraction, which we validated using a model system: Pseudomonas putida mt-2 degrading toluene. cDNA from P. putida mt-2 grown on toluene (model pollutant) or acetate (control substrate) was subjected to our prokaryotic SSH PCR cDNA subtraction protocol to generate subtraction clone libraries. Over 90% of the sequenced clones contained gene fragments encoding toluene-related enzymes, and 20 distinct toluene-related genes from three key operons were sequenced. Based on these results, prokaryotic SSH PCR cDNA subtraction shows promise as a targeted method for gene identification.

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Gust, Bertolt, Kerstin Spatz, Alexander Spychaj, and Matthias Redenbach. "Region-Specific Transcriptional Activity in the Genome of Streptomyces coelicolor A3(2)." Applied and Environmental Microbiology 67, no. 8 (2001): 3598–602. http://dx.doi.org/10.1128/aem.67.8.3598-3602.2001.

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ABSTRACT Transcriptional analysis of microbial genomes is an important component of functional genomics. Strategies such as hybridization of labeled total RNA against ordered clone libraries or differential-display approaches have already been carried out to identify expressed genes. We describe here an additional method which applies subtractive hybridization between genome-specific DNA and total RNA followed by a PCR approach to identify expressed microbial genes. With the new strategy, the expression of genes in the terminal regions of the linear Streptomyces coelicolor A3(2) chromosome and the accessory linear plasmid SCP1 was analyzed. The results indicate that the method is useful for the identification of expressed genes in actinomycetes and other microbial systems. We demonstrate for the first time that at least 24 genes in the chromosome end regions (silent regions) of S. coelicolor are actively expressed. In addition, several expressed SCP1 genes were identified, including a gene which shows high similarity to microbialdnaN genes and which seems to play a role in SCP1 maintenance.

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Seta, Karen A., and David E. Millhorn. "Functional genomics approach to hypoxia signaling." Journal of Applied Physiology 96, no. 2 (2004): 765–73. http://dx.doi.org/10.1152/japplphysiol.00836.2003.

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Mammalian cells require a constant supply of oxygen to maintain energy balance, and sustained hypoxia can result in cell death. It is therefore not surprising that sophisticated adaptive mechanisms have evolved that enhance cell survival during hypoxia. During the past few years, there have been a growing number of reports on hypoxia-induced transcription of specific genes. In this review, we describe a unique experimental approach that utilizes focused cDNA libraries coupled to microarray analyses to identify hypoxia-responsive signal transduction pathways and genes that confer the hypoxia-tolerant phenotype. We have used the subtractive suppression hybridization (SSH) method to create a cDNA library enriched in hypoxia-regulated genes in oxygen-sensing pheochromocytoma cells and have used this library to create microarrays that allow us to examine hundreds of genes at a time. This library contains over 300 genes and expressed sequence tags upregulated by hypoxia, including tyrosine hydroxylase, vascular endothelial growth factor, and junB. Hypoxic regulation of these and other genes in the library has been confirmed by microarray, Northern blot, and real-time PCR analyses. Coupling focused SSH libraries with microarray analyses allows one to specifically study genes relevant to a phenotype of interest while reducing much of the biological noise associated with these types of studies. When used in conjunction with high-throughput, dye-based assays for cell survival and apoptosis, this approach offers a rapid method for discovering validated therapeutic targets for the treatment of cardiovascular disease, stroke, and tumors.

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Hu, Wei-Ping, Sun Kuie Tay, and Yi Zhao. "Endometriosis-Specific Genes Identified by Real-Time Reverse Transcription-Polymerase Chain Reaction Expression Profiling of Endometriosis Versus Autologous Uterine Endometrium." Journal of Clinical Endocrinology & Metabolism 91, no. 1 (2006): 228–38. http://dx.doi.org/10.1210/jc.2004-1594.

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Abstract Context: The etiology and molecular pathogenesis of endometriosis, a prevalent estrogen-dependent gynecologic disease, are poorly understood. Objective: The objective of the study was to identify the differentially expressed genes between autologous ectopic and eutopic endometrium. Design: Subtractive hybridization was used for a genome-wide search for differentially expressed genes between autologous ectopic and eutopic endometrium. Real-time RT-PCR was used for gene expression profiling in the paired tissue samples taken from multiple subjects. Patients: The paired pelvic endometriosis and uterine endometrium tissue biopsies were procured from 15 patients undergoing laparoscopy or hysterectomy for endometriosis. Results: Seventy-eight candidate genes were identified from the subtractive cDNA libraries. Seventy-six of these genes were investigated in approximately 8000 real-time PCR for their differential expression in 30 paired tissue biopsies from 15 patients affected by endometriosis. Cluster analysis on gene expression revealed highly consistent profiles in two groups of genes, despite the clinical heterogeneity of the 15 cases. Thirty-four genes specific to early disease point to their potential roles in establishment and evolution of endometriosis. Most interestingly, 14 genes were consistently dysregulated in the paired samples from the majority of the patients. Of these, there were two uncharacterized transcripts and two novel genes, and 10 were matched to known genes: IGFBP5, PIM2, RPL41, PSAP, FBLN1, SIPL, DLX5, HSD11B2, SET, and RHOE. Conclusions: Dysregulation of 14 genes was found to be overtly associated with endometriosis. Some of these genes, known to participate in estrogen activities and antiapoptosis, may play a role in the pathogenesis of endometriosis and may represent potential diagnostic markers or therapeutic targets for endometriosis.

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Lombardi, M. Paola, Maurice J. B. van den Hoff, Jan M. Ruijter, et al. "Expression analysis of subtractively enriched libraries (EASEL): a widely applicable approach to the identification of differentially expressed genes." Journal of Biochemical and Biophysical Methods 57, no. 1 (2003): 17–33. http://dx.doi.org/10.1016/s0165-022x(03)00083-6.

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Zhou, Yanhong, Zhaoyang Zeng, Wenling Zhang, et al. "Identification of candidate molecular markers of nasopharyngeal carcinoma by microarray analysis of subtracted cDNA libraries constructed by suppression subtractive hybridization." European Journal of Cancer Prevention 17, no. 6 (2008): 561–71. http://dx.doi.org/10.1097/cej.0b013e328305a0e8.

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Ye, Z. "Identification of iron responsive genes by screening cDNA libraries from suppression subtractive hybridization with antisense probes from three iron conditions." Nucleic Acids Research 28, no. 8 (2000): 1802–7. http://dx.doi.org/10.1093/nar/28.8.1802.

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Zhou, Yan Hong, Zhao Yang Zeng, Wen Ling Zhang, et al. "Identification of candidate molecular markers of nasopharyngeal carcinoma by microarray analysis of subtracted cDNA libraries constructed by suppression subtractive hybridization." Cell Biology International 32, no. 3 (2008): S40. http://dx.doi.org/10.1016/j.cellbi.2008.01.174.

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