{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T08:30:53Z","timestamp":1767861053745,"version":"3.49.0"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biotechnol"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>DNA microarrays are among the most widely used technical platforms for DNA and RNA studies, and issues related to microarrays sensitivity and specificity are therefore of general importance in life sciences. Compatible solutes are derived from hyperthermophilic microorganisms and allow such microorganisms to survive in environmental and stressful conditions. Compatible solutes show stabilization effects towards biological macromolecules, including DNA.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We report here that compatible solutes from hyperthermophiles increased the performance of the hybridization buffer for Affymetrix GeneChip<jats:sup>\u00ae<\/jats:sup> arrays. The experimental setup included independent hybridizations with constant RNA over a wide range of compatible solute concentrations. The dependence of array quality and compatible solute was assessed using specialized statistical tools provided by both the proprietary Affymetrix quality control system and the open source Bioconductor suite.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Low concentration (10 to 25 mM) of hydroxyectoine, potassium mannosylglycerate and potassium diglycerol phosphate in hybridization buffer positively affected hybridization parameters and enhanced microarrays outcome. This finding harbours a strong potential for the improvement of DNA microarray experiments.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1472-6750-7-82","type":"journal-article","created":{"date-parts":[[2007,11,23]],"date-time":"2007-11-23T19:13:42Z","timestamp":1195845222000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Compatible solutes from hyperthermophiles improve the quality of DNA microarrays"],"prefix":"10.1186","volume":"7","author":[{"given":"Nicoletta","family":"Mascellani","sequence":"first","affiliation":[]},{"given":"Xiuping","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Simona","family":"Rossi","sequence":"additional","affiliation":[]},{"given":"Jlenia","family":"Marchesini","sequence":"additional","affiliation":[]},{"given":"Davide","family":"Valentini","sequence":"additional","affiliation":[]},{"given":"Diego","family":"Arcelli","sequence":"additional","affiliation":[]},{"given":"Cristian","family":"Taccioli","sequence":"additional","affiliation":[]},{"given":"Mauro","family":"Helmer Citterich","sequence":"additional","affiliation":[]},{"given":"Chang-Gong","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Rita","family":"Evangelisti","sequence":"additional","affiliation":[]},{"given":"Giandomenico","family":"Russo","sequence":"additional","affiliation":[]},{"given":"Jorge M","family":"Santos","sequence":"additional","affiliation":[]},{"given":"Carlo M","family":"Croce","sequence":"additional","affiliation":[]},{"given":"Stefano","family":"Volinia","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,11,23]]},"reference":[{"key":"257_CR1","doi-asserted-by":"crossref","unstructured":"Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays. Nat Genet. 1999, 10-14. 10.1038\/4434. Suppl 1","DOI":"10.1038\/4434"},{"key":"257_CR2","doi-asserted-by":"crossref","unstructured":"Syv\u00e4nen AC: Toward genome-wide SNP genotyping. Nat Genet. 2005, S5-S10. 10.1038\/ng1558. Suppl 1","DOI":"10.1038\/ng1558"},{"key":"257_CR3","doi-asserted-by":"crossref","unstructured":"Pinkel D, Albertson DG: Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005, S11-S17. 10.1038\/ng1569. Suppl 1","DOI":"10.1038\/ng1569"},{"key":"257_CR4","doi-asserted-by":"crossref","unstructured":"Van Steensel B: Mapping of genetic and epigenetic regulatory networks using microarrays. Nat Genet. 2005, S18-S24. 10.1038\/ng1559. Suppl 1","DOI":"10.1038\/ng1559"},{"key":"257_CR5","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1046\/j.1462-2920.2002.00335.x","volume":"4","author":"H Santos","year":"2002","unstructured":"Santos H, Da Costa MS: Compatible solutes of organisms that live in hot saline environments. Environ Microbiol. 2002, 4: 501-509. 10.1046\/j.1462-2920.2002.00335.x.","journal-title":"Environ Microbiol"},{"key":"257_CR6","doi-asserted-by":"crossref","first-page":"3591","DOI":"10.1128\/AEM.64.10.3591-3598.1998","volume":"64","author":"P Lamosa","year":"1998","unstructured":"Lamosa P, Martins LO, Da Costa MS, Santos H: Effects of temperature, salinity, and medium composition on compatible solute accumulation by thermococcus spp. Appl Environ Microbiol. 1998, 64: 3591-3598.","journal-title":"Appl Environ Microbiol"},{"key":"257_CR7","doi-asserted-by":"crossref","first-page":"4020","DOI":"10.1128\/aem.63.10.4020-4025.1997","volume":"63","author":"A Ramos","year":"1997","unstructured":"Ramos A, Raven N, Sharp RJ, Bartolucci S, Rossi M, Cannio R, Lebbink J, Van Der Oost J, De Vos WM, Santos H: Stabilization of Enzymes against Thermal Stress and Freeze-Drying by Mannosylglycerate. Appl Environ Microbiol. 1997, 63: 4020-4025.","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"257_CR8","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s007920100236","volume":"6","author":"N Borges","year":"2002","unstructured":"Borges N, Ramos A, Raven ND, Sharp RJ, Santos H: Comparative study of the thermostabilizing properties of mannosylglycerate and other compatible solutes on model enzymes. Extremophiles. 2002, 6 (3): 209-216. 10.1007\/s007920100236.","journal-title":"Extremophiles"},{"issue":"8","key":"257_CR9","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1002\/cbic.200300574","volume":"4","author":"TQ Faria","year":"2003","unstructured":"Faria TQ, Knapp S, Ladenstein R, Ma\u00e7anita AL, Santos H: Protein stabilisation by compatible solutes: effect of mannosylglycerate on unfolding thermodynamics and activity of ribonuclease A. Chembiochem. 2003, 4 (8): 734-741. 10.1002\/cbic.200300574.","journal-title":"Chembiochem"},{"key":"257_CR10","doi-asserted-by":"publisher","first-page":"48680","DOI":"10.1074\/jbc.M408806200","volume":"279","author":"TQ Faria","year":"2004","unstructured":"Faria TQ, Lima JC, Bastos M, Ma\u00e7anita AL, Santos H: Protein stabilization by osmolytes from hyperthermophiles: effect of mannosylglycerate on the thermal unfolding of recombinant nuclease a from Staphylococcus aureus studied by picosecond time-resolved fluorescence and calorimetry. J Biol Chem. 2004, 279: 48680-48691. 10.1074\/jbc.M408806200.","journal-title":"J Biol Chem"},{"key":"257_CR11","doi-asserted-by":"publisher","first-page":"1974","DOI":"10.1128\/AEM.66.5.1974-1979.2000","volume":"66","author":"P Lamosa","year":"2000","unstructured":"Lamosa P, Burke A, Peist R, Huber R, Liu MY, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C, Santos H: Thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile Archaeoglobus fulgidus. Appl Environ Microbiol. 2000, 66: 1974-1979. 10.1128\/AEM.66.5.1974-1979.2000.","journal-title":"Appl Environ Microbiol"},{"key":"257_CR12","doi-asserted-by":"publisher","first-page":"4606","DOI":"10.1046\/j.1432-1033.2003.03861.x","volume":"270","author":"P Lamosa","year":"2003","unstructured":"Lamosa P, Turner DL, Ventura R, Maycock C, Santos H: Protein stabilization by compatible solutes. Effect of diglycerol phosphate on the dynamics of Desulfovibrio gigas rubredoxin studied by NMR. Eur J Biochem. 2003, 270: 4606-4614. 10.1046\/j.1432-1033.2003.03861.x.","journal-title":"Eur J Biochem"},{"key":"257_CR13","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1007\/s007920050116","volume":"3","author":"S Knapp","year":"1999","unstructured":"Knapp S, Ladenstein R, Galinski EA: Extrinsic protein stabilization by the naturally occurring osmolytes beta-hydroxyectoine and betaine. Extremophiles. 1999, 3: 191-198. 10.1007\/s007920050116.","journal-title":"Extremophiles"},{"key":"257_CR14","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1038\/nbt1296-1675","volume":"14","author":"DJ Lockhart","year":"1996","unstructured":"Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996, 14: 1675-1680. 10.1038\/nbt1296-1675.","journal-title":"Nat Biotechnol"},{"key":"257_CR15","unstructured":"Gautier L, Irizarry R, Cope L, Bolstad B: Description of affy. [http:\/\/bioconductor.org\/packages\/1.9\/bioc\/vignettes\/affy\/inst\/doc\/affy.pdf]"},{"key":"257_CR16","unstructured":"Affymetrix Technical Support: Manual. [http:\/\/www.affymetrix.com\/support\/technical\/manual\/expression_manual.affx]"},{"key":"257_CR17","unstructured":"Affymetrix Technical Documentation: GeneChip\u00ae expression analysis technical manual, data analysis fundamentals. [http:\/\/www.affymetrix.com\/support\/technical\/manuals.affx]"},{"key":"257_CR18","unstructured":"Bolstad B: affyPLM: model based QC assessment of Affymetrix GeneChips. [http:\/\/bioconductor.org\/packages\/1.9\/bioc\/vignettes\/affyPLM\/inst\/doc\/QualityAssess.pdf]"}],"container-title":["BMC Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1472-6750-7-82.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T09:43:21Z","timestamp":1630489401000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiotechnol.biomedcentral.com\/articles\/10.1186\/1472-6750-7-82"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,23]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["257"],"URL":"https:\/\/doi.org\/10.1186\/1472-6750-7-82","relation":{},"ISSN":["1472-6750"],"issn-type":[{"value":"1472-6750","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,11,23]]},"assertion":[{"value":"29 June 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 November 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 November 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"82"}}