{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["224308"],"full_dataset_link":["https://pax-db.org/dataset/224308/3452104403"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Due to the physicochemical properties of nanoparticles, the use of nanomaterials increases every year in industrial and medical processes. At the same time, the increasing number of bacteria becoming resistant to many antibiotics, mostly by a horizontal gene transfer process, is a major public health concern. We herein report, for the first time, the role of nanoparticles in the physiological induction of horizontal gene transfer in bacteria. Besides the most well-known impacts of nanoparticles on bacteria, i.e. death or oxidative stress, two nanoparticles, n-ZnO and n-TiO<sub>2</sub>, significantly and oppositely impact the transformation efficiency of Bacillus subtilis in biofilm growth conditions, by modification of the physiological processes involved in the induction of competence, the first step of transformation. This effect is the consequence of a physiological adaptation rather than a physical cell injury: two oligopeptide ABC transporters, OppABCDF and AppDFABC, are differentially expressed in response to nanoparticles. Interestingly, a third tested nanoparticle, n-Ag, has no significant effect on competence in our experimental conditions. Overall, these results show that nanoparticles, by altering bacterial physiology and especially competence, may have profound influences in unsuspected areas, such as the dissemination of antibiotic resistance in bacteria."],"pubmed_title":["Impact of nanoparticles on the Bacillus subtilis (3610) competence."],"pubmed_authors":["Eymard-Vernain Elise E, Luche Sylvie S, Rabilloud Thierry T, Lelong Cécile C"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"pubmed_title_synonyms":["Bacillus subtilis var. natto, Bacillus natto, Nanoparticle, Materials, Material, Nanocrystalline Materials, Vibrio subtilis, Bacillus mesentericus, Bacillus subtilis subsp. natto, Nanocrystalline, Bacillus subtilis8, Bacillus uniflagellatus., Nanocrystals, Natto Bacteria, Bacillus globigii, E430016J11Rik, Bacillus subtilis/Bacillus globigii, Ximpact, RWDD5, Bacillus subtilis (natto), impact-a, Nanocrystalline Material, Nanocrystal"],"name_synonyms":["Koerper., organism, whole body, multi-cellular organism, whole organism, animal, body"],"pubmed_abstract_synonyms":["DNA Oxidative, deceased, nebb, Materials, Resistances, CG10718, antimicrobials, Compounds, Wound, postnatal development, Physical, aneurysmal cyst of bone, antimicrobial agents, Nitrative Stress, growth and development, Progress Reports, Cardiac Death, End-Of-Life, injury, Damage, Nanocrystal, Long Term, Productivity, trauma, Drug Antimicrobial Resistance, SUB, Drug Resistances, dmTAF[[II]]230, Prokaryota., microbicides, Oxidative DNA, Roles, Oxidative, DmelCG12298, Anti Mycobacterial Agent, Summary Report, Bacillus subtilis subsp. natto, GRP1, Nitro-Oxidative Stress, sl(2)ry, Grp1, Concepts, SCRAMBLED, Nitro-Oxidative Stresses, Bacteriocide, Oxidative Injury, Effect, Summary Reports, DNA Damage, KIF20A, Research-Related, aneurysmal bone cyst (disease), antimicrobial, ABC, Antimycobacterial Agents, Oxidative Injuries, Eubacteria, TFIID TAF250, Interspecific, Progress Report, Bacillus mesentericus, cel, Aneurysmal, Antibiotika, PTPSTEP, Oxidative Cleavage, klp38B, Anti Bacterial Compound, End Of Life, ABC14, Oxidative DNA Damages, Community Health, Anti-oxidative, Anti-Bacterial Compounds, Bacteria Woese et al. 2024, Progress, Horizontal Gene Transfer, Oxidative Stress Injuries, Oxidative Stresses, Field Reports, Bacteria <bacteria>, Prokaryotae, l(2)k08110, Role Concepts, Drug Antimicrobial Resistances, Antimycobacterial Agent, MCOPCB7, Procaryotae, KLP 38B, Long-Term Effects, MTABC3, GPH, antibiotic, dTAF[[II]]230, anatomical protrusion, KIF14, Nanocrystalline Materials, Injury and Wounds, PRP, STRUBBELIG, Longterm Effect, TAF200, Physical Traumas, Antibacterial Agent, TAFII-250, TAF250/230, Microbial, tio, results, TAFII250, Role Concept, Investigative Report, aneurysmal bone cyst, Oxidative and Nitrosative Stress, 3.1.3.48, Role, prokaryotes, microbicide, Near-Death Experience, DNA Oxidative Damages, Physical Trauma, Biofilm, Anti Bacterial Agent, aneurysmal bone cysts, Bacteriocides, Anti-Mycobacterial Agent, Antimycobacterial, Gene Transfers, Recombination, growth pattern, Antibacterial, Determination of Death, Step, CG11628, aneurysmal cyst of the bone, non-developmental growth, Field, Striatum-enriched protein-tyrosine phosphatase, Oligopeptide, CG17603, TAF[[II]], Bacillus subtilis (natto), Antibacterial Agents, Nitro-Oxidative, Health, Report, Agents, Interspecies Recombination, Taf250, Antimicrobial Drug Resistance, Material, spine, STEP, SR3-5, Interspecific Recombination, Research-Related Injuries, Preventive Medicine & Public Health, Oxidative Stress Injury, Mot, Bacillus globigii, Research-Related Injury, Antimicrobial Resistance, Preventive Medicine and Public Health, DNA, E430016J11Rik, Prokaryota, TAF230, umat, Community, Oxidative Damage, AT1G11140, Research Related Injuries, Oxidative Stress, d230, 38B.12, GRP1/cytohesin 1, antibiotique, 38B.10, Effects, Antioxidative, Nanocrystalline, DmKlp38B, Drug Antimicrobial, number, genetic exchange, Antioxidative Stress, dTAFII250, Bone Cysts, eubacteria, Ximpact, EfW1, Injuries and Wounds, DUH3, DmelCG10718, Bacillus uniflagellatus, KLP-38B, CG12298, protrusion, Stresses, Agent, CG11633, Antimicrobial Drug Resistances, cytohesin/GRP1, Cardiac, Investigative, Oxidative Nitrative, Wounds, Antibiotic Resistance, Stress Injury, dmTAF1, Taf230, Klp38B, Oxidative Cleavages, Antibiotic, Bacteriocidal, Bacteriobiota, l(2)k00802, abacavir, Oxidative Damages, antibiotics, TAF250, KLP38B, Taf200, Injury, dTAF[[II]]250, Longterm, cell, mei-1794, Bacillus subtilis8, Anti Bacterial Compounds, l(2)SH2 0323, Taf1p, Long-Term, Monera, Anti-Mycobacterial, Bacteria (ex Cavalier-Smith 1987), dTAF250, Anti-Bacterial, Neural-specific protein-tyrosine phosphatase, Anti-Mycobacterial Agents, Anti oxidative Stress, Oxidative DNA Damage, Neb, Antioxidative Stresses, Vibrio subtilis, Traumas, Nanocrystals, Natto Bacteria, Long-Term Effect, Antibiotics, SRF9, fungi, Investigative Reports, TAF, LAN, Nanocrystalline Material, Antibiotikum, bacteria, Nanoparticle, TAF[[II]]250, Antimicrobial Resistances, l(3)84Ab, stepk, BG:DS00004.13, function, Anti-oxidative Stresses, Bacillus subtilis/Bacillus globigii, impact-a, Cell, Anti Mycobacterial Agents, Concept, dTAF230, STRUBBELIG-RECEPTOR FAMILY 9, development, Oxidative Nitrative Stress, l(2)03552, traumatic injury, Wounds and Injury, Public, Oxidative Nitrative Stresses, p230, Trauma, Long Term Effects, Research Reports, post-mortem, Resistance, TAF[[II]]250/230, TFIID, Bacteriocidal Agents, Environment, Death, l(2)SH0323, CYH1, Bacillus subtilis var. natto, Taf[[II]]250, Interspecies, death, Bacillus natto, Anti Bacterial Agents, l(2)k07614, Anti-oxidative Stress, TAF[[II]]230, DNA Oxidative Damage, not Bacteria Haeckel 1894, {(1S-cis)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol, Dub, postnatal growth, wound, Lateral Gene Transfer, TAF[II]250, Cleavage, Longterm Effects, DmelCG11628, Injuries, Bacteriocidal Agent, Drug, Anti-Bacterial Agent, Lateral Gene Transfers, Lateral, DmelCG17603, Klp38, Reports, Compound, prokaryote, Dm0332, cardinality, Stress, Anti-Bacterial Compound, sl(2)ry3, Summary, Nitro Oxidative Stress, Gene Transfer, T19D16.8, growth, SCM, RWDD5, Field Report, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"B.subtilis - Whole organism, iBAQ (Eymard-vernainetal,scirep2018)","description":"abundance based on iBAQ, Interaction consistency score: 7.0, Coverage: 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