You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: ["HealthCareActivity", "InjuryOrPoisoning", "BodySubstance", "IntellectualProduct", "AnatomicalStructure", "SpatialConcept", "Chemical", "Bacterium", "MedicalDevice", "Organization", "BiomedicalOccupationOrDiscipline", "Finding", "BiologicFunction", "Virus", "ResearchActivity", "ClinicalAttribute", "PopulationGroup", "Eukaryote", "BodySystem", "Food", "ProfessionalOrOccupationalGroup"].

Please return the output as a JSON object of the format: {"Virus": ["HIV", ...], "Bacterium": ["MRSA", ...], "AnatomicalStructure": ["Lung", ...], "BodySystem": ["CNS", ...], "BodySubstance": ["Serum", ...], "Finding": ["Headache", ...], "InjuryOrPoisoning": ["Fracture", ...], "BiologicFunction": ["Death", ...], "HealthCareActivity": ["Biopsy", ...], "ResearchActivity": ["Clinical trial", ...], "MedicalDevice": ["Lenses", ...], "SpatialConcept": ["Camps", ...], "BiomedicalOccupationOrDiscipline": ["Forensic medicine", ...], "Organization": ["WHO", ...], "ProfessionalOrOccupationalGroup": ["Provider", ...], "PopulationGroup": ["Swimmers", ...], "Chemical": ["Gold", ...], "Food": ["Rice", ...], "IntellectualProduct": ["RPAM", ...], "ClinicalAttribute": ["Biomarker", ...], "Eukaryote": ["Dogs", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].

Only output the JSON object and do not include any additional text.

Abstract:

The genome -scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp -like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a β-alanine aminotransferase gene, which is involved in β-alanine degradation. In contrast to classical Lrp -like transcription factors, BarR is not responsive to any of the α-amino acids but interacts specifically with β-alanine. Besides the juxtaposed β-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although β-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome -wide perspective. We characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp -like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the β-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators. BarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized β-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between β-alanine and α-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp -like regulators.
{"AnatomicalStructure": ["genomic sites", "glutamine synthase operon", "glutamine synthase genes", "\u03b2-alanine aminotransferase gene", "genomic", "genome", "\u03b2-alanine aminotransferase", "operon", "regulon"], "Bacterium": [], "BiologicFunction": ["Regulation", "DNA-binding", "expression", "\u03b2-alanine", "binding", "\u03b2-alanine degradation", "binding regions", "\u03b1-amino acid metabolism"], "BiomedicalOccupationOrDiscipline": [], "BodySubstance": [], "BodySystem": [], "Chemical": ["operator structure", "Lrp", "glutamine synthase", "regulatory transcription factors", "family", "\u03b1-amino acids", "multiple (major and auxiliary) operators", "\u03b2-alanine", "coenzyme A", "intergenic regions", "Leucine-responsive Regulatory Protein", "\u03b2-alanine aminotransferase promoter region", "transcription factors", "precursor", "BarR protein", "metabolite", "promoter", "transcription factor", "BarR", "semi-palindromic"], "ClinicalAttribute": [], "Eukaryote": [], "Finding": ["ChIP-seq profile", "not responsive"], "Food": [], "HealthCareActivity": ["electrophoretic mobility shift assays", "profile", "qRT-PCR analysis", "genome-wide binding profile", "chromatin immunoprecipation"], "InjuryOrPoisoning": [], "IntellectualProduct": [], "MedicalDevice": [], "Organization": [], "PopulationGroup": [], "ProfessionalOrOccupationalGroup": [], "ResearchActivity": ["ChIP-seq", "study", "high-throughput sequencing"], "SpatialConcept": ["loci", "local", "conserved", "binding motif"], "Virus": []}