Portosystemic shunt placement reveals blood signatures for the development of hepatic encephalopathy through mass spectrometry.

Autor: Dantas Machado AC; Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA., Ramos SF; Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA.; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA., Gauglitz JM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Fassler AM; Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA., Petras D; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany., Aksenov AA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Department of Chemistry, University of Connecticut, Storrs, CT, USA., Kim UB; Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA., Lazarowicz M; Department of Radiology, Division of Interventional Radiology, College of Medicine, University of Florida, Gainesville, FL, USA., Barnard Giustini A; Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA.; Division of Gastroenterology, Department of Medicine, Veterans Affairs Puget Sounds Health Care System, Seattle, WA, USA.; Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, WA, USA., Aryafar H; San Diego Imaging, San Diego, CA, USA.; Departments of Radiology, University of California San Diego Medical Center, La Jolla, CA, USA., Vodkin I; Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA., Warren C; Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA., Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA., Zarrinpar A; Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA. ali.zarrinpar@surgery.ufl.edu.; Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA. ali.zarrinpar@surgery.ufl.edu.; J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA. ali.zarrinpar@surgery.ufl.edu., Zarrinpar A; Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA. azarrinpar@ucsd.edu.; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. azarrinpar@ucsd.edu.; Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA. azarrinpar@ucsd.edu.; Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA. azarrinpar@ucsd.edu.

Publikováno v: Nature communications [Nat Commun] 2023 Aug 31; Vol. 14 (1), pp. 5303. Date of Electronic Publication: 2023 Aug 31.

Pre- and Post-Portosystemic Shunt Placement Metabolomics Reveal Molecular Signatures for the Development of Hepatic Encephalopathy.

Autor: Dantas Machado AC, Ramos SF, Gauglitz JM, Carpenter AM, Petras D, Aksenov AA, Kim UB, Lazarowicz M, Giustini AB, Aryafar H, Vodkin I, Warren C, Dorrestein PC, Zarrinpar A, Zarrinpar A

Publikováno v: MedRxiv : the preprint server for health sciences [medRxiv] 2023 Jan 04. Date of Electronic Publication: 2023 Jan 04.

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome.

Autor: Dantas Machado AC; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Brown SD; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Lingaraju A; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Sivaganesh V; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Martino C; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Chaix A; Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA., Zhao P; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA., Pinto AFM; Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA., Chang MW; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Richter RA; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Saghatelian A; Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA., Saltiel AR; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA., Knight R; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Panda S; Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, USA., Zarrinpar A; Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; VA Health Sciences, San Diego, La Jolla, CA, USA. Electronic address: azarrinpar@ucsd.edu.

Publikováno v: Cell reports [Cell Rep] 2022 Jul 05; Vol. 40 (1), pp. 111008.

The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.

Autor: Lara-Gonzalez S; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States., Dantas Machado AC; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States., Rao S; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States., Napoli AA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States., Birktoft J; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States., Di Felice R; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.; Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.; CNR-NANO Modena, Via Campi 213/A, 41125 Modena, Italy., Rohs R; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States.; Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States.; Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.; Department of Computer Science, University of Southern California, Los Angeles, California 90089, United States., Lawson CL; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States.

Publikováno v: Biochemistry [Biochemistry] 2020 Dec 08; Vol. 59 (48), pp. 4523-4532. Date of Electronic Publication: 2020 Nov 18.

Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.

Autor: Dantas Machado AC; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Cooper BH; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Lei X; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA., Di Felice R; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA., Chen L; Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA., Rohs R; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA.; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.; Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2020 Sep 04; Vol. 48 (15), pp. 8529-8544.