RabLab March 2023

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Science (New York, N.Y.)

Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.

2023-03-09

PubMed:36893255; DOI:10.1126/science.abm3452

Kevin G Hicks¹, Ahmad A Cluntun¹, Heidi L Schubert¹, Sean R Hackett², Jordan A Berg¹, Paul G Leonard³, Mariana A Ajalla Aleixo⁴, Youjia Zhou⁵, Alex J Bott¹, Sonia R Salvatore⁶, Fei Chang⁶, Aubrie Blevins¹, Paige Barta¹, Samantha Tilley¹, Aaron Leifer¹, Andrea Guzman¹, Ajak Arok¹, Sarah Fogarty¹, Jacob M Winter¹, Hee-Chul Ahn⁷, Karen N Allen⁸, Samuel Block⁹, Iara A Cardoso⁴, Jianping Ding¹⁰, Ingrid Dreveny¹¹, William C Gasper¹², Quinn Ho¹², Atsushi Matsuura⁷, Michael J Palladino¹³, Sabin Prajapati¹⁴, Pengkai Sun¹⁰, Kai Tittmann¹⁴, Dean R Tolan¹², Judith Unterlass¹⁵, Andrew P VanDemark¹⁶, Matthew G Vander Heiden⁹, Bradley A Webb¹⁷, Cai-Hong Yun¹⁸, Pengkai Zhao¹⁸, Bei Wang⁵, Francisco J Schopfer⁶, Christopher P Hill¹, Maria Cristina Nonato⁴, Florian L Muller¹⁹, James E Cox¹, Jared Rutter¹

Affiliations

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
Calico Life Sciences LLC, South San Francisco, CA, USA
Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
School of Computing, University of Utah, Salt Lake City, UT, USA
Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
Department of Chemistry, Boston University, Boston, MA, USA
The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
Department of Biology, Boston University, Boston, MA, USA
Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
Department of Biochemistry, West Virginia University, Morgantown, WV, USA
Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA

MIDAS: Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase https://science.org/doi/10.1126/science.abm3452…

2023-05-15

Nice work from our friends in Utah highlighting new metabolite-enzyme interactions in metabolism. #metabolism

2023-05-15

Research on Visualizations for Metabolic Networks by the Kahlert School’s Dr. Youjia Zhou and Prof. @BeiWangPhillips published in prestigious Nature Cell Biology and Science https://cs.utah.edu/kahlert-school-research-on-visualizations-for-metabolic-networks-published-in-nature-cell-biology-and-science/… https://doi.org/10.1038/s41556-023-01117-9…

2023-05-31

IT WAS ALREADY TOO COMPLICATED
#Science

2023-05-14

cancer-and-disease

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Nutrients

Reduction of Plasma BCAAs following Roux-en-Y Gastric Bypass Surgery Is Primarily Mediated by FGF21.

2023-03-31

PubMed:37049555; DOI:10.3390/nu15071713

Harsh Shah¹, Alyssa Kramer¹, Caitlyn A Mullins¹, Marie Mattern¹, Ritchel B Gannaban¹, R Leigh Townsend², Shawn R Campagna³, Christopher D Morrison², Hans-Rudolf Berthoud², Andrew C Shin¹

Affiliations

Neurobiology of Nutrition Laboratory, Department of Nutritional Sciences, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA
Neurobiology of Nutrition & Metabolism Department, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA 70808, USA
Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA

Check out our most recent publication with @PBRCNews and @ttucohs
Reduction of Plasma BCAAs following Roux-en-Y Gastric Bypass Surgery Is Primarily Mediated by FGF21 https://mdpi.com/2225564 #mdpinutrients via @Nutrients_MDPI

2023-04-06

Frontiers in molecular biosciences

Using mass spectrometry imaging to visualize age-related subcellular disruption.

2023-03-08

PubMed:36968274; DOI:10.3389/fmolb.2023.906606

Kelly A Hogan¹, Julianna D Zeidler², Heather K Beasley³, Abrar I Alsaadi¹, Abdulkareem A Alshaheeb¹, Yi-Chin Chang⁴, Hua Tian⁵, Antentor O Hinton³, Melanie R McReynolds¹

Affiliations

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, United States
Department of Chemistry, Pennsylvania State University, University Park, PA, United States
Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States

My first publication as a member of the @mcreynolds_lab made possible by an absolute dream team of co-authors. Not to mention: what a powerful tool for interrogating the process of aging at the subcellular level!

2023-03-10

@AtHinton is excited to have collaborated with
@dr_ohsopretty & @mcreynolds_lab. Her staff is amazing, especially @Loose_Lab_Rat (congrats)! Congrats to @HKbeasley who helped with this great article @VUBasicSciences @VICB_Vanderbilt
@phdgprotein86

2023-03-15

Cancer prevention research (Philadelphia, Pa.)

Metabolomic, DNA Methylomic, and Transcriptomic Profiling of Suberoylanilide Hydroxamic Acid Effects on LPS-Exposed Lung Epithelial Cells.

2023-03-03

PubMed:36867722; DOI:10.1158/1940-6207.CAPR-22-0384

Pochung Jordan Chou¹, Md Shahid Sarwar¹, Lujing Wang¹, Renyi Wu¹, Shanyi Li¹, Rasika R Hudlikar¹, Yujue Wang², Xiaoyang Su², Ah-Ng Kong¹

Affiliations

Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey

From the June issue—
Metabolomic, DNA Methylomic, and Transcriptomic Profiling of Suberoylanilide Hydroxamic Acid Effects on LPS-Exposed Lung #EpithelialCells, by Chou et al.
https://bit.ly/45JsZy0
@RutgersU

2023-06-01

evolution

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Nature ecology & evolution

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees.

2023-03-20

PubMed:36941345; DOI:10.1038/s41559-023-02001-3

Beryl M Jones¹, Benjamin E R Rubin¹, Olga Dudchenko², Callum J Kingwell¹, Ian M Traniello¹, Z Yan Wang¹, Karen M Kapheim³, Eli S Wyman¹, Per A Adastra², Weijie Liu¹, Lance R Parsons⁴, S RaElle Jackson⁴, Katharine Goodwin⁴, Shawn M Davidson⁴, Matthew J McBride⁴, Andrew E Webb¹, Kennedy S Omufwoko¹, Nikki Van Dorp¹, Mauricio Fernández Otárola⁵, Melanie Pham², Arina D Omer², David Weisz², Joshua Schraiber⁶, Fernando Villanea⁶, William T Wcislo³, Robert J Paxton⁷, Brendan G Hunt⁸, Erez Lieberman Aiden², Sarah D Kocher⁹

Affiliations

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
Smithsonian Tropical Research Institute, Panama City, Republic of Panama
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
Biodiversity and Tropical Ecology Research Center (CIBET) and School of Biology, University of Costa Rica, San José, Costa Rica
Department of Biology, Temple University, Philadelphia, PA, USA
Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
Department of Entomology, University of Georgia, Athens, GA, USA
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.

Not only beautiful but also a great model system for evolutionary studies: https://nature.com/articles/s41559-023-02001-3…

2023-04-12

New paper out today from ⁦@KocherLab⁩ and many collaborators!

2023-03-20

microbes

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mBio

Listeria monocytogenes GlmR Is an Accessory Uridyltransferase Essential for Cytosolic Survival and Virulence.

2023-03-20

PubMed:36939339; DOI:10.1128/mbio.00073-23

Daniel A Pensinger¹, Kimberly V Gutierrez¹, Hans B Smith¹, William J B Vincent¹, David S Stevenson², Katherine A Black³, Krizia M Perez-Medina¹, Joseph P Dillard¹, Kyu Y Rhee³, Daniel Amador-Noguez⁴, TuAnh N Huynh⁴, John-Demian Sauer¹

Affiliations

Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
Weill Cornell Medical College, New York, New York, USA
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA

Listeria monocytogenes GlmR Is an Accessory Uridyltransferase Essential for Cytosolic Survival and Virulence:

https://pubmed.ncbi.nlm.nih.gov/36939339/
@mbiojournal #Listeria

2023-03-21

mSystems

Systematic Analysis of Metabolic Bottlenecks in the Methylerythritol 4-Phosphate (MEP) Pathway of Zymomonas mobilis.

2023-03-30

PubMed:36995223; DOI:10.1128/msystems.00092-23

Daven B Khana¹, Mehmet Tatli¹, Julio Rivera Vazquez¹, Sarathi M Weraduwage², Noah Stern¹, Alexander S Hebert¹, Edna Angelica Trujillo¹, David M Stevenson¹, Joshua J Coon¹, Thomas D Sharky², Daniel Amador-Noguez¹

Affiliations

DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA

Check out the latest publication from the @theDANlab about Z. mobilis! Congrats to MDTP students Daven Khana (1st author) and Julio Rivera Vazquez on the paper!

2023-04-03

mass-spec

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Briefings in bioinformatics

FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism.

2023-03-01

PubMed:36857618; DOI:10.1093/bib/bbad064

María I Alcoriza-Balaguer¹, Juan C García-Cañaveras¹, Marta Benet¹, Oscar Juan-Vidal¹, Agustín Lahoz¹

Affiliations

Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia 46026, Spain

I am excited to share the final version of our paper:
FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbad064/7066347#.Y_9tFsOjvg4.twitter…
@LahozLab @IISLaFe @Marta44Benet @ojuan2001

2023-03-01

human-health

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bioRxiv

Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy

2023-03-19

DOI:10.1101/2023.03.16.532852

C. A. Perez-Ramirez, H. Nakano, R. C. Law, N. Matulionis, J. Thompson, A. Pfeiffer, J. O. Park, A. Nakano, H. R. Christofk

Affiliations

University of California, Los Angeles

bioRxiv

Therapeutic targeting of ACLY in T-ALL in vivo

2023-03-28

DOI:10.1101/2023.03.27.534395

V. da Silva-Diz, A. Singh, O. Lancho, M. Aleksandrova, K. Mandleywala, P. R. Nunes, J. Khatun, O. Kim, H. Affronti, E. Chiles, X. Su, H. Khiabanian, K. Wellen, D. Herranz

Affiliations

Rutgers Cancer Institute of New Jersey

kedalionlabs.com

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