Archive for 2017

December 2017

Yekaterina wins 3rd Place in the poster competition at the Chemistry-Biology Interface Symposium, congrats!

Our collaboration with the Zaret lab (UPenn) taking a multi-omics approach to identify heterochromatin factors that impede activation of gene expression patterns necessary for cell fate specification is published in Molecular Cell.

Ben is named to the Advisory Committee in the Division of Biological Sciences for the National Science Foundation (NSF).

Ben gives a short research talk at the Eastern PA section of the Leukemia and Lymphoma Society.

November 2017

A multi-Penn lab collaborative effort linking TDP-43 to chromatin remodeling complexes important for induction of protective disease gene expression in amyotrophic lateral sclerosis and frontotemporal dementia is published in Current Biology.

Bernard Delanghe from Thermo (creator of the Proteome Discoverer software) visits the Garcia Lab and gives a workshop on the capabilities of the latest software version.

The Garcia Lab returns from the Department/BMB graduate group retreat in the Poconos Mountains. Joe, Simone, Kasia, Yekaterina, Dylan, Kevin, Abby, Laura, Zuo-Fei, Mariel C, Amber and Sam presented posters, and Kelly gave a great talk. Additionally, Mariel C won 2nd Place for her poster in the Biophysics category, congrats!

Congratulations to Qi, as her manuscript “Assessment of quantification precision of histone post-translational modifications by using an ion trap and down to 50,000 cells as starting material” is published in the Journal of Proteome Research.

Peder gives a talk at the Penn/CHOP Microbiome Program Symposium.

Amber’s manuscript “GiaPronto: a one-click graph visualization software for proteomics datasets” is accepted by Molecular and Cellular Proteomics, and is picked up by the Proteomics news blogspot, congrats! GiaPronto can be accessed here.

Visiting graduate student Mariana Lopes (Instituto Butantan, Brazil) joins the lab, welcome!

A collaboration with the Gorbunova lab (Univ. of Rochester) on the naked mole rat epigenome (implications for cancer resistance and longevity ) is published in Stem Cell Reports., while another collaborative study with the Sykes lab (Fox Chase Cancer Center) describing the role of the kinase PKCε in supporting cell survival and disease progression in acute myeloid leukemia is published in Clinical Cancer Research.

 

October 2017

The Garcia Lab has their first Halloween/Murder Mystery Party. It was a great time, as Yekaterina was murdered by Laura, who went on to blow up the entire planet. Simone won best costume, and Joe won best actor. Awards for best carved pumpkins went to Khadija/Audri/Amber for their angry pumpkin and Bhanu for her double helix DNA pumpkin.

Johayra’s studies on the connection between metabolism and histone acyl modifications is published in Nature Communications, congrats!

Ben and Mariel M return from the SACNAS Conference in Salt Lake City, UT, where Mariel presented a research poster, and Ben recruited future graduate students for BGS and the BMB Program.

Kelly’s research on histone ADP-ribosylation is published in Molecular BioSystems, congrats!

The Garcia Lab comes back from the Epigenetics Institute Retreat at Citizens Bank Park (home of the Philadelphia Phillies). Mariel C gave a talk, and Kasia, Simone, Peder and Laura presented posters.

The Garcia Lab welcomes new postdoc Geoff Dann to the group.

Collaborations with the Bonasio lab (UPenn) on methods to determine RNA-binding protein domains, with the Weitzman lab to identify proteomes on viral genomes, and with the Berger lab on the role of cytoplasmic chromatin in senescence are published in JoVEMolecular and Cellular Proteomics, and Nature, respectively.

 

September 2017

Collaborations with the Klein lab (UPenn), Eckenhoff lab (UPenn) and Lazar lab (UPenn) focusing on the GSK-3 phosphoproteome,  identification of drug-binding sites on the transient receptor potential ankyrin 1 ion channel,  and the HDAC3 interactome are published in JBC, the Biophysical Journal and Nature Communications, respectively.

The Garcia Lab comes back from a GRAAM (Garcia-Roeder-Allis-Armstrong-Muir) meeting at Rockefeller University where John presented his latest research.

Laura and Kevin present their research progress at the department Friday Research Discussion.

The Garcia Lab wishes Yanping well in her new position at Johnson & Johnson.

The Garcia Lab welcomes a new Research Specialist Joseph Cesare to the Quantitative Proteomics Resource Core.

PGG graduate student Khadija Wilson joins the group for the Fall rotation, welcome!

August 2017

Yekaterina’s research on global non-histone acetylation dynamics is published in Scientific Reports! Collaboration with the Bonasio lab (UPenn) on role of the peptide corazonin on Ant caste identity is published in  Cell, and another study in collaboration with the Kang lab (Princeton) describing Nidogen 1 as an inducer cancer metastasis is published in Genes & Development.

Very sad to hear about the recent tragic events in Charlottesville, VA, but a nice reminder on the impact this town has had on the proteomics field can be found here.

The Garcia Lab is excited to hear about the Cell and Molecular Biology graduate subprogram Genetics and Gene Regulation being renamed as the Genetics and Epigenetics Program!

July 2017

Collaborative work with the Zaret lab (UPenn) to identify biomarkers of pancreatic ductal adenocarcinoma is published in Science Translational Medicine. Also check out the CBS News piece on the research work here. Also, a collaboration with Ramalho-Santos lab (UCSF) on vitamin C induction of demethylation of histone H3  in ES cells is published in Epigenetics & Chromatin.

The Garcia Lab welcomes new graduate students Richard Lauman and Mariel Mendoza (joint with the Berger lab) to the group!

Simone’s work to make Middle Down MS for histone PTMs more quantitative by incorporating SILAC labeling is published in Epigenetics & Chromatin. Additionally, our collaborative work with the Moazed lab (Harvard Univ.) on heterochromatin formation is published in Nature.

June 2017

Congrats to our honorary lab member Jarrett Remsberg (Mitch Lazar’s lab) who defended his PhD thesis and will be off for a postdoc in Ben Cravatt’s lab at the Scripps Research Institute.

Our collaboration with the You lab (UPenn) on Brd4 phosphorylation in carcinoma is published in PNAS. Simone’s review on Middle Down MS for chromatin biology research is also published in Expert Reviews in Proteomics.

The Garcia Lab welcomes three high school students for summer research: Aaron Garcia, Ryan Liu and Ayushi Jain.

Research Specialist Sara Montanez and Postdoc Jen Liddle (joint with Matt Weitzman/CHOP) join the Garcia Lab, welcome!

The Garcia Lab comes back from a fun and successful American Society for Mass Spectrometry  Conference. We had 13 posters and Peder, Laura, Kelly, Kevin and Simone gave great talks. Ben helped co-organize a workshop and then won the Indy 500, and Dylan was fired and then re-hired. All in all, it was a great time!

The Garcia Lab welcomes incoming BMB graduate students Mary Szurgot and Hee Jong Kim for summer rotations.

An article highlighting Penn’s Presidential Professors is published online.

May 2017

Kevin presents a poster on his RNA MS work at the RNA Biology & Cancer Symposium here at Penn.

Simone returns from representing the lab in collaborator meetings at the Broad Institute and at the Instituto Butantan in São Paulo, Brazil.

Ben participates in a virtual meeting to kickoff the International Partnership between Helmholtz Zentrum München (HMGU) in Munich and the Penn Epigenetics Institute.

The Garcia Lab says goodbye to Qi, who will take a year off before coming back to begin graduate school at Penn. Good luck and see you again soon!

Kevin has received a travel award from the Delaware Valley Mass Spectrometry Discussion Group to attend the American Society for Mass Spectrometry Conference next month, congrats!

Our collaborative work with the Wysocka lab (Stanford University) on MLL3/MLL4 H3K4me1 independent function is published in Molecular Cell, while a collaboration with the Martinez lab (UT Southwestern) on JumonjiC inhibitors as therapeutic treatments for non-small cell lung cancer is published in Cell Reports. Another collaboration with the Morrisey Lab (UPenn) examining how lncRNA transcription factor interactions regulate tissue development is published in Genes and Development.

April 2017

Visiting graduate student Minghui Chen (Shanghai Jiao Tong University) joins the lab, welcome!

Laura has passed her 2nd year prelim exam, congrats!

Edwin has defended his PhD thesis in Pharmacology. Congratulations Dr. Yoo!

Mariel’s review article on investigating proteolytic cleavage by mass spectrometry is published in Expert Review of Proteomics, nice work!

The Garcia Lab welcomes first-year BMB graduate student Richard Lauman to the group for a Spring rotation.

The Garcia Lab is awarded a PennCHOP Microbiome Program pilot grant to fund studies into the crosstalk between the gut microbiome and host epigenetic mechanisms. Big props to Peder, who did all the heavy lifting on the proposal. Congrats!

Yekaterina Kori has officially joined the lab for her graduate thesis work, welcome aboard!

The Garcia Lab welcomes our new Technical Director Hyoungjoo Lee and new postdoctoral researcher Josue Baeza (who has been awarded a Penn  Academic Diversity Postdoctoral Fellowship) to the group.

Congratulations to Qi, who has accepted the offer to join the Biochemistry and Molecular Biophysics graduate program here at Penn for her PhD studies!

Collaborations with the Birkholtz lab to map the histone PTMs changes during the malaria parasite life cycle is published in Scientific Reports., while other collaborations to characterize epigenome alterations in melanoma, and to identify RNA-protein interactions critical for root hair cell development in Arabidopsis thaliana are published in Cell Reports and Developmental Cell, respectively.

March 2017

Shu’s research publication “Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells” was selected as a “Highlight of 2016″ for the Journal of Biological Chemistry!

The Garcia Lab attends the Epigenetics Institute party to celebrate the elevation of the program to Institute status at Penn. Congrats!

The Garcia Lab returns from the 13th annual US HUPO Conference. Dylan, Mariel, Amber, Simone, Yekaterina, Kasia, Peder and Kevin all gave lightning talks, Ranran gave a short talk, and Ben also gave a talk and led an evening workshop. We also had 10 poster presentations as well. Dylan and Yekaterina were awarded student travel awards to attend the conference, and Mariel won first place in the poster competition!

The Garcia Lab welcomes Abigail Lemmon our new undergraduate researcher to the group.

Our collaborative project with the Kutateladze lab (University of Colorado School of Medicine) on understanding recognition of histone crotonyl modifications by the monocytic leukemia zinc-finger protein-related factor (MORF) is published in Structure. Another collaboration with the Eckenhoff lab (Penn) on investigating the mechanisms of  inhaled general anesthetics is published in ACS Chemical Biology.

Ben returns from representing the US HUPO organization at FASEB’s Capitol Hill Day, where he spoke to congress about the importance of continued funding of scientific research.

Garcia Lab has 19 presentations (13 poster and 6 oral) accepted for the American Society for Mass Spectrometry (ASMS) conference in Indianapolis in June.