Full Text Journal Articles by
Author Brian D Dill

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Publisher Correction: A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, 16(10):1149]

Cited: 0 times

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A mass spectrometry-based proteome map of drug action in lung cancer cell lines.

Benjamin Ruprecht, Julie Di Bernardo, Zhao Wang, Xuan Mo, Oleg Ursu, Matthew Christopher, Rafael B Fernandez, Li Zheng, Brian D Dill, Huijun Wang, Yuting Xu, Andy Liaw, Jonathan D Mortison, Nirodhini Siriwardana, Brian Andresen, Meir Glick, James R Tata, Victoria Kutilek, Ivan Cornella-Taracido, An Chi,

Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein-drug associations substantially improved ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2020, 16(10):1111-1119]

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Dysregulation of a long noncoding RNA reduces leptin leading to a leptin-responsive form of obesity.

Olof S Dallner, Jill M Marinis, Yi-Hsueh Lu, Kivanc Birsoy, Emory Werner, Gulya Fayzikhodjaeva, Brian D Dill, Henrik Molina, Arden Moscati, Zoltán Kutalik, Pedro Marques-Vidal, Tuomas O Kilpeläinen, Niels Grarup, Allan Linneberg, Yinxin Zhang, Roger Vaughan, Ruth J F Loos, Mitchell A Lazar, Jeffrey M Friedman,

Quantitative changes in leptin concentration lead to alterations in food intake and body weight, but the regulatory mechanisms that control leptin gene expression are poorly understood. Here we report that fat-specific and quantitative leptin expression is controlled by redundant cis elements and trans factors interacting with the proximal promoter together ... Read more >>

Nat. Med. (Nature medicine)
[2019, 25(3):507-516]

Cited: 10 times

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Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription.

Steven Z Josefowicz, Miho Shimada, Anja Armache, Charles H Li, Rand M Miller, Shu Lin, Aerin Yang, Brian D Dill, Henrik Molina, Hee-Sung Park, Benjamin A Garcia, Jack Taunton, Robert G Roeder, C David Allis,

The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 ... Read more >>

Mol Cell (Molecular cell)
[2016, 64(2):347-361]

Cited: 16 times

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Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.

Hani Goodarzi, Hoang C B Nguyen, Steven Zhang, Brian D Dill, Henrik Molina, Sohail F Tavazoie,

Transfer RNAs (tRNAs) are primarily viewed as static contributors to gene expression. By developing a high-throughput tRNA profiling method, we find that specific tRNAs are upregulated in human breast cancer cells as they gain metastatic activity. Through loss-of-function, gain-of-function, and clinical-association studies, we implicate tRNAGluUUC and tRNAArgCCG as promoters of ... Read more >>

Cell (Cell)
[2016, 165(6):1416-1427]

Cited: 97 times

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Transcriptomic characterization of fibrolamellar hepatocellular carcinoma.

Elana P Simon, Catherine A Freije, Benjamin A Farber, Gadi Lalazar, David G Darcy, Joshua N Honeyman, Rachel Chiaroni-Clarke, Brian D Dill, Henrik Molina, Umesh K Bhanot, Michael P La Quaglia, Brad R Rosenberg, Sanford M Simon,

Fibrolamellar hepatocellular carcinoma (FLHCC) tumors all carry a deletion of ∼ 400 kb in chromosome 19, resulting in a fusion of the genes for the heat shock protein, DNAJ (Hsp40) homolog, subfamily B, member 1, DNAJB1, and the catalytic subunit of protein kinase A, PRKACA. The resulting chimeric transcript produces ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2015, 112(44):E5916-25]

Cited: 30 times

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Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in.

Morgan M Steffen, Stephen P Dearth, Brian D Dill, Zhou Li, Kristen M Larsen, Shawn R Campagna, Steven W Wilhelm,

ISME J (The ISME journal)
[2014, 8(10):2152-2152]

Cited: 0 times

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A crucial role for β2 integrins in podosome formation, dynamics and Toll-like-receptor-signaled disassembly in dendritic cells.

Christian Gawden-Bone, Michele A West, Vicky L Morrison, Alexander J Edgar, Sarah J McMillan, Brian D Dill, Matthias Trost, Alan Prescott, Susanna C Fagerholm, Colin Watts,

The dynamic properties of podosomes, their ability to degrade the underlying matrix and their modulation by Toll-like receptor (TLR) signaling in dendritic cells (DCs) suggests they have an important role in migration. Integrins are thought to participate in formation and dynamics of podosomes but the multiplicity of integrins in podosomes ... Read more >>

J. Cell. Sci. (Journal of cell science)
[2014, 127(Pt 19):4213-4224]

Cited: 11 times

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Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis.

Morgan M Steffen, Stephen P Dearth, Brian D Dill, Zhou Li, Kristen M Larsen, Shawn R Campagna, Steven W Wilhelm,

The cyanobacterium Microcystis aeruginosa is a globally distributed bloom-forming organism that degrades freshwater systems around the world. Factors that drive its dispersion, diversification and success remain, however, poorly understood. To develop insight into cellular-level responses to nutrient drivers of eutrophication, RNA sequencing was coupled to a comprehensive metabolomics survey of ... Read more >>

ISME J (The ISME journal)
[2014, 8(10):2080-2092]

Cited: 23 times

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Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.

Patrick K H Lee, Brian D Dill, Tiffany S Louie, Manesh Shah, Nathan C Verberkmoes, Gary L Andersen, Stephen H Zinder, Lisa Alvarez-Cohen,

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and ... Read more >>

Appl. Environ. Microbiol. (Applied and environmental microbiology)
[2012, 78(5):1424-1436]

Cited: 12 times

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Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.

Ritin Sharma, Brian D Dill, Karuna Chourey, Manesh Shah, Nathan C VerBerkmoes, Robert L Hettich,

The expanding use of surfactants for proteome sample preparations has prompted the need to systematically optimize the application and removal of these MS-deleterious agents prior to proteome measurements. Here we compare four detergent cleanup methods (trichloroacetic acid (TCA) precipitation, chloroform/methanol/water (CMW) extraction, a commercial detergent removal spin column method (DRS) ... Read more >>

J Proteome Res (Journal of proteome research)
[2012, 11(12):6008-6018]

Cited: 32 times

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Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.

Yongqin Jiao, Patrik D'haeseleer, Brian D Dill, Manesh Shah, Nathan C Verberkmoes, Robert L Hettich, Jillian F Banfield, Michael P Thelen,

In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbial physiology. ... Read more >>

Appl. Environ. Microbiol. (Applied and environmental microbiology)
[2011, 77(15):5230-5237]

Cited: 22 times

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Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community.

Ryan S Mueller, Brian D Dill, Chongle Pan, Christopher P Belnap, Brian C Thomas, Nathan C VerBerkmoes, Robert L Hettich, Jillian F Banfield,

Proteomes of acid mine drainage biofilms at different stages of ecological succession were examined to understand microbial responses to changing community membership. We evaluated the degree of reproducibility of the community proteomes between samples of the same growth stage and found stable and predictable protein abundance patterns across time and ... Read more >>

Environ. Microbiol. (Environmental microbiology)
[2011, 13(8):2279-2292]

Cited: 28 times

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The multifaceted role of oestrogen in enhancing Chlamydia trachomatis infection in polarized human endometrial epithelial cells.

Jennifer Vanover Hall, Maria Schell, Sophie Dessus-Babus, Cheryl G Moore, Judy D Whittimore, Melanie Sal, Brian D Dill, Priscilla B Wyrick,

The oestrogen receptor (ER) α-β+ HEC-1B and the ERα+β+ Ishikawa (IK) cell lines were investigated to dissect the effects of oestrogen exposure on several parameters of Chlamydia trachomatis infection. Antibody blockage of ERα or ERβ alone or simultaneously significantly decreased C. trachomatis infectivity (45-68%). Addition of the ERβ antagonist, tamoxifen, ... Read more >>

Cell. Microbiol. (Cellular microbiology)
[2011, 13(8):1183-1199]

Cited: 12 times

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Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.

Christopher J Gobler, Dianna L Berry, Sonya T Dyhrman, Steven W Wilhelm, Asaf Salamov, Alexei V Lobanov, Yan Zhang, Jackie L Collier, Louie L Wurch, Adam B Kustka, Brian D Dill, Manesh Shah, Nathan C VerBerkmoes, Alan Kuo, Astrid Terry, Jasmyn Pangilinan, Erika A Lindquist, Susan Lucas, Ian T Paulsen, Theresa K Hattenrath-Lehmann, Stephanie C Talmage, Elyse A Walker, Florian Koch, Amanda M Burson, Maria Alejandra Marcoval, Ying-Zhong Tang, Gary R Lecleir, Kathryn J Coyne, Gry M Berg, Erin M Bertrand, Mak A Saito, Vadim N Gladyshev, Igor V Grigoriev,

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2011, 108(11):4352-4357]

Cited: 88 times

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Identification of iron-responsive proteins expressed by Chlamydia trachomatis reticulate bodies during intracellular growth.

Brian D Dill, Sophie Dessus-Babus, Jane E Raulston,

The obligate intracellular bacterium Chlamydia trachomatis serovar E is the most prevalent cause of bacterial sexually transmitted disease. With an established requirement for iron, the developmental cycle arrests at the intracellular reticulate body stage during iron restriction, resulting in a phenomenon termed persistence. Persistence has implications in natural infections for ... Read more >>

Microbiology (Reading) (Microbiology (Reading, England))
[2009, 155(Pt 1):210-219]

Cited: 13 times

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Examination of an inducible expression system for limiting iron availability during Chlamydia trachomatis infection.

Brian D Dill, Jane E Raulston,

The obligate intracellular bacterium Chlamydia trachomatis requires iron in order to complete its developmental cycle. Addition of an iron-chelating drug, Desferal (deferoxamine mesylate), to infected cell culture causes Chlamydia to enter persistence. Here, we explore the ability of a stably-transfected cell line with inducible over-expression of the eukaryotic iron efflux ... Read more >>

Microbes Infect (Microbes and infection)
[2007, 9(8):947-953]

Cited: 9 times

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