Search Results - "Williamson, James R."

Overflow metabolism in Escherichia coli results from efficient proteome allocation by Basan, Markus, Hui, Sheng, Okano, Hiroyuki, Zhang, Zhongge, Shen, Yang, Williamson, James R., Hwa, Terence

“…Overflow metabolism refers to the seemingly wasteful strategy in which cells use fermentation instead of the more efficient respiration to generate energy,…”
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Structure and dynamics of bacterial ribosome biogenesis by Davis, Joseph H., Williamson, James R.

“…Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical,…”
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A global resource allocation strategy governs growth transition kinetics of Escherichia coli by Erickson, David W., Schink, Severin J., Patsalo, Vadim, Williamson, James R., Gerland, Ulrich, Hwa, Terence

“…A new approach to modelling bacterial growth removes the need to know kinetic parameters for metabolic and regulatory processes and can be used to model…”
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Modular Assembly of the Bacterial Large Ribosomal Subunit by Davis, Joseph H., Tan, Yong Zi, Carragher, Bridget, Potter, Clinton S., Lyumkis, Dmitry, Williamson, James R.

“…The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of…”
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A universal trade-off between growth and lag in fluctuating environments by Basan, Markus, Honda, Tomoya, Christodoulou, Dimitris, Hörl, Manuel, Chang, Yu-Fang, Leoncini, Emanuele, Mukherjee, Avik, Okano, Hiroyuki, Taylor, Brian R., Silverman, Josh M., Sanchez, Carlos, Williamson, James R., Paulsson, Johan, Hwa, Terence, Sauer, Uwe

“…The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial resources, affecting, for example, the expression levels of…”
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Quantitative Analysis of rRNA Modifications Using Stable Isotope Labeling and Mass Spectrometry by Popova, Anna M, Williamson, James R

“…Post-transcriptional RNA modifications that are introduced during the multistep ribosome biogenesis process are essential for protein synthesis. The current…”
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Assembly of Bacterial Ribosomes by Shajani, Zahra, Sykes, Michael T, Williamson, James R

“…The assembly of ribosomes from a discrete set of components is a key aspect of the highly coordinated process of ribosome biogenesis. In this review, we…”
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Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria by Hui, Sheng, Silverman, Josh M, Chen, Stephen S, Erickson, David W, Basan, Markus, Wang, Jilong, Hwa, Terence, Williamson, James R

“…A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to…”
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Characterization of the Ribosome Biogenesis Landscape in E. coli Using Quantitative Mass Spectrometry by Chen, Stephen S., Williamson, James R.

“…The ribosome is an essential and highly complex biological system in all living cells. A large body of literature on the assembly of the ribosome in vitro is…”
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Proteome partitioning constraints in long-term laboratory evolution by Mori, Matteo, Patsalo, Vadim, Euler, Christian, Williamson, James R., Scott, Matthew

“…Adaptive laboratory evolution experiments provide a controlled context in which the dynamics of selection and adaptation can be followed in real-time at the…”
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Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates by Rabuck-Gibbons, Jessica N., Lyumkis, Dmitry, Williamson, James R.

“…Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability…”
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Detecting Parkinson's Disease from Wrist-Worn Accelerometry in the U.K. Biobank by Williamson, James R, Telfer, Brian, Mullany, Riley, Friedl, Karl E

“…Parkinson's disease (PD) is a chronic movement disorder that produces a variety of characteristic movement abnormalities. The ubiquity of wrist-worn…”
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Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways by Dong, Xiyu, Doerfel, Lili K, Sheng, Kai, Rabuck-Gibbons, Jessica N, Popova, Anna M, Lyumkis, Dmitry, Williamson, James R

“…Abstract Understanding the assembly principles of biological macromolecular complexes remains a significant challenge, due to the complexity of the systems and…”
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Assembly landscape for the bacterial large ribosomal subunit by Sheng, Kai, Li, Ning, Rabuck-Gibbons, Jessica N., Dong, Xiyu, Lyumkis, Dmitry, Williamson, James R.

“…Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge…”
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Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly by Popova, Anna M, Jain, Nikhil, Dong, Xiyu, Abdollah-Nia, Farshad, Britton, Robert A, Williamson, James R

“…Abstract Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across…”
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Assembly of the bacterial ribosome with circularly permuted rRNA by Dong, Xiyu, Sheng, Kai, Gebert, Luca F R, Aiyer, Sriram, MacRae, Ian J, Lyumkis, Dmitry, Williamson, James R

“…Abstract Co-transcriptional assembly is an integral feature of the formation of RNA–protein complexes that mediate translation. For ribosome synthesis, prior…”
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Seizure prediction using EEG spatiotemporal correlation structure by Williamson, James R, Bliss, Daniel W, Browne, David W, Narayanan, Jaishree T

“…Abstract A seizure prediction algorithm is proposed that combines novel multivariate EEG features with patient-specific machine learning. The algorithm…”
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ArcA overexpression induces fermentation and results in enhanced growth rates of E. coli by Basan, Markus, Hui, Sheng, Williamson, James R.

“…Overflow metabolism in the presence of oxygen occurs at fast growth rates in a wide range of organisms including bacteria, yeast and cancer cells and plays an…”
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Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry by D’Ascenzo, Luigi, Popova, Anna M., Abernathy, Scott, Sheng, Kai, Limbach, Patrick A., Williamson, James R.

“…Mass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer…”
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Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth by Dai, Xiongfeng, Zhu, Manlu, Warren, Mya, Balakrishnan, Rohan, Patsalo, Vadim, Okano, Hiroyuki, Williamson, James R., Fredrick, Kurt, Wang, Yi-Ping, Hwa, Terence

“…Bacteria growing under different conditions experience a broad range of demand on the rate of protein synthesis, which profoundly affects cellular resource…”
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