Article
Biochemical Research Methods
Muir Morrison, Manuel Razo-Mejia, Rob Phillips
Summary: This study explores the correspondence between theoretical frameworks of transcriptional regulation in the context of the simple repression motif, finding that different models cannot be distinguished at the level of mean gene expression but can be differentiated by studying higher moments of the gene expression distribution, supporting a minimal kinetic model. The research highlights the challenges in distinguishing between various models of transcriptional regulation and suggests a two-state model with a distribution of burst sizes as the most effective for describing the simple-repression motif.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kedar Karkare, Huei-Yi Lai, Ricardo B. R. Azevedo, Tim F. Cooper
Summary: In 8 out of 24 populations of Escherichia coil evolved for 8,000 generations in lactose-containing environments, no detectable repressor mutations were found. Despite the potential benefit, repressor mutations were shown to become neutral or deleterious in populations where they were not detected. Populations not fixing repressor mutations reached the same fitness as those fixing them, suggesting an alternative evolutionary path led to equivalent benefit.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert
Summary: Vivarium is a software tool for building integrative multiscale models, providing an interface that allows computational biologists to easily define mechanistic models and combine them as an integrated multiscale model. It streamlines the integrative modeling effort by making individual models into modules that can be wired together and run with Vivarium's discrete-event simulation engine. This tool has been demonstrated to successfully build composite models that combine various modeling frameworks, and it has the potential to support future efforts in integrating more types of models at different biological scales.
Article
Biophysics
Daniel Schultz, Mirjana Stevanovic, Lev S. Tsimring
Summary: Cellular responses to toxic compounds require prompt expression of appropriate enzymes regulated by transcription factors. Different regulatory strategies are optimized based on selective pressures, with costs associated with drug, enzyme, and repressor concentrations influencing gene regulation.
BIOPHYSICAL JOURNAL
(2022)
Article
Mathematics
Tatiana N. N. Lakhova, Fedor V. V. Kazantsev, Aleksey M. M. Mukhin, Nikolay A. A. Kolchanov, Yury G. G. Matushkin, Sergey A. A. Lashin
Summary: This study aims to automatically reconstruct genome models for different bacteria by considering all possible interactions of transcription factors and their binding sites in an operon's promoter region. The obtained models are of great significance for researchers studying the regulatory effects of transcription factors on bacterial gene expression.
Article
Cell Biology
Douglas L. Rothman, Peter B. Moore, Robert G. Shulman
Summary: Since the discovery of the lac operon & SIM by Jacob and Monod in 1960, genetic explanations have dominated the understanding of metabolic adaptations. However, the roles of metabolism in adaptation have been largely overlooked. This article argues that metabolic adaptations, including changes in gene expression, depend heavily on the metabolic state of the organism prior to environmental changes, and the flexibility of that state. Using examples of E. coli adaptation to lactose growth and the Crabtree effect in yeast, the authors reevaluate these adaptations based on metabolic control analysis and emphasize the importance of understanding the metabolic properties of organisms prior to environmental changes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
Summary: The study analyzed the expression dynamics of thousands of genes with inducible promoters, revealing the impact of RNA polymerase and LacI repressor binding site strengths on gene expression. By fitting a statistical mechanics model, properties of theoretically optimal inducible promoters were accurately modeled. Through the examination of three alternative promoter architectures, the study showed how repositioning binding sites within promoters influences the combinatorial effects observed between promoter elements.
NATURE COMMUNICATIONS
(2021)
Article
Biophysics
Prasanna M. Bhogale, Robin A. Sorg, Jan-Willem Veening, Johannes Berg
Summary: The lactose uptake pathway of E. coli serves as a paradigmatic example of multistability, with transitions between induced and uninduced states driven by fluctuations. The induced state is found to be highly stable, and methods for systematically reducing circuit complexity while retaining rate-limiting fluctuations have been developed.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Anjali Doshi, Marian Shaw, Ruxandra Tonea, Soonhee Moon, Rosalia Minyety, Anish Doshi, Andrew Laine, Jia Guo, Tal Danino
Summary: Bacteria naturally self-organize into durable macroscale patterns on solid surfaces via swarming motility. Researchers engineered Proteus mirabilis to modify pattern features and developed quantitative approaches to decoding, demonstrating the ability to record dynamic environmental changes. This work expands the framework for engineering emergent microbial behaviors.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Microbiology
Yu Xia, Zhi-Yuan Wei, Rui He, Jia-Huan Li, Zhi-Xin Wang, Jun-Da Huo, Jian-Huan Chen
Summary: The study identified a new beta-galactosidase in Erwinia sp. E602 and conducted de novo genome assembly using a combination of Illumina and PacBio sequencing technology. The genome of E602 revealed a large plasmid with genes related to lactose metabolism and regulation, including a novel lac operon lacking the lacA gene. Phylogenetic analysis indicated positive selection in lacY and lacZ genes, suggesting adaptation of lactose metabolism in Erwinia sp. E602. The hybrid de novo genome assembly and metabolic pathway analysis provided a useful strategy for understanding the evolution of undiscovered microbial species or strains.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Mathematics, Applied
G. P. Neverova, E. Ya Frisman
Summary: This study investigates a simple model of stage-structured population with density-dependent birth rate. The model shows that increasing intraspecific competition results in subcritical period-doubling bifurcation, leading to periodic, quasiperiodic, and chaotic oscillations. The evolutionary development of the population can occur in three ways depending on the genetic composition, resulting in monomorphic populations, polymorphism, or 2-cycle of genotype's frequencies.
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2021)
Article
Mathematics, Applied
Yeyin Xu, Ying Wu
Summary: In this paper, analytical predictions of the firing cascades in a Hindmarsh-Rose neuron system are completed via an implicit mapping method. The obtained results provide new perspectives to the complex firing dynamics of the HR neuron system and present a potential strategy to regulate the firings of neurons.
Article
Biotechnology & Applied Microbiology
Alexander Gill, Tanis McMahon, Forest Dussault, Karen Jinneman, Rebecca Lindsey, Haley Martin, Devon Stoneburg, Nancy Strockbine, June Wetherington, Peter Feng
Summary: Two outbreaks of Shiga toxin-producing Escherichia coli O121:H19 associated with wheat flour in the USA and Canada involved strains with delayed lactose utilization (DLU), attributed to the insertion sequence IS600. This insertion might reduce the expression of fi-galactoside permease, resulting in the DLU phenotype. Considering the high probability of DLU is important when using lactose-containing media for the isolation of STEC O121.
Article
Microbiology
Sara Del Duca, Christopher Riccardi, Alberto Vassallo, Giulia Fontana, Lara Mitia Castronovo, Sofia Chioccioli, Renato Fani
Summary: This study analyzed the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer of histidine biosynthesis genes in a group of phylogenetically close bacteria with different surviving strategies. The analysis revealed different scenarios with genes organized in various ways, suggesting that various forces have played a role in shaping the gene structure in this bacterial superphylum.
Article
Biochemistry & Molecular Biology
Richard Charczenko, Madeline McMahon, Kimberly Kandl, Robert Rutherford
Summary: LacOp is a free web-based simulation designed to enhance learning of prokaryotic gene regulation and pathways for high school and undergraduate students. Through LacOp, students can experiment with different genotypes to understand their effects on E. coli lactose metabolism and regulation. Students who used LacOp showed measurable gains in conceptual understanding of the lac operon and had a positive opinion of the simulation as an instructional tool.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2022)
Article
Microbiology
Atul Narang, Stefan Oehler
JOURNAL OF BACTERIOLOGY
(2017)
Article
Biophysics
Eric R. May, Dmitry I. Kopelevich, Atul Narang
BIOPHYSICAL JOURNAL
(2008)
Article
Mathematical & Computational Biology
Carla J. Davidson, Atul Narang, Michael G. Surette
BMC SYSTEMS BIOLOGY
(2010)
Article
Biology
Jason T. Noel, Atul Narang
BULLETIN OF MATHEMATICAL BIOLOGY
(2009)
Review
Biology
Atul Narang
JOURNAL OF BIOSCIENCES
(2009)
Article
Cell Biology
Ved P. Sharma, Vera DesMarais, Colin Sumners, Gerry Shaw, Atul Narang
JOURNAL OF LEUKOCYTE BIOLOGY
(2008)
Article
Biology
Jason T. Noel, Sergei S. Pilyugin, Atul Narang
JOURNAL OF THEORETICAL BIOLOGY
(2009)
Article
Microbiology
Shraddha Maitra, Atul Narang
Article
Multidisciplinary Sciences
Krishna Choudhary, Stefan Oehler, Atul Narang
Article
Biotechnology & Applied Microbiology
Shraddha Maitra, Atul Narang
BIOTECHNOLOGY FOR BIOFUELS
(2019)
Article
Biophysics
Krishna Choudhary, Atul Narang
BIOPHYSICAL JOURNAL
(2019)
Article
Biology
Atul Narang
JOURNAL OF THEORETICAL BIOLOGY
(2007)
Article
Physics, Fluids & Plasmas
Eric R. May, Atul Narang, Dmitry I. Kopelevich
Letter
Microbiology
Atul Narang
NATURE REVIEWS MICROBIOLOGY
(2009)