Nick Buchler
fungi, cell cycle, circadian clocks, quantitative biology, evolution
Works (43)
Updated: April 3rd, 2024 18:35
2022 journal article
Diploid-dominant life cycles characterize the early evolution of Fungi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(36).
author keywords: life cycle evolution; phylogenomics; aquatic fungi; plesiomorphy
MeSH headings : Diploidy; Fungi / classification; Fungi / genetics; Genome, Fungal / genetics; Life Cycle Stages; Phylogeny
TL;DR:
It is shown, using the estimated heterozygosity of these genomes, that many fungal lineages have diploid-dominant life cycles (diplontic).
(via Semantic Scholar)
doi.org (publisher)
Sources: Web Of Science, ORCID
Added: December 19, 2022
2022 article
Gene expression noise accelerates the evolution of a biological oscillator
Lin, Y. T., & Buchler, N. E. (2022, March 23). (Vol. 3). Vol. 3.
TL;DR:
It is shown that noise counter-intuitively accelerates the evolution of a biological oscillator and, thus, can impart a benefit to living organisms and suggest that noise can help dynamical systems evolve or learn new behavior by revealing cryptic dynamic phenotypes outside the bifurcation point.
(via Semantic Scholar)
Source: ORCID
Added: March 30, 2022
2021 journal article
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
GENOME RESEARCH, 31(7), 1216-+.
Contributors: Y. Zhang *, T. Ho*, N. Buchler n & R. Gordan *
TL;DR:
It is shown that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns, and an approach is proposed for studying this competition in a quantitative and high-throughput manner.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: May 12, 2021
2020 journal article
MeSH headings : Animals; Biological Evolution; Cell Cycle; Fungi / classification; Fungi / cytology; Fungi / genetics; Fungi / physiology; Gene Expression Regulation, Fungal
TL;DR:
Medina and Buchler provide an introduction to chytrid fungi, an early diverging fungal lineage exhibiting characteristics found in both animals and fungi.
(via Semantic Scholar)
Source: ORCID
Added: May 25, 2020
2020 journal article
Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology
ELife.
Contributors: E. Medinal, K. Robinson*, K. Bellingham-Johnstun n, G. Laniri, C. Laplante n, L. Fritz-Laylin *, N. Buchler n
MeSH headings : Actins / metabolism; Biological Evolution; Cell Cycle; Cell Movement; Chytridiomycota / cytology; Chytridiomycota / genetics; Chytridiomycota / growth & development; Fungal Proteins / metabolism; Genome, Fungal; Microorganisms, Genetically-Modified; Mitosis; Morphogenesis; Spores, Fungal / physiology; Transformation, Genetic
TL;DR:
It is shown that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’, which makes Spizellomyces a genetically tractable model for comparative cell biology and understanding the evolution of fungi and early eukaryotes.
(via Semantic Scholar)
Source: ORCID
Added: May 12, 2020
2019 journal article
Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes
CELL REPORTS, 26(5), 1174-+.
Contributors: L. Chen*, Y. Lin *, D. Gallegos*, M. Hazlett*, M. Gomez-Schiavon *, M. Yang *, B. Kalmeta*, A. Zhou *
MeSH headings : Acetylation; Action Potentials; Alleles; Animals; Basic Helix-Loop-Helix Transcription Factors / genetics; Basic Helix-Loop-Helix Transcription Factors / metabolism; CRISPR-Associated Protein 9 / metabolism; CRISPR-Cas Systems; Cell Membrane / metabolism; Enhancer Elements, Genetic / genetics; Gene Expression Regulation; Histones / metabolism; Mice; Neurons / metabolism; Nuclear Proteins / metabolism; Promoter Regions, Genetic; Proto-Oncogene Proteins c-fos / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
Activity-inducible histone acetylation tunes the transcriptional dynamics of experience-regulated genes to affect selective changes in neuronal gene expression and cellular function.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: February 18, 2019
2019 journal article
Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise
PLOS COMPUTATIONAL BIOLOGY, 15(10).
Contributors: M. Gomez-Schiavon * & N. Buchler *
MeSH headings : Adaptation, Physiological / genetics; Animals; Biological Evolution; Computer Simulation; Environment; Epigenesis, Genetic / genetics; Epigenesis, Genetic / physiology; Epigenomics / methods; Gene Regulatory Networks / genetics; Genotype; Humans; Models, Genetic; Models, Theoretical; Mutation; Phenotype; Selection, Genetic / genetics
TL;DR:
This work uses computer simulations to evolve a mechanistic, biophysical model of a self-activating genetic circuit, which can both adapt genetically through mutation and exhibit epigenetic switching, and shows a trade-off between either minimizing the adaptation time or increasing the robustness of the phenotype to biochemical noise.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: December 30, 2019
2019 review
Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain
[Review of ]. CURRENT OPINION IN GENETICS & DEVELOPMENT, 58-59, 103–110.
Contributors: E. Medina *, E. Walsh n & N. Buchler n
MeSH headings : DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Evolution, Molecular; Fungi / genetics; Fungi / metabolism; Gene Transfer, Horizontal / physiology; Membrane Proteins / chemistry; Membrane Proteins / genetics; Membrane Proteins / metabolism; Nuclear Proteins / chemistry; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Phylogeny; Protein Conformation; Protein Domains / genetics; Repressor Proteins / chemistry; Repressor Proteins / genetics; Repressor Proteins / metabolism; Saccharomyces cerevisiae Proteins / chemistry; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Schizosaccharomyces pombe Proteins / chemistry; Schizosaccharomyces pombe Proteins / genetics; Schizosaccharomyces pombe Proteins / metabolism; Transcription Factors / chemistry; Transcription Factors / genetics; Transcription Factors / metabolism; Viral Regulatory and Accessory Proteins / genetics
TL;DR:
A family of fungal transcription factors derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: December 16, 2019
2019 journal article
Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts
The Journal of Chemical Physics.
Contributors: Y. Lin * & N. Buchler n
MeSH headings : Algorithms; Bayes Theorem; Gene Expression; Models, Genetic; Monte Carlo Method; Single-Cell Analysis
TL;DR:
It is shown that time-dependent mRNA distributions of discrete-state models of gene expression are dynamic Poisson mixtures, whose mixing kernels are characterized by a piecewise deterministic Markov process, and Bayesian evidence selects the true model and outperforms approximate metrics typically used for model selection.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: July 10, 2019
2019 journal article
Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression
MOLECULAR CELL, 76(6), 909-+.
Contributors: G. Gowans*, J. Bridgers*, J. Zhang*, R. Dronamraju*, A. Burnetti n, D. King*, A. Thiengmany*, S. Shinsky*
MeSH headings : Acyl Coenzyme A / metabolism; Energy Metabolism / genetics; Fatty Acids / metabolism; Gene Expression Regulation, Fungal; Histones / genetics; Histones / metabolism; Homeostasis; Lysine; Oxidation-Reduction; Protein Processing, Post-Translational; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Signal Transduction; Transcription Factor TFIID / genetics; Transcription Factor TFIID / metabolism; Transcription, Genetic
TL;DR:
These findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Web Of Science
Added: January 6, 2020
2018 journal article
Daily humidity oscillation regulates the circadian clock to influence plant physiology
NATURE COMMUNICATIONS, 9.
Contributors: M. Mwimba*, S. Karapetyan *, L. Liu *, J. Marques*, E. McGinnis *, N. Buchler n, X. Dong *
MeSH headings : Arabidopsis / microbiology; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Circadian Clocks / physiology; DNA-Binding Proteins / genetics; Gene Expression Regulation, Plant; Humidity; Mutation; Photoperiod; Plant Immunity; Plants, Genetically Modified; Repressor Proteins / genetics; Transcription Factors / genetics
TL;DR:
It is reported that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: October 29, 2018
2018 journal article
Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes
Journal of The Royal Society Interface, 15(138), 20170804.
Contributors: Y. Lin * & N. Buchler *
author keywords: mathematical model; gene expression; circadian rhythm; intrinsic noise; stochastic cycles
MeSH headings : Biological Clocks; Gene Expression Regulation; Gene Regulatory Networks; Markov Chains; Models, Genetic; Stochastic Processes
TL;DR:
A simple analytical framework, known as a piecewise deterministic Markov process (PDMP), is introduced that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime and is generalized to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2018 journal article
The evolution of a G1/S transcriptional network in yeasts
Current Genetics, 64(1), 81–86.
Contributors: A. Hendler*, E. Medina *, N. Buchler *, R. Bruin * & A. Aharoni *
author keywords: Cell cycle; Evolution; Gene expression; G1-to-S transition; MBF and SBF
MeSH headings : Biological Evolution; Evolution, Molecular; G1 Phase / genetics; Gene Expression Regulation, Fungal; Gene Regulatory Networks; S Phase / genetics; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic; Yeasts / physiology
TL;DR:
The co-evolution of G1/S transcriptional network is reviewed and the evolutionary dynamics and specificity of the MBF–MCB and SBF–SCB interactions in different fungal species are discussed.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2017 journal article
BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells
Genome Biology, 18(1).
Contributors: M. Gomez-Schiavon *, L. Chen *, A. West * & N. Buchler *
author keywords: Gene expression; Stochastic process; Chemical master equation; Likelihood methods; Monte Carlo sampling; Bayesian posterior probability
MeSH headings : Animals; Basic Helix-Loop-Helix Transcription Factors / genetics; Bayes Theorem; Cells, Cultured; Computational Biology / methods; Female; In Situ Hybridization, Fluorescence; Male; Mice; Models, Genetic; Neurons / metabolism; Probability; RNA / genetics; Software; Stochastic Processes; Transcription, Genetic
TL;DR:
A computational pipeline (BayFish) is developed to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction, using a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFish data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2017 journal article
Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family
Proceedings of the National Academy of Sciences, 114(19), 4942–4947.
Contributors: T. Liban*, E. Medina *, S. Tripathi *, S. Sengupta*, R. Henry*, N. Buchler *, S. Rubin *
author keywords: cell cycle; tumor suppressor protein; E2F; protein-protein interactions; evolution
MeSH headings : Crystallography, X-Ray; E2F Transcription Factors / chemistry; E2F Transcription Factors / genetics; E2F Transcription Factors / metabolism; Humans; Protein Domains; Retinoblastoma Protein / chemistry; Retinoblastoma Protein / genetics; Retinoblastoma Protein / metabolism; Retinoblastoma-Like Protein p107 / chemistry; Retinoblastoma-Like Protein p107 / genetics; Retinoblastoma-Like Protein p107 / metabolism
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2017 journal article
Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
PLOS Genetics, 13(5), e1006778.
Ed(s): M. Snyder
MeSH headings : Binding Sites; Evolution, Molecular; G1 Phase / genetics; Gene Duplication; Gene Regulatory Networks; Genetic Fitness; Protein Binding; S Phase / genetics; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
Experimentally exploring how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2017 journal article
Long-term growth data of Escherichia coli at a single-cell level
Scientific Data.
Source: ORCID
Added: February 11, 2019
2016 journal article
Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates.
Molecular Biology of the Cell, 27(1), 64–74,
MeSH headings : Biological Clocks / physiology; Cell Cycle / genetics; Cell Cycle / physiology; Cell Division / genetics; Cell Division / physiology; DNA Replication; Oxygen / metabolism; Oxygen Consumption / physiology; Partial Pressure; Saccharomycetales / cytology; Saccharomycetales / metabolism
TL;DR:
The interaction of two oscillators (cell division cycle and yeast metabolic cycle) with different frequencies is studied and Cell cycle Start is coupled with the initiation of high oxygen consumption and breakdown of storage carbohydrates across diverse strains and different growth rates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2016 journal article
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi
ELife, 5.
MeSH headings : Cell Cycle; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Evolution, Molecular; Fungi / cytology; Fungi / genetics; Fungi / physiology; Gene Transfer, Horizontal; Transcription Factors / genetics; Transcription Factors / metabolism
Source: ORCID
Added: February 11, 2019
2016 journal article
The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling
Genome Biology and Evolution, 8(1), 109–125,
Contributors: P. Schaap *, I. Barrantes *, P. Minx, N. Sasaki *, R. Anderson*, M. Beinard, K. Biggar*, N. Buehler
author keywords: Amoebozoa; tyrosine kinase receptor; two-component system; signaling; phytochrome
MeSH headings : Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Evolution, Molecular; Genetic Loci; Genome, Protozoan; Physarum polycephalum / genetics; Protozoan Proteins / genetics; Protozoan Proteins / metabolism; Receptor Protein-Tyrosine Kinases / genetics; Receptor Protein-Tyrosine Kinases / metabolism; Signal Transduction; Transcriptome
TL;DR:
The analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts, and argues against the later emergence of tyrosine kinase signaling in the opistHokont lineage.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2015 journal article
A noisy linear map underlies oscillations in cell size and gene expression in bacteria
Nature, 523(7560), 357–360.
Contributors: Y. Tanouchi, A. Pai*, H. Park*, S. Huang *, R. Stamatov*, * , L. You *
MeSH headings : Cell Division / genetics; Cell Size; Computer Simulation; Escherichia coli / classification; Escherichia coli / cytology; Escherichia coli / genetics; Escherichia coli / growth & development; Feedback, Physiological; Gene Expression Regulation, Bacterial; Homeostasis / genetics; Models, Biological; Single-Cell Analysis; Time Factors
TL;DR:
This work measures and analyses long-term, single-cell growth and division across different Escherichia coli strains and growth conditions and demonstrates that a subset of cells in a population exhibit transient oscillations in cell size with periods that stretch across several (more than ten) generations, revealing that a simple law governing cell-size control—a noisy linear map—explains the origins of these cell- size oscillations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2015 journal article
Different mechanisms confer gradual control and memory at nutrient- and stress-regulated genes in yeast
Molecular and Cellular Biology, 35(21), 3669–3683.
Contributors: A. Rienzo*, D. Poveda-Huertes*, S. Aydin *, * , A. Pascual-Ahuir * & M. Proft *
MeSH headings : Galactokinase / genetics; Galactokinase / metabolism; Galactose / metabolism; Gene Expression Regulation, Fungal; Genes, Regulator; Histones / genetics; Histones / metabolism; Mitogen-Activated Protein Kinases / metabolism; Oxidoreductases / genetics; Oxidoreductases / metabolism; RNA Polymerase II / metabolism; Saccharomyces cerevisiae / cytology; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Stress, Physiological; Trans-Activators / metabolism; Transcription Factors / metabolism
TL;DR:
Investigating the dose-dependent modulation of gene expression at high temporal resolution in response to nutrient and stress signals in yeast reveals important differences in the way dynamic signals create dose-sensitive gene expression outputs.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2015 journal article
Redox rhythm reinforces the circadian clock to gate immune response
Nature, 523(7561), 472–476.
Contributors: M. Zhou *, W. Wang *, S. Karapetyan *, M. Mwimba*, J. Marqués*, * , X. Dong *
MeSH headings : Arabidopsis / growth & development; Arabidopsis / immunology; Arabidopsis / metabolism; Arabidopsis / microbiology; Arabidopsis Proteins / biosynthesis; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Nucleus / metabolism; Circadian Clocks / drug effects; Circadian Clocks / genetics; Circadian Clocks / physiology; Circadian Rhythm / genetics; Circadian Rhythm / immunology; Circadian Rhythm / physiology; Darkness; Gene Expression Regulation, Plant / drug effects; Gene Expression Regulation, Plant / genetics; Genes, Plant / genetics; Oxidation-Reduction / drug effects; Plant Diseases / microbiology; Plant Immunity / genetics; Plant Immunity / immunology; Pseudomonas syringae / physiology; Salicylic Acid / immunology; Salicylic Acid / metabolism; Salicylic Acid / pharmacology; Transcription Factors / biosynthesis; Transcription Factors / genetics; Transcription, Genetic / genetics
TL;DR:
It is reported that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant’s redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2015 journal article
Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.
Physical Review E, 92(6), 062712,
Contributors: S. Karapetyan * & N. Buchler *
MeSH headings : Binding Sites; Circadian Clocks / genetics; DNA / genetics; DNA / metabolism; Kinetics; Models, Genetic; Stochastic Processes
TL;DR:
This work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2014 journal article
Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy
Molecular Biology of the Cell, 25(22), 3699–3708.
Contributors: A. Mazo-Vargas *, H. Park*, M. Aydin* & *
MeSH headings : Animals; Cell Cycle / genetics; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Coleoptera / chemistry; Coleoptera / enzymology; Fireflies / chemistry; Fireflies / enzymology; Gene Expression Regulation, Fungal; Insect Proteins / chemistry; Insect Proteins / genetics; Insect Proteins / metabolism; Luciferases / chemistry; Luciferases / genetics; Luciferases / metabolism; Luminescent Measurements; Microfluidic Analytical Techniques; Microscopy, Fluorescence; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Single-Cell Analysis / methods; Time-Lapse Imaging
TL;DR:
It is shown that luciferase reporters are better than fluorescent proteins at tracking gene expression and time-lapse luminescence microscopy was optimized to measure the dynamics of cell cycle genes in yeast with subminute time resolution.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2014 journal article
Two-Faced Cyclins with Eyes on the Targets
Cell Cycle, 4(1), 125–130.
Contributors: V. Archambault *, * , G. Wilmes, M. Jacobson & F. Cross
author keywords: Clb5; hydrophobic patch; B-type cyclin; RXL; DNA replication
MeSH headings : Amino Acid Motifs; Amino Acid Sequence; Cell Cycle / genetics; Cell Cycle / physiology; Cyclin B / chemistry; Cyclin B / genetics; Cyclin B / physiology; Cyclin-Dependent Kinases / genetics; Cyclin-Dependent Kinases / physiology; Cyclins / genetics; Cyclins / physiology; DNA Replication; Gene Expression Regulation, Fungal; Hydrophobic and Hydrophilic Interactions; Molecular Sequence Data; Origin Recognition Complex / chemistry; Origin Recognition Complex / genetics; Origin Recognition Complex / physiology; Protein Structure, Tertiary; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / physiology; Saccharomyces cerevisiae Proteins / chemistry; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / physiology; Signal Transduction / genetics; Signal Transduction / physiology
TL;DR:
The observations as well as work from other groups suggest that HP-RXL interactions are functionally important for cyclin-Cdk signaling to other targets, and the evolutionary conservation of the HP motif suggests that it allows cyclins to carry out important and specialized functions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 16, 2022
2012 journal article
Programming stress-induced altruistic death in engineered bacteria
Molecular Systems Biology, 8.
Contributors: Y. Tanouchi, A. Pai*, * & L. You *
author keywords: altruistic death; antibiotic response; eagle effect; programmed cell death; synthetic biology
MeSH headings : Apoptosis; Escherichia coli / cytology; Escherichia coli / growth & development; Genetic Engineering; Microbial Viability; Models, Biological; Reproducibility of Results; Stress, Physiological
TL;DR:
Using a mathematical model, the existence of an optimal programmed death rate that maximizes population growth under stress is predicted and the ‘Eagle effect’, a counter‐intuitive phenomenon where bacteria appear to grow better when treated with higher antibiotic concentrations is predicted.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2011 journal article
MeSH headings : Chromatin / metabolism; DNA-Binding Proteins / metabolism; Galactokinase / genetics; Galactokinase / metabolism; Gene Expression Regulation, Fungal / genetics; Gene Expression Regulation, Fungal / physiology; Nucleosomes / metabolism; Promoter Regions, Genetic / genetics; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Transcription Factors / metabolism
TL;DR:
A novel RSC-nucleosome complex is identified that both strongly phases flanking nucleosomes and presents regulatory sites for ready access, and these results challenge several widely held views.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2011 journal article
Evolution of networks and sequences in eukaryotic cell cycle control
Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1584), 3532–3544.
Contributors: F. Cross *, * & J. Skotheim *
author keywords: cell cycle; eukaryotes; evolution; opisthokonts; plants
MeSH headings : Amino Acid Sequence; Animals; Cell Cycle Checkpoints; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Conserved Sequence; Eukaryota / classification; Eukaryota / cytology; Eukaryota / genetics; Eukaryota / metabolism; Evolution, Molecular; Mammals; Phylogeny; Plant Cells / metabolism; Plants / classification; Plants / genetics; Plants / metabolism; Sequence Alignment; Yeasts / classification; Yeasts / cytology; Yeasts / genetics; Yeasts / metabolism
TL;DR:
Forward genetics in non-opisthokonts, such as plants or their green algal relatives, will provide direct information on cell cycle control in these organisms, and may elucidate the potentially more complexcell cycle control network of the last common eukaryotic ancestor.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2009 journal article
Protein sequestration generates a flexible ultrasensitive response in a genetic network
Molecular Systems Biology, 5.
Contributors: * & F. Cross *
author keywords: all-or-none; inhibitor; threshold; titration; transcription
MeSH headings : Basic-Leucine Zipper Transcription Factors / genetics; Basic-Leucine Zipper Transcription Factors / metabolism; Fungal Proteins / genetics; Fungal Proteins / metabolism; Gene Expression Regulation, Fungal; Gene Regulatory Networks; Genes, Dominant; Genetic Engineering / methods; Models, Genetic; Mutation; Saccharomycetales / genetics; Trans-Activators / genetics; Transcription, Genetic
TL;DR:
It is shown that sequestration of a basic leucine zipper transcription factor by a dominant‐negative inhibitor converts a graded transcriptional response into a sharply ultrasensitive response, with apparent Hill coefficients up to 12.5, which could explain the frequent evolutionary emergence of dominant negatives.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2008 journal article
Molecular Titration and Ultrasensitivity in Regulatory Networks
Journal of Molecular Biology, 384(5), 1106–1119.
Contributors: * & M. Louis *
author keywords: dominant negative; sequestration; threshold; titration; ultrasensitive
MeSH headings : Animals; Bacteria; Dimerization; Gene Regulatory Networks; Kinetics; Models, Molecular; Protein Processing, Post-Translational; Saccharomyces cerevisiae; Transcription Factors / metabolism
TL;DR:
It is demonstrated that molecular titration can generate ultrasensitivity on timescales compatible with most cell-fate decisions, and it is suggested that dominant negatives are abundant in gene regulatory circuits and might be generating an ultrasensitive response in these networks.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2007 journal article
Designing sequential transcription logic: A simple genetic circuit for conditional memory
Systems and Synthetic Biology, 1(2), 89–98.
Contributors: G. Fritz *, * , T. Hwa * & U. Gerland *
TL;DR:
Deterministic and stochastic analysis of the circuit dynamics indicate that an experimental implementation is feasible based on well-characterized genes and proteins based on existing protein–protein interactions and simple transcriptional regulation.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2005 journal article
Nonlinear protein degradation and the function of genetic circuits
Proceedings of the National Academy of Sciences of the United States of America, 102(27), 9559–9564.
Contributors: * , U. Gerland * & T. Hwa *
author keywords: amplification; dimerization; bistability; oscillation
MeSH headings : Bacteria / genetics; Gene Expression Regulation; Models, Biological; Multiprotein Complexes / metabolism; Protein Engineering / methods; Protein Subunits / metabolism; Proteins / metabolism; Transcription Factors / metabolism
TL;DR:
This work examines a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins and demonstrates that a few-fold difference between the degradation rate of monomers and dimers can enhance the function of these circuits substantially.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2005 journal article
Transcriptional regulation by the numbers: Applications
Current Opinion in Genetics and Development, 15(2), 125–135.
Contributors: L. Bintu *, * , H. Garcia *, U. Gerland *, T. Hwa *, J. Kondev *, T. Kuhlman *, R. Phillips *
MeSH headings : Animals; Bacteria / genetics; DNA / chemistry; Gene Expression Regulation; Humans; Models, Theoretical; Promoter Regions, Genetic / genetics; Quantitative Trait Loci; Thermodynamics; Transcription, Genetic; Transcriptional Activation
TL;DR:
Thermodynamic models provide a useful framework for the quantitative analysis of bacterial transcription regulation that can facilitate the quantification of vastly different forms of gene expression from several well-characterized bacterial promoters that are regulated by one or two species of transcription factors.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2005 journal article
Transcriptional regulation by the numbers: Models
Current Opinion in Genetics and Development, 15(2), 116–124.
Contributors: L. Bintu *, * , H. Garcia *, U. Gerland *, T. Hwa *, J. Kondev *, R. Phillips *
MeSH headings : Gene Expression Regulation; Humans; Models, Theoretical; Thermodynamics; Transcription, Genetic
TL;DR:
Interactions of activators, repressors, helper molecules and RNAP are described by a single function, the "regulation factor", which culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2019
2005 journal article
Two-faced cyclins with eyes on the targets
Cell Cycle, 4(1), 125–130. http://www.scopus.com/inward/record.url?eid=2-s2.0-14844287697&partnerID=MN8TOARS
Source: ORCID
Added: February 11, 2019
2003 journal article
On schemes of combinatorial transcription logic
Proceedings of the National Academy of Sciences of the United States of America, 100(9), 5136–5141.
Contributors: * , U. Gerland * & T. Hwa *
MeSH headings : Bacteria / genetics; Models, Genetic; Transcription, Genetic
TL;DR:
This work shows explicit schemes to implement regulatory logic functions of increasing complexity by appropriately selecting the strengths and arranging the relative positions of the relevant protein-binding DNA sequences in the cis-regulatory region.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 11, 2019
2000 journal article
Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus
The Journal of Chemical Physics.
TL;DR:
A solvation model was demonstrated to give identical designability results to previous models, and was shown to be inherently related to thermodynamically relevant energetic measures of protein folding, such as the foldability F and energy gap Δ10.
(via Semantic Scholar)
Source: ORCID
Added: February 16, 2022
1999 journal article
Effect of alphabet size and foldability requirements on protein structure designability
Proteins: Structure, Function and Genetics, 34(1), 113–124.
Contributors: N. Buchler & R. Goldstein *
TL;DR:
The designability of lattice proteins over a wide range of amino acid alphabets and foldability requirements is compared and it was noticed that those structures that were highly designable for the two‐letter amino acidAlphabet are not especially designable with higher‐letter alphABets.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education
(OpenAlex)
Source: ORCID
Added: February 11, 2019
1999 journal article
Universal correlation between energy gap and foldability for the random energy model and lattice proteins
The Journal of Chemical Physics.
TL;DR:
The random energy model is revisited to derive the statistical distributions of the various energy gaps and foldability and the resulting joint distribution allows us to explicitly demonstrate the positive foldability of proteins.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 16, 2022
1997 journal article
Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing
Journal of Magnetic Resonance, 125(1), 34–42.
Contributors: N. Buchler *, E. Zuiderweg *, H. Wang & R. Goldstein *
MeSH headings : Computer Simulation; Magnetic Resonance Spectroscopy / methods; Molecular Weight; Proteins / chemistry
TL;DR:
A mean-field method that reports the resonance assignments in a probabilistic fashion, displaying the certainty of assignments in an unambiguous and quantitative manner was applied to the NMR data of the 172-residue peptide-binding domain of the E. coli heat-shock protein, DnaK.
(via Semantic Scholar)
Source: ORCID
Added: February 16, 2022
1997 journal article
Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing
Journal of Magnetic Resonance, 125(1), 34–42. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031083526&partnerID=MN8TOARS
Contributors: N. Buchler, E. Zuiderweg, H. Wang & R. Goldstein
Source: ORCID
Added: February 11, 2019
1994 journal article
BL HERCULIS MODEL PULSATIONS .3. LIVERMORE OPACITIES
Astronomy & Astrophysics. https://publons.com/publon/51431452/
Contributors: . Buchler & N. Buchler
Source: ORCID
Added: February 16, 2022
Employment
Updated: July 11th, 2018 20:21
2018 - present
North Carolina State University Raleigh, NC, US
Associate Professor
Molecular Biomedical Sciences
2009 - 2018
Duke University Durham, NC, US
Assistant Professor
Biology
Education
Updated: October 16th, 2014 13:59
1995 - 2001
University of Michigan Ann Arbor, MI, US
Ph.D.
Biophysics
1991 - 1995
University of California San Diego La Jolla, CA, US
B.S.
Physics
Funding History
Funding history based on the linked ORCID record. Updated: October 15th, 2019 15:25
grant
April 1, 2018 - March 31, 2022
Measuring and perturbing metabolic rhythms and the cell division cycle in single cells
National Institute of General Medical Sciences
grant
February 1, 2018 - January 1, 2021
Determining mechanisms of rewiring of the eukaryotic cell cycle by a virus without disrupting network function
National Science Foundation
grant
November 1, 2011 - January 1, 2015
Biochronicity: Time, Evolution, Networks, and Function
Defense Sciences Office, DARPA
grant
September 30, 2011 - June 30, 2016
Rewiring the yeast brain: Redundancy and interference in genetic networks
Office of the Director
award
July 1, 2006 - June 1, 2016
Career Award at the Scientific Interface
Burroughs Wellcome Fund
grant
July 1, 2001 - June 30, 2003
Postdoctoral Research Fellowship in Biological Informatics for FY2001
Directorate for Biological Sciences
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