Final Presentation Videos
Discussions 10 & 11
Lecture 24
Lecture 23
Lecture 22
In-class code
Data for in-class code
Lecture 21
Slides
Lecture Video
Papers Referenced
Jasuja, et al., “Chemotactic Responses of Escherichia coli to Small Jumps of Photoreleased l-Aspartate”, Biophysical Journal 76, 1706-1719 (1999): the authors investigate the swimming response of E. coli to a sudden jump in aspartate concentration [journal] [pdf]
Essock-Burns, et al., “Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis”, mBio 11, e00853-20 (2020): with confocal imaging, the authors observe the colonization of the squid Euprymna scolopes by the Vibrio fischeri bacteria [journal] [pdf]
Waters and Bassler, “QUORUM SENSING: Cell-to-Cell Communication in Bacteria”, Annual Review of Cell and Developmental Biology 21, 319-346 (2005): a detailed review of quorum sensing in bacteria [journal] [pdf]
Miller and Bassler, “Quorum Sensing in Bacteria”, Annual Review of Microbiology 55, 165-199 (2001): a review of quorum sensing in bacteria [journal] [pdf]
Süel, et al., “An excitable gene regulatory circuit induces transient cellular differentiation“, Nature 440, 545-550 (2006): by dynamically measuring the expression of genes associated with competence (physiological state where DNA can be taken up from the environment) and comparing data to a mathematical model, the authors argue that entry into competence is an excitable process along the lines of a neuronal action potential [journal] [pdf]
Ahmer, et al., “Salmonella typhimurium Encodes an SdiA Homolog, a Putative Quorum Sensor of the LuxR Family, That Regulates Genes on the Virulence Plasmid” Journal of Bacteriology 180, 1185-1193 (1998): the discovery of regulation of virulence by quorum sensing [journal] [pdf]
Piper, et al., “Conjugation factor of Agrobacterium tumefaciens regulates Ti plasmid transfer by autoinduction”, Nature 362, 448-450 (1993): the discovery of regulation of DNA conjugation by quorum sensning [journal] [pdf]
Kaplan and Greenberg, “Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system”, Journal of Bacteriology 163, 1210-1214 (1985): bioluminescence inuced by quorum sensing is investigated quantitatively as a function of auto-inducer concentration [journal] [pdf]
Elowitz and Leibler, “A synthetic oscillatory network of transcriptional regulators”, Nature 403, 335–338 (2000): the creation of a synthetic genetic circuit in E. coli that produces GFP at periodic intervals [journal] [pdf]
Danino, et al., “A synchronized quorum of genetic clocks”, Nature 463, 326–330 (2010): by linking a synthetic gene circuit to quorum sensing, the authors create a robust genetic oscillator [journal] [pdf]
Lecture 20
Slides
Lecture Video
Papers Referenced
Howard Berg, E. coli in Motion (2004): a book by Howard Berg on E. coli swimming [link]
Jasuja, et al., “Chemotactic Responses of Escherichia coli to Small Jumps of Photoreleased l-Aspartate”, Biophysical Journal 76, 1706-1719 (1999): the authors investigate the swimming response of E. coli to a sudden jump in aspartate concentration [journal] [pdf]
Menolascina, et al., “Logarithmic sensing in Bacillus subtilis aerotaxis“, npj Systems Biology and Applications 3, 16036 (2017): an investigation into B. subtilis swimming toward high concentrations of oxygen [journal] [pdf]
Cluzel, et al., “An Ultrasensitive Bacterial Motor Revealed by Monitoring Signaling Proteins in Single Cells”, Science 287, 1652-1655 (2000): technical tour de force single-cell measurement of flagellar rotation and concentrations of chemotactic messenger proteins [journal] [pdf]
Sourjik and Berg, “Functional interactions between receptors in bacterial chemotaxis“, Nature 428, 437–441 (2004) : authors find cooperative activity of chemotactic receptors in E. coli [journal] [pdf]
Lecture 19
Slides
Lecture Video
Papers Referenced
Turner, et al., “Real-Time Imaging of Fluorescent Flagellar Filaments”, Journal of Bacteriology 182, 2793-2801 (2000): the authors develop a fluorescent labeling method for E. coli flagella and observe new aspects of flagellar dynamics [journal] [pdf]
DeRosier, “The Turn of the Screw: The Bacterial Flagellar Motor”, Cell 93, 17-20 (1998): a short review on bacterial flagella [journal] [pdf]
Simon and Silverman, “Flagellar rotation and the mechanism of bacterial motility“, Nature 249, 73-74 (1974): by immobilizing flagella on a glass slide, the authors observe whole cells rotating, supporting the hypothesis that flagella rotate to propel bacteria through fluids [journal] [pdf]
Kralj, et al., “Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein“, Science 333, 345-348 (2011): the authors develop a genetically encoded fluorescent sensor of membrane potential and show, among other things, a correlation between membrane potential and flagellar rotation [journal] [pdf]
Lecture 18
Slides
Lecture Video
Papers Referenced
Rellan-Alvarez, et al., “GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems“, eLife 4:e0759 (2015): the authors introduce a method to image growing plant roots in soil [journal] [pdf]
Süel, et al., “An excitable gene regulatory circuit induces transient cellular differentiation“, Nature 440, 545-550 (2006): by dynamically measuring the expression of genes associated with competence (physiological state where DNA can be taken up from the environment) and comparing data to a mathematical model, the authors argue that entry into competence is an excitable process along the lines of a neuronal action potential [journal] [pdf]
Hochbaum, et al., “All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins“, Nature Methods 11, 825–833 (2014): a system for both stimulation and measurement of neuronal action potentials with light [journal] [pdf]
Süel, et al., “Tunability and Noise Dependence in Differentiation Dynamics“, Science 315, 1716-1719 (2007): by creating a mutant strain where bacterial cells elongate, but do not divide, the authors average out cell-to-cell noise and observe different dynamics in differentiation into the competence state [journal] [pdf]
Lecture 17
Slides
Lecture Video
Papers Referenced
Dunlop, et al., “Regulatory activity revealed by dynamic correlations in gene expression noise”, Nature Genetics 40, 1493-1498 (2008): using single-cell measurements and a stochastic model, the authors isolate intrinsic and extrinsic noise in an E. coli regulatory circuit [journal] [pdf]
Süel, et al., “An excitable gene regulatory circuit induces transient cellular differentiation“, Nature 440, 545-550 (2006): by dynamically measuring the expression of genes associated with competence (physiological state where DNA can be taken up from the environment) and comparing data to a mathematical model, the authors argue that entry into competence is an excitable process along the lines of a neuronal action potential [journal] [pdf]
Waymack, et al., “Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic”, eLife e59351 (2019): shadow enhancers are shown to reduce noise in Drosophila development [journal] [pdf]
McAdams and Arkin, “Stochastic mechanisms in gene expression”, Proceedings of the National Academy of Sciences 94, 814-819 (1997): a stochastic model of gene expression shows that cells in the same state can have notably different dynamics of gene expression due to the inherent stochasticity of the process [journal] [pdf]
Elowitz, et al. “Stochastic Gene Expression in a Single Cell”, Science 297, 1183-1186 (2002): intrinsic noise in gene expression is measured in bacteria by monitoring the variation in two nearly identical copies of the same gene [journal] [pdf]
Lecture 16
Slides
Papers Referenced
Shen-Orr, et al., “Network motifs in the transcriptional regulation network of Escherichia coli“, Nature Genetics 31, 64-68 (2002): the paper that introduced network motifs in the regulatory network of E. coli [journal] [pdf]
Rosenfeld, et al., “Negative Autoregulation Speeds the Response Times of Transcription Networks“, Journal of Molecular Biology 323, 785-793 (2002): the authors construct auto-repressed and constitutive promoters that reach the same steady-state concentration and show that the auto-repressed circuit responds faster than the constitutive one [journal] [pdf]
Atkinson, et al., “Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli“, Cell 113, 597-607 (2003): a synthetic toggle-switch circuit exhibits bi-stable dynamics [journal] [pdf]
Mangan, et al., “The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks“, Journal of Molecular Biology 334, 197-204 (2003): the E. coli ara network is shown to be a feed-forward loop and a sign-sensitive delay element [journal] [pdf]
Alon, “Network motifs: theory and experimental approaches“, Nature Reviews Genetics 8, 450–461(2007): a review on network motifs [journal] [pdf]
Lecture 15
Slides
Papers Referenced
Shen-Orr, et al., “Network motifs in the transcriptional regulation network of Escherichia coli“, Nature Genetics 31, 64-68 (2002): the paper that introduced network motifs in the regulatory network of E. coli [journal] [pdf]
Rosenfeld, et al., “Negative Autoregulation Speeds the Response Times of Transcription Networks“, Journal of Molecular Biology 323, 785-793 (2002): the authors construct auto-repressed and constitutive promoters that reach the same steady-state concentration and show that the auto-repressed circuit responds faster than the constitutive one [journal] [pdf]
Atkinson, et al., “Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli“, Cell 113, 597-607 (2003): a synthetic toggle-switch circuit exhibits bi-stable dynamics [journal] [pdf]
Lecture 14
Slides
Papers Referenced
Miller, et al., “Visualization of Bacterial Genes in Action“, Science 24, 392-395 (1970): electron microscope measurement of DNA in the process of being transcribed reveals that in bacteria translation and transcription can be directly coupled with mRNAs being translated into proteins as they are being synthesized [journal]
Bernstein, et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays“, Proceedings of the National Academy of Sciences 99, 9697-9702 (2002): measurement of the degradation half-life of mRNAs in E. coli [journal] [pdf]
Nath and Koch, “Protein Degradation in Escherichia coli: I. MEASUREMENT OF RAPIDLY AND SLOWLY DECAYING COMPONENTS“, Journal of Biological Chemistry 245, 2889-2900 (1970): a measurement of the fraction of E. coli proteins that are actively degraded [journal] [pdf]
Ko and Lee, “Development of specific l-methionine sensors by FRET-based protein engineering“, RSC Advances 9, 15648-15656 (2019): a FRET sensor for methionine [journal] [pdf]
Lecture 13
Slides
Papers Referenced
Miller, et al., “Visualization of Bacterial Genes in Action“, Science 24, 392-395 (1970): electron microscope measurement of DNA in the process of being transcribed reveals that in bacteria translation and transcription can be directly coupled with mRNAs being translated into proteins as they are being synthesized [journal]
de Peppo, et al. “Engineering bone tissue substitutes from human induced pluripotent stem cells“, Proceedings of the National Academy of Sciences 110, 8680-8685 (2013): authors engineer bone from induced pluripotent stem cells [journal] [pdf]
Emert, et al., “Variability within rare cell states enables multiple paths toward drug resistance”, Nature Biotechnology : authors find rare cancer cell types that survive durg treatment [journal] [pdf]
Süel, et al., “An excitable gene regulatory circuit induces transient cellular differentiation“, Nature 440, 545-550 (2006): by dynamically measuring the expression of genes associated with competence (physiological state where DNA can be taken up from the environment) and comparing data to a mathematical model, the authors argue that entry into competence is an excitable process along the lines of a neuronal action potential [journal] [pdf]
Lopez, et al. “Generation of multiple cell types in Bacillus subtilis“, FEMS Microbiology Reviews 33, 152-163 (2009): a review on different phenotypic states of B. subtilis and their regulation [journal] [pdf]
Monod, “From Enzymatic Adaptation to Allosteric Transitions“, Science 154, 475-483 (1966): Jacques Monod’s Nobel acceptance speech published in Science; it outlines the experiments that built toward the discovery of gene regulation [journal] [pdf]
Herrgård, et al. “Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures“, Genome Research 13, 2423-2434 (2003): an attempt at the full genome regulatory network of E. coli [journal] [pdf]
Gotta, et al. “rRNA transcription rate in Escherichia coli“, Journal of Bacteriology 173, 6647-6649 (1991): measurement of transcription rate in E. coli [journal] [pdf]
Young and Bremer, “Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate“, Biochemical Journal 160, 185-194 (1976): measurement of translation rate in E. coli [journal] [pdf]
Bernstein, et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays“, Proceedings of the National Academy of Sciences 99, 9697-9702 (2002): measurement of the degradation half-life of mRNAs in E. coli [journal] [pdf]
Nath and Koch, “Protein Degradation in Escherichia coli: I. MEASUREMENT OF RAPIDLY AND SLOWLY DECAYING COMPONENTS“, Journal of Biological Chemistry 245, 2889-2900 (1970): a measurement of the fraction of E. coli proteins that are actively degraded [journal] [pdf]
Ko and Lee, “Development of specific l-methionine sensors by FRET-based protein engineering“, RSC Advances 9, 15648-15656 (2019): a FRET sensor for methionine [journal] [pdf]
Lecture 12
Slides
Papers Referenced
Van Valen, et al. “A Single-Molecule Hershey-Chase Experiment“, Biophysical Journal 22, 1339-1343 (2012): single-cell-level dynamic measurements of bacteriophages transfecting bacteria [journal] [pdf]
Luria and Delbrück, “Mutations of Bacteria from Virus Sensitivity to Virus Resistance“, Genetics 28, 491-511 (1943): by measuring the number of resistant colonies repeatedly and comparing the results to the predictions of two different statistical models, the authors rule out induced resistance as a mechanism for bacteria acquiring resistance to viruses [journal] [pdf]
Lecture 11
Slides
Papers Referenced
Stewart, et al., “Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division“, PLoS Biology 3, e45 (2005): this paper studies aging in E. coli and contains a beautiful video of exponentially growing cells [journal] [pdf]
Xiang, et al., “Solvent quality and chromosome folding in Escherichia coli“, bioArxiv https://doi.org/10.1101/2020.07.09.195560 (2020): the authors investigate the quality of the bacterial cytoplasm as a solvent for DNA
Wiggins, et al., “Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament“, Proceedings of the National Academy of Sciences 107, 4991-4995 (2010): the authors investigate the linear order of different loci in the E. coli genome and find that their order is conserved instead of being random [pdf]
Wang and Rudner, “Spatial organization of bacterial chromosomes“, Current Opinion in Microbiology 22, 66-72 (2014): a review on common spatial organizational structures of bacterial DNA [journal] [pdf]
Marbouty, et al. “Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging“, Molecular Cell 59, 588-602 (2015): a study of Bacillus subtilis chromosome organization with Hi-C measurements [journal] [pdf]
Brandão, et al. “RNA polymerases as moving barriers to condensin loop extrusion“, Proceedings of the National Academy of Sciences 116, 20489-20499 (2019): interplay of DNA-condensing proteins and gene expression machinery is investigated in bacteria with Hi-C measurements [journal] [pdf]
Le, et al. “High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome“, Science 342, 731-734 (2013): a pioneering study of bacterial chromosome organization using chromosome capture techniques and C. crescentus as a model [journal] [pdf]
Lecture 10
Slides
Lecture Video
Papers Referenced
Abreu, et al., “Microbial communities display alternative stable states in a fluctuating environment”, PLoS Computational Biology 16, e1007934 (2020): the authors investigate competition and coexistence of two microbial species in an environment that fluctuates in time [journal] [pdf]
Abreu, et al., “Mortality causes universal changes in microbial community composition”, Nature Communications 10, 2120 (2019): the authors create a multi-species model that includes a global mortality effect and test its predictions experimentally [journal] [pdf] [supplementary information]
Mehnaz, “Secondary Metabolites of Pseudomonas aurantiaca and Their Role in Plant Growth Promotion”, Plant Microbe Symbiosis: Fundamentals and Advances, 373-393 (2013): metabolites in P. aurantiaca are measured; this paper was used only for its photo of P. aurantiaca [journal]
Montes, et al., “A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential“, Environmental Microbioome 11, 76 (2016): genome of P. veronii; includes images of P. veronii [journal] [pdf]
Celiker and Gore, “Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment“, Nature Communications 5, 4643 (2014): authors measure abundances of many species growing together for long periods of time and classify long-term states into one of several types [journal] [pdf]
Lecture 9
Slides
Lecture Video
Papers Referenced
Limoli, et al., “Interspecies interactions induce exploratory motility in Pseudomonas aeruginosa“, eLife 8, e47365 (2019): this paper observes induced motility in P. aeruginosa in the presence of S. aureus cells [journal] [pdf]
Lecture 8
iPython notebook file
Slides
Lecture Video
Lecture 7
Slides
Lecture Video
Papers Referenced
Stewart, et al., “Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division“, PLoS Biology 3, e45 (2005): this paper studies aging in E. coli and contains a beautiful video of exponentially growing cells [journal] [pdf]
Hudson, “Collared Doves in Britain and Ireland”, British Birds, 65, 139-155 (1972): this paper contains data tracking the number of collared doves in Britain after their arrival on the island in 1952 [journal]
Monod, “The Growth of Bacterial Cultures”, Annual Review of Microbiology 3, 371-394 (1949): a famous review about quantitative features of bacterial growth curves [journal] [pdf]
van Niel, “The Culture, General Physiology, Morphology, and Classification of the Non-sulfur Purple and Brown Bacteria“, Microbiology and Molecular Biology Reviews 8, 1-118 (1944): van Niel studies growth of “purple” and “brown” bacteria and includes a very entertaining description of growth media [journal] [pdf]
Lecture 6
Slides
In-class python code
Papers Referenced
Forchhammer and Lindahl, “Growth rate of polypeptide chains as a function of the cell growth rate in a mutant of Escherichia coli 15“, Journal of Molecular Biology 55, 563-568 (1971): the authors determine that E. coli achieves faster cell growth not by having ribosomes synthesize faster but by making more ribosomes [journal] [pdf]
Scott, et al. “Interdependence of Cell Growth and Gene Expression: Origins and Consequences”, Science 330, 1099-1102 (2010): the authors quantitatively investigate the relationship between exponential growth rate and ribosome levels in E. coli, revealing several linear equations accounting for gene expression during exponential growth [journal] [pdf] [supplementary info pdf]
Lecture 5
Slides
Lecture Video
Papers Referenced
Stewart, et al., “Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division“, PLoS Biology 3, e45 (2005): this paper studies aging in E. coli and contains a beautiful video of exponentially growing cells [journal] [pdf]
Karr, Sanghvi, et al. “A Whole-Cell Computational Model Predicts Phenotype from Genotype“, Cell 150, 389-401(2012): the authors attempt to model literally an entire cell [journal] [pdf]
van Niel, “The Culture, General Physiology, Morphology, and Classification of the Non-sulfur Purple and Brown Bacteria“, Microbiology and Molecular Biology Reviews 8, 1-118 (1944): van Niel studies growth of “purple” and “brown” bacteria and includes a very entertaining description of growth media [journal] [pdf]
Monod, “The Growth of Bacterial Cultures”, Annual Review of Microbiology 3, 371-394 (1949): a famous review about quantitative features of bacterial growth curves [journal] [pdf]
Scott, et al. “Interdependence of Cell Growth and Gene Expression: Origins and Consequences”, Science 330, 1099-1102 (2010): the authors quantitatively investigate the relationship between exponential growth rate and ribosome levels in E. coli, revealing several linear equations accounting for gene expression during exponential growth [journal] [pdf] [supplementary info pdf]
Lecture 4
Discussion 1
iPython notebook template file
Video
Lecture 3
Slides
Lecture Video
Lecture 2
Papers Referenced
Theillet, et al., “Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins“, Chemical Reviews 114, 6661-6714 (2014): a review examining the effects on physical and chemical properties of cells (e.g. ion concentration) on intrinsically disordered proteins (i.e. proteins that do not fold into stable spatial conformation [journal] [pdf]
Wilks and Slonczewski, “pH of the Cytoplasm and Periplasm of Escherichia coli: Rapid Measurement by Green Fluorescent Protein Fluorimetry“, Journal of Bacteriology 189, 5601-5607 (2007): the authors measure the pH of the E. coli cytoplasm [journal] [pdf]
Blattner, Plunkett III, et al., “The Complete Genome Sequence of Escherichia coli K-12“, Science 277, 1453-1462 (1997): the complete genome sequence of E. coli [journal] [pdf]
Bennett, et al., “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli“, Nature Chemical Biology 5, 593-599 (2009): the authors attempt to measure the absolute concentration of many metabolites in E. coli [journal] [pdf]
Pedersen, et al., “Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates“, Cell 14, 179-190 (1978): the authors measure the proportions of 140 different proteins in E. coli under several different growth conditions [journal] [pdf]
Cai and Inouye, “EnvZ-OmpR Interaction and Osmoregulation in Escherichia coli“, Journal of Biological Chemistry 277, 24155-24161 (2002): the authors measure the levels of osmoregulatory genes in E. coli [journal] [pdf]
Lu, et al., “Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation“, Nature Biotechnology 25, 117-124 (2007): a powerful technique for measuring absolute protein concentrations gives insight into transcriptional and translational regulatory patterns in E. coli [journal] [pdf]
Pandey and Mann, “Proteomics to study genes and genomes“, Nature 405, 837-846 (2000): a review of proteomics [journal] [pdf]
A section from Milo, Phillips, and Orme’s Cell Biology By the Numbers: http://book.bionumbers.org/what-is-the-macromolecular-composition-of-the-cell/
Bionumbers Database: https://bionumbers.hms.harvard.edu/search.aspx
Pekkurnaz, et al., “Glucose Regulates Mitochondrial Motility via Milton Modification by O-GlcNAc Transferase“, Cell 158, 54-68 (2014): the authors observe a relationship between intracellular mitochondrial motility and metabolism [journal] [pdf]
McGuffee and Elcock, “Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm“, PLoS Computational Biology 6, e100069 (2010): computational simulations show a plausible view of diffusion and crowding inside a bacterial cell [journal] [pdf]
Reck-Petersen, et al., “Single-Molecule Analysis of Dynein Processivity and Stepping Behavior“, Cell 126, 335-348 (2006): one of many remarkable measurements of motor protein activity by Sam Reck-Petersen, Ron Vale, et al. [journal] [pdf]
Htet, et al., “LIS1 promotes the formation of activated cytoplasmic dynein-1 complexes“, Nature Cell Biology 22, 518-525 (2020): the authors explore the formation of the massive dynein motor protein complex [journal] [pdf]
Schnitzer, et al., “Force production by single kinesin motors“, Nature Cell Biology 2, 718-723 (2000): the authors measure the forces exerted by a single motor protein [journal] [pdf]
Lecture 1
Papers Referenced
Hug, et al., “A new view of the tree of life“, Nature Microbiology 1, 16048 (2016): using new data from previously unexamined environments, the authors propose a revised tree of life with greatly a greatly expanded repertoire of microbial species [journal] [pdf]
Flemming and Wuertz, “Bacteria and archaea on Earth and their abundance in biofilms“, Nature Reviews Microbiology 17, 247-260 (2019): the authors attempt to estimate what proportion of Earth’s microbial biomass resides in biofilms [journal] [pdf]
Kuypers, et al., “The microbial nitrogen-cycling network“, Nature Reviews Microbiology 16, 263-276 (2018): the authors review environmental nitrogen cycling by microbes across environments [journal] [pdf]
Breznak and Pankratz, “In situ morphology of the gut microbiota of wood-eating termites“, Applied and Environmental Microbiology 33, 406-426 (1977): remarkable electron microscope images of the termite gut microbiome [journal] [pdf]
Adams, et al., “DNA-uptake pili of Vibrio cholerae are required for chitin colonization and capable of kin recognition via sequence-specific self-interaction“, Nature Microbiology 4, 1545-1557 (2019): DNA uptake pili are shown to be essential for surface colonization and cell aggregation in V. cholerae; strain to strain variability suggest such pili interactions may be a form of kin recognition [journal] [pdf]
Süel, et al., “An excitable gene regulatory circuit induces transient cellular differentiation“, Nature 440, 545-550 (2006): by dynamically measuring the expression of genes associated with competence (physiological state where DNA can be taken up from the environment) and comparing data to a mathematical model, the authors argue that entry into competence is an excitable process along the lines of a neuronal action potential [journal] [pdf]
Yang, Bialecka-Fornal, et al., “Encoding Membrane-Potential-Based Memory within a Microbial Community“, Cell Systems 10, 417-423 (2020): the authors observe that exposure to blue light results in a permanent phase shift of membrane potential oscillations in Bacillus subtilis biofilms, facilitating the encoding of spatial patterns in bacterial communities [journal] [pdf]
Le, et al., “High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome“, Science 342, 731-734 (2013): using Hi-C technology, the authors argue that the Caulobacter crescentus genome is physically organized into a series of supercoiled filaments similar to a pipe-cleaner or bottle-brush [journal] [pdf]
Johnson, et al., “The Type II Secretion System Delivers Matrix Proteins for Biofilm Formation by Vibrio cholerae“, Journal of Bacteriology 196, 4245-4252 (2014): V. cholerae cells secrete components of the biofilm extracellular matrix with a type-II secretion system [journal] [pdf]