Lecture 4

Slides
Chocolate chip cookie data
Prussian army data
Papers Referenced

Lecture 3

Slides
Bacterial growth data
Papers Referenced

Lecture 2

Slides
E. coli chemical composition image
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

Slides

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]