Bibliography
“10 Global Health Issues to Track in 2021.” 2020. World Health Organization. December 24, 2020. https://www.who.int/news-room/spotlight/10-global-health-issues-to-track-in-2021. An urgent but concise overview of humanities greatest health crises, ultimately an advertisement for donations and WHO public stature.
Alberts, Bruce, Alexander Johnson, and Julian Lewis. 2002. Molecular Biology of the Cell. 4th ed. New York: Garland Science. An introductory textbook providing general and specific overview of eukaryotic and bacterial structures.
Anthropocene Working Group. 2019. “Results of Binding Vote by AWG Released 21st May 2019.” http://quaternary.stratigraphy.org/working-groups/anthropocene/. An in-group summary of minutes. I didn’t read it, just looked for the citation defining the Anthropocene and how it is stratigraphically different from other eras but not yet ratified, which I thought it was.
Aryal, Sagar. 2022. “Nutrient Agar: Composition, Preparation and Uses.” MicrobiologyInfo.Com. August 10, 2022. https://microbiologyinfo.com/nutrient-agar-composition-preparation-and-uses/. A DIY, step-wise recipe for preparing nutrient agar plates.
Benyus, Janine. 1997. Biomimicry: Innovation Inspired by Nature. HarperCollins. Literary pop-science that is lovely but conceptually dated, it has a strong dualism contrasting nature’s elegance to human (masculine) mismanagement; tends to explore fewer examples in greater depth rather than many examples briefly.
“Biosafety Level (BSL) 1: Hazard Control.” 2021. UC San Diego. June 29, 2021. https://blink.ucsd.edu/safety/research-lab/biosafety/containment/bsl-1.html. A brief overview for researchers at UC San Diego, it is simple, clear, to the point, and has examples for consideration.
Bolt, Adam, director. Human Nature. News and Guts Films, 2019. An excellent documentary that should be shown to students in small sections to explain the basic mechanisms of CRISPR-Cas9 and the story of its discovery.
Borin, Joshua M., Sarit Avrani, Jeffrey E. Barrick, Katherine L. Petrie, and Justin R. Meyer. 2021. “Coevolutionary Phage Training Leads to Greater Bacterial Suppression and Delays the Evolution of Phage Resistance.” Proceedings of the National Academy of Sciences 118 (23). https://doi.org/10.1073/pnas.2104592118. A difficult to read research paper and theory overview about “training,” aka coevolving, l-phage with E. coli to produce a lunt-phage that was several generations “evolved,” anticipating any resistance mechanisms the E. coli might produce but only delayed acquisition of resistance.
CDC. 2013. “ANTIBIOTIC RESISTANCE THREATS in the United States.” https://www.cdc.gov/drugresistance/pdf/ar-threats-2013-508.pdf. A dated summary of antibiotic resistance that summarizes where the U.S. was in its infection rates at the time.
Center for Biological Evaluation and Research. 2021. “Science and Regulation of Bacteriophage Therapy.” Washington, D.C. https://www.fda.gov/media/159400/download. Black-and-white Congressional reports that justifies the FDA is carefully monitoring successful clinical trials and there are barriers to widespread application of phage therapy.
Chow, Denise. 2020. “Why Are Viruses Hard to Kill? Virologists Explain Why These Tiny Parasites Are so Tough to Treat.” NBC News, May 7, 2020. https://www.nbcnews.com/science/science-news/why-are-viruses-hard-kill-virologists-explain-why-these-tiny-n1202046. An annoying, COVID-contextualized info-piece for the lay public with “sound-bites” from five or six virologists outlying the basic anatomy of a virus and how they differ from other biological systems.
Cohan, Frederick M, Matthew Zandi, and Paul E Turner. 2020. “Broadscale Phage Therapy Is Unlikely to Select for Widespread Evolution of Bacterial Resistance to Virus Infection.” Virus Evolution 6 (2). https://doi.org/10.1093/ve/veaa060. A short and effective review of phage features that contribute to the titular hypothesis that viruses are unlikely to induce the same antimicrobial resistance currently plaguing human health care.
Darwin, Charles. 1859. On the Origin of Species by Means of Natural Selection, or, The Preservation of Favoured Races in the Struggle for Life. Wanted to cite the OG.
“Diarrhoeal Disease.” 2017. World Health Organization. May 2, 2017. https://www.who.int/news-room/fact-sheets/detail/diarrhoeal-disease. A surprisingly brief set of statistics with no emotional impact that lack of clean water and basic hygiene infrastructure is still the number two kill of human children and hundreds of thousands of children are still suffering every year as a result. But sure, prioritize private space flight.
“DNA Is a Structure That Encodes Biological Information.” 2014. Scitable by NatureEducation. 2014. https://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050/. An educational webpage from 2014 seemingly developed to be student facing, accessible introduction to the basics of DNA.
Eldredge, Niles. 2001. “The Sixth Extinction.” ActionBioscience.Org. June 2001. https://www.biologicaldiversity.org/programs/population_and_sustainability/extinction/pdfs/Eldridge-6th-extinction.pdf. An old and poorly constructed webpage with early statistics about the Sixth Extinction and basic comparisons to non-extinction timelines.
Foster, Jane A., Glen B. Baker, and Serdar M. Dursun. 2021. “The Relationship Between the Gut Microbiome-Immune System-Brain Axis and Major Depressive Disorder.” Frontiers in Neurology 12 (September). https://doi.org/10.3389/fneur.2021.721126. A research paper identifying the mechanisms of gut-microbial influence on the human brain, useful in this context for establishing that such a connection exists.
Gillett, Grant, and Felicity McKergow. 2007. “Genes, Ownership, and Indigenous Reality.” Social Science and Medicine 65 (10): 2093–2104. https://doi.org/10.1016/j.socscimed.2007.06.024. A readable narrative with strong author voice identifying secular and Indigenous objections to legal concepts of genetic ownership.
Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report 2022. 2022. https://www.who.int/publications/book-orders. A WHO report with the most recently available information on global antimicrobial resistance; useful reference statistics.
Gottfried, Joseph. 2005. “History Repeating? Avoiding a Return to the Pre-Antibiotic Age.” http://nrs.harvard.edu/urn-3:HUL.InstRepos:8889467. An undergraduate article by a law student that is useful for its background information.
Greene, Shannon, and Anne Reid. 2013. “Moving Targets: Fighting the Evolution of Resistance in Infections, Pests, and Cancer.” https://www.ncbi.nlm.nih.gov/books/NBK561252/pdf/Bookshelf_NBK561252.pdf. A thorough and concise introduction to the acquisition and spread of genetic resistance to chemical interventions in different biological systems.
“Grow Bacteria On Homemade Agar Plates.” 2017. Mad About Science. July 26, 2017. https://www.madaboutscience.com.au/shop/science-extra/post/grow-bacteria-on-homemade-agar-plates. A step-wise DIY instruction aimed at adults working with young people on how to make agar plates.
Hanauer, David I., Mark J. Graham, Laura Betancur, Aiyana Bobrownicki, Steven G. Cresawn, Rebecca A. Garlena, Deborah Jacobs-Sera, et al. 2017. “An Inclusive Research Education Community (IREC): Impact of the SEA-PHAGES Program on Research Outcomes and Student Learning.” Proceedings of the National Academy of Sciences 114 (51): 13531–36. https://doi.org/10.1073/pnas.1718188115. An impact review of SEA-PHAGES research program outcomes for undergraduates across several institutions.
Health Equity and Antibiotic Resistance. (n.d.). Centers for Disease Control and Prevention. Retrieved July 23, 2023, from https://www.cdc.gov/drugresistance/pdf/Health-Equity-Antibiotic-Resistance-FS-508.pdf. An excellent info-sheet detailing how different antimicrobial threats have disparate impacts on communities in the United States.
Howard Hughes Medical Institute. 2023. “SEA PHAGES Phage Discovery Guide.” In . https://seaphagesphagediscoveryguide.helpdocsonline.com/home. Readable and clear stepwise protocols for isolating novel bacteriophage from the environment.
Huynh, Miki. 2017. “New Findings of Early Life on Earth Date Back 3.77 Billion Years.” Astrobiology at NASA. March 3, 2017. https://astrobiology.nasa.gov/news/oldest-evidence-for-early-life-on-earth-dated-to-at-least-377-billion-years/. A pop-sci article reporting NASA findings, strange formatting of text and images.
Kean, Sam. 2014. “Book Review: ‘The Amoeba in the Room’ by Nicholas P. Money & ‘Missing Microbes’ by Martin J. Blaser A Human Being Consists of 30 Trillion Cells but 100 Trillion Microbes. .” Wall Street Journal, April 18, 2014. https://www.wsj.com/articles/SB10001424052702304117904579501444059499148. Did not read, just wanted the “sound-bite” that bacteria outnumber eukaryotes by magnitudes.
Keeling, Patrick J., and Jeffrey D. Palmer. 2008. “Horizontal Gene Transfer in Eukaryotic Evolution.” Nature Reviews Genetics. https://doi.org/10.1038/nrg2386. A dated overview of mechanisms for horizontal gene transfer; I only read enough to cite that it exists.
Kortright, Kaitlyn E, Benjamin K Chan, Jonathan L Koff, and Paul E Turner. 2019. “Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria.” Cell Host & Microbe 25 (2): 219–32. https://doi.org/https://doi.org/10.1016/j.chom.2019.01.014. An elegant and thorough overview of history, application, and limits to consider when using phage therapy; novel mechanisms for controlling bacterial evolution was mind-blowing.
Kortright, Kaitlyn E., Simon Doss-Gollin, Benjamin K. Chan, and Paul E. Turner. 2021. “Evolution of Bacterial Cross-Resistance to Lytic Phages and Albicidin Antibiotic.” Frontiers in Microbiology 12 (June). https://doi.org/10.3389/fmicb.2021.658374. An effective and readable methods paper describing a multigeneration bacterial challenge using three different antimicrobials and comparing the development of cross-resistance.
Kutateladze, M, and R Adamia. 2010. “Bacteriophages as Potential New Therapeutics to Replace or Supplement Antibiotics.” Trends Biotechnol 28 (12): 591–95. https://doi.org/10.1016/j.tibtech.2010.08.001. A context of antimicrobial resistance and a history that suggests phage therapy is actually not new.
Learn.Genetics. n.d. “Beyond the Central Dogma.” Genetic Science Learning Center. A clear and relatively concise educational overview of exceptions to biology’s central dogma illustrated with a paragraph of explanation for each.
Lee Ventola, C. 2015. “The Antibiotic Resistance Crisis Part 1: Causes and Threats.” Vol. 40. A seeming passion project that includes a fair overview of AMR.
MacLean, M. R., & Harper, D. R. (2021). Intellectual Property Issues for Bacteriophages. In Bacteriophages (pp. 731–749). Springer International Publishing. https://doi.org/10.1007/978-3-319-41986-2_23. Cited the brief section confirming that patenting of bacteriophage has grounds in a 1980 Supreme Court case over the novelty of genetically modified materials compared to what is found naturally.
Minero, Emelina. 2019. “Place-Based Learning: A Multifaceted Approach Connecting Learning to Students’ Surroundings—the Buildings, the Landscape—Covers Content Goals and Builds Community Pride.” Edutopia. April 19, 2019. https://www.edutopia.org/practice/place-based-learning-connecting-kids-their-community. A shallow article whose resources were tangential at best.
Murray, Christopher JL, Kevin Shunji Ikuta, Fablina Sharara, Lucien Swetschinski, Gisela Robles Aguilar, Authia Gray, Chieh Han, et al. 2022. “Global Burden of Bacterial Antimicrobial Resistance in 2019: A Systematic Analysis.” The Lancet 399 (10325): 629. https://doi.org/10.1016/S0140-6736(21)02724-0. Global health facing article explaining the basics of AMR and evaluating where in the world has been and will be most impacted by it.
Myers, William. Biodesign. New York: The Museum of Modern Art, 2018. Beautiful and lushly produced collection of designers inspired by biology.
National Human Genome Research Institute. 2023. “Central Dogma.” July 14, 2023. https://www.genome.gov/genetics-glossary/Central-Dogma. Concise and illustrated overview of biology’s central idea and molecular machinery whereby DNA is transcribed to RNA which is translated to proteins.
Oechslin, Frank. 2018. “Resistance Development to Bacteriophages Occurring during Bacteriophage Therapy.” Viruses 10 (7): 351. https://doi.org/10.3390/v10070351. A short paper summarizing existing research reporting in vitro and in vivo examples of when bacteria developed resistance to one phage or multiple phages.
Pires, D P, S Cleto, S Sillankorva, J Azeredo, and T K Lu. 2016. “Genetically Engineered Phages: A Review of Advances over the Last Decade.” Microbiol Mol Biol Rev 80 (3): 523–43. https://doi.org/10.1128/MMBR.00069-15. An exhaustive and only slightly-dated overview of methods for genetically engineering phages; a practitioner’s guidebook.
Prangishvili, David, Patrick Forterre, and Roger A. Garrett. 2006. “Viruses of the Archaea: A Unifying View.” Nature Reviews Microbiology 4 (11): 837–48. https://doi.org/10.1038/nrmicro1527. A summary paper of what was known about viruses of the obscure and difficult-to-study archaea, it feels “wacky” because it had a few grand statements that had not been experimentally verified.
Ramirez, Jaime, Francisco Guarner, Luis Bustos Fernandez, Aldo Maruy, Vera Lucia Sdepanian, and Henry Cohen. 2020. “Antibiotics as Major Disruptors of Gut Microbiota.” Frontiers in Cellular and Infection Microbiology 10 (November). I only read the abstract. It said what I wanted it to say, and I do not care that the journal has a low impact factor.
Reinking, Larry. 2007. “Examples of Image Analysis Using ImageJ.” Millersville University Department of Biology. June 2007. https://imagej.nih.gov/ij/docs/pdfs/examples.pdf. A three-page college worksheet for practicing surface area quantification using ImageJ.
“Replication and Distribution of DNA during Meiosis.” 2014. Scitable by NatureEducation. 2014. https://www.nature.com/scitable/topicpage/replication-and-distribution-of-dna-during-meiosis-6524853/. An education-facing, poorly formatted but brief article with illustrations describing DNA processing during gamete production.
Roper, Daniel C. 1938. “RATE TABLES AND GENERAL TABLES FOR THE UNITED STATES WITH SUPPLEMENTAL STATISTICS FOR HAWAII, PUERTO RICO, AND THE VIRGIN ISLANDS.” https://www.cdc.gov/nchs/data/vsushistorical/mortstatsh_1936.pdf. An old PDF with pages and pages of different ways to category disease demographics in the US in the 1930s.
Ryu, Wang-Shick. 2017. “Virus Life Cycle.” In Molecular Virology of Human Pathogenic Viruses, 31–45. Elsevier. https://doi.org/10.1016/B978-0-12-800838-6.00003-5. A concise and well-illustrated overview of basic viral anatomy and infection strategies.
Scheele, Leonard A, and Halbert L Dunn. 1955. “PUBLIC HEALTH SERVICE VITAL STATISTICS OF THE UNITED STATES 1952 VOLUME H MORTALITY DATA PREPARED UNDER THE SUPERVISION OF.” https://www.cdc.gov/nchs/data/vsus/VSUS_1952_2.pdf Another PDF of mortality data in the U.S., this one was searchable.
Squidonius. Mobio-Header.svg. 2008, May 13. Image. Wikimedia Foundation. https://commons.wikimedia.org/wiki/Category:Central_dogma_of_molecular_biology#/media/File:Molbio-Header.svg A Wikimedia foundation image representing DNA being copied to RNA being translated into a protein.
Twort, F.W. 1915. “AN INVESTIGATION ON THE NATURE OF ULTRA-MICROSCOPIC VIRUSES.” The Lancet 186 (4814): 1241–43. https://doi.org/10.1016/S0140-6736(01)20383-3. Upon reading the original publication, I felt like Twort got a lot of shade for “not discovering” bacteriophages. He proposes the observed antimicrobial property is due to viruses in the title and clearly explains the changes in bacterial plates that led him to hypothesize the existence of something smaller than he could identify with given tools.
“UN Report: Nature’s Dangerous Decline ‘Unprecedented’; Species Extinction Rates ‘Accelerating.’” 2019. UN Sustainable Development Goals. May 6, 2019. https://www.un.org/sustainabledevelopment/blog/2019/05/nature-decline-unprecedented-report/. General overview of species decline in the anthropogenic 6th mass extinction.
VanderWal, Arica. 2023. “Viruses of Microbes Conference 2023 Highlights.” San Diego. Zoom lecture given to Turner Lab and other virtual attendees summarizing notes from experiences at the Viruses of Microbes conference in Tbilisi, Georgia during the first week in July 2023.
Wang, Ming-Te, and Jessica L. Degol. 2017. “Gender Gap in Science, Technology, Engineering, and Mathematics (STEM): Current Knowledge, Implications for Practice, Policy, and Future Directions.” Educational Psychology Review 29 (1): 119–40. https://doi.org/10.1007/s10648-015-9355-x. I only read the abstract to confirm a statement that I heard verbally in an education workshop.
Weiner-Lastinger, Lindsey M., Sheila Abner, Jonathan R. Edwards, Alexander J. Kallen, Maria Karlsson, Shelley S. Magill, Daniel Pollock, et al. 2020. “Antimicrobial-Resistant Pathogens Associated with Adult Healthcare-Associated Infections: Summary of Data Reported to the National Healthcare Safety Network, 2015–2017.” Infection Control & Hospital Epidemiology 41 (1): 29. https://doi.org/10.1017/ice.2019.296. An awful set of statistic-containing colored rectangles that misused space and were poorly organized.
Wright, Rosanna C. T., Ville-Petri Friman, Margaret C. M. Smith, and Michael A. Brockhurst. 2018. “Cross-Resistance Is Modular in Bacteria–Phage Interactions.” PLOS Biology 16 (10): e2006057. https://doi.org/10.1371/journal.pbio.2006057. Very cool article detailing that bacteria can develop resistance to not just one phage but several at once depending on whether a structural feature or regulatory mechanism is mutated during successive generations of bacterial evolution under selective pressure by phages.
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