Dr. B's microbio stuff

Quick guide on how to look up a 16S sequence using the BLAST tool.Applies to BIO203A and BIO205A.

Audio only!

What to expect during the week 2 activities of BIO205A? Microbiology: oral bacteria and Gram staining.A&P: nervous system, endocrine system, cardiovascular.Get ready for some dissections! Sheep brain and heart.Blood typing and ECG measurements and

This episode is primarily intended for the students currently enrolled in a new National University course, BIO205A. The episode provides a recap of the goals and activities of the first week.

Quick rundown about what is similar and what is different between Staphylococci and Streptococci, and how you differentiate S. aureus from other Staph, as well as some of the characteristics of the main Streptocci.

Protein catabolism reactions: gelatinase, urease, SIM, ImViCGelatinase: https://youtu.be/z3mlfia9oQo?si=SXy48lhNZQ5GFYxqUrease: https://www.youtube.com/watch?v=5_wdyQPIk4wSIM https://youtu.be/ng_8Mye4mu0?si=wzVlsn1MTKTUtcOtIMViC https://youtu.be/az0dXYmXgAg?si=WMqLbsNx8HPMpKh4

Lecture notes for the July 2024 BIO407 (Molecular Biology) class, based on Tropp's Principles of Molecular Biology textbook. Chapter 1: Intro to Mol Bio, some of the big discoveries, brief intro to nucleic acid structure. Some useful links: DNA structure discovery: ⁠https://www.youtube.com/watch?v=1vm3od_UmFg⁠ Encode and the human genome: ⁠https://www.youtube.com/watch?v=TwXXgEz9o4w&t=32s

Quick rundown on some of the major diseases/microbes seen in class. Plus a bit of "big picture view" of how to see microbes and the diseases they cause.

Lots of information out there!Vibrio vulnificus https://youtu.be/6M9-nd2ejcY?si=eowlC630JtXiquqdCholera https://youtu.be/cvMN_YjDiCI?si=lGigqLxgdHVoq9AZHepatitis C: https://youtu.be/vRvyV1x2t60?si=r1DOZ_gWEficfjguHBV serology https://youtu.be/21eVTf0otUw?si=vga6Gn_YcErzsAXg

Chapter 24. Openstax book.Typhoid Mary https://youtu.be/THLZpWJMK7M?si=kkiHDYwKV87XL5zMRevisiting the gut with a camera inside: https://youtu.be/5ufESc1bK78?si=naYpjqA5wff_wKb-

Ch.23 Openstax Microbiology groupChlamydia: https://youtu.be/2Gcf_frNtJQ?si=BOZHX21EZK3xPVhgSyphilis clinical presentation: https://youtu.be/050m9qyYI30?si=8DInAsYGQFyk4NTH

Openstax: https://openstax.org/books/microbiology/pages/25-introduction Septic shock https://youtu.be/-MXi4mOMmI4?si=yw94sdgMzuIc7Yc2 Rheumatic fever https://youtu.be/iDnuQdycidc?si=T8nw4sWFTmPaE871 Malaria https://youtu.be/HkmL7A--MKY?si=264tfj6e9LqVrD-J Leishmaniasis info in Spanish https://youtu.be/7VDdPcrkiB8?si=coTCZA7CyeyZsrwT

Openstax chapter https://openstax.org/books/microbiology/pages/26-introduction Meningitis https://youtu.be/G1E_uX746cM?si=vbsMj8ZFRut5otzW Terrifying video about the effect of rabies https://youtu.be/kxBIJvNHZg4?si=raBL8NnQh7t_wKXC Info about polio https://youtu.be/27MAgWSYrvI?si=LgtXed9AwJZrDNKl Naegleria the brain eating amoeba https://youtu.be/IUlhwvUsa0U?si=FT5sRwuX7AqnktSt West Nile virus https://youtu.be/VIGaytaTBNk?si=N1rhhufESBVL0bZH Long but relevant about Coccidioidomycosis https://youtu.be/C8vwxm5GJwU?si=RcZXeQF458q1AdTl

DNA barcoding, skin and throat cultures.

Dr. B going over the lab exam study guide, from special media to the end of respiration and anaerobes.

Respiratory infections, emphasis on Streptococci, pneumonia (different types) and TB. Openstax Nursing insights about pneumonia https://youtu.be/q9dKz8UwEcY?si=vFjxMcR8Mz8erMcf Detailed explanation about TB: https://youtu.be/6P6zBHpWiGA?si=u4LultNDlqdViixZ Histoplasmosis https://youtu.be/FDI6tls7Vzs?si=_tDJ50U1OZJYV_B2 Aspergillosis https://youtu.be/N1UUazCiL78?si=aR-zceCFRda0D8F_ Valley fever https://youtu.be/aWmw_cLiuOk?si=c7JVjl46TUrfI4ZW

Overview of skin defenses. Bacterial, viral, fungal, and parasitic diseases of the skin and eye. MRSA https://www.youtube.com/watch?v=iGgobi91LOA Staphylococcal infections https://youtu.be/5t7BqsXFvOg?si=znYVi01YCYo5TX61 Danger of smallpox? https://youtu.be/7KJsVKlJC7U?si=ufB9Cq7HdLVeu71- Monkeypox https://youtu.be/_ePucQaZpRU?si=kGmE-HAjiRV_UoAM Loa loa video https://youtu.be/vr5xjDWppv8?si=niDt1gs8VRi_B-vO

Humoral and Cellular Immune response. Antibody characteristics. Antigen presentation via MHC I and MHC II. For intro microbio course using the Openstax book. https://openstax.org/books/microbiology/pages/18-1-overview-of-specific-adaptive-immunity How does the immune system able to make so many antibodies: https://youtu.be/o2Pa664PHxo?si=yBUiVKTsTVBFsquf Antigen presentation simple: https://youtu.be/oiwMwMREd-M?si=lMtAMxEx4DCPPlNO This is video similar to the TLR one for innate, but if you go to 2:40 min you will see a cool MHC II antigen presentation animation https://youtu.be/iVMIZy-Y3f8?si=HgMPEMT1oERWR_zo

Intro immunology based on Ch.17 of the OpenStax book https://openstax.org/books/microbiology/pages/17-introduction Crash course video on innate response: https://youtu.be/GIJK3dwCWCw?si=l0snWIZCIZSs0BTr Animation of how TLRs recognize and act on pathogens, disregard all the abbreviations of the many intermediaries and components https://youtu.be/d0fgMaQfAQw?si=TnNYKd2wSdKw2pvM Detailed video about white blood cells https://youtu.be/MHdVJZUfeR4?si=N6znoG6GkF_BkSLW Complement system: https://youtu.be/E4dZ5w3D9ZM?si=0xt3YL4eF8g5nyEu

Intro microbiology based on Openstax book. Episode covers basic concepts in epidemiology, morbidity/mortality, incidence, prevalence, types of epidemiology studies, reservoirs, carriers, and transmission types. Openstax chapter 16 https://openstax.org/books/microbiology/pages/16-introduction CDC Morbidity and Mortality Weekly Report https://www.cdc.gov/mmwr/index.html Contagion scene https://youtu.be/4sYSyuuLk5g?si=0XBTj9xv3PL8fYAD Incidence and Prevalence https://youtu.be/HnBYw8_-azw?si=qDSDhWAJ7y150Ek9

Intro micro based on the Openstax book. This covers virulence factors especially toxins. Example of an exotoxin type (AB toxins): https://youtu.be/JTAOQHtClxA?si=Jkvf8S7dJ7aJ2ysE

Intro microbiology chapter 15 pathogenicity (part 1). Covers concepts related to microbial diseases, different types, signs and symptoms, Koch's postulates, pathogenicity vs virulence and ID50, stages of disease, stages of infection.

Intro microbiology lab, recap of biochemical reactions around carbohydrate metabolism: Starch agar https://www.youtube.com/watch?v=FEf_ecmD_Uk&t=1s OF medium https://www.youtube.com/watch?v=ofiBrGIzY7w Phenol Red broths https://www.youtube.com/watch?v=msDezRcixKg&t=2s MRVP https://www.youtube.com/watch?v=JxmrPar5qzI Simmons citrate https://www.youtube.com/watch?v=LZ_mVPRLayQ&t=1s

Intro microbiology chapter 14. Covers mechanisms of action of antibiotics, major groups, as well as resistance mechanisms. Openstax chapter :https://openstax.org/books/microbiology/pages/14-2-fundamentals-of-antimicrobial-chemotherapy Video how showing how antibiotics inhibit protein synthesis: https://youtu.be/RedO6rLNQ2o?si=zhE94YPyCmq18q52 Evolution of antibiotic resistance in real life: https://youtu.be/plVk4NVIUh8?si=h2EZrTZIy8eJPKhj

Intro microbiology chapter 13. Covers BSL levels, types of microbial control, brief intro to physical and chemical methods. Openstax book chapter link: https://openstax.org/books/microbiology/pages/13-introduction Summary of disinfectants: https://www.cfsph.iastate.edu/Disinfection/Assets/characteristics-of-selected-disinfectants.pdf Video about how to evaluate disinfectants on surfaces https://youtu.be/ArWyKfR4h54?si=cTZkiD0O8ugfnwJo

Openstax ch.11 https://openstax.org/books/microbiology/pages/11-4-protein-synthesis-translation Cult classic from the 1970s: Stanford students visualize translation https://youtu.be/u9dhO0iCLww?si=ALRdY13skRNheR3o More modern version: https://youtu.be/41_Ne5mS2ls?si=H9K-6RatTWnxbJm2 More advanced one: https://youtu.be/TfYf_rPWUdY?si=rfN_eK6zTaz5R1cx Another animation: https://youtu.be/2dV5s6v2v8Q?si=SyFfKHDEP7EFbSsM

Openstax ch.11 https://openstax.org/books/microbiology/pages/11-introduction Simpler DNA replication https://youtu.be/TNKWgcFPHqw?si=iKA-HkSMTkgpEtjZ DNA replication https://youtu.be/4jtmOZaIvS0?si=vd-ZVUusT1e2E3KT Transcription and translation https://youtu.be/41_Ne5mS2ls?si=U8SS_tdzOAgt3k4F

Ch.10 Openstax: https://openstax.org/books/microbiology/pages/14-2-fundamentals-of-antimicrobial-chemotherapy Watson shows base pairing: https://youtu.be/PDeaLxoL75M?si=CeHpaXdSxKdg0fU2 If you thought genomics was boring, the genomics of beer: https://youtu.be/VmxdU-M0eXY?si=ZM6k6Xwv7BxrSPPY DNA/RNA structure video: https://youtu.be/nuC1_jiqq5g?si=k2ssReTA4wvUiiCd

Openstax chapter https://openstax.org/books/microbiology/pages/9-introduction Recap of serial dilutions https://youtu.be/l8HgDPajsMI?si=i0Ci3ttcpY4Umbuk Timelapse of bacterial growth https://youtu.be/XLmk0zYIFjE?si=1CtntArben22eJWa

Openstax chapter https://openstax.org/books/microbiology/pages/8-introduction Oxidation & reduction video https://learn.genetics.utah.edu/content/metabolism/carbon Metabolic pathways interactive https://learn.genetics.utah.edu/content/metabolism/pathways/ Glycolysis with music https://youtu.be/6JGXayUyNVw?si=_mER382t3mRBlwm4 Cheese and microbes https://youtu.be/9krRP2aSewo?si=vOQzWzzXqw9Qxrl- Electron transport chain animation https://youtu.be/LQmTKxI4Wn4?si=avKQVNCrtuiGJd8l

Sorry it is a long one! Openstax chapter 8: https://openstax.org/books/microbiology/pages/8-1-energy-matter-and-enzymes Rap song about redox stuff: https://youtu.be/VCpNk92uswY?si=aIy97qYRdR0AI6ve How enzymes work https://youtu.be/yk14dOOvwMk?si=BMZgIIDsHA4XSoN3

Openstax chapter: https://openstax.org/books/microbiology/pages/6-introduction Cool animation of a bacteriophage infection: https://youtu.be/uFXuxGuT7H8?si=QiFJPQFQ5SzomlnJ HIV & reverse transcriptase: https://youtu.be/PlSvywlLuNw?si=1qZZA_7oVHl0HYHw Covid virus infection: https://youtu.be/LoVJCx6XXMM?si=LNk2HZIxGAGK7UjN Infectious encephalitis (including measles): https://youtu.be/unleaXRtsC0?si=abuK1r-B1lErKTzb

Openstax book https://openstax.org/books/microbiology/pages/5-introduction Candida auris https://youtu.be/jw8TB4jw-jM?si=4wgtjbHItDm7hf86

Tough mudder and Aeromonas infection https://news.yahoo.com/tough-mudder-near-san-francisco-022410696.html Aeromonas is an enteric btw https://en.wikipedia.org/wiki/Aeromonas Here is Conan the bacterium: https://www.smithsonianmag.com/smart-news/conan-the-bacterium-has-what-it-takes-to-survive-on-mars-180981019/

The first couple of weeks of micro lab may feel overwhelming with so many new techniques and lots of information. Dr. B puts it in the context of "real life" especially as related to clinical lab and health care.

Cool clip of the inside of a cell https://youtu.be/wJyUtbn0O5Y?si=It07OzeTMnrcMFhz Flagella, pili, and fimbriae https://youtu.be/VzqC7nag6KM?si=1aoHq31RLff2ChcO This is a cool video about modern day endosymbionts with some amazing live microscopy of amoebas https://youtu.be/4LhBZ2H5SwM?si=bCIHPjzext8UIGje

Ch.3 of Openstax: https://openstax.org/books/microbiology/pages/3-introduction Cool interactive for cells https://learn.genetics.utah.edu/content/cells/insideacell20/ Intro to plasmids (they can be used as tools of genetic engineering) https://youtu.be/SdqJFA6mOkI?si=ro8jXgtgtNVPfbXg Endospores in the food industry: https://youtu.be/L9uAf9Bsmvg?si=5vTKw6Pfv-5j9J50

Openstax book chapter 7: https://openstax.org/books/microbiology/pages/7-introduction How gamers can help figuring out the 3-d structure of a protein: https://www.youtube.com/watch?v=axN0xdhznhY&list=PLCB386EB2B4D1097A&index=13

Opnestax appendix about chemistry: https://openstax.org/books/microbiology/pages/a-fundamentals-of-physics-and-chemistry-important-to-microbiology NaCl bonding song: https://youtu.be/ljvX-RMv_lw?si=yoV6RwhIjlWI3aBn TEAS test prep chemistry video: https://youtu.be/j9rLiSLIsh4?si=4Gl9FmiVBAywprGo Same TEAS series but with chemistry questions: https://youtu.be/B3_nogbF8ZM?si=j4qsi_O5Ap5dSWND

Chapter 2 of Openstax book: https://openstax.org/books/microbiology/pages/2-introduction Cell size and scale https://learn.genetics.utah.edu/content/cells/scale/ Virtual microscope https://learn.genetics.utah.edu/content/cells/microscope Intro to electromagnetic spectra https://youtu.be/lwfJPc-rSXw?si=tyklygzUV3cDsTFI Preparing smears https://youtu.be/OrSmJst_lPM?si=iqurYByQ70SSuEx9

Tiny Earth website: https://tinyearth.wisc.edu/ Intro video for TE: https://youtu.be/fZtjAfEUHyo?si=gWZUqQu8IcOoaObL Soil sampling: https://youtu.be/4KlKQT9YGL8?si=vnwzMskq73I4ous6 Screening for antibiotic production https://youtu.be/MKRRkrad6K8?si=y5G6P44IWiOwU_jt More such videos at TE Instructional In 2017, NU students got a honorary mention for this video: https://youtu.be/HIxA356o-jU?si=EoV5fiaP7yHt4U0t (it was called Small World Initiative then)

Taxonomy 101, microbial groups. Openstax chapter 1 https://openstax.org/books/microbiology/pages/1-3-types-of-microorganisms

Intro to microbiology: brief history and types of microbiology. Openstax chapter 1: https://openstax.org/books/microbiology/pages/1-introduction Like cheese? Here is a cool video about how microbes contribute to cheese (in a good and bad way): https://youtu.be/9krRP2aSewo?si=hzBer-ilH2EpzRAM History of microscope: https://youtu.be/TJyOQmdwHhE?si=ZDiWeASukVUJQBRZ Mrs. Fleming dr. Voureka https://en.wikipedia.org/wiki/Amalia_Fleming How penicillin changed the world https://youtu.be/q2yd3lGN7xA?si=rn8DgQCNa95cmCzH GATTACA official trailer: https://youtu.be/NIIZ2P-fiyI?si=0C0QPfEV7rIodTZt

Summary videos: https://www.youtube.com/watch?v=5bLEDd-PSTQ https://www.youtube.com/watch?v=Ikq9AcBcohA Kirky Stanford video: https://library.ucsd.edu/dc/object/bb90484996 (best quality video) and a story of its making: https://stanmed.stanford.edu/protein-synthesis-an-epic-on-the-cellular-level/

Recap: https://www.youtube.com/watch?v=Ikq9AcBcohA

Summary siRNA and miRNA https://www.youtube.com/watch?v=cK-OGB1_ELE&t=45s MiRNA https://www.youtube.com/watch?v=5YsTW5i0Xro 2024 review article https://www.cell.com/trends/molecular-medicine/fulltext/S1471-4914(24)00190-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1471491424001904%3Fshowall%3Dtrue

Lariat splicing https://www.youtube.com/watch?v=CdwLKwseP9Q Spliceosomes https://www.youtube.com/watch?v=YgmoHtLGb5c Spliceosome regulation https://www.youtube.com/watch?v=q63JCoLDR2w

Gal pathway regulation https://www.youtube.com/watch?v=vDWEHlQw6Jk Epigenetic modification, HAT/HDAC https://www.youtube.com/watch?v=eYrQ0EhVCYA

Eukaryotic transcription, RNA polymerases, initiation, core and regulatory promoters. Promoters, enhancers, silencers https://www.youtube.com/watch?v=mK4wzCTrj9k

Long but excellent explanation of the attenuation mechanism starting around minute 12: https://youtu.be/v7L9aCVPEcs?si=F41uin76paXEr0j-