BIOL 260 Microbiology   fall 2017

Seattle Central College

Lauren Yasuda, Ph.D. 

Fri 11/17:  Current topic assignment due
Google Drive for sharing current topic #2 - 2 extra credit points if posted (w/ subject title) by Mon 11/20 at 5 pm 

Tues 11/21: Analyze biochemical tests & start Unknowns Project:  Gram stain, TSA slants & streak plates. Before lab, please review the gram stain procedure (p.38-39), & read the biochemical tests handout & p.8 of the lab supplement 

Tues 11/21:  Review session at 2:30 in rm303

Weds 11/22:  Exam II (Ch.8, 9, 10, 13). For extra time, you can start the test as early as 10:00 in rm102.  At 10:55, we will move to rm105.  If you are unable to start early, let Lauren know & you can have extra time after 11:50.  Please bring a scantron form 882-E.  

Study questions notes:


Ch.8 SQ 2 -  A bacterial gene mutation (eg, base substitution) can result in a slightly different protein (eg, one amino acid difference).  An antibiotic (abx) binds to a bacterial protein (ie, target) to inhibit &/or kill bacteria.  If an abx doesn't bind well to a bacteria's slightly different protein, that bacteria will be less susceptible to the abx (less sensitive to an abx = more abx resistant).

Ch.8 SQ 3 - A bacteria can acquire new bacterial genes by horizontal gene transfer. The new gene can confer abx-resistance by encoding a protein that inactivates the abx or prevents the abx from getting into the cell or from binding to its target inside the cell (e.g., efflux).

Ch.8 SQ 4 - Natural selection as a force for bacterial evolution:  In certain surroundings, some bacteria in a population are more likely to survive to reproduce than others.  Over time, these bacteria will increase in proportion & spread (i.e., colonize more environments & hosts).

Example of how natural selection can lead to a new abx-resistant bacterial strain: In a bacterial population, some proportion of the organisms may be less susceptible to an abx (more abx-resistant).  In the presence of that abx (or possibly other inhibitory chemicals), the more susceptible are inhibited or killed, but the more resistant bacteria can survive. The surviving bacteria reproduce & their descendants spread.


Ch.9 SQ 3 - A DNA microarray (DNA chip) is composed of specific probes arrayed on a solid surface. Each probe consists of identical, single-stranded short DNAs of known sequence (specific oligonucleotides).  A fluorescently-labeled DNA sample applied to the microarray will only bind (i.e., hybridize by complementary base pairing) to probes that match sequences present in the DNA sample.

a)  Gene expression analysis: mRNAs isolated from cells (eg, bacteria growing under certain conditions) are reverse transcribed (in vitro), resulting in cDNA copies labeled with a colored chemical tag (e.g., red).  The labeled cDNAs are hybridized with a microarray of bacterial genes (probes).  Genes expressed in the cells are identified as the probes that bind those labeled cDNAs.

Under different conditions, bacteria express different genes:  some genes are "on" (transcribed), while others are "off". A microarray experiment can compare which genes are on vs off under certain conditions, compared to a control. Different colors are used to label the cDNAs from genes expressed by experimental (e.g., red) vs control (e.g., green) bacteria. In this example, after hybridization and visualization, genes that are on in the experimental but off in the control sample would be identifiable as the red spots; genes that are off in the experimental but on in the control would be green spots. (genes on in both samples are yellow spots, genes off in both samples are black). 

b)  DNA sequence analysis:  Specific regions of a microorganism's genome (eg, genes) are amplified by PCR & labeled with a colored tag.  When these are applied to a microarray of specific probes, the DNA sequences present in the bacteria (or virus) can be identified.  This allows detection/identification, for example, of a particular bacterial species (eg, rRNA genes as probes) or strain (eg, sequence variants as probes).


Ch.13 SQ 12 - A host's immune system (innate & adaptive) can prevent viruses from infecting cells & eliminate infected cells.  When exposed to a virus, the host's immune system recognizes (binds to) parts of the viral surface proteins & carbohydrates (antigens). If the immune response is fast & strong enough, viral infection & multiplication can be prevented & the host will be protected (immune) from infection & disease.

When an individual who lacks immunity is exposed to a virus, the virions can infect cells, multiply & transmit to other hosts. In an infected host, the virus may cause no symptoms, mild disease, or severe, even life-threatening disease.

Ch.13 SQ 13 - As long as the virus is multiplying, it can be transmitted to new hosts (infectious virus), whether or not the infected host has disease symptoms.

Ch.13 SQ 20, part 1 - A mutation in a viral gene can alter the encoded viral protein. A virus with mutation that alters a viral antigen (surface protein or carbohydrate) can escape the host's immune system (e.g., go unrecognized by host antibodies or immune system cells), or infect different types of host cells (e.g., can bind to a different type of receptor). Such changes can enable a virus to be more virulent &/or infect more hosts. 

Ch.13 SQ 20, part 2 - A virus with an altered version of a protein that an antiviral drug is designed to bind to may be able to keep multiplying in the presence of that drug (e.g., drug resistant HIV).

Ch.13 SQ 21, part 1 - Antigenic drift:  A virus with a mutation that alters an antigen (surface protein or carbohydrate) can escape the host's immune system (not be bound by host's antibodies or immune system cells).

Ch.13 SQ 21, part 2 - A vaccine exposes the individual to a pathogen's antigens, stimulating the adaptive immune response, which includes production of long-lasting memory cells.  If the individual is exposed in the future to the actual pathogen, the immune response is much faster & stronger, & can prevent the virus from multiplying & causing disease (ie, immunity).

However, if the individual is exposed to a virus with an altered antigen, the immune response may not be as effective (but may still prevent some viral multiplication & prevent severe symptoms).

Ch.13 SQ 22 - If different strains of influenza virus (eg, human & pig variants) infect the same host cells, genetic reassortment can occur, resulting in a viral strain with a new combination of genome segments.

Antigenic shift:  Reassortment occurs that results in a viral strain with new surface proteins not recognized by the host's immune system.  The virus can infect & transmit easily (possibly new hosts), & cause an epidemic. 

BIOL 260 links

Global pathogen surveillance system

UW microbiology dept seminars (Tuesdays at 4)

This Week in Microbiology (TWiM) podcasts (microbe TV)

Center for Infectious Disease Research (CIDR)

Infectious Disease Research Institute (IDRI)

Center for Disease Dynamics, Economics & Policy

TEDTalks: How our microbes make us who we are

The Scientist - human microbiome

National Ctr for Emerging & Zoonotic Diseases (NCEZID)

World Health Organization (WHO)

Science Global Health 9/14

Sequencing to track Ebola's spread