Category Archives: Important

Some Holiday spirit for the class

In searching through the Internet this morning, I found some microbiology art to help us get into the season!

Staphylococcus and Serratia; Author(s):Tasha Sturm, Cabrillo College

Staphylococcus and Serratia; Author(s):Tasha Sturm, Cabrillo College

Another Christmas tree!

fungal-christmas; via Stephanie Mounaud, JCVI

Star: Talaromyces stipitatus; Tree: Aspergillus nidulans Ornaments: Penicillium marneffei; Trunk: Aspergillus terreus – via Stephanie Mounaud, JCVI

Some yummy cookies!

Not OK to eat in lab, via Ms. Humble

Not OK to eat in lab, via Ms. Humble

Uh, Ebola and MRSA!

Lots of yuckier examples if you click the picture, via Wendy Staples

Lots of yuckier examples if you click the picture, via Wendy Staples

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Critically ill patients and intestinal microbiota

An article entitled The intestinal microbiota and host immune interactions in the critically ill, by TJ Schuitj and co-workers, and published recently in Trends in Microbiology, nicely reviews the complex set of issues caregivers need to be aware of with this set of patients (note: this article may be downloaded without cost while logged into the York College network.) All BIO230 students should find the article relatively easy to follow, particularly as we work through Chapter 15 on Innate Immunity. The article begins by summarizing the diversity of microorganisms in the healthy human gut. Surprisingly, across all human cultures, the composition of the intestinal microbiota can be organized into three broad clusters or enterotypes, and these clusters are independent of continental or national location. Recent research suggests that people with the different enterotypes might potentially respond differently to different drugs and diets, and so further study of the specific composition between healthy individuals and the role that these enterotypes play in normal health is important.

Interrelationship between various groups of bacteria and food intake (Fig 1c) from Schuitj et al

Interrelationship between various groups of bacteria and food intake (Fig 1c) from Schuitj et al

It is easy to think of the microorganisms of the mammalian gut as being free loaders with little contribution to the host, however the presence of the normal microbiota is actually very important for proper health. The principle of competitive exclusion or microbial antagonism has been brought up previously in class; the presence of relatively benign microorganisms can prevent the overgrowth of more pathogenic microorganism. This principle has been further used to postulate that microorganisms now missing from frequent human contact (parasitic worms for instance) have led to increased levels of autoimmune and allergic diseases in modern human societies, in a hypothesis called the “hygiene hypothesis.” However, the benefit of these normal organisms goes significantly further than that, as illustrated by Figure 1c from this article. The presence of the normal microbial flora is also critical to break down dietary components into a form that the human intestine can adsorb, and these organisms also produce a number of compounds such as vitamins that our bodies are unable to make on their own. In the absence of these microorganisms, the majority of foodstuff passes through the small intestine essentially undigested and moves out of the body.

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End of Course Material, Fall 2012

The final exam for Prof. Singleton’s sections of BIO230 is scheduled for the following times, and will be held in the computer lab in PAC185:

  • MWF  11 AM section:  Monday, Dec 17th, 10:15-12:15 PM
  • MWF 1PM section: Monday, Dec 17th, 12:45-2:45 PM

New material following the 3rd exam will include:

  • Gram positive bacteria: Chapter 19
  • Gram negative bacteria: Chapter 20
  • Viruses: Chapter 13
  • Specific viruses: Chapters 24 and 25
  • Additionally, the chapter on Introduction to Genetics (Chapter 7) will be VERY helpful to understand viruses

The above schedule is ambitious, and I do not expect that we will get through it all. We will cover the material on viruses by the last lecture.

The final exam for this course is cumulative. A significant portion of the final (approximately 40%) will draw on the final series of lectures dealing with our discussion of the above listing of pathogenic microorganisms. However, there are a number of topics that I consider of critical importance for which we will be responsible from the first 3 exams. Material that you should be familiar with will include:

  • Chapter 3 Cell Structure; pp 56-66,72-76,80-85
  • Chapter 4 Microscopy; pp 97-105,108-112
  • Chapter 6 Nutrition; pp 166-172, 176-179, 185-189
  • Chapter 9 Control; pp 258-261, 263-270, 277
  • Chapter 10 Antibiotics; pp 285-299 (understand the mechanisms of drug killing, not specific examples of antibiotics)
  • Chapter 14 Infection; pp 402-416, 418-420, 423
  • Chapter 15, Innate Immunity; pp 436-440, 444-448,451-453
  • Chapter 16, Adaptive Immunity, pp 460, 463-464, 466-471, 482-485
  • Chapter 17, Immunization, pp 491-497
  • Chapter 18, Immune Disorders, pp 512-522

Proper reading of cultures: still important

As I cannot stay away from the Micro lab, even on the weekend, I made my Saturday morning pilgrimage to make sure nothing was amiss. I did find two things of note: first, even though there was a practical question dealing with the proper discarding of cultures that essentially everyone got correct, in practice people seem to miss what the proper procedure is. All to-be-discarded culture tube need to go in the appropriate rack, with all tape removed prior to discard. Second, I found about a dozen cultures in the incubator. Those of you who left cultures in the incubator for the weekend will need to run them again. I do feel somewhat like a broken record in this regard, as I did specifically state it to everyone repeatedly on Wednesday and Thursday, and wrote about it here previously, but perhaps it is time to reemphasize things that are important for success in a lab.

Names blurred, since this is on teh interwebs! One culture appears to belong to Lord Voldemort, He Who Must Not Be Named!

All of our cultures need to be run, incubated, and interpreted according to specific guidelines, or else the interpretation of the culture is completely invalid. The Clinical and Laboratory Standards Institute is a national organization that establishes guidelines for the proper way to set up and read clinical assays in laboratories. If a test is run for too short of an interval, there is a significant possibility of obtaining a false negative result, and if a test is run for too long of an interval, there is a possibility of obtaining a false positive result. Either case represents the possibility of a poor patient outcome: for the false negative, they might not receive notice that they have a given infection, and for the false positive, they might be started on an inappropriate treatment regimen.

End of Course Material, Fall 2011

The final exam for BIO230 is scheduled for the following times:

  • MWF  11 AM section:  Monday, Dec 19th, 10:15-12:15 PM
  • MWF 1PM section: Monday, Dec 19th, 12:45-2:45 PM
  • MW 5 PM section: Friday, Dec 17th, 5:00-7:00 PM

New material following the 3rd exam will include:

  • Gram positive bacteria: Chapter 19
  • Gram negative bacteria: Chapter 20
  • Viruses: Chapter 13
  • Specific viruses: Chapters 24 and 25
  • Additionally, the chapter on Introduction to Genetics (Chapter 7) will be VERY helpful to understand viruses

The above schedule is ambitious, and I do not expect that we will get through it all. We will cover the material on viruses by the last lecture.

The final exam for this course is cumulative. A significant portion of the final (approximately 40%) will draw on the final series of lectures dealing with our discussion of the above listing of pathogenic microorganisms. However, there are a number of topics that I consider of critical importance for which we will be responsible from the first 3 exams. Material that you should be familiar with will include:

  • Chapter 3 Cell Structure; pp 56-66,72-76,80-85
  • Chapter 4 Microscopy; pp 97-105,108-112
  • Chapter 6 Nutrition; pp 166-172, 176-179, 185-189
  • Chapter 9 Control; pp 258-261, 263-270, 277
  • Chapter 10 Antibiotics; pp 285-299 (understand the mechanisms of drug killing, not specific examples of antibiotics)
  • Chapter 14 Infection; pp 402-416, 418-420, 423
  • Chapter 15, Innate Immunity; pp 436-440, 444-448,451-453
  • Chapter 16, Adaptive Immunity, pp 460, 463-464, 466-471, 482-485
  • Chapter 17, Immunization, pp 491-497
  • Chapter 18, Immune Disorders, pp 512-522

Human Papillomavirus: a vaccination update!

Papilloma. Human papillomavirus (HPV)

Human Papillomavirus lesion, Image via Wikipedia

Via the New York Times, a story detailing the very recent recommendation by an advisory panel at the Centers for Disease Control to endorse vaccination against Human Papillomavirus (HPV) for boys ages 11 and 12. Currently, the CDC recommendation for the HPV vaccine (Gardisil) is for all girls at this age. The vaccine is designed to prevent infection by this very common, primarily sexually transmitted virus, which in turn is responsible for causing a significant number of cervical cancers in women. The move by the advisory committee would be followed up by a decision by the Director’s office at the CDC, with a likely recommendation to the Secretary of Health and Human Services presidential cabinet office for final approval.

The vaccine is currently rather expensive, at approximately $300 for the three dose regimen, however it is covered by most insurance programs at present.  The Department of Health and Human Resources recommended in 2006 that girls be vaccinated by age 12 for HPV, and the vaccine is widely available, however the NYT article does note that so far compliance rates have been “disappointing,” suggesting a fair amount of public resistance. This negative perception has of course occurred in part due to public pronouncements by people such as Michelle Bachmann (see here for a rant from last month,) where she attributed a link between HPV vaccine and mental retardation.

Although the recommendation is likely to make it to full approval status resulting in a national recommendation for the HPV vaccine in both boys and girls, it is unclear to what extent it will make in cancer rates in the short term. Cervical cancer rates have been declining over the past few decades, even prior to the availability of an HPV vaccine, likely due to increased surveillance and early detection. However, as summarized here, forms of cancer (mouth and throat) attributable to HPV infection have been increasing in males very recently. These cancers would likely greatly diminish with common vaccination. And considering the cost of treating cancer (and hoping that you survive the disease,) the upfront $300 investment then seems like a real bargain.

I also came across this link via io9.com, which gives a current update on how the vaccine is constructed. Vaccines are typically made using two general approaches. In the first one, called attenuation, a virulent pathogen is manipulated in the laboratory to become avirulent, so that its ability to cause disease is diminished or eliminated. When the attenuated pathogen is introduced via vaccination, the immune system recognizes it at the bona fide pathogen, and generates a long term response that confers immunity to reexposure. This approach carries with it the danger that the attenuated pathogen reacquires virulence and then could potentially cause disease as a side effect. The “live” influenza vaccine and most current forms of polio vaccine are of this type, and the classic example of using cowpox to confer immunity to smallpox is the same thing in principle.

The second approach uses a killed pathogen, where the pathogen is grown in the laboratory and then is treated with chemicals to eliminate any chance that the pathogen can reacquire virulence. The killed pathogen still is able to induce a long term immune response, however there is no risk of getting the disease from this vaccine. The potential side effects are limited to adverse reactions to a vaccine component, such as the chemicals used to inactivate the pathogen. The flu “shot” is an example of this form of vaccine.

Assenbly of HPV virus-like particles

HPV vaccines such as Gardisil are using a new approach that wasn’t possible 10 or 20 years ago, where the genes of the pathogen are manipulated in the laboratory to make a novel kind of vaccine. In the HPV vaccine, individual virus components are assembled together in the lab by using the yeast Saccharomyces cerevisiae to make all of the virus pieces. For a virus to be infectious, it requires both a set of virus proteins (the capsid proteins) and a genome (nucleic acids that encode the instructions to make that virus.) In the case of the HPV vaccine, only the capsid proteins are present, and no genome is included in the virus-like particles that are included in the vaccine. This makes for vaccine preparation that effectively induces a long term immune response, has no risk of reacquiring virulence, and has not been treated with the chemicals that may be involved in adverse reactions to vaccine components.

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