Tag Archives: microbiology

Antigen Presentation #2: B Cells

Antigen Presentation

Presentation by B Cells

Before thinking about B Cells presenting antigen, first recall that B Cells are lymphocytes bearing antigen receptors on their surface called B Cell Receptors (BCRs). These BCRs have been randomized during development such that every B Cell can theoretically bind a unique antigen. See Lymphocyte Development for a refresher on this if you need it.  The major function of B Cells is to make antibody that is nearly identical to its receptor protein, which will be secreted and can then bind to antigens of the same shape.


B Cell with specific BCR engages an antigen on a bacterium (Left). After activation this B Cell will become a Plasma Cell secreting antibody with identical specificity as the original BCR (Right).

A major distinction between B Cell phagocytosis and that by Macrophages is that B Cells only take up materials they have bound with their BCRs, while macrophages take up material indiscriminately. The reason for this, of course, is that B Cells are gearing up to produce antibody, and the best way to ensure this antibody will bind anything of use is if only B Cells bearing specific BCRs known to bind antigen are activated. Macrophages have no antigen-specific receptors, so this specificity is not required by those cells. The membrane bound BCR is exactly the same molecule as secreted antibody – except for the small portion that anchors the BCR to the membrane.

Like macrophages, B cells are ‘professional’ antigen presenting cells (APCs) that take up exogenous antigen, break it down within lysosomes and present the resulting peptide fragments within MHC Class II Molecules. As with other professional APCs, this is intended to pick up foreign, invasive particles for present them to T cells to elicit a specific immune response.

ImageJust by binding to antigen with their BCRs, the B Cell will become (at least partially) activated, stimulating proliferation of this cell and processing/presentation of antigen as indicated above. In order to complete its activation, this B Cell must receive ‘help’ from T Cells capable of binding the presented antigen in the context of MHC II. Because T Cells have also been selected for ‘Non-Self’ exclusivity, this provides additional insurance that this B Cell was truly activated by a ‘Non-Self’ antigen.  The MHC II :: TCR + CD4 interaction between the antigen-presenting B Cell and the helper T Cell results in activation of the T Cell, that immediately gives activation signals (cytokines) back to the B Cell.


Keep in Mind the Big Picture!

To summarize with an example:

  1. A bacteria gets into the host
  2. B Cells with BCRs capable of binding any part of that bacteria catch ahold of it
  3. These B Cells gobble up the bacteria (endocytosis)
  4. Inside the B Cell, the bacteria is killed and broken into a bunch of little pieces
  5. The little bacteria pieces are picked up by MHC II molecules
  6. MHC II molecules move to the cell surface and ‘present’ antigen
  7. T Cells with TCRs capable of binding this bacteria piece within MHC II, do so
  8. These T Cells become activated, proliferate and produce activation factors (cytokines)
  9. These activation factors trigger the B Cell to go on proliferating and changing into Plasma Cells.

10. Plasma Cells no longer make BCR on the surface, they make a soluble form of that BCR, called Antibody, and spew that forth in great amounts.

11. Antibody can coat, gum up, and signal the disposal of bacteria all over the body.

Resting and Activated T Cells from “Immune System History” by Dr. Harry Louis E. Trinidad 
All that ER expansion is to accommodate the heavy load of secreted protein this cell will churn out.



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Posted by on December 8, 2013 in Uncategorized


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Antigen Presentation #1: Macrophages

Antigen Presentation

Presentation by Macrophages

Macrophages (‘Big Eater Cells) exist in a variety of flavors with slightly different functions throughout the body. For out purposes, we’ll just consider a macrophage that is responding to some inflammation. Like a number of other cells, macrophages can react to inflammatory signals generated by damaged cells at the site of a wound. Once there, the macrophages will eat up (by phagocytosis) whatever they find : cellular debris, dirt, bacteria, anything.

ImageOnce they take up this material, the macrophages will begin to ‘Process and Present’ them. Processing involves the digestion of internalized material by fusion of the phagosome with enzyme-containing lysosomes and reactive-oxygen-species-containing peroxisomes. This treatment breaks up materials into small units that can be bound by Major Histocompatability Complex (MHC) Class II molecules and transported to the cell surface. In this way, the MHC ‘presents’ antigens(Ag) such that they can be tested for binding with the T Cell Receptors (TCRs) on T Cells.

MHC Class II molecules with Ag can be engaged by TCRs with the aid of CD4 acting as a stabilizing molecule between the T Cell and the MHC. However, only TCRs that can soundly bind the MHC+Ag will trigger a reaction that promotes the T Cell to become activated. These activated CD4 Helper T Cells will proliferate and begin secreting molecules (cytokines) that activate other cells in turn. The interaction of T Cells with APCs occurs across a highly organized ‘immune synapse’ where numerous cell-cell recognition molecules come together (see the fluorescent microscopy image below)


      Borrowed from

Helper T Cells provide help to a number of other, effector cells, such as B Cells, Killer CD8 T Cells (also called Cytotoxic T Cells, or CTLs) and macrophages.

It is important to recall that T Cells, like B Cells have undergone negative selection during development so that they only bear TCRs that can bind Non-Self material. Therefore, although self molecules may be presented by APCs, there should be no corresponding  T Cells that recognize these Ags.

Keep in Mind the Big Picture!

To summarize with an example:

  1. A bacteria gets into the host through some wound
  2. The wound stimulates inflammation recruiting Macrophages
  3. Macrophages gobble up the bacteria (endocytosis) in a non-specific manner
  4. Inside the Macrophage, the bacteria is killed and broken into a bunch of little pieces
  5. The little bacteria pieces are picked up by MHC II molecules
  6. MHC II molecules move to the cell surface and ‘present’ antigen
  7. T Cells with TCRs capable of binding this bacteria piece within MHC II, do so
  8. These T Cells become activated, proliferate and produce activation factors (cytokines)
  9. These activated T Cells can now go on to ‘help’  (primarily) B Cells and CD8 ‘Killer’ T Cells  do their jobs

The Immune Synapse


HTLV-I capsid protein (Gag) at the cell-cell 
junction. Tubulin-alpha (green), HTLV-I Gag p19 (red). 
Bar = 5 μm. Source


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Posted by on December 8, 2013 in Uncategorized


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Three posts on Antigen Presentation

Having recently finished teaching a semester of microbiology ending with my favorite topic, immunology, I thought I would provide some summaries of three different types of antigen presentation:

1. Presentation of antigen by macrophages (MHC II + Ag) to CD T Cells (TCR + CD4) resulting in the activation of CD4+ Helper T Cells

2. Presentation of antigen by B Cells (MHC II + Ag) to CD T Cells (TCR + CD4) resulting in the activation of CD4+ Helper T Cells – specifically capable of activating B Cells that have ‘seen’ and taken up antigens that bind to their unique BCRs.

3. Presentation of antigen by Epithelial Cells (MHC I + Ag) to CD T Cells (TCR + CD8) resulting in the activation of Cytotoxic T Lymphocytes (CTLs) that will kill cells presenting this antigen. All Cells bear MHC I, enabling them to present endogenous, intercellular antigens such as infecting virus particles.

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Posted by on December 8, 2013 in Uncategorized


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The End of Days is upon us


The semester is drawing to a close. There is only one last day of regular class left before we have our jeopardy review session and then Final Exam. Finals this year will be held on Tuesday, December 10. Officially, Microbiology starts at 9am and General Biology at 12pm, however all students are welcome to come at either time according to their own convenience.

On our last day of Microbiology we will be reviewing antigen presentation and talk about the basic processes associated with Lymphocyte Development. How does the body discriminate between self and non-self?


                      World Demographics – Into the 21st century

In General Biology, we will review the Hardy Weinberg equations and what they can tell us. I’m also hoping to demonstrate the effect of population size on genetic drift (and maybe even genetic draft). We will also be discussing populations and how speciation occurs as well as associated topics of sympatric and allopatric speciation.  We’ll also look at survival strategies (k and r) and finish with human demographics and how some of these features also appear in human populations.

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Posted by on December 1, 2013 in Uncategorized


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Finishing Offit’s Vaccine Course

ImageI just finished up Paul Offit’s Vaccines course offered for free through I found this course to be an excellent introduction to the science and history of vaccines which anyone could benefit from regardless of their background. This is particularly important because the act of having children has such a low barrier to entry, yet it immediately puts one in the position to be responsible for another’s life.

I highly recommend this course to anyone who is interested in vaccines, interested in immunology, interested in disease, has children, might have children in the future and really anyone who wants to take their citizenship in the world seriously.

The last lecture on vaccine exemptions was especially informative to me as it discussed not only the current trend in vaccine refusal, but also explored the historical and legal history. Listening to this lecture reminded me of a question that has always bubbled on the back burner of my mind: What are the legal ramifications of vaccine refusal for the physicians who care for these patients? My feeling is that allowing parents to elect to refuse vaccines for their children is akin to asking their doctor to practice sub-standard medicine, something that is often prosecuted in malpractice cases.

ImageConsider the case of Typhoid Mary, who spread her eponymous disease through preparing baked goods in New York. When she was finally tracked down, she was forced to become “quarantined on North Brother Island in a tiny cottage separated from Manhattan by the East River.” Her freedom was certainly infringed upon for the good of the public. Was this a reasonable course of action by the authorities?

I haven’t read this book yet having just discovered in today, but I will be looking into it shortly.Image

You can explore this topic more in Christine Vara’s article here or read Art Caplan’s article on a much more recent case here.


Posted by on November 4, 2013 in Uncategorized


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MicroBiology Test Questions


Mixed Culture

Despite the surfeit of responses to my call for General Biology Test questions earlier this week that I had to wade through (read sarcastically), I thought I would yet again offer the opportunity for anyone (Students!?) to present potential test questions. If there is anyone out there who would like to try their hand at it, please respond here in the comments section with your proposed question(s).

Topics for this exam include:

-Laboratory techniques (primarily microscopy and culturing methods)

-Cell composition/organelles/functions, comparing and contrasting prokaryotes and eukaryotes

-Prokaryotic cell biology

-Eukaryotic cell biology

-Viral biology

-metabolism / flow of energy through living systems

-cell culture / growth patterns / nutrition

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Posted by on October 23, 2013 in Uncategorized


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This Week in MicroBiology Class



Instead of starting our chapter on Eukaryotic micro-organisms / parasites, we spent much of Thursday’s class discussing the second Chapter of ‘Vaccinated’. This chapter digs in and discusses how a number of vaccines were tested in the children of the Willowbrook institution in New York. We talked about how researchers must balance the (sometimes) competing interests of doing the best experiments to answer a question and looking out for the interests of those who can not look after themselves (the children of Willowbrook, in this case).

This chapter looked at the work of several investigators; Most evaluating vaccines, but one (Krugman) was also doing experiments to investigate how Hepatitis was spread. His work included the infection of a number of children with live virus, but no attempt at protecting them from infection.

This is presented as the most condemnable work of the lot as it presented no potential benefit to the children. In saying this we define the principle by which other work was done, ‘does the study do no intentional harm and does it provide at least some potential benefit to the subjects?’

This principle provides a challenge to doing the (scientifically) ideal experiment outlined below.

A basic, direct vaccine test would divide patients into two groups (vaccinated and unvaccinated) and then challenge half of each group with live virus (or whatever the vaccine is to protect against).

Ideal results:

vaccinated –> unchallenged –> 100% healthy

vaccinated –> challenged –> 100% healthy

unvaccinated –> unchallenged –> 100% healthy

unvaccinated –>challenged –> 100% sick

However, this means that the researcher would be knowingly (assume s/he is not blinded) injecting unprotected patients with live virus – an obvious ethical issue.

In looking through some old work done to investigate how hepatitis is spread, there was a mention of work conducted in just such a manner:


Bellin and Bailet J. Ped 1952

It’s unclear from this reference to a personal communication what, exactly the word ‘volunteer’ means.

I’ll bring up this paper in class the next time we discuss Vaccinated. I have an interesting person connection to it.

Instead of a experimentally controlled challenge, modern vaccine tests (as the other work described in this chapter) use much larger populations chosen because of their ‘at risk’ nature and then we wait and see if there are statistical differences between the infection rates of each group.

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Posted by on September 6, 2013 in Uncategorized


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Paul Offit’s Vaccine class

ImageIn my microbiology class, students read Paul Offit’s ‘Vaccinated’, an excellent account of the life and work of Maurice Hilleman, creator of many vaccines in common use today. I don’t know how many of my students are aware of it, but is a free online university offering courses in a number of subjects taught by senior faculty from many distinguished universities. Today marked the first day of Paul Offit’s Vaccine course, which covers topics related to the history, development, use and misinformation surrounding vaccines. From the course website:

1) History of Vaccines – Viruses

2) History of Vaccines – Bacteria

3) Current and ‘Alternate’ Schedule

4) Common Questions About Vaccines

5) Vaccines in the media

6) Creation of a Vaccine – Case Study: The Rotavirus Vaccine

7) Vaccine Exemptions

I can’t promise that this course is still open, but I expect it is – and best of all it’s FREE.

Furthermore, if you sign up and only decide to watch one or two class lectures, there’s no risk: just drop out or simply stop signing in. So, if you have any interest in the subject, or would simply like to see what it’s like, go onto and type ‘vaccines’ in the search bar.

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Posted by on September 3, 2013 in Uncategorized


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Cool Virtual lab for my Micro Students


An excellent example of a streak plate

I was looking around online and found this site that has a virtual lab for doing streak plates. Since we will likely be doing these very soon, I thought you might find this to be a pretty neat preview from Michigan State University. 

It took a little playing around before I got it, but click on the ‘module’ button to get started and then drag the inoculating loop to the burner. I think once you do that, the rest is pretty intuitive. There is a pdf of instructions as well to get you started.

The purpose of streak-plating, you should recall, is that it allows you to pick individual colonies that have grown out from individual cells. 

Streak Plate Simulation 

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Posted by on August 28, 2013 in Uncategorized


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first day jitters

Yesterday was the first day of my Bio and MicroBio classes for the Fall semester and I’m trying some new things including using iPads as clicker devices and media delivery. I’ve had some problems moving my iBooks onto the devices, but with some help from Apple’s technical services, I hope to have that worked out soon.


Won’t get Fooled Again

One problem I did stumble into was getting used to the eClicker interface while trying to keep my cool at the same time. Worse, in my fluster I confused the approach of 11 o’clock with 12, and rushed my way into ending class a full hour early.

in the event that anyone reading this is a student in my class, I want to mention that I would like you all to read the first chapter of the textbooks and write out the end-of-chapter questions (MC&TF for Micro, Testing Yourself for GenBio). You should also read the first chapter of the complementary book by Thursday, Aug 29.

All in all, I think everything went fine and I’m eager to get working on core material in the coming classes.

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Posted by on August 21, 2013 in Uncategorized


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