Course Corrections

I've been teaching a course for the last 15+ years. I love this course because I conceived it and brought it to fruition. Since its inception, it has been modified a lot, primarily through interactions with the students who take the course. Initially it was a 'lecture' course, but from its inception it involved plenty of reading the scientific literature, discussion of said readings, and writing. 

One of the first major changes to the course was to make it writing intensive. In practice this did not change the course significantly, but did add an overt writing instruction component that was there but less explicit. It was about this time that I was much more active in writing to a general audience and actively engaged in science communication. These are still critically important to me, but my communication to a general audience have moved to the periphery as other commitments and responsibilities have taken over much more of my time. Regardless, my direct involvement in science communication impacted the changes occurring concomitant with the change to making the course writing intensive.

From here

While every year the course changes due to which scientific papers we use and to student interests/involvement, the fundamental structure has remained intact. This summer I am making some relatively significant changes to the course, at least in how it is delivered. The course is structured around a weekly schedule, where Monday is a didactic lecture in the organism we are discussing and relevant background related to the papers we are reading. Wednesday involves short student presentations on two primary research papers the entire class reads (the students address five specific questions related to the paper, but do not present the entire paper). Friday is a discussion related to specific aspects of the organism, papers from Wednesday, and student input from online responses.These discussion are completely open and are hard to prepare for as the discussions can go in many different directions. Regardless, the following Monday we move on to a different organism and set of papers.

Based on student feedback, I am making some significant changes. First, I am changing the M/W.F schedule to  a F/M/W schedule. Because students are reading two primary research papers for presentation/discussion, they have asked for the extra time the weekend provides to read and digest the material, as opposed to the Monday to Wednesday turn around time. This makes a lot of sense to me, so I am making this change for next semester, although it requires me to make some substantial changes to the course schedule. Second, students overwhelmingly indicate that the discussions occurring on Wednesday post-paper presentation and Friday facilitated their learning and engagement with the material. However they also noted it was difficult to see the link among organisms and topics. To be fair, there is no obvious link between these organisms/topics, other than all eukaryotes living today descended from a universal ancestral population. However, this is important and while I highlight similarities between what we were discussing in week 1 versus week 4, it occurs in passing during lecture or the discussions. So to more directly show the linkage, however disparate among organisms/topics, I am developing weekly worksheets for students to fill out asking questions like how does paper X discussed this week relate to topic Y from two weeks ago. Instead of trying to convince students of how analyses in one area can inform a distinct area, I am going to ask them to do that work in a directed way. In some cases there may be no clear links, but these higher level thinking exercises can be extremely informative to the students during discussion, but also to me (the instructor) to observe student perspectives/understanding. Third, I am developing at least one new type of writing assignment or at least making it overt that a writing assignment is distinct in style/approach than other assignments. Currently, students submit four essays that fall under the umbrella of 'essay exam'. Although these essays are completely distinct (one involves assessing a specific scientific paper, another a compare-contrast essay addressing a biological question in two distinct organisms), it appears (based on student feedback) that the distinction is not apparent. This coming semester, I am going to grade several distinct writing assignments that are completely independent...in other words do not fall under an umbrella of 'essay exams'. We already have another writing assignment, a blog post, that students do not report the same concerns with the 'essay exam' assignments even though grade associated with the blog post is slightly more than the individual 'essay exams'.

Basically, I want to facilitate student learning and embracement of, at least, some of the writing assignments. Why do I want do to this? There is much literature noting that writing facilitates learning (this is my personal experience as well).I'm not sure much more is needed to justify these approaches. However, science communication is sorely needed in society, especially societies where a significant population is more than willing to embrace non-scientific modes of thinking to justify policy decisions.

Will these changes improve student learning? I think so, but will need to make the adjustments and see how it works. The good things are these changes built on a solid foundation and are easy to alter if they do not appear to be working.

Eukaryotic Microbiology: The Blogs Are Coming

Despite my desire to keep updating the blog with course information, which has been an abject failure in regards to updates, I still want to post when I can. To be fair, I'm behind on grading, so I can't in good conscience be blogging about the course when assignments need to be graded.

However, I'll take a minute to make this brief post. It's getting to my favorite time of year: Student Blog Posts at Traveling Small with a Nucleus! I know for many students this is a writing assignment they truly enjoy. (Of course I'm sure some students do not like this assignment, but I have yet to hear from them.)

S0, I invite you to check out some previous students posts in the interim. The majority are quite good and there are some real gems in there. It's possible TSw/aN may be invaded with some organisms lacking a nucleus too. I'll keep you posted. 

Eukaryotic Micro: Week 3 the last of the fungi

So this week (actually last week) we covered what is probably the last unit concerning fungi: Cryptococcus neoformans. The first two weeks covered two ascomycetes, Candida albicans and Fusaruim species, and now we move over to the basidiomycetes, otherwise known as 'if I asked you to draw a fungus this is what you would draw'.

The primary research papers were:

• Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation. Gerstein AC, Fu MS, Mukaremera L, Li Z, Ormerod KL, Fraser JA, Berman J, NielsenK. MBio. 2015 Oct 13;6(5):e01340-15. doi: 10.1128/mBio.01340-15.
• Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. Huang M, Hebert AS, Coon JJ, Hull CM. PLoS Genet. 2015 Aug 27;11(8):e1005490. doi: 10.1371/journal.pgen.1005490. eCollection 2015 Aug.

This is an interesting point in the semester. Upon completion of this week, we are ~25% of the way through the semester and exactly 25% of the way through the 12 modules. This is the point where students have completed the short writing assignment four times now, so hopefully they are comfortable with what I am looking for. I lay out the guidelines on day 1, and then model what I expect. There are two difficulties. 1: Getting students to explain a dataset of their choosing such that someone would walk away knowing what was done, what it showed, and most importantly be able to ask informed questions about the data set. Students are reasonably good at explaining the data after a week or two, but struggle to give enough experimental information such that you would know how the data was obtained. 2: Identifying limitations with the data set. This is in fact difficult, but it is an important skill to foster if we really want people who are critical thinkers. I ask them that their limitation answers the question 'how does this affect the authors' conclusions or interpretations?' This latter issue usually takes a couple more weeks to get better at for most of the class.

Cryptococcus neoformans normal and titan cells

It's also interesting because Cryptococcus follows up the ascomycetes we already discussed extremely well. Like Candida albicans, C. neoformans is a budding yeast, which is distinct from Fusarium, which although more closely related to C. albicans, is a filamentous fungus. However, like Fusarium, C. neoformans forms dikaryotic filaments during sexual reproduction and grows in a filamentous form during asexual spore production. 

I like these two papers (this is the first year I've used the Gerstein paper) because they deal with different aspects of development/differentiation in different ways.  The Gerstein paper is focused on a role titan cells play using primarily genomic approaches; the Huang paper is focused on spore formation and development using classical genetic approaches.

Gerstein et al ties in conceptually with the Selmecki and Ma papers from the Candida and fusarium modules respectively. All are centered on the acquisition of additional genetic information and the outcomes of this. I'm certain creationists always talk about the inability for an organism to acquire new 'information'. Well here are three independent examples.

Huang et al ties in, slightly, with the Lui paper from the Fusarium module by dealing with cellular differentiation and development. This is something we will come back to in the future frequently and is a biological concept I think is often underappreciated in microbes.  

First Eukaryotic Microbiology Classes

Since we do not start classes until after Labor Day, the first week represents a Wednesday, Friday week for my writing intensive Eukaryotic Microbiology course. I designed the course to run on a M/W/F cycle, so this first W/F week might seem problematic, but it is not. In fact, it works out extremely well.

The first day of class (today), involves discussing what is going on in the course and going over the syllabus. Similar to last year, in the first class I try getting students involved by having describe their goals and defining plagiarism. This year I focused the first lecture on the structure of the course and less time going in detail on the syllabus. It was only partially successful because I didn't get through the course set up but got through most of it. Luckily there's time to finish on Friday.

Although I don't get too deep into the syllabus (the students can read), I do cover grades and how they are determined because this is an issue that cuts to the heart of many students. One thing I started doing last year in another class, is determining the course GPA. That is the GPA for the course, determined by the student grades. The last two years my Eukaryotic Microbiology course had a GPA of 3.0 and 2.7. I'm pretty happy with these GPAs overall, it means I am not giving out a ton of A's but the GPA is higher than one might expect for an introductory class (this is not an introductory class and is taken primarily by seniors in the major with a smattering of graduate students).

The class is generally set up as follows:

• Monday: I give a standard lecture introducing the students to an organism and the relevant topics for the week.

• Wednesday: Students present primary research papers. However, they don't actually present the paper, I have them answer some specific questions:

• A. What question is the paper addressing and why do we care?
• B. Which conclusion do you think is the most interesting/important and why?
• C. Pick one figure that you think best supports your favorite conclusion and explain in detail how the data support the conclusion.
• D. What are the limitations of the data?
• E. Why are the conclusions important?

Questions A and E are only answered by the presenters, which is why they are struck out. These questions are derived from a document by Little and Parker (no longer available online, but they were at the University of Arizona). I like these because they focus the students in on a specific aspect of the paper, their favorite conclusion, which may be completely different than the press release or authors' overall conclusion.

The students then focus in on the data that supports that conclusions and not the entirety of the paper. Essentially, I do not want the presenters to reiterate the paper to the class, everyone is required to read the papers so there is no need to reiterate them.

The most difficult part is finding limitations or some issue(s) with the data/interpretation of data. I think students are trained to accept the literature and not rigorously go after the authors and their arguments, which, is in a nutshell, how science works. This one takes time and experience to get good at. Even excellent papers can have issues and I think one of my jobs is to get students comfortable with finding issues.

One thing I haven't told the students about is that the presenters have to give a 30 second elevator talk about the paper. I started doing this several years ago and I think it is extremely important. Basically, if you were an author and someone in the grocery store asked you about your work, how do you explain cogently and succinctly such that they are impressed and glad their tax dollars are supporting the work.

• Friday: Discussion of things. This varies markedly and is dependent on the students. I have a discussion board for them to ask questions, raise issues, provide feedback, etc. I do not post to these boards unless things are going off the rails and try to keep it a student oriented discussion board. (Once a prof posts a comment, all additional comments cease in my experience.)

On Friday, the second day of class, I will model what I expect out of the student presentations. We are reading "Complementary Adhesin Function in C. albicans Biofilm Formation' by Nobile et al. I also provided a review article 'Adhesion in Candida spp.' by Paula Sundstrom.

I will give a 30" elevator talk and then give an oral presentation that covers answers to the above questions A-E. Students are required to provide written responses to questions B-D to get us started.

Starting Monday we really kick into gear, although we will stay with Candida albicans. FYI the topics we are covering are drug resistance and host environmental adaptation.

My goal is to keep blogging about the course throughout the semester.

Preparing for Eukaryotic Microbiology Class

For the second year in a row, my advanced microbiology course, Eukaryotic Microbiology, is up and running. Technically this is the 11th iteration of the course, but the second year I'm going to try and blog about the course concomitantly. So the website is went live to students today and has a bunch of business related things about the course and a the first few weeks of modules available.

Before we met, in just under two weeks, there is an online quiz and a number of introductory papers for the course as a primer for the students. The papers are:

• The eukaryotic tree of life from a global phylogenomic perspective. Burki F. Cold Spring Harb Perspect Biol. 2014 May 1;6(5):a016147
• The origin and early evolution of eukaryotes in the light of phylogenomics.  Koonin EV. Genome Biol. 2010;11(5):209.
• The hybrid nature of the Eukaryota and a consilient view of life on Earth. McInerney JO, O'Connell MJ, Pisani D. Nat Rev Microbiol. 2014 Jun;12(6):449-55.
• An archaeal origin of eukaryotes supports only two primary domains of life. Williams TA, Foster PG, Cox CJ, Embley TM. Nature. 2013 Dec 12;504(7479):231-6.
• The common ancestor of archaea and eukarya was not an archaeon. Forterre P. Archaea. 2013;2013:372396. doi: 10.1155/2013/372396.
• A new view of the tree of life. Hug LA., Baker BJ., et al. Nature Microbiology. 2016 Apr 11; 1(article number 16408)
• Predation and eukaryote cell origins: a coevolutionary perspective. Cavalier-Smith T. Int J Biochem Cell Biol. 2009 Feb;41(2):307-22.

Figure 1 from the Hug paper

I ask the students to read the Burki paper first, which is a great overview of the current eukaryotic tree and how it was established. The Koonin and McInerney next, followed by the Williams and Forterre papers. There's a fair bit of overlap among the Koonin, McInerney, and Williams papers that I suggest they skim through. Once those are done, I ask that they read through the Hug paper, which is the only primary research paper of the list. Finally,  the Cavalier-Smith paper on what is a eukaryotic cell in some detail.

I particularly like the two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not. 

New Student Posts en route

As Thanksgiving is over and another semester winds down, a time of great celebration is soon to be upon us. By which I mean student blog posts from my Eukaryotic Microbiology course! As I await the submission of the final drafts to roll in, I discovered some older posts in a folder that never made it onto Traveling Small with a Nucleus. So look through some of the older ones or check those that were not previously posted until now. Feel free to leave a comment or two for the students!

Eukaryotic Microbiology Intro Readings

My advanced microbiology course, Eukaryotic Microbiology, is up and running. At least the website is. I have assigned several introductory papers for the course as a primer for the students. The papers include:

• Predation and eukaryote cell origins: a coevolutionary perspective. Cavalier-Smith T. Int J Biochem Cell Biol. 2009 Feb;41(2):307-22.
• The origin and early evolution of eukaryotes in the light of phylogenomics.  Koonin EV. Genome Biol. 2010;11(5):209.
• The hybrid nature of the Eukaryota and a consilient view of life on Earth. McInerney JO, O'Connell MJ, Pisani D. Nat Rev Microbiol. 2014 Jun;12(6):449-55.
• An archaeal origin of eukaryotes supports only two primary domains of life. Williams TA, Foster PG, Cox CJ, Embley TM. Nature. 2013 Dec 12;504(7479):231-6.
• The common ancestor of archaea and eukarya was not an archaeon. Forterre P. Archaea. 2013;2013:372396. doi: 10.1155/2013/372396.

From McInerney et al

I've used the Cavalier-Smith and Koonin papers in the past to introduce the basic ideas surrounding where eukaryotic cells come from (I think the Koonin paper is more clear here) and what is a eukaryotic cell (Cavalier-Smith wins here).

This year I've introduced the other three papers to provide additional perspective on the origin issues. The McInerney paper does a good job summarizing the four basic hypotheses for the origin of the eukaryotic cell (see the figure) and I think it is good to come after the first two papers as they deal more directly with the science behind the origin of eukaryotic cells.

I particularly like the last two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not. 

First Class in the Books

The state fair is over indicating the end of summer and the beginning of a new semester. I taught my first class today, which of course means I basically met the students and introduced them to the course. In other words, we went over the syllabus…kind of. The course I am talking about is Eukaryotic Microbiology, an upper division course that focuses/uses the primary literature to teach students about eukaryotic microbes, scientific thinking, argument, etc.

The third slide in this lecture is the following (from here with slight modification)

This slide gets used throughout the course but I use it in the Introduction lecture to highlight how little almost all students are familiarized with the diversity in the eukarya. Basically students are familiar with green plants at 12:05, fungi (except for the microsporidia) at 3:15, and the animals, including sponges, at 4:00. Other than the Opisthokonts (in blue) and a minor fraction of Archeaoplastids (in green), the vast vast diversity of the eukaryotic lineages are basically ignored in biology courses. Admittedly there is lip service played to Plasmodium falciparum (the primary agent of malaria) over in the Alveolates. But just look at how little is brought up! Of the eight major eukaryotic lineages, only two are routinely discussed, think of all the biology out there we know so little about! This, in my opinion, is incredibly exciting.

Aspects of this problem were recently brought up by Larry Moran and PZ Myers (by way of   Jeffrey Ross-Ibarra). Again all that diversity noted above falls into the choice C.

Now that I hopefully have instilled some small sense of awe or at least lighted a candle of interest in my students, we deal with the syllabus and some course specific issues. I do want to point out this course is writing intensive, which means a bunch of things but basically we do a fair amount of writing (surprising huh?).

There are two things we did today I want to mention. First, I asked them what their goals are in relation to the course. (Other than getting an A.) So I had them spend a couple of minutes writing down their thoughts and then we discussed them. This represents one easy way to get the students talking in a relatively stress free environment. Open discussions are an integral part of the course and the sooner I get students comfortable speaking up the better. My goals were: 1, to give the students a broad sense of that importance of eukaryotic microbiology; 2, to increase their fluency with the scientific literature; 3, to hone their critical thinking skills. I won't divulge the students' goals.

Second, we discussed plagiarism as it is a writing intensive course. I have found that students know what plagiarism is, but if you ask 20 students for a definition, you'll get 12 - 15 different variants. I also have the students write down what they think the consequence for plagiarism should be. This leads to yet another relatively stress free discussion and serves develop a sense of student ownership for the course. Once the discussion is complete, we agree to a definition and consequences that is posted onto the course website. This year we came up with:

The 4161W class of 2014 has agreed to define plagiarism as not giving credit for others' work, including words and ideas, that is not common knowledge.

and the penalty:

Students who are found to have plagiarized will receive an F on the assignment and be reported to the Office for Student Conduct and Academic Integrity for the 1st offense. A subsequent offense will result in an F for the course and another report to the Office for Student Conduct and Academic Integrity.

As normal for the first lecture, I did not get through everything. Luckily Friday allows time to finish up going over the course and to discuss our first paper. This discussion allows me to demonstrate what I expect of the students when they do presentations and gets the students started reading papers. The paper we discuss on Friday is:

Complementary adhesin function in C. albicans biofilm formation. Nobile CJ, Schneider HA, Nett JE, Sheppard DC, Filler SG, Andes DR, Mitchell AP.Curr Biol. 2008 Jul 22;18(14):1017-24. doi: 10.1016/j.cub.2008.06.034.

My Favorite Time of the Year

From here

One of the courses I teach culminates with blog posts written by the students. This is the third year I have used this assignment and is one assignment the students actually enjoy doing (at least based on student feedback from previous years). Students will be submitting their final essays on some aspect of research on eukaryotic microbes in the next few days and you will be able to find them here. Until the new ones are posted, you can see some essays written previously.

FYI: The assignment is to write an essay of 1000 - 1500 words for a lay audience of science enthusiasts that incorporates at least primary research papers on a eukaryotic microbe. (Microbe being defined in the course as an organism that exists primarily as a single celled organism, thus excluding microscopic multicellular animals.) Students were allowed to write in any voice and use any style of writing.

If you read through an essay, please leave a comment for the student.

Poor Communication of Essentially Good Research

It is no surprise to see a press release on scientific research that inflates the conclusions of the study or its potential impact. But usually the basic biology is correct, not so with the press release I read today. (I thank the twitterverse for bringing this to my attention.) Since I'll go through the press release paragraph by paragraph, you can thank the twitterverse too,

The release starts out well enough, but quickly goes off the rails. In fact, the writers couldn't get out of the first paragraph, which is also the first sentence, without stating half-truths.

Targeting serious and sometimes deadly fungal infections, a team of researchers at Worcester Polytechnic Institute (WPI) and the University of Massachusetts Medical School (UMMS) has discovered a chemical compound that prevents fungal cells from adhering to surfaces, (This would be a great place for a period.) which, typically, is the first step of the infection process used by the human pathogen Candida albicans (C. albicans). (Red note by AbC.)

The point being made is that 'adherence' is the first step of the infection process. Whatever the hell 'infection process' is escapes me, but it does sound pretty awesome and scary. However, the press release completely misses a key point, Candida albicans is a commensal in humans. C. albicans is easily culturable from 60% of all people and is almost certainly found in all humans. Let me be clear, C. albicans causes serious and sometimes deadly infections as noted in the first line of the press release. However, in the vast vast majority of people, C. albicans is not a problem. Herein lies the problem or obvious question ignored in order to write overimpactful press releases. Does C. albicans only adhere to surfaces during infection? Does C. albicans in most people simply float free in saliva, gastric juices, or vaginal fluids? (The answer to these questions is 'No'.)

After screening 30,000 chemical compounds in a series of tests with liveC. albicans, the team found one molecule that prevented the yeast from adhering to human cells or to polystyrene, a common plastic used in many medical devices. Named "filastatin" by the researchers, this molecule now emerges as a candidate for new anti-fungal drug development and as a potential protective material to embed on the surfaces of medical devices to prevent fungal infections.

This is all pretty good. It hits on the major finding and the potential impact of the research.  What is not explicit here, but comes up later, is that the major source of C. albicans in deadly systemic infections is contaminated medical devices, like catheters.

The team, led by co-principal investigators Paul Kaufman, PhD, professor of molecular medicine at UMMS, and Reeta Rao, PhD, associate professor of biology and biotechnology at WPI, reports its findings in the paper "Chemical screening identifies filastatin, a small molecule inhibitor of Candida albicansadhesion, morphogenesis, and pathogenesis," published online in advance of print by the journalProceedings of the National Academy of Sciences (PNAS).

Again nothing to complain about regarding the press release here. We are basically describing the leaders of the research teams and the source of the article. I do have an issue with part of the title of the paper 'a small molecule inhibitor of...morphogenesis...' The title suggests that filastatin inhibits the formation of cell structure or shape. In actuality, the drug inhibits the ability of yeast cells to form filamentous cells. This is a morphological transition, but it does not encompass the entirety of C. albicans structure and shape. A yeast cell making more yeast cells is an example of morphogenesis. The abstract makes this point clear, but the title is a bit colloquial. This is a problem in the field and not specific to the authors, I have probably used similarly short-hand. 

"In humans, the most widespread fungal pathogen is Candida albicans, which is also one of the most frequent causes of hospital-acquired infections," the authors write. "We conclude that filastatin is not toxic to the human cell line under our assay conditions, but is unique in that it can impair fungal adhesion both to inert surfaces and to cultured human epithelial cells."

I am not sure in what context filastatin is unique as a quick literature search revealed HIV-protease inhibitors, a 23 amino acid peptide, cranberry derived compounds, as well as antibodies have all been reported to inhibit C. albicans adhesion. (This is an issue of the authors inflating their work not of the press release writer(s).)

Infection by C. albicans causes common chronic illnesses like thrush and vaginitis, which affect millions of people globally each year and are not easily cleared by the handful of anti-fungal drugs now available. While most fungal infections do not cause serious harm, if one spreads to the bloodstream it can be deadly.

All good. Minor issue with referring to thrush and vaginitis as chronic illnesses as the vast majority of cases are not chronic.

Hospitalized patients with catheters or central intravenous lines are at risk as the fungi can grow on those devices and enter the body. Similarly, patients with implanted medical devices like pacemakers or prosthetic hips or knees are also at risk if the implant carries a fungus into the body. Also, people with compromised immune systems are at greater risk for serious fungal infections. Because of the lack of effective drugs against C. albicans and other pathogenic fungi, the mortality rate for systemic fungal infections is between 30 and 50 percent.

Again all good, but now we come to it. The paragraphs of FAIL.

Typically, a blood stream infection of C. albicans or a similar pathogen begins with fungal cells attaching to a surface—a catheter, for example, or epithelial cells lining the mouth—to form what is known as a biofilm. Next, the ovoid shaped yeast cells morph into an invasive filamentous form, extending pointed filaments that penetrate and damage surrounding tissues. In the current study, the team found that filastatin curtailed both steps: it largely prevented C. albicans from adhering to various surfaces, and it significantly reduced filamentation (inspiring the name filastatin).

First of all, we have established that C. albicans adheres to things independently of infection. So a basic part of C. albicans lifestyle is to adhere to things, things like epithelial cells which are the structures C. albicans normally finds itself on. This is a function of biology not infection.

Second, this press release builds on a dead mythos that yeast cells are commensals and filaments are infectious. This was the conventional wisdom 20+ years ago, but the field has (or has tried to) move on. It is true the filamentous cells do things related to disease that yeast cells do not. Filamentous cells secrete gobs of proteases which help degrade the host tissues. Filamentous cells are invasive. But you know what, yeast cells do things related to disease that filamentous cells do not. Yeast cells do not stimulate the immune response as much as filamentous cells do. Yeast cell populations grow much faster than filamentous cell populations. Yeast cells can readily disseminate throughout the body via the bloodstream, filamentous cells cannot. But ignoring these facts, there are basic predictions we can make based on the press release premise. For example, we should not observe filamentous cells in non-diseased individuals, but we do. We should not observe yeast cells during bloodstream infections, but we do. Other fungal pathogens should show similar morphological transitions, they don't. In fact, Candida glabrata, the second most common Candida species causing human disease only grows in the yeast form.

Third, filastatin inhibits adherence and filamentation. This becomes problematic because those who work on C. albicans are already aware that filamentous cells are extremely adherent, but yeast cells are not. Thus, if you inhibit filamentation you by definition inhibit adherence. However the press release tells us why this result is really the SHITZ (emphasis mine).

As a next step, the team tested filastatin's impact on C. albicans cells that had grown unfettered in test wells and had already adhered to the polystyrene walls. When the compound was added to the culture mix, it knocked off many of the fungal cells already stuck to the polystyrene. The inhibitory effects of filastatin were further tested on human lung cells, mouse vaginal cells, and live worms (C. elgans) exposed to the fungus to see if it would reduce adhesion and infection. In all cases, the novel small molecule had significant protective effects without showing toxicity to the host tissues.

Based on the bolded statement, you now think 'HOLYFUCKBALLS, that's interesting,' because the cells were already stuck to something. While the press release is technically correct, the implications are flat out wrong. First, in almost every experiment the drug was present throughout the experiment, in other words as soon as the cells were added, aka before adherence occurred. Thus, inhibition of filamentation is an obvious and unsurprising likelihood to explain these data. Second, in the one experiment referred to above, the effect of the drug was minor (see data from paper below). Even this minor effect could be an attribute of growth. 

From PNAS Figure 2D

In one case, the black bars, the cells were kept without (left) or with (right) drug for 8 hours and there is a profound difference between the two conditions. In the other case, the striped bars, the cells were grown for 4 hours and then drug left out (left) or added (right) and cells grown an additional 4 hours. Both samples lacking drug are similar (compare the leftmost of the black and striped bars). The authors suggest that the reduction observed 4 hours with drug (rightmost striped bar) represents a reversal of adherence, but this conclusion is not necessarily the best. How about growth after 4 hours is always ~8000 Fluorescence units, but when drug is added no further growth is observed. Knowing what the Fluorescence looked like at 4 hour in this experiment is lacking and important. Note the press release states the drug did something active, 'it knocked off many fungal cells already stuck to the polystyrene.' I say the drug inhibited growth or prevented additional adherence, like by preventing additional filamentous growth as observed in all the other experiments.

Research is now focused on teasing out the precise molecular mechanisms filastatin uses to prevent adhesion and filamentation. "We need to find the target of this molecule," Rao said. "We have some good leads, and the fact that we aren’t seeing toxicity with host cells is very encouraging, but there is more work to be done."

Why does the target of filastatin need to be found? It seems important, but I am not sure why and I wonder if a general audience reader knows why.

Additional studies on filastatin are underway at both WPI and UMMS. "The molecule affects multiple clinically relevant species, so we're pursuing the idea that it provides a powerful probe into what makes these organisms efficient pathogens," Dr. Kaufman said. "In this era of budget gridlock in Washington, our ability to get funding from the Center for Clinical and Translational Research at UMMS to support this work was essential for allowing us to pursue our ideas for novel ways to approach this important class of hospital-acquired infections."

What makes these organisms efficient pathogens? These organisms are shit pathogens. Virtually no one had issues with deadly fungal infections before the 1960s and even after 1960 that number was minute. It is only recently that these organisms have risen to the forefront of importance and it's not the organism that has changed. Rather it is the host, us, or more specifically modern medicine that is the culprit. Now we have a large and growing population of people who are immunocompromised because of cancer therapy, organ transplants, HIV, even extreme old age. But as noted 'in this era of budget gridlock in Washington,' we must inflate and oversell our studies 'to get funding from the Center of Clinical and Translational Research....' There fixed it.

Look, I agree filastatin is an interesting molecule worthy of additional research and development as a coating for catheters and other medical devices. These are some interesting studies and the fact the drug does not appear to be toxic to human cell lines and in a mouse vaginal model is extremely encouraging. It is important to know how this drug acts systemically in a mouse because the bloodstream infections are the critical ones to combat. But these studies are an important first step. 

The project was also funded by a grant from a WPI/UMMS pilot program established to promote collaborations between researchers at the universities to advance early stage translational research. "Joint research programs, such as the pilot program between our institutions, are central to WPI's work in the life sciences," said Michael Manning, PhD, associate provost for research ad interim, at WPI. "As this collaboration between Professors Rao and Kaufman demonstrates so well, both institutions can leverage their complementary expertise for the ultimate advancement of scientific discovery and public health."

Terence R. Flotte, MD, UMMS executive deputy chancellor, provost, and dean of the School of Medicine, agreed. "The faculty of UMass Medical School and WPI possess scientific knowledge and expertise in disciplines that complement each other," he said. "The creation of this type of multidisciplinary team collaboration between the two universities allows us to work synergistically to solve problems important for improving human health."

Synergistically, √. Novel, √. Translational, √. Paradigm shifting, oops missed that one.

I feel bad, slightly, picking on this press release and the author statements. We often give answers to question that upon reflection wish we had a do over. However, this is my field of interest and C. albicans is the organism I primarily study, so I am intimately familiar  with the issues in the field. I am sure the approach I take here could be applied to many press releases. I would like us, as scientists and communication officers, to work harder at getting the stories out, keeping it interesting and informative without jumping the shark. This likely requires some back and forth between the scientists and communications people with a touch of editorial oversight by an independent scientist.

Student Blog Posts: Read 'em and Comment

There is a new blog Traveling Small with a Nucleus I want to draw your attention to. It is on the writings of students from my Eukaryotic Microbiology course. Go and read them, enjoy them, and comment if a spirit moves you to do so.

Paramecium, nice to meet you

How many of you recall one of the first cool science related thing you experienced? I bet if you think about it, even if you no longer give a rat's ass about science, you can come up with something from childhood. Maybe seeing puppies or kittens being born, watching a frog or butterfly develop from a tadpole or caterpillar respectively, seeing light split into diverse colors through a prism.

Malamute puppies

Prism

Chrysalis

I can think of two things that got me hooked on the wonder and awesomeness of biology. One was 'discovering' my brother's microscope. It's a single eyepiece light microscope. I still have the beast and it still works, although it needs a new bulb. Once this device was discovered, it opened a whole new world to me: pondscum. That was when I was first introduced to a beautiful little beast. I didn't know its name or even what the hell I was looking at. What I did know is that it was love at first sight. Now I admit our relationship faltered when I met colecovision and was ruined when I realized the opposite sex was more than just a cootie factory. However, it ignited a longing that burned deep within me, forever influencing my...well let's not get overly dramatic.

The shear awesomeness that comes from seeing these little beasts swimming around in the pond behind your house with your own eyes, well eye since it was a monocular scope is inspiring. Here's a video using a much better scope than I had, which I hope can give you an inkling into that sense of wonder that arose in a child.



There are many aspects of Paramecium biology worthy of discussion: separation of 'somatic' and 'germ line' nuclei, the trichocyst, digestive progression, whole genome duplications, macronuclear development, RNA editing, endosymbiosis, etc. We will touch on a few of these in the next few weeks.

Its Official: Fungi Kick Mammalian Butt

Bats with WNS

Since 2006 certain species of hibernating bats have been dying off in dramatic fashion by what has been called White Nose Syndrome (WNS). It is named as such because of some fungal growth around the nose of many affected bats. In 2008, Blehert and colleagues identified the fungus as Geomyces destructans and showed in early 2009 that the fungus was widespread throughout affected populations. In previous posts on these issues, I raised concerns because there was no data demonstrating causation. In fact, while noting that G. destructans could indeed be the etiologic agent of WHS, I also noted that it could be an indirect effect of some underlying problem. For example, the bat immune system could be impaired by a biological or chemical agent that allows G. destructans to infect and ultimately kill the bats (akin to HIV in people).

Well Lorch et al report in Nature that G. destructans is directly causing WNS in bats. Lorch et al essentially test the third of Koch's postulates, which are:

1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
2. The microorganism must be isolated from a diseased organism and grown in pure culture.3. The cultured microorganism should cause disease when introduced into a healthy organism.
4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Now even Koch realized his postulates are not universal laws. For example, asymptomatic carriers kind of screw over postulate #1 and non-culturable organisms make #2 an impossibility. However, when fulfilled even partially, these postulates provide powerful information in the etiology of disease.

In the case of G. destructans, postulate #2 was fulfilled previously. In the study by Lorch et al, postulate #3 is shown to be true. If you grow G. destructans in culture and then expose healthy (but susceptible) bats to the fungus, they get l00% infection (Treated in table below), but similarly treated, but without the fungus, control animals should absolutely no development of WNS. More than 95% of infected bats succumbed to WNS within 3 months on infection! (Although it sucks for the bats, this provides definitive evidence that the fungus is the causative agent of WNS!!!1111!

Nature Table 1 (partial)

Furthermore, the authors found the fungi in lesions on the wings where most of the disease damage is thought to occur (despite the 'nose' being part of the name). This helps fulfill postulate #4.

This work is important because it affixes a firm target on the culprit. We can rule out other biological or chemical agents causing susceptibility to WNS. This also helps deal with postulate #1. Postulate #1 has been a complete dick in the case of WNS. This is due to the fact that G. destructans is found associated with European bats that are healthy. What Lorch et al's work tells us is that the situation is more complex than initially realized (but the truth of the matter is that life is always more complex). Maybe European bat species have immune mechanisms that prevent WNS. Maybe the G. destructans strain in the US is more pathogenic than the European isolates. Regardless, these are testable hypotheses. We can also definitively add mammals to the animals fungi feed on. Happy Halloween!


Lorch, J., Meteyer, C., Behr, M., Boyles, J., Cryan, P., Hicks, A., Ballmann, A., Coleman, J., Redell, D., Reeder, D., & Blehert, D. (2011). Experimental infection of bats with Geomyces destructans causes white-nose syndrome Nature DOI: 10.1038/nature10590

Fungal research does not need death threats

As scientists we have to sell our work. We need to make our ideas as compelling and WOW!!! as possible to obtain funding, get published in the S/N/C glamour journals, and justify ourselves to the greater community and our peers. But we should never jump the shark.


A recent paper from Fungal Biology proceeds to do just that (subscription required). The press glommed onto to this paper with such objective titles as "'My Dishwasher Is Trying to Kill Me': New Research Finds Harmful Fungal Pathogens Living in Dishwasher Seals" and let's not overlook "My dishwasher is trying to kill me! Deadly bacteria found in household appliances" (Really!?! bacteria!?! Really!?!) A reality based article can be found at MinnPost, for which I provided some thoughts.


Now maybe this is the fault of the media, but maybe not. Actually it's not. Well it's both. As far as the media simply reporting what they were told, they are not at fault. As far as the media actually doing their damn job and not simply being a mouthpiece, they are at fault.

The actual title of the paper is "Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens." That seems fairly benign, although the authors are already introducing the "OMG! We're all going to die!!!" meme by focusing on human opportunistic fungal pathogens. (As an aside, I've always been torn by the phrase fungal pathogen. Is it a pathogen that's a fungus or a pathogen of fungi?)

Fungi live here

So the researchers swabbed dishwashers from all over the world, including the US, and found fungi. This is not interesting. Microbes are everywhere. I am not exaggerating, they are everywhere. The freaking original buildings in Antarctica are being destroyed by fungi. What is interesting is that they found certain fungi frequently, suggesting the environmental factors associated with the dishwasher is most favorable to these types of fungi.

E. dermatitidis

The most common fungus obtained was Exophiala  dermatitidis followed closely by Exophiala phaeomuriformis. As expected these yeast grow remarkably well at high temperature (>45°C), high pH (>10 and even up to 12.5), and high salt (17%). These are all conditions, and harsh ones by most accounts, found intermittently in your dishwasher. Personally, I do find this interesting, albeit descriptive. If you check out your dishwasher seals (or even your refrigerator seals), you can often find some dark gunk growing there. In the case of the dishwasher, you have an idea of what the main fungus might be. (I wonder what's growing on the frig, its certainly a different environment from the dishwasher.)


OK, so how is this related to human health, remember the article's title? Well, E.  dermatitidis has been associated with disease in humans, although it is extremely rare. The word 'opportunistic' in the article's title means something. In the case of E. dermatitidis it means there is something wrong with your immune system. Several studies demonstrate that E. dermatitidis colonizes the lungs of Cystic Fibrosis (CF) patients. However, finding something there does not mean that something is causing a problem. Indeed, the very first sentence of the most recent paper on E. dermatitidis and CF reads "The black-pigmented fungus Exophiala dermatitidis is considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients." (emphasis mine) Ooohhh, that's some scary shit.


Hopefully, I've noted how the media went off the rails here. The question now is why? Did they make this hype up? Let's see if the authors of the paper in question have anything to say on the topic. The following quotes are directly from the paper.


"The ability of opportunistic fungi to survive near-boiling temperatures needs special attention." Yeah, yeah, we all think our research needs special attention, but why do these authors think this? Is it because this potentially deadly fungus is coming to get us?


"Roughly one-third of sampled dishwashers was infested mostly with one of the two Exophiala species." Anyone else think the word 'infested' was used primarily to elicit an emotional response?


"The presence of such fungi in dishwashers increases the risk of infection through tableware or otherwise." Well that's pretty damned definitive! Im sure there's a reference with data backing that statement up. What? There's not?!? Well, we all know E. dermatitidis infections have increased markedly since the 1970s when dishwashers became common in US households, wait, we don't know that? How about E. dermatitidis infection rates correlate with number of dshwashers/capita, we don't know that either? Hmm, well are E. dermatitidis infection rates higher in employees how spend their days working with dishwashers than others, we don't know that either? Fine! Let's consider this latter sentence  Fonzi's shark.


You know what jerks my chain the most? This is interesting work. The authors have looked in a previously ignored niche and found some interesting bugs. They provide physiological evidence for why these organisms, and not other organisms, are there. This work provides a way to identify natural niches for E. dermatitidis, look for hot high pH high salt locales. This work also highlights how very little we actually know about the microbial world in which we live. There's no reason to pump up the volume with fear (don't believe there was fear, read the comments following the Daily Mail article).

P. Zalara, M. Novak, G.S. de Hoog, & N. Gunde-Cimerman (2011). Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens Fungal Biology DOI: 10.1016/j.funbio.2011.04.007