Tag Archives: students

No powerpoint allowed

4 Dec
2014-11-06 14.44.10

One of the students in my class (Arturo Altamirano) as he is giving a talk about Influenza virus. The drawings on the whiteboard were a very helpful for understanding his presentation.

One of the things I did in my seminar this semester was to prohibit the use of Powerpoint or any other presentation software. For their talks, the students had to use the whiteboard or handouts or anything that didn’t require a projector. Most of them used the whiteboard. Initially some of them didn’t like it much. But every student had to give three short presentations during the semester and so they had a chance to improve their whiteboard skills during the semester.

Focus on the story

I asked them not to use Powerpoint because I wanted to make sure that they did not spend a lot of time preparing beautiful slides. Instead, I wanted them to you to focus on the story of their presentation and the connection with their audience. I’m happy that I made this decision because the presentations that students did were really nice and I think they wouldn’t have been as good if I had allowed Powerpoint. All of the students improved their presentation skills during the semester and as the semester progressed, it got more more fun to listen to their talks.

Whiteboard exercises

One thing I will do differently next time is that I will start the semester with some exercises to become familiar with using the whiteboard. I am thinking about asking each student in the first class to introduce themselves using the whiteboard. For example, they could draw (very roughly) the geographic location of the cities or neighborhoods in which they have lived. The exercise would be to combine drawing on the whiteboard and talking to an audience. And hopefully, such an exercise would take away some of the fear they may have about talking without slides.

The picture I attach to this blog is of one of the students in the class (Arturo Altamirano) as he is giving a talk about Influenza virus. The drawings on the whiteboard were a very helpful for understanding his presentation.

Student blogpost: on bad-small-things and small animals

11 Nov

Nicolas Cole (MSc student at SFSU) does a great job explaining the Hersft et al 2012 paper on airborne Influenza A in ferrets using only the 1000 most common words of the English language. Enjoy!  


Figure 2 from Herfst et al 2012 Science

There is a “bad-small-thing” that goes from one flying animal to another flying animal, causing death. It can also go from a flying animal to a human, if a human touches that flying animal while it is dead. This causes the human to get sick. Does this “bad-small-thing” go from human to human through the air? A group of doctors studied the “bad-small-thing” in “small animals” that do not fly. The “small animals” can also die because of the “bad-small-thing” being in their bodies.

First, the doctors changed the “bad-small-thing” in small ways that could make it go from “small animal” to “small animal” through the air. At first, the “bad-small-thing” and the “changed-bad-small-thing” did not move through the air from one “small animal” to the next.

Then they passed the “bad-small-thing” from one “small animal” to the next, to change it more. They did this ten times with both the “bad-small-thing” and the “changed-bad-small-thing”. They found that the “changed-bad-small-thing” grew easier and more often after passing from “small animal” to “small animal”.

Next, they wanted to see if the “passed-changed-bad-small-thing” could pass from “small animal” to another “small animal” through the air. The doctors put the “small animals” in boxes that did not let the “small animals” touch, but air could pass between them. They put small animals with the normal “bad-small-thing” next to boxes of not-sick “small animals” and they put the “small animals” with the “passed-changed-bad-small-thing” next to not-sick “small animals”.

So, if the “passed-changed-bad-small-thing” could be passed, it could not pass by touch but could pass by air. Sure enough, the doctors found that the “passed-changed-bad-small-thing” passed from sick “small animals” to not-sick “small animals” but the “normal-bad-small-thing” did not pass through the air. However, none of the not-sick “small animals” that became sick through the air died.

The doctors took a closer look at the “air-passed-changed-bad-small-thing” and the “changed-bad-small-thing” and found that the “bad-small-thing” only needs 5 changes to be able to pass through the air from “small animal” to “small animal”. The doctors also say that even though the “small animals” were able to get sick from the “air-passed-changed-bad-small-thing” through the air, this does not mean that humans can change the “bad-small-thing” in the same way as the “small animals” so that it could pass through the air.

Finally, the doctors studied “man-made-human-good-stuff” that is meant to stop “bad-small-thing” from passing from humans to humans. They put the “man-made-human-good-stuff” in the “small animals” that were sick from the “air-passed-changed-bad-small-thing”. The “man-made-human-good-stuff” was able to stop the “air-passed-changed-bad-small-thing”!!!!!!!!!!!!!!!!!!!! (because happy points are free).

For the first time doctors were able to show that a “bad-small-thing” can pass from animal to animal enough that it can become a “air-passed-changed-bad-small-thing” and that can be bad for humans.

Students write about a vaccine-derived polio outbreak

16 Oct

Last week we read a paper about an outbreak of vaccine-derived polio virus in Dominican Republic and Haiti in 2000 – 2001. Such outbreaks are uncommon, but they do happen. For me, this paper made clear that no vaccine is 100% safe. As an evolutionary biologist, I find it exciting that it may be possible to study how the attenuated virus evolves to become virulent again.

Here is some of the homework from the students in my class.

Make a graphical abstract of the paper


Cameron Soulette

What kind of data are used in the paper?

Most of the data used in this paper were viral isolates obtained from the stool samples of two patients in the Dominican Republic and Haiti. These were collected (presumably) by the authors because the patients were exhibiting signs of Acute Flaccid Paralysis (AFP). Individuals can have nonpolio AFP, but these two patients were exhibiting characteristics that led the authors to believe their AFP was caused by wild poliovirus, of which very few infections had been observed since the 1980’s.

Nucleic acid probe hybridization identified Vaccine-Derived Polio Virus (VDPV) in these samples. They then performed a sequence characterization of the major capsid surface protein VP1 and compared the isolates from samples to wild-type. The authors looked for more polio cases in the area, and obtained 31 more samples from which they isolated VDPV. They used bioinformatic approaches to analyze their data, including maximum-likelihood and neighbor-joining trees. Using these methods they were able to figure out the timeline for this outbreak of the virus.

Jennifer Gilbert

How much impact did this paper have?

According to Google scholar, this paper has been cited 441 times with the most recent being this year. I found two articles about the paper: one from the Telegraph and the other was a story from Reuters Health (I could not find the original article, but I found it on two separate forums). I think this paper is very influential, but it also has the potential to be used in ways that the authors did not intend. The paper emphasizes the need for continued vaccination and increased surveillance to further the effort of poliomyelitis eradication. However, it seems that this paper has also been picked up as fodder for those in the anti-vaccination movement (one of the forums was hosted by a group called The American Iatrogenic Association – a group focused on raising awareness for illness/ injury caused by physicians).

Links to articles:




Bradley Bowser

Students write about a Dengue outbreak in Australia

22 Sep

It is the fourth week of the semester in San Francisco and the students in my class keep producing interesting content! This week we read a paper on a Dengue outbreak in Australia. One of the conclusions of the paper was that the outbreak was started by a person who traveled to Indonesia and brought back the virus to Australia. The students were a little surprised when they realized all the seemingly unlikely things that must have taken place for the epidemic to get started: the traveler must have been bitten by a dengue-infected mosquito in Indonesia, then they* traveled back to Australia, where they must have been bitten by a mosquito again, and this mosquito must then have survived long enough (the extrinsic incubation period of the virus) so that it could transmit the virus to other humans, and finally this mosquito must have actually bitten one or more other humans to transmit the virus to them.

*Edited on Sep 26 to use the gender neutral singular “they” in stead of s/he.

The students in my class are all master’s students in the Biology Department of SF State.

Here is some of the homework the students did this week:

Make a graphical abstract for the paper


Kadie-Ann Williams

Write two tweets about the paper


Steven Flammer

Who are the authors of the paper?

This article focuses on the epidemic of DENV-3 in Cairns Australia. Dr. Scott A. Ritchie works in the school of public health; tropical medicine and rehabilitative science at James Cook University, Cairns Queensland Australia. He leads a group dedicated to the study of vector-borne diseases. He is the principal investigator in the Eliminate Dengue Program funded by the Bill and Melinda Gates Foundation. He is involved with research projects ranging from global warming to monitoring the course of Dengue and other viral diseases. He has received numerous grants from different institutions to aid the control of mosquito related infections.

Dr. Andrew F. Van Hurk also focuses on Dengue virus. His research is related to molecular studies and phylogenetic studies of virus and has 83 publications. Dr. Hurk is a supervising scientist-entomology at the Queensland Health Forensic and Scientific Services in Australia.

Maricela Prado

Summarize the paper using only the 1000 most common words of the English language

When it is raining and warm outside, there are more small flying things with six legs that bite. They drink people’s blood for food. Sometimes, they have even tinier bad things living inside them. These tiny things can get into the blood if a person is bitten, make them sick, and even kill them. This happened in the land down under two times during 1998 and 2008. People studying this found out that the really tiny bad things needed to live in the flying things for a shorter time in 2008 than 1998 before they can move into people. It is very interesting to know that the time spent in the flying six legged thing can change how quickly and how many people can get sick. Even though the 1998 kind can get into people more often, the 2008 sort doesn’t have to wait as long in the flying thing in order to get into the blood so they end up having about the same chances of getting into people and making them sick. The people studying this also found out that the 2008 tiny bad thing probably came from a person who went to another land then came back with the tiny thing in their blood. They know this because they found that the 2008 tiny thing was more like other tiny things from the other lands than tiny things from the land down under from the past.

Roxanne Bantay

The Devil’s advocate

I felt that the introduction was lacking in background. It moves from broad to narrow too quickly, and left me with questions about Dengue and DALYs values. When discussing environmental conditions, the authors do not extrapolate on how certain conditions enhance Dengue outbreak. They also state that Figure 3 has 100% bootstrap support. From my limited knowledge of bootstrapping, this seems a little too good to be true. So every time they bootstrapped their data, it came out with the same tree every time? And some of the results sections like “Vector Competence Experiments” actually read more like methods than results. Overall I thought the paper didn’t have many ethical issues, and they made a good case for why their work was important, but the actual experiments, data, and relevant background were lacking in detail and made the paper boring.

Jennifer Gillbert

Genomics of the Ebola outbreak in Sierra Leone

14 Sep

I am teaching a graduate seminar at SF State on contemporary evolution of human viruses. Colleagues advised me to pick the papers for the entire semester beforehand, to reduce work during the semester. I didn’t do that, however, because I wanted to be flexible and choose (partly) based on what the students liked or what the students had trouble with. The result was that in the second week of class, I could hand out a brand new paper on the 2014 Ebola outbreak. Now that is contemporary!

The only trouble is that from now on, every other paper I choose will seem old; a Dengue outbreak in 2008? How ancient!

Here is some of the homework by the students in my class. I hope you enjoy reading it.

The context and main question of the paper

This paper focused on identifying the transmission route of the Ebola virus disease (EVD) outbreak throughout West Africa, whether the outbreak continues to be supplied by new vectors, and how the virus has changed to infect humans. The scientists used parallel viral sequencing and they ended up generating 99 EBOV genome sequences from 78 confirmed EVD patients. Phylogenetic comparison of all genomes from earlier outbreaks, suggests that the 2014 EBOV likely spread from Middle Africa within 10 years. Patients sharing intrahost variation showed specific transmission patterns in West Africa, and this suggests that transmission of viral genetics may be common.

Something new found in this study was that in contrast to previous EVD outbreaks, human-reservoir exposure is unlikely to have contributed to the growth of this epidemic. In addition, the EBOV catalog of mutations will aid in future studies. One main question that this paper addresses is whether or not future studies can monitor viral changes and adaptation, and understand how to contain this expanding epidemic.

Ryan Marder

The main conclusion of the paper

As this paper was largely descriptive in nature, I am wary to try to define the main scientific conclusion. With regard to concrete discoveries, however, their data suggests quite strongly a single point of origin for the outbreak of Ebola virus disease (EVD) in Sierra Leone, involving two different strains of the virus introduced simultaneously. Additionally, they document with high fidelity possible transmission links between groups of patients.

More important is the demonstration of the utility and information density available through the types of rapid sequencing and analysis employed in this work. Although not a protocol paper, the authors have produced a technical tour de force with a great deal of insight into the disease dynamics involved in the recent Ebola outbreak. I am sure that, as sequencing costs continue their steep decline techniques of this sort will only become more common, and the community will begin to adopt standard practices for these types of studies.

This sort of adoption and standardization will have broad implications for the future of disease mitigation. Tempered by the human genome project’s underwhelming applicability to medical breakthroughs, I remain optimistic that as genetic data is more readily applied to patient treatment, it is likely that information of this kind will contribute to tangible medical interventions which will directly benefit patients around the world.

Graham Larue

The devil’s advocate

The paper mentioned that when the first Sierra Leone case of Ebola virus disease (EVD) was confirmed, the tracing led to 13 more sick females who attended the burial of a traditional healer. It was misleading to seem the females are more prone to contract the disease than the males because the gender ratio of the funeral attendees wasn’t provided.

It was informative but boring to read when a bunch of numbers were given like single nucleotide polymorphisms (SNPs) between the 2014 EBOV genome sequences and the previous EBOV outbreak, and the numbers of intrahost single nucleotide variant (iSNV) in Sierra Leone patients. The wording was a bit confusing sometimes. One ethical issue could be sequencing for other pathogens when the 35 EDV suspected cases turned out negative for EBOV.

Emily Chang

Make a graphical abstract of the paper


Nicolas Cole

Two tweets about the paper


Arturo Altamirano (@articluateartie)

Reading about using phylogenetics in court

5 Sep

In my new job at SFSU, I am teaching a seminar on the evolution of human viruses. We are reading one paper every week and every student gets a different assignment for each paper. We’ve done one week now and I am very happy with the results. The paper we read was Metzker et al (PNAS, 2002), it is about using phylogenetic methods in an HIV infection case that went to court (thanks to Graham Coop for suggesting the paper).

I asked the students if I could publish some of their work. Here we go:

Describe the context and main question of the paper

The Metzker et al. study details the first instance of the admission of phylogenetic analysis as forensic evidence in a criminal case. It sought to determine whether scientific support existed for the proposed viral transmission event between the suspect (via injection of blood from an HIV-positive patient) and the victim by inferring phylogenies of the patient, victim, and HIV-infected control strains from the same geographic region using two loci under different selective pressures. In trees generated from both loci, the isolates from the victim clustered with the patient’s, supporting a close relationship between victim and patient HIV strains. Phylogenetic analysis has previously been used in inferring HIV transmission events, notably in the “Florida dentist case”. Five individuals were inferred to have contracted HIV-1 from their dentist based on the distinct clustering of their strains with the dentist’s relative to geographically similar HIV-positive controls.

Roxanne Bantay

Who are the (main) authors of the paper?

Dr. Michael Metzker, the primary author of Molecular evidence of HIV-1 transmission in a criminal case (2012), is an associate professor at Baylor college of Medicine and Rice University where he teaches human genetics. Additionally, he is president & CEO at RedVault Biosciences, a technology company that aims to advance personalized genomic medicine. Metzker is also an active researcher in the field of bioinformatics and next-generation sequencing.

The last author of the preceding publication is Dr. David Hillis, who is a current evolutionary biology professor and former director of the biology and bioinformatics department at the University of Texas (Austin). Hillis’ research focuses on experimental laboratory evolution; he believes that by studying this process we can ultimately gain insight into the underlying mechanisms that drive evolution.

Eduardo Lujan

Explain the main results of the paper using only the 1000 most common English words

This paper is about a doctor who tried to kill his girlfriend by using blood from a sick person. The doctor got the blood from their work and stuck their girlfriend during a fight. The important part of this case is the way that they showed that it really was the doctor who made the woman sick. For this case, tiny changes that happened in the thing that made the woman sick were found. These changes can show which person made the other people sick and show the relationships between all of the sick people.   By looking at these changes and the relationships, they showed that the doctor was the one who was at fault for making the woman sick.

Bradley Bowser

(see http://splasho.com/upgoer5/)

Make a graphical abstract of the paper


Peter Manzo