A first look at my exome variants from 23andMe

About 5 months after I sent my saliva to 23andMe, I received an email that my exome results were ready. The data were in a large (4.2 GB) encrypted file folder, that could be opened only after I had downloaded and installed TrueCrypt. Eventually I was able to download and unpackage my data. These data consist of 4 files, all labeled with my identifier: “LF1396″ and ending with a .bam, .bai, .vcf.gz, and .report.pdf. The .bam file contains the alignments of the Illumina reads to the human reference sequence, the hg19 release. The .bai file is an index file of the read alignments. The .vcf.gz is a zipped .vcf  file, for “variant call format” developed by the 1000 Genomes Project, in the latest version 4.1. And the pdf report is a 17-page summary explaining the file formats, my “exome at a glance” summary statistics, and a description of the filtering scheme used to select 21 variants of interest. The rest of the report describes each of the 21 variants, sequentially filtered for high or moderate predicted effect, occurring at low frequency (<1%), in genes involved in Mendelian disorders.

Figre 1. Bases sequenced and exome coverage. A: number of bases sequenced; top line indicates total coverage of 117X. B: Number of called bases in exome. Small red sliver indicates variants from reference genome (hg19).

Figure 1A shows that a little under 4 billion bases align to or near the targeted exons. These on-target and near-target bases map to about 120 million exonic positions. The vast majority of the exonic base calls are identical to the human reference genome.

Figure 1C: Variant calls listed in the vcf file.

About 0.1% of the exonic base calls are variant compared to the reference sequence. Figure 1C shows that these variants consist of about 100,000 single-nucleotide polymorphisms (SNPs) and 10,000 insertions/deletions (indels). These numbers are consistent with unrelated humans sharing 99.9% DNA sequence identity.

Given over 100,000 total variants, which should I look at first? Which of these are most likely to influence my health or appearance or behavior? Which of these have the most impact on me being me? Although 23andMe specifically stated that no consumer-level interpretation would be provided as part of their pilot exome sequencing project, they do provide annotation of the variant calls, in the vcf file.

Figure 2. Classification of variants by predicted impact on gene function.

Figure 2 from the 23andMe exome report shows the distribution of my approximately 110,000 variants categorized according to their predicted impact on gene function.

• High impact variants include gain of premature stop codons (nonsense mutations), frameshifts, splice site alterations, and loss of stop codons. My exome sequence contains 634 of these.
• Moderate impact variants include non-synonymous substitutions (amino acid changes) and codon insertions and deletions (addition or deletion of amino acid residues). My exome sequence contains 11,504 of these.
• Low impact variants include synonymous substitutions (no change in amino acid sequence) or gain of a start codon.
• Unknown impact variants are those “unlikely to affect gene products” – presumably because they occur in non-exonic (intergenic or intronic) sequences.

Another way to look at these variants is by frequency in the human population. Variants that occur at high frequency are less likely to have serious adverse consequences. Conversely, it’s tempting to think that rare and unique variants may contribute to me being such a unique and rare individual.

Figure 3. Variant frequencies.

Figure 3 shows that about 15% of my exome variants are rare (occur at <1% frequency) or previously unidentified (unique). As more exomes and whole genomes are sequenced, the proportion of “unique” variants will diminish, but the 15% proportion of rare variants is unlikely to shift significantly. After all, you have to figure that most of the common variants have already been identified.

These classifications can be combined to filter the variants, first by predicted effect, then by frequency, to identify those variants with high or moderate predicted impact, that are rare. Then 23andMe asked whether any of these filtered variants occur among a list of 592 genes “involved in Mendelian disorders” (Figure 4).

Figure 4. Variant filtering process.

This filtering scheme resulted in a list of 21 variants. All 21 on my report were predicted to have “moderate” impact, and all were non-synonymous substitutions. But even a cursory look through these 21 amino acid changes reveals that some are more likely to affect protein structure or function than others. For example, some are conservative amino acid changes, where the variant amino acid has similar physico-chemical properties as the original amino acid. Examples are L25V (leucine at amino acid position 25 changed to valine; both have hydrophobic side chains) and I929V (again, isoleucine and valine are both hydrophobic). Other changes are more potentially disruptive, where the variant amino acid has very different properties from the original. Examples are R1125W, with arginine (a positively charged side chain) replaced by tryptophan (large hydrophobic side chain); E158K and E482K, which substitute positively charged lysine for a negatively charged glutamic acid; and R150C, which puts cysteine in place of arginine.

The report does not say whether I am homozygous or heterozygous for any of these 21 variants. I presume that I am heterozygous for all of them (23andMe excluded X and Y chromosome genes). I can check these myself by looking them up in the vcf file (that will be a later post).

This post then gives curious readers what they can expect at this point if they have their exome sequenced by 23andMe. Clearly, this barely scrapes the surface of one tiny corner of the exome sequence data. In my next post, I will present some open-source tools for looking at and sifting through the data yourself. In the meantime, I am making my vcf file publicly available here: http://dl.dropbox.com/u/69564734/LF1396.vcf.gz

Did Life Begin with “RNA on Steroids”?

The “RNA world” hypothesis posits that life, and biological evolution, began with self-replicating RNA molecules. Before DNA, before protein enzymes, RNA molecules both stored hereditary information, and performed the catalytic functions required for replication. All cells today still depend on RNA catalysis for some core functions such as protein synthesis by the ribosomes, where the ribosomal RNA molecule forms the peptidyl transferase catalytic center, rather than any of the ribosomal proteins. Other enzymatic RNAs (ribozymes) catalyze self-splicing, RNA cleavage, RNA ligation, and RNA polymerase activities.

All reactions involving ribozymes require divalent cations, preferably Mg2+. Recent and ongoing research by the laboratories of Loren Williams, Nick Hud, Roger Wartell, and Stephen Harvey at Georgia Tech asked whether Fe2+ could substitute for Mg2+ in RNA folding and catalysis (Athavale et al. 2012). Fe2+ is a soluble form of iron that was abundant in the Earth’s early oceans until cyanobacterial ancestors began to produce large quantities of molecular oxygen (O2), around 2.7 billion years go. In the presence of O2, Fe2+ is oxidized to Fe3+, which is insoluble and precipitates in the form of iron oxide (rust). This massive precipitation of iron oxide onto ocean sediments formed banded iron formations that can be found around the world.

Athavale et al. discovered that Fe2+, with coordination geometry similar to Mg2+, could indeed substitute for Mg2+ in folding and catalysis by ribozymes. Moreover, Fe2+ enhanced ligation by the Tetrahymena Group I intron by 25-fold and cleavage by a hammerhead ribozyme by 3-fold compared to equivalent concentrations of Mg2+.

Athavale et al. 2012 Fig. 3 Ribozyme activity is enhanced by Fe2+ compared to Mg2+.
A) L1 ribozyme ligase activity is enhanced in Fe2+ compared to Mg2+. Reaction progress was monitored by gel electrophoresis. B) Hammerhead ribozyme activity is enhanced in Fe2+ compared to Mg2+. Reactions were monitored by both gel electrophoresis and capillary electrophoresis, which gave similar results.

These results help address one of the criticisms of the RNA world hypothesis, that RNA catalysis is slow and inefficient. In the anoxic oceans of the Archaean eon (from the origin of life to circa 2.5 billion years ago), dissolved Fe2+ would have greatly enhanced the catalytic activities of RNA molecules. In the words of Loren Williams, RNA in the presence of Fe2+ was like “RNA on steroids” (H Thompson 2012).

References:

Athavale SS, AS Petrov, C Hsiao, D Watkins, CD Prickett, JJ Gossett, L Lie, JC Bowman, E O’Neill, CR Bernier, NV Hud, RM Wartell, SC Harvey, LD Williams, 2012. RNA folding and catalysis mediated by Iron (II), PLoS ONE 7(5): e38024. doi:10.1371/journal.pone.0038024

H Thompson 2012, Dissolved iron may have been key to RNA-based life, Nature News Blog http://blogs.nature.com/news/2012/06/dissolved-iron-may-have-been-key-to-rna-based-life.html

Cell Membrane Permeability – a Teaching Tidbit from SERSI12

This summer I was privileged to be the facilitator for the Cell/Development group at the Southeast Regional Summer Institute (SERSI), one of 7 replicate progeny of the National Academies/HHMI Summer Institute for advancing undergraduate biology teaching in the nation’s research universities. In an intense, week-long workshop, participants from universities around the Southeast learn the principles and practices of Scientific Teaching (Handelsman et al. 2004). They then apply these principles by developing a Teachable Tidbit, that aligns learning goals and learning objectives, formative and summative assessments, learning activities, and issues of classroom diversity.

My group chose the concept of semi-permeability of cell membranes, for a large-enrollment (>250 students) freshman biology for majors lecture course. This is the tidbit they came up with, with suggestions to how to implement this in the lecture hall.

Cell Membrane Permeability
Group 2- Cell Development
Gladys Alexandre (1), Cristina Calestani (2), John Koontz (1), Silvia Moreno (3), Brian Ring (2), William Said (3)

(1) University of Tennessee; (2) Valdosta State University; (3) University of Georgia

Learning objectives: Students should be able to:

• Explain the concept of selective permeability.
• Predict the movement of molecules across the phospholipid membrane based on their structure.
• Interpret and graph kinetics of molecule transport across a phospholipid membrane.

Learning activities:

It begins with a short demonstrative play – 4 student volunteers are recruited to the front of the lecture hall, in a central location visible to all students. Two students join hands to form a barrier. One student simulating random movement runs into the barrier and bounces off. A second student is allowed passage through the barrier (the students that form the barrier unlink their hands and allow passage). The previous student tries again, and is rejected again by the barrier. The selectivity should be based on any easily distinguishable characteristic, such as gender, color of clothing, etc.

Clicker Question #1 follows the demonstration. This question assesses whether students have read the assigned chapter and can define the concept of selective permeability of phospholipid membranes (Learning Objective #1).

CQ#1: A semi-permeable membrane allows…

1. Only small molecules to cross.
2. Only charged molecules to cross.
3. Certain molecules to enter the membrane but not cross to the other side.
4. Molecules to cross the membrane until they reach equal concentration on both sides.
5. Molecules to cross dependent upon their chemical characteristics.

After addressing any student misconceptions revealed by student responses, the students are given the following scenario:

Sally went to the doctor for a fever and she was prescribed a sulfa-drug antibiotic. The doctor and her pharmacist insisted that she took her medication with food.
Sally wonders why.

Why does she have to take the drug with meals?

Let’s find out…

In this group project, students discuss in groups how to categorize the 6 molecules shown in the figure. The instructor should explain that this is a pure phospholipid bilayer (no proteins are shown), the molecules are added to the side at the top, and students should not only decide which molecules cross the membrane fast, slow, or not at all, and write their reasoning. After the allotted time, different groups are called upon to answer which molecules they placed in each category. The discussion should lead to the conclusion that lipids molecules (like estrogen) and small, non-polar molecules (like oxygen) will cross the lipid bilayer rapidly; that small polar molecules (like glycerol and acetic acid at pH 1.5) will cross slowly; and that large polar molecules (like sucrose) or charged molecules (like acetic acid at pH 7) will not cross at all.

Next, students are asked to consider real cell membranes, where 50% of the weight consists of membrane proteins.

In the next slide, students are asked to discuss the question with a neighbor, then answer the question using their clickers. In the table, “+” indicates the compound enters the cell from the outside, and “-” indicates that the compound cannot enter the cell.

Another think-pair-share clicker question asks students to identify which molecule crosses the membrane by simple diffusion, based on the same table.

After discussion of the differences between active transport and diffusion, and the role of transport proteins and channels, students then consider kinetics. How does the mode of transport (active transport, facilitated diffusion, or simple diffusion) affect the kinetics (rate of transport as a function of the concentration difference across the membrane)? This presumes that students have already learned about enzyme kinetics.

In groups, students are asked to plot the kinetics of the transport of each of the molecules from the same table above:

In the presentation to the SERSI participants, observers thought the X-axis would be difficult for students to conceptualize, and would require further explanation. Perhaps the instructor should explain that this is the concentration of the compound added to the outside the cell, when the concentration of the compound inside the cell is zero. The ultimate goal is to get the students to describe and draw saturation kinetics for compound B.

The teachable tidbit then returns to the original question Sally posed:

These figures are all from the attached Powerpoint file, provided with permission from members of the group. The file also contains the test questions (summative assessment) that students should be able to answer as a result of these learning activities and formative assessments.

So this is an example of what one group of faculty produced in the form of a teachable tidbit after 4 days of hard work. They all learned a lot about backwards design, active learning, and scientific teaching. We all agreed that, given how much work it takes to produce even one tidbit, it would be wonderful to be able to share them with each other, and with other instructors. Although all the tidbits, packaged into a Powerpoint, are shared among all the Regional Summer Institute participants in a Dropbox folder, we want a forum where people can comment on tidbits after they try them out, and upload revisions and additions.

So consider this a trial run, with one tidbit. Please feel free to download the materials, try them out in your classes, and provide feedback. If other groups want to share their tidbits on this site, please let me know and I’ll post them, or better yet, allow you to post them as a guest author.

Tidbit-Group 2 Cell Development v7

The Lac Operetta – can Monty Python and Richard Wagner help students grasp gene regulation?

The E. coli lac operon is featured as the paradigm for prokaryotic gene regulation in our Biology 1510 Introduction to Biological Principles course. I want my students to learn the following key concepts):

1. gene expression is regulated by proteins (transcription factors) that bind to specific sites on DNA to either repress or activate transcription;
2. RNA polymerases initiate transcription at specific sites in the DNA called promoters;
3. prokaryotic genes that function in the same pathway are often organized into operons, where all the genes in the operon are transcribed from a single promoter into a single mRNA molecule that is translated to produce multiple proteins.

Unfortunately, in 25 years of teaching Intro Biology and sophomore-level Genetics courses, I found that even after repeated textbook reading and lectures on the topic, many students have trouble answering questions such as:

If a mutation eliminates the CAP protein binding site, then the E. coli lac operon

• a) will be fully induced whenever glucose is present, regardless of lactose
• b) will be fully induced whenever glucose is absent, regardless of lactose
• c) will be fully induced whenever lactose is present, regardless of glucose
• d) will be fully induced whenever lactose is absent, regardless of glucose
• e) will never be fully induced

A few years ago, rather than lecture yet again about the lac operon, I devised and staged the Lac Operetta, where student volunteers act out the parts of the RNA polymerase, Lac Repressor, and CAP. The actors also sing short ditties, and the chorus (all the other students in the lecture hall) sings the refrain.

I thought that students would be able to conceptualize how the lac operon works if they thought of the different key proteins as characters with assigned roles. I also observed that many people have amazing memories for music. People have passed on stories and knowledge through song from pre-literate times. And getting students to participate by singing would break the usual class routine, and could further serve to stick the lesson in their memories. Oh, and I use props: Milky Way bars to represent lactose, any hard candy for glucose, and Red Hots for cyclic AMP.

You can click on this link to download my powerpoint: lac operetta_presentation

I ran the Lac Operatta for 3 years, immediately after a 30-min lecture on prokaryotic genomes and gene regulation. My wife also staged it in her freshman biology class at Clark-Atlanta University (before they fired her from her tenured position). It’s always lots of fun,  and students remember this class years afterwards. But does it actually enhance their understanding beyond what I present in lecture?

This year, as part of my flipped class, students were asked to view the lecture video before class.

In class, I did an assessment of whether the Lac Operetta increased student understanding of the lac operon model. I used 4 of my standard test & clicker questions, and polled the class with clickers both before and after the Lac Operetta. At the start of class, I polled all 4 questions and collected the answers without comment. Then I sprang the Lac Operetta on them, and then polled the same questions again, in the same order. Students were free to discuss the questions with each other, both times the questions were polled, as per the usual procedure with clicker questions in my class.

Q1: Under which conditions will E. coli cells express (transcribe and translate) lots of beta-galactosidase?

• a) In medium with glucose as the only sugar
• b) In medium with glucose and lactose
• c) In medium with lactose as the only sugar
• d) In medium with galactose
• e) All of the above

This first question is a lower-order factual recall question, to see whether students have done the assigned reading or viewed the lecture video before coming to class. The histogram of the student clicker responses are shown below, with the pre-Operetta response percentages on the left in blue, and the post-Operetta response percentages on the right in red, for each answer choice:

Comparison of student clicker responses for question 1, before the Lac Operetta staging (blue, n= 125), and after (red, n= 144).

At this point I was feeling pretty smug. Then I got to a much higher-order question:

Q2: If the repressor gene is mutated, so that no repressor protein is made, then

• a) The lac operon will never be induced
• b) The lac operon will always be induced
• c) The lac operon will be induced whenever lactose is present
• d) The lac operon will be induced whenever glucose is absent
• e) The lac operon will be induced only when both lactose and glucose are present

Comparison of student clicker responses to Question #2, before the Lac Operetta staging (blue, n = 130) and after (red, n=142).

Now I was shocked and devastated. My efforts with the Lac Operetta staging had apparently strengthened a misapplication of the model. But instead of correcting them, I asked them to discuss with their peers again, but also to think about what they had just seen in the Lac Operetta, and think about what the Repressor and Cap did. And I repolled.

Comparison of student responses to question #2, the first time polled after the Lac Operetta presentation (blue, n = 142), and repolled after peer discussion with explicit guidance to apply the Lac Operetta to the question (red, n= 145).

The repolling showed a dramatic change, so that now the majority chose the best answer. I like to think that perhaps students had first thought of the Lac Operetta as mostly entertainment, but then realized that it could be used to think through how the lac operon model actually works.

Q3: What causes induction of the lac operon?

• a) When Repressor binds to the operator, regardless of CAP
• b) When CAP binds to the promoter, regardless of Repressor
• c) When Repressor binds to inducer
• d) When both a) and b) occur
• e) When CAP binds to the promoter and Repressor is not bound to the operator

Comparison of student responses to question #3 before the Lac Operetta staging (blue, n = 133) and after (red, n = 142)

Q4: In wild-type E. coli cells in medium with glucose, and no lactose:

• a) CAP binds to promoter
• b) Repressor binds to operator
• c) Both CAP and Repressor bind to promoter and operator, respectively
• d) Neither bind

Comparison of student responses to question #4 before staging of the Lac Operetta (blue, n = 135) and after (red, n = 144)

The last two questions showed the highest percentages of correct responses to these questions than I had ever seen, posed either as clicker questions or exam questions. Questions #3 and #4 are not as difficult as question #2, but clearly viewing the Lac Operetta and then applying it helped many students to work out the correct answer.

Dear student (why I don’t want to lecture)

Is this your brain during lecture?

Student’s electrodermal activity From “A Wearable Sensor for Unobtrusive, Long-term Assessment of Electrodermal Activity” (by Poh, M.Z., Swenson, N.C., Picard, R.W. in IEEE Transactions on Biomedical Engineering, vol.57, no.5)

Note that the electrodermal activity for this particular student shows the same flatline during class as while watching TV. While the paper does not indicate what went on during this student’s classes, in all likelihood they were lectures from a professor standing in front of the class, probably using Powerpoint.

But, you say, this isn’t you. Maybe you are one of the diminishing fraction of students who take notes. But are you really as mentally engaged, even taking notes, as while you’re studying, or doing homework? Study after study has shown that students attending lectures learn the least. If you are interested in looking into these studies, these articles or links reflect the current state of pedagogical thinking about lectures versus other modes of active learning. The first article from 30 years ago already provides plenty of references, and these findings have been amply confirmed since.

http://www.brookes.ac.uk/services/ocsld/resources/20reasons.html

http://discovermagazine.com/2011/dec/16-impatient-futurist-science-finds-better-way-to-teach

And here are a couple of the latest studies published in Science, with college biology and physics classes. Unfortunately, they are pay-walled and you’ll need either a personal subscription or access them through an institutional subscription (like the Georgia Tech library).

Haak, DC, J HilleRisLambers, E Pitre and S Freeman 2011. Increased structure and active learning reduce the achievement gap in introductory biology. Science 332:1213-1216

Deslauriers L, E Schelew and C Wieman, 2011. Improved learning in a large-enrollment physics class. Science 332:862-864

Regardless of method, however, I firmly believe that the strongest indicator of student learning is the student’s desire to learn, and willingness to engage in the hard work and struggle to learn. It is work. Some of it will be hard. And you may struggle to even know what you know and know what you don’t know. And that’s what I think class time should be used; for you to discover how good your understanding is, and learn by discussing with your peers who are going through the same process of discovery.

So I’m not saying that no one learns from lecture. Some people do. But I think I can safely say that everyone learns more from using and applying the concepts and ideas. Science is a skill, that requires the learner to practice and exercise. How well can you learn to play a piano or basketball, just by attending lectures or watching videos?

Recording lecture videos for the flipped intro biology course

In the flipped classroom, recorded lectures are the baseline and a failsafe. No matter what I and my students do in the classroom or lecture hall, students can still watch the videos and their learning won’t be any worse than in the traditional lecture course. When I decided to flip my large intro biology lecture course in fall 2011, I had to produce my own set of lecture videos for the first time. Fortunately, I was responsible for only 1/2 of the course, rather than an entire semester’s worth of lectures.

I set out to produce Khan-academy style videos with polished illustrations, but no other frills. I used a free, open-source application called CamStudio (camstudio.org) to capture streaming audio and screen activity on my HP tablet PC, while I talked and annotated Powerpoint slides with the tablet pen. This was how I gave lectures in previous years, interspersed with clicker questions. For the video lectures, I removed the clicker question slides (these were used in class). At the end of the lecture session, I stopped the recording in CamStudio. I used Windows Movie Maker to review the session, trim the start and end, and sometimes to split the video into multiple parts. I saved the movie “for computer” 640 x 480 display with a manageable file size.

My first recorded lectures suffered from poor synchronization of audio with video, so that the pen on the screen was writing a few seconds behind the voice. Students complained that this was distracting. In later videos, I eliminated this problem by using a higher frame-rate in CamStudio (50 frames/second). This led to larger (1 GB) avi file sizes, and there may be a better solution, but this worked for me. Your mileage may vary with your particular machine. Fortunately, Windows Movie Maker greatly reduced the file size in the exported wmv format. I uploaded these videos to T-square, Georgia Tech’s custom implementation of the Sakai course-management system, and to YouTube. I registered to get my own channel and to be able to upload videos longer than 15 min. The YouTube channel turned out to be important because students with Macs could not view the wmv files on T-square.

Recording the lectures turned out to be more time-consuming than I had anticipated. For 30 minutes of video, I spent several hours preparing the Powerpoint slides. Although I had slides from my previous years of lecturing, with my intent to put them on YouTube I wanted to remove all copyrighted material (textbook figures!). Because of time constraints I could not find acceptable substitutes for all of them. Then rough-scripting the lecture, recording the first take, reviewing the take, and preparing a second and sometimes third or fourth take consumed several additional hours. I had to wait until I could find a quiet place where I would not be interrupted by students, wife, telephone, or hungry/bored cats. Finally, uploading 100-Mb video files to T-square and YouTube took agonizingly long times. Although my goal was to upload each video at least 24 hours before class, some videos were uploaded just the evening before.

Now that I have a complete set of lecture videos already on-line, students next year will have plenty of time to view the videos in advance. However, I am not done with them. As my first effort, these videos are serviceable, but I’m sure they can stand a good bit of refinement. Over time, I will redo most of them, in shorter, tighter and more focused segments of 10 minutes or less.

Oh, and how did students like my videos? I think the majority did not like having to watch them. Typical student comments in the end-of-course evaluations:

Expecting us to listen to lectures before class, so that group activities could be done during class, was not fair to the students time wise. Listening to the lectures, doing the homework, and reading the chapters was more work than should be necessary for this class.

Watching the videos outside of class was an unfair expectation- if both 50 minutes of lectures and 20 minutes of video are required then the lecture should be worth more than 3 hours.

I had a hard time with the video lectures. They were very useful on occasions when I watched them before coming to class but combined with my courseload and in someways lack of discipline, this didn’t happen often.

Yes, I had a few complaints that the lecture videos were uninteresting/boring, but most of the complaints were about the additional work and time it took to view the videos, and the use of class time to do group activities. As the third student commented above, only about half of the students watched the assigned video before class. I could tell because straightforward clicker questions based on the video content elicited only about 50% correct answers.

On the other hand, many students appreciated the on-line video lectures:

I loved his strategy of the recorded lectures followed by the clicker questions. I felt like I understood the material much better than just reading the book before lecture. His videos were concise, to the point, and very representative of what would be on the test.

The video lectures are what taught me everything i needed to know for the material he taught.

I thought the lecture videos were very helpful, especially when reviewing for the exams.

I know many people did not like the lecture videos, but I would much rather watch the videos than read the book. I feel as if I did a lot better when I watched the videos, or at least I feel like I learned much more. They helped because it was like having my own private lecture where I could pause it at my own leisure to write information down. This also helped me to focus on everything that was said because when I noticed that I was no longer paying attention to the video, I could just pause and take a break as opposed to a real lecture. The diagrams and pictures that are used are also very helpful.

Overall, I do believe that lecture videos on-line can be very helpful for student learning. And the whole point is that it frees up class time for process skills and applications – real science! I can also see the student perspective that this is an extra demand on their time. For my next go-around, I will have to think carefully about how to integrate lecture videos, textbook readings, Mastering Biology and in-class activities to better enable students to manage their time and learn most efficiently.

All my lecture videos are available on my YouTube Channel:

http://www.youtube.com/user/jungchoigt?feature=guide

As always, your comments and suggestions are welcome.

What do human infants and philodendrons have in common?

One answer is that they both smell bad at times. Philodendrons include skunk cabbage and even stinkier species such as the dead horse arum. If we look deeper into the odoriferousness of philodendrons, what we see is that they heat their male flower parts to help disperse their odor. We often see skunk cabbage flowers that have melted the snow around them.

Localization of thermogenic cells in the spadix of skunk cabbage (Onda et al., 2008). A, An intact inflorescence. B, The spathe has been cut to reveal the heat-producing spadix. C, Longitudinal sectioning of the spadix. D, Thermal image of the plant shown in C using a high-resolution infrared thermal camera. Bar, 1 cm. Image from Roger Seymour, Plant Physiology Online Essay 11.6 Respiration by thermogenic flowers http://5e.plantphys.net/article.php?ch=e&id=503

Some species are able to thermoregulate; they can maintain nearly uniform set temperature over a wide range of ambient air temperatures.

Rate of oxygen consumption and heat production (top) and temperature of the central receptacle (bottom) in the sacred lotus Nelumbo nucifera, in relation to ambient temperature (Seymour and Schultze-Motel, 1998). The dashed line is isothermal, showing that evaporative heat loss predominates at high ambient temperatures, but metabolic heat production prevails at low ambient temperature. The means were derived from intact flowers in the field, during the thermoregulatory period associated with female receptivity. Image from Roger Seymour, Plant Physiology Online Essay 11.6 Respiration by thermogenic flowers http://5e.plantphys.net/article.php?ch=e&id=503

How these plants generate heat is by uncoupling respiration from ATP synthesis in their mitochondria. The flower cell mitochondria transfer electrons from food to oxygen, but make very little ATP. Instead, all of the energy of respiration is released as heat.

Uncoupling respiration from ATP synthesis is the second, and more significant, way that thermogenic flowers resemble human babies. Newborn mammals have a special organ, called brown adipose tissue, or brown fat, that helps warm the newborns via non-shivering thermogenesis. Brown fat differs markedly from ordinary adipose tissue (white fat) that we see in adult mammals. White fat cells are storage tissues with large lipid droplets, little cytoplasm, few mitochondria, and low oxygen consumption. Brown fat cells have smaller lipid droplets, lots of mitochondria, and high levels of oxygen consumption. The brown color of brown fat results from the numerous blood vessels that supply oxygen to these cells.

Brown adipocytes (left panel) are polygonal in shape, have a considerable volume of cytoplasm and contain multiple lipid droplets of varying size. Their nuclei are round and almost centrally located. White adipocytes (right panel) have a scant ring of cytoplasm surrounding a single large lipid droplet. Their nuclei are flattened and eccentric within the cell. from Laura Austgen and R. Bowen http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/brownfat.html

Both mammalian brown fat and thermogenic skunk cabbage cells make an uncoupling protein (UCP) in their mitochondria. UCP is a gated proton channel in the mitochondrial inner membrane, that when opened facilitates diffusion of protons across the membrane.

Questions: Why does uncoupled respiration generate more heat per molecule of sugar or fat burned than respiration that generates ATP via oxidative phosphorylation?

When UCP is open, what will happen to the proton gradient in the mitochondria? Will the rate of ATP synthesis increase, decrease, or stay the same? What will happen to oxygen consumption (if there is no change in the rate of the citric acid cycle)?

Question: What part of a fat molecule contains most of the energy available to cells: glycerol or fatty acids?

Fats are broken down to glycerol and fatty acids. Glycerol is converted to pyruvate. Fatty acid chains are cleaved two carbons at a time to generate acetyl-CoA.

Question: in what part of the cell does fat metabolism take place?

Question: which form of exercise will burn more fat: moderate, aerobic exercise or strenuous exercise leading to anaerobiosis?

I like this as a way to stimulate students to explore fat metabolism (aerobic respiration), the relationship between oxygen consumption and heat generation, and coupling of respiration to oxidative phosphorylation. I hope that it will also help students to fully embrace the concept that plants have mitochondria and respire in the same way as animals.

References and sources:

Roger Seymour, Respiration by thermogenic flowers. Plant Physiology Online Essay 11.6 http://5e.plantphys.net/article.php?ch=e&id=503

Laura Austgen and R. Bowen, Brown Adipose Tissue. http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/brownfat.html

http://www.nytimes.com/2012/01/25/health/brown-fat-burns-ordinary-fat-study-finds.html?_r=1&hp