New And Precise Figures And Figure Legends
Reading and evaluating science is often about looking at and interpreting figures and figure legends. What makes a good figure? What makes a good figure legend? When we go to read a figure legend what are we looking for? This assignment is about reading, and producing figure legends.
Introduction: The parts of a good figure legend. The object of a good figure legend is to give your audience the overall conclusion of the figure, and all of the technical aspects that they need to understand what you are doing in that figure. However, this is a fairly short piece of writing. Thus, you are often required to assume a certain amount of knowledge from your audience. The purpose of talking about “variables” in our techniques section was partly to give you some knowledge of what you need to know in order to interpret figure legends.
The labeling on the figure also plays a big role in your audience’s ability to understand and interpret your figure. Thus, unlabeled or poorly labeled figures are some of the worst elements of science. A well labeled figure and its legend should almost stand alone, and an experienced scientist can generally understand and evaluate the majority of a figure without having to read the associated text. We are going to practice this here, but first, what are the parts of a figure legend?
Figure legends can be broken into 3 parts
1) The big picture conclusion sentence: This sentence is designed tell your reader what you found overall in the experiments depicted in the figure.
2) The experimental details, this gives your reader all of the variables they need to look at the figure and understand what you did (the labels on the figures are also very important for this)
3) Statistics – for quantitative figures the number of “n’s” and the p values often go at the bottom of the figure legend.
This assignment is broken into 3 parts. We will start by looking at a figure and its associated legend, and you will be asked interpret what the figure is showing you, then you will be given a figure without a legend, and you will describe the results of the figure, and write your own figure legend, and finally I will ask you to draw your own figure with labels and figure legends. When you are drawing your own figure you can do this on the computer, or just draw on a piece of paper and scan it or take a picture of it and turn it in. Id you are taking a picture please be sure any labels are legible in your image.
The figures we are using here are from a paper that is the continuation of the experiments that we examined last week. This is partly to give you some background about basically what they are doing, so that we can look at these figures in isolation from the paper. In class on Friday we will briefly look at these figures, and then we will go on and try to look at the figures from a completely unrelated paper, and see if we can understand and interpret those figures on their own.
Although I am sure you could go find this paper, please don’t. The purpose of this is to practice looking at and evaluating figures without the associated words.
Part 3 of this assignment mimics something that I might ask you to do on an exam. (Although in that case I often let you design your own experiment rather then giving you an experiment and results). Thus, you can think of this as exam practice.
Here is a great example of a figure and legend (in this case I have removed A-C to make this a single experiment)
Figure 1: Depletion of Gαq/11 inhibits traffic-pulse-dependent SFKs activation at the Golgi complex. D) HeLa cells were treated with non-targeting siRNAs (Ctrl), siRNAs against Gαq/11 and Gαs (Gαq/11, Gαs siRNA) for 72 h, or 400 ng/ml PTX for 16 h. After infection with VSV for 45 min, the cells were incubated at 401C for 3 h (temperature block) and then shifted to 321C for 30 min (block release). Control cells and siRNAs-treated cells were fixed and stained for active SFKs (p-SFKs, grey scale) and giantin (marker for Golgi area definition). Merged images following the temperature-block release are shown (p-SFKs/Giantin; red and green respectively). Scale bars, 10 mm. (E) Quantification of data illustrated in (D). The p-SFKs IF intensities at the Golgi complex are expressed as arbitrary units (AU). Data are mean values (±s.d.) from four independent experiments. ***Po0.001 compared with 321C control (ANOVA analysis). (F) Western blotting reveals decreases in Gαq/11 and Gαs levels in siRNA-treated cells, compared with control cells. HeLa cells were treated with non-targeting siRNAs (Ctrl) and siRNAs against Gαq/11 and Gαs (siRNA) for 72 h, and then homogenized. The cell lysates were analysed by immunoblotting for the different Gα subunits, with actin as the loading control.
Part1 : Going through the figure, What it tells you and what it doesn’t
1) What do the labels on the left hand side of the images in part D tell you about? Given that they are doing siRNA, what can you tell me about Gαq/11 and Gαs…what are they? What is happening when we do siRNA on them? What about PTX – what might this be? – Note this is one of those places where the figure legend may not provide all of the info you need.. you would probably go look this up in the paper.
2) What are the labels at the bottom of part D showing you? Given that this work is a continuation of the paper we did last week, what is the temperature shift doing for them here?
3) What are labels at the top of part D telling you?
4) For each of the four horizontal sets of images in Part D in one sentence describe for me what is shown in these 4 images (You should have 4 sentences, one for control, one for Gαs si RNA, one for Gαq/11- siRNA, and one for PTX)
5) In Part E what are all the stars telling you?
6) Part F is not a very well organized or labeled figure. In this case the label siRNA is not very informative because they are showing you two experiments with different siRNA targets… I know this partly because they show you actin twice. Why are they showing you actin, what does this control for? What does this figure show?
7) How would you redraw or reorganize this figure to make the experiments clearer? If they really wanted to convince you that their siRNA was working as intended what else might they do in this figure? (Hint: Since Gαs and Gαq/11 are pretty similar, might Gαq/11 levels be affected by an siRNA that targeted Gαs? How would they ensure that was not the case?)
Part 2 – Here is the very next figure from the same paper as shown above (remember this is a continuation of the work that we looked at in class last week so p-SFK’s are the protein kinase family that becomes phosphorylated during traffic pulses, and VSVG is a viral protein that is exported to the plasma membrane. Just like Gigantin in the previous figure GM130 is a golgi marker.
1) Describe for me what this figure is showing. What happens to VSVG at these time points in the 3 conditions (control and the 2 siRNA’s) What is the difference between total VSVG and external VSVG?
2) Write a figure legend to accompany this figure.
Part 3 – They want to show that KDELR and these G –proteins (Gαs and Gαq/11) physically interact. To do this they use a Co-IP where they pull on KDELR and use a western blot to look for individual members of this family of G-proteins. They find that KDELR interacts with both Gαs and Gαq/11, but not with the related G-protein, Gαi3/0. Construct your own figure to show the results of this experiment. Make sure to show any controls that would be required for this type of experiment. Label your figure and write a figure legend.