Demo Edit 3 (Optional)

This is the third of three optional modules in which I’m going to share a demo at it, that I did of a student’s work in a previous course. This module is optional but it may help you to see how I approach editing an entire essay.

It will help prepare you for the period that you’re going to do in a couple of weeks.

So if this paper was a biological paper, and when I’m going to have you do now is pause the video.

And we did over a couple of times so that you’re familiar with it before you restart the video, and I’ll lead you through how I would approach editing the paper

So now that you’ve read the paper a couple of times through, you can see it’s about a experimental technique that you can use to actually control cell behavior. So it’s a really cool technique.

This is one actually a little bit more technical than the last two demo edits that I did. The author of this paper has actually done a really good job of trying to explain all of the technical material.

So every time he introduced a technical term, he tried to explain what that term was. So he’s done a very good job.

I think we can even go one step further in making this more understandable to a general audience, who doesn’t necessarily have a biology background.

So especially if you weren’t coming from biology, you may have found that you struggled a little bit to get through the technical parts of this.

Because again, it is a much more technical paper than the other edits that I showed you. So, I think we can bring it one step further by removing a little bit of clutter, and setting the things up a little bit, so we get the pertinent details when we’re ready for them.

I think we can take it one step further to make it even a little bit more understandable.

And so, that’s what I’m going to focus on in this edit. Again, the author has done a really good job, and I think we can just take it one step further to make it a little bit more understandable to a general audience.

So we’re going to jump right in with the first paragraph. So it has a great start to this paper.

So it says traditional methods for controlling biological signals in cells or a sledgehammer.

That’s a wonderful picture right up front. And then, the author says they are global, slow and often nonspecific.

We actually don’t see that they are there, so am going to get rid of that.

But then, they’re global, slow and nonspecific, the author starts with that and then kind of dovetails off from that and says that, the authors of this new paper describe a technique to do local fast and targeted cell signalling.

So that’s a really nice contrast. The author set up a really nice introduction here.

So I’m going to leave those first two sentences. I’m going to just change one thing in the second sentence. So in the authors of this paper, that’s a little bit general, the authors of this paper.

Let’s dive right in and say exactly what paper we’re talking about and what specific authors in this first paragraph so I said.

But in a 2009 paper in nature.

So let’s just edit at nature paper, so we can give that detail. And then, let’s use the author’s specific names so Levskaya Et Al, I will just pop that up here, Levskaya Et Al describe.

And then, I don’t think we need there. I think a new technique. A new technique to generate local, fast, and targeted cell signalling and live cells.

So that works really nicely. This idea of genetically altered to have light sensitive proteins, I think that’s a little bit too much detail up front, so let’s move that down.

I’m going to get that detail in back later, but we don’t need it quite yet in the introduction. I want to keep the introduction sort of big picture, so it’s easy to ease the reader into the story. So we get this nice technique to generate local, fast, and targeted cell signalling and live cells.

There we get a few extra details here, that I’m also going to push down a little bit further into the paper.

So they engineered a cellular perturbation system applicable to many signaling proteins that cellular perturbation system is just kind of very jargony and sitting there that’s a little bit hard to digest early on.

So we’re going to move that down.

We’ll get those. All right. We’ll get those details in backlog or so all of those details are going to put back in in various spots in the second paragraph.

The idea that this like proteins have to be activated by a membrane that’s a very important detail for understanding this system.

But I’m again going to move it down a little bit. We’re not quite ready for that detail yet. I think once the system has been described, then that detail makes more sense. So I’m going to push that down.

In the opening paragraph, what I’m going to add is I’m going to the very bottom of this paper to the last sentence.

The authors has great detail in the last sentence. So they show in movies that they effectively guided the direction followed by the new lamellopodium, the first reported control of cell movement in real time using light sensitive proteins.

And when I got to that I thought well, that’s one of the biggest, most significant pieces of this work.

So don’t put it to the ending, let’s put that right at the beginning. That’s a nice use of the dash by the author there by the way.

So we’re going to put that at the beginning. The author also did a nice job of using a colon. So that’s great.

But let’s get this idea right in here. This is one of the most significant things at the work, they actually control the movement of a cell.

They were able to force the cell to move in the direction they wanted using light sensitive protein.

So let’s just say that right in the first paragraph, they reported the first control of cell movement in real time using light sensitive proteins.

And so, we can kind of introduce that idea of light sensitive proteins being critical to this whole system, without getting into too much detail yet.

I’m going to get to that detail very quickly in the second paragraph. Again, all of these details here I’m going to incorporate into the second paragraph.

So I’m going to skip them for now. This stuff is going to get put into this paragraph starting with this genetically altered part.

So, since we just named the researchers, I’m going to change this to the researchers.

So the researchers, and Let’s instead of saying built this membrane recruitment system, let’s say genetically altered.

So we’ll start in with that genetically altered idea. Genetically altered cells to contain.

And I’m going to say that genetically altered cells to contain these light sensitive proteins. Now again, this idea of the membrane recruitment system I don’t think we’re ready for that concept yet.

I’m going to put that further down into this paragraph. So we’ll get that, but it’s going to come later.

So, the researchers genetically altered cells to contain photosensitive proteins named Phytochromes.

And actually, I don’t mean the word photosensitive here because I just said in the end of the last paragraph light sensitive proteins, which is the same thing as photosensitive.

So we don’t need to repeat that. And I’m also going to very quickly say what these proteins do. Which is that they respond to light, so I don’t need to use the word photosensitive it would be repetitive here

. So the researchers genetically altered cells to contain proteins named Phytochromes. These proteins from plants detect red and near-infrared light.

Okay. Well, all they’re from plants, these proteins are from plants.

That’s an important detail, but I can get that in right here by saying these, the researchers genetically altered cells to contain plant proteins named Phytochromes.

And then we can just dive right into what they do, which detect red in your infrared light. This detail through the Photoisomerization of a bound chromophore.

I think that’s quite jargony and technical and actually is not yield to understand the system, so I’m just going to cut that. I don’t think we need that detail. So then, let’s jump back into just exactly how it is that the Phytochrome respond to red and near-infrared light.

So that’s what the author does in this next sentence.

I’m just going to streamline this just slightly, so the idea is that the phytochromes, when they get hit with red light, they bind to a particular protein called the PIF, the phytochrome interacting factor. When they are exposed to infrared light, they don’t bind to that protein.

So that’s the idea and I think we can say that just a little bit more quickly.

So how about we just say, when exposed to red light, phytochromes, we don’t need apostrophe here. Phytochromes, the idea that it changes conformation I don’t think is important, and I think we can just say that it binds.

Phytochromes bind. We don’t need to directly. Bind to a phytochrome interacting factor.

Just say, bind to phytochrome interacting factor (PIF). I’m not going to let the author keep in this one acronym, because they do use this phytochrome interacting factor quite a bit in the article, and it is a little bit long.

So if that’s the only acronym in the paper, we’ll let that one acronym stay. So, when exposed to red light, phytochromes bind to phytochrome interacting factor.

And then when exposed, I’m going to use a semi-colon here, when exposed to infrared light, it’s just a little quicker to say when exposed to rather than under a state of. When exposed to infrared light, they release PIF.

Rather than saying they don’t bind to PIF, I think it’s a little more accurate to say they release PIF, I like that verb there.

So that now tells you exactly how it is that phytochromes respond to red and near-infrared light.

So when exposed to red light, they bind this protein, when they are exposed to infrared light, they release this protein. Right. Now we’re going to get into the most important details of this system.

So how does this system work? This scientists added a piece of domain to the phytochrome protein that they’ve engineered, so that it will stick to the cell membrane.

So that’s one key part. So the phytochromes are therefore going to be located at the cell membrane. So we need that. Detail is important. The other detail that’s important is that the scientists attached a signaling protein to this phytochrome interacting factor. So, that’s the whole idea. And are you going to test any signaling protein you want there.

The important detail is that it has to be a signaling protein that is activated by interactions with the memory.

So, the system is going to bring that PIF into the memory, and bring that signaling protein into the membrane under certain conditions when exposed to red light and that’s going to turn on the signaling protein.

So that’s the idea and I think the author have done a good job of describing it. I’m just going to tweak a few things here. Since we already said the researchers, I might go back to using the actual researcher’s name here just for variety.

So that is the scientists, Levskaya Et Al added a membrane localization, rather than part, I kind of prefer the word domain to the phytochrome and attached the signaling protein to the PIF.

I don’t think we need this ‘to complete their system either’. I think those are just extra words, so we can cut that.

So that’s the key, they change the phytochromes in this way, they change the PIF in this way.

And the key to making, to understanding this whole thing is what you have to know is that, you need to bring the signaling protein to the membrane, and the signaling protein has to be any signaling protein that’s activated by interacting with the membrane.

So remember, I already got this idea in, this detail here about the candidate signaling protein has to be activated by interactions with the memory.

I’m now going to introduce that idea now that we understand that the phytochromes are sitting on the membrane.

So, I’m going to say, the system works for any signaling proteins that are activated by interactions with the membrane. So I think we’re ready for that detail now, because now you see oh!

Okay. Because it’s about bringing a signaling protein to the membrane. We weren’t quite ready for that detail before.

So I think now we’ve got all of those details, and so we can cut all of that material that was originally in the first paragraph.

I’ve now brought it into the second paragraph. We can cut it because we’ve incorporated it. So now we know the system works for any signaling proteins that are activated by interactions with the membrane.

Let me get this, a cell illuminated with infrared light will have inactive free-floating PIF attached signaling proteins. In other words, the signaling proteins will be floating around, they won’t be on the membrane.

Actually, I’m going to get rid of that whole sentence and just jump into that sort of the off state.

I’d rather jump into the on state. So the author goes, had described the off state and then they’re going to describe the on state, and then they’re going to describe the off state again at the end of this paragraph.

In fact, I think we can just jump in and describe the on state and then describe the off state.

We don’t actually need the entire sentence. So, we can just start writing on. When a scientist points a red laser at the cell membrane, membrane-bound phytochromes.

So I’m going to get this picture across that these phytochromes are now sitting on the membrane.

So I kind of like the idea of membrane-bound phytochromes.

So, when the scientists point to a red laser at the cell membrane, membrane-bound, so we know that they’re sitting on the membrane, phytochromes bind to PIF, thus bringing the signaling proteins, which of course are attached to PIF, we’ve just said that.

The signaling proteins close to the membrane and increasing their activity. Since I just said that they need to be next to the membrane, membrane to have activity makes sense to the reader that if you bring them into the membrane, it will increase their activity we’re kind of now ready for that.

So, when a scientist points a red laser at the cell membrane, membrane-bound phytochromes bind to PIF, thus bringing the signaling proteins stay close to the membrane and increasing their activity.

And we don’t need to repeat ‘of the signaling proteins.’ So, thus increasing their activity. And then we get turning off the red laser freeze the proteins and turns off the cellular signal. Notice how we don’t need that prior sentence about turning the cellular signal off.

So, I think now we’ve streamlined this a little bit, so it’s a little bit easier for the reader to get through, and a little bit easier to understand what’s going on here.

So, the author of this paper has on a nice job of organizing by the way, because they put all the details about the system in the second paragraph.

In the third paragraph, they put all the details about the experiments that were used to test the system. So, we have a nice organization here. Again, for this third paragraph, I’m just going to streamline and just slightly, there’s a few places where we can condense things so we get it across to the reader a little more quickly.

So, to demonstrate the feasibility of this new technique, they focused on the signaling proteins, Tiam and intersectin. I actually think in this case we don’t need more details about what the precursors of the Rho-GTPases.

That’s getting a little bit too technical and in fact, I don’t think you need these details to understand this whole section.

So I’m just going to cut all of those and go right in to what Tiam and intersectin do. They have critical roles in organizing the actin skeleton.

So we can just jump right into that Tiam and intersectin which help in the organization of, instead of in the organization of which is a noun, let say which help organize actins cytoskeleton during cell movements.

So you notice that we didn’t really need all those extra details. Just knowing that these two proteins that were going to be attaching to PIF, their job is to help organize the actin cytoskeleton during cell movement, that’s sufficient.

Next the author say they performed three main experiments.

Actually I can get rid of this ‘three main experience’ thing, and just fold it into the first sentence just to be a little more concise here. So we’re already talking about the experiments of the first sentence.

So what if I just said, to demonstrate the feasibility of this new technique, they performed three main experiments focusing on the signaling proteins Tiam and intersectin.

So I think we can fold that three main experiments into that first sentence.

Just kind of again cutting a little bit here and you’re getting rid of clutter, making things a little bit more streamlined.

Then what I’m going to do for the next two sentences, so the author then describes these three experiments as nicely organised, this is a very nice logical organization.

So the author goes to the first, the second and third experiment.

So what I’m going to do is I’m going to streamline things a little bit because for example; in the next two sentences, the author in the first sentence describes what was done in the first experiment. And then, the second sentence, here they described what was found in that first experiment.

In fact, I think we can say it all in one sentence, we can just directly say what was found in the sort of implying what was done, so try this. The first experiment let’s just go right into that, not what they tested but what it showed.

The first experiment showed that membrane recruitment of a small part of intersectin.

And again, I don’t think we knew this detail about regulating Cdc42. That’s not important here.

So, the first experiment showed that membrane recruitment transiently increased local protein activity, that’s what it’s supposed to do. So that’s kind of a proof of principle.

And we don’t need to know that they showed images. We can just say again what they found the first to ensure that membrane recruitment transiently increase local protein activity.

And then again, we don’t need the detail about Cdc4 activity. So you noticed we already get protein activity, so we can just get rid of that.

And then we can say, and then that this fact disappeared a few seconds after turning off the red laser. So note how we got all those two sentences, we condensed them into one.

The first experiment showed that membrane recruitment of a small part of intersectin transiently increased local protein activity, and that this effect disappeared a few seconds, you need an a there.

A few seconds after turning off the red laser. So we get it all in one. We can streamline the description of the second experiment a little bit as well.

So this second experiment, let’s go right into it showed, the second experiment showed that membrane recruitment of a small part of Tiam was sufficient to induce changes in the shape of these particular types of cells.

And I’m just going to use that. I’m going to have a comma in here, so I’m saying exactly what was shown, I’m going to give the details of what was shown after the call.

So when they illuminated the whole cell with red light for 20 minutes. Now, notice we get a lot of details about ‘they counted the Lamellipodia.’

We can actually go right into what they found. So I’m going to just say when they illuminated the whole cell with red light for 20 minutes, almost 80% of cells made new Lamellipodia.

So notice how we don’t really lose anything by cutting out the ‘they counted.’ It’s implied that they counted them right, if we know how many there were.

So we can just go right into that when they illuminate the whole cell with a red light for 20 minutes, almost 80% of cells made new.

Now we need to define this word here, so I’m going to put back in that definition of what Lamellipodia. That’s these little actin skeletal projections on the mobile edge of the cell that definition. So we need that definition for those who don’t know what that is.

Now we don’t need to repeat under a red light treatment so we can delete that. So you know how much we can cut compared with 10%. We don’t need the A there, with 10% of control population and I would say control cells here. It’s okay to repeat the word cells.

So when they illuminate the whole cell with red light for 20 minutes, almost 80% of cells made new Lamellipodia.

Here’s the definition compared with 10% of control cells. And I think that’s sufficient. And then we can jump right into this last thought.

So, they say to make things even more interesting, I think we can streamline this just slightly by saying, even more interesting, in a third experiment they pointed a red laser dot on the edge of one cell, and gradually moved it outwards slowly extending this red targeted region from the cell body.

I think that’s a really nice description of this, the good verb there and going to leave that as it is. They show movies that they effectively guided the direction followed by the new Lamellipodium.

And I’ve already moved this detail up. I’m going to keep this dash here and say thus controlling the movement of the cell. So kind of summarizing exactly what’s going on here.

A little bit repeating what we said at the beginning, but this is giving more details about exactly how they’re controlling the movement of the cell.

And then that’s not quite enough to end on. So what I’m going to hound the author hand here is and short, we need a short conclusion here.

Add a short conclusion and what that conclusion should say is what are other potential applications of this research. So, I’m going to go back to the author here and say in the revision I’d like to know.

I need kind of a concluding paragraph that gives me the wider implications of this work. So, I know now that I can control the movement of a cell now with a red laser. What other potential applications does this system have?

I imagine there is a wide variety of potential applications that are pretty important here. So we need a nice conclusion that says exactly what are those other potential applications.

It might be just one or two sentences as a fourth paragraph here. So I’m going to go back to the author and ask them to add that in.

Say, what are the other picture implications of this? How else might we be able to apply this? What other types of cell behavior? Might we be able to control now that we have this system?

Other than that, I think the paper is now reading really well. We’ve streamlined it a little bit. Made it a little bit easier to follow the technical details, the organization was already pretty good.

I just moved a few of the technical details out of that first paragraph, so that the first paragraph wasn’t too intimidating for the reader. And now I think it’s reading really well.