Can you prepare for research?

[grivacobae]

I just got a research position with a professor of Immunology and his lab works with Multiple Sclerosis and autoimmune diseases. I have no background in immunology but he said it was fine, but I want to be more thank just a mice breeder and pcr person in their lab so I got a book and am starting to read. But I was told I would be breeding mice to keep the population lineage constant for their research, what does that entail? How will I be doing this? Also, I think he said I'd be PCR'ing... making more and more DNA sequences? No clue really, how should I prepare for this?
I don't want to be the **** who ruins the mice population for their lab haha!

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[gtbROX]

For starters, read the most recent (<5 years) publications that have your PI or graduate students as primary/secondary authors. You only need to read the abstract to get an idea of what their project goal is and then skim the methods section to get an idea of what experiments/tests they run. Otherwise, have fun and be sure to shadow/partner up with graduate students, especially when they're about to run experiments besides PCR.

 

[kraskadva]

^yeah, that's probably not going to help much, since the OP probably won't understand most of the papers.

Look OP, there isn't much you can do to prepare. You've already told the PI you don't have an immuno background and he probably saw your CV. He knows what it is that you don't know. And if he's any kind of decent PI at all, he'll explain what you need to know along the way.
I wouldn't spend a lot of time doing random Internet searches and freaking out right now. Totally not necessary and a waste of time. Just chill and you'll be fine. Besides, you don't even know what it is that you don't know, so most internet searches would be fruitless.

If you do want to google things, you'd be better starting at the low end, so you are aware of basic lab techniques.
Like PCR: go make sure you understand the concept and how it works theoretically, maybe also google a PCR protocol so you have a general idea of the steps. This is something they would walk you through the first time though, so don't get caught up in Internet details.
Maybe also google the concept of maintaining a mouse line so you understand what you're doing in theory, though the reality will probably be much more boring than you're imagining now. Playing matchmaker for mice will get old quickly.

Enjoy the experience though, it's the first step on the ladder, but you can keep moving up from there
And never be afraid to ask your PI or the grad students questions. That's the best way to learn.

 

[hoihaie]

know the concept of PCR, know common mistakes that people make.

For mice, know basic mice handling, know how to treat lab mice, how breeding works (i.e. crosses...etc), how the lab was able to develop that specific mice model you will be taking care of

 

[sat0ri]

I totally disagree with @kraskadva.
Reading papers can be a big help. Asking them for relevant literature is probably better than reading only what they do (they likely know the seminal papers and good review papers), to get an idea of the type of work going on. Read the papers slowly and deliberately and look up anything you don't know, especially in their methods section. It's a skill you need to have. It's basically what kraskadva said, but you need to know what basics to be looking up to begin with. Also, you might need to crack open a few old text books on things they do in lab, and youtubing videos of methods can help too. Plus when it comes times for interviews, youre going to need to know why you lab was PCRing and growing mice, and that won't come without actually going to the literature. Without the literature, yuore just a lab monkey.
When I did a summer internship in a field I was totally new at, you had to start with the literature, which was true for everyone in the program.

 

[kraskadva]

I totally disagree with @kraskadva.
Reading papers can be a big help. Asking them for relevant literature is probably better than reading only what they do (they likely know the seminal papers and good review papers), to get an idea of the type of work going on. Read the papers slowly and deliberately and look up anything you don't know, especially in their methods section. It's a skill you need to have. It's basically what kraskadva said, but you need to know what basics to be looking up to begin with. Also, you might need to crack open a few old text books on things they do in lab, and youtubing videos of methods can help too. Plus when it comes times for interviews, youre going to need to know why you lab was PCRing and growing mice, and that won't come without actually going to the literature. Without the literature, yuore just a lab monkey.
When I did a summer internship in a field I was totally new at, you had to start with the literature, which was true for everyone in the program.

oh, I don't think we totally disagree. I wasn't saying the OP should never read the PI's papers (s/he should eventually), only that jumping into dense scientific literature without even a solid understanding of PCR is likely not the best use of time in preparing to start lab work.
Trying to read a paper where you have to look up a dozen terms is one thing. Trying to read a paper where you look up every term is another...

 

[grivacobae]

Thanks for all the responses! Lots of good info, we'll see how it goes, theses safety courses on line are annoying though ha

 

[Avicenna]

All you'll be doing is carrying out your PI's instructions. What's there to prepare for?

 

[Doctor Strange]

Wikipedia is your friend.

 

[mimelim]

Do not read papers. It will be a complete and total waste of your time. You need to learn some basic Immunology. I'd try to find and old copy of Janeway's, brand new is only like $25, but someone in the lab probably has one on the bookshelf collecting dust. It is easy enough to read and as long as there is a grad student or someone else that can answer basic questions, you should be all set.

 

[ithd]

My lab does extensive mouse genetics. Maintaining mouse lines means that you take your male mice and cross them to female mice to produce pups that have the desired genotype (maybe double or triple transgenic). The PCRing is probably just genotyping the mice offspring and confirming the correct genes of interest. You keep the mice that have the correct genotype and euthanize the rest. Just keep setting up the females with the males, get pups, genotype them, keep the ones you need, set up the mom with the male again, and repeat. Not that complicated, just requires some organizational skills and time.

 

[grivacobae]

Awesome overview thanks! So I can assume that's relatively simple to learn and do I think, thanks again everyone

 

[sat0ri]

oh, I don't think we totally disagree. I wasn't saying the OP should never read the PI's papers (s/he should eventually), only that jumping into dense scientific literature without even a solid understanding of PCR is likely not the best use of time in preparing to start lab work.
Trying to read a paper where you have to look up a dozen terms is one thing. Trying to read a paper where you look up every term is another...

Fair enough. I see where you're coming from. I thought you were advocating not even touching a paper but clearly not.

Do not read papers. It will be a complete and total waste of your time. You need to learn some basic Immunology. I'd try to find and old copy of Janeway's, brand new is only like $25, but someone in the lab probably has one on the bookshelf collecting dust. It is easy enough to read and as long as there is a grad student or someone else that can answer basic questions, you should be all set.

Starting with all of immunology with no orientation to what information is important to her field and what is not immediately relevant would also be a waste of time. Balance is needed. A girl in my summer program had no experience, not even bio 2 or organic, and she started from scratch--you learn so much faster when you're thrown in the deep in; you could drown I guess is the minor drawback. It's a skill you need to pick up (for the MCAT for instance), to be able to process something you're unfamiliar with. So many undergraduate researchers are just glorified lab monkeys, and this person shouldn't develop the habit since they are just starting.

 

[grivacobae]

Soooo my first day was definitely humbling. I haven't started research but I did sit in on their weekly meeting/presentation and their publications discussions. I am a relatively humble person but do assume I can learn anything if I set time and would be relatively easy if I love the subject... You only know how stupid you really are when you talk to an expert and are surrounded by experts in their field. I thought I could come in and pick up a book, read it, and understand it and do really well like in a biology class, boy is that far from the truth. 2 and a half ours of complete daze and confusion, to make it worse, the PI and grad student I'm working under barely acknowledge me, which gets me to believe they want me as a lab monkey, but nah, hopefully I can prove them wrong. Thanks for all the input!

 

[mimelim]

Starting with all of immunology with no orientation to what information is important to her field and what is not immediately relevant would also be a waste of time. Balance is needed. A girl in my summer program had no experience, not even bio 2 or organic, and she started from scratch--you learn so much faster when you're thrown in the deep in; you could drown I guess is the minor drawback. It's a skill you need to pick up (for the MCAT for instance), to be able to process something you're unfamiliar with. So many undergraduate researchers are just glorified lab monkeys, and this person shouldn't develop the habit since they are just starting.

"Learn basic immunology" is not the same as "start with all of immunology". If you are going to be working in the field, there are fundamentals that you need to know. The way to have a productive time in a lab is to have a strong foundation to grow on, not trying to fit in as a niche worker. And hey, you might actually learn something. This isn't about learning faster. This is about how to be more than a scut monkey which is about development of good habits and being efficient. Reading papers is a skill and something that is developed over time. Learning methods is how you become a good technician. Learning science is how you do good research.

I don't know how much experience you have with research. I run a group of 4 students and 3 residents and for all practical purposes have been doing research in some flavor for the last decade and the fundamental difference between productive and non-productive is attitude. If you see it as a check box or focusing on methods, you will always be a scut monkey. You have to know how to do that stuff, but it is just a tool, nothing more. If you want to actually produce something, learn the Science.

 

[kraskadva]

Soooo my first day was definitely humbling. I haven't started research but I did sit in on their weekly meeting/presentation and their publications discussions. I am a relatively humble person but do assume I can learn anything if I set time and would be relatively easy if I love the subject... You only know how stupid you really are when you talk to an expert and are surrounded by experts in their field. I thought I could come in and pick up a book, read it, and understand it and do really well like in a biology class, boy is that far from the truth. 2 and a half ours of complete daze and confusion, to make it worse, the PI and grad student I'm working under barely acknowledge me, which gets me to believe they want me as a lab monkey, but nah, hopefully I can prove them wrong. Thanks for all the input!

Yeah, it always starts out that way. Just breathe and learn how to do your job there.
Good lab monkeys get to move up the ladder
Also, the lab meeting is not the time when they'll take things slow and hold your hand through it. Doesn't mean they don't want you to learn. Just take it one day at a time and ask questions as you go. First one will be "how do I do this?". After you master that, move on to "why am I doing this* and what is the relevance to your project?"
You'll be fine. One step at a time. 2 years ago I was in office hours with my genetics professor every week, now it's likely I'll end up listed as a middle author on his next pub. But you gotta start small.

*not in a whiny sense, but in a what's the underlying principle sense

 

[grivacobae]

Yeah, it always starts out that way. Just breathe and learn how to do your job there.
Good lab monkeys get to move up the ladder
Also, the lab meeting is not the time when they'll take things slow and hold your hand through it. Doesn't mean they don't want you to learn. Just take it one day at a time and ask questions as you go. First one will be "how do I do this?". After you master that, move on to "why am I doing this* and what is the relevance to your project?"
You'll be fine. One step at a time. 2 years ago I was in office hours with my genetics professor every week, now it's likely I'll end up listed as a middle author on his next pub. But you gotta start small.

*not in a whiny sense, but in a what's the underlying principle sense

Should read and study for immunology like a class?

 

[kraskadva]

Should read and study for immunology like a class?

mmm... I'm not going to say no, but I also wouldn't rush into it. Like I said before, you don't know what it is you don't know- i.e. you have no idea where to start. So buying a textbook (as mentioned above) may not be a bad idea, but I wouldn't start by reading it cover to cover.
Right now I'd focus on figuring out your job in the lab. Then as terms come up, go look them up and read up on those bits. Study what you need to know at the moment to understand what's being said around you.
And ask questions....always ask questions.

 

[sat0ri]

"Learn basic immunology" is not the same as "start with all of immunology". If you are going to be working in the field, there are fundamentals that you need to know. The way to have a productive time in a lab is to have a strong foundation to grow on, not trying to fit in as a niche worker. And hey, you might actually learn something. This isn't about learning faster. This is about how to be more than a scut monkey which is about development of good habits and being efficient. Reading papers is a skill and something that is developed over time. Learning methods is how you become a good technician. Learning science is how you do good research.

I don't know how much experience you have with research. I run a group of 4 students and 3 residents and for all practical purposes have been doing research in some flavor for the last decade and the fundamental difference between productive and non-productive is attitude. If you see it as a check box or focusing on methods, you will always be a scut monkey. You have to know how to do that stuff, but it is just a tool, nothing more. If you want to actually produce something, learn the Science.

Well I think we're boarding on moot, but I love moot things. So it's like saying "learn the basics of neuroscience" to work in any sort of neuro lab. Yeah, technically the "basics" does not mean "all of", but the basics usually mean the breadth of everything, but just not the depth. So I work in a few labs, one being a oxytocin/fMRI lab,. If someone told me to learn the "basics", I would have spent a third of the time learning about action potentials, and a third learning about the PNS...well you get my point: I would have wasted a lot of time going through stuff that would not have helped me directly, despite learning the fundamentals. This lab is very systems level, and not molecular, so the structure of this nonapeptide or 5HT would likely not help me. If I worked my way through their publications first, and asked for relevant papers and meta-studies, I can cut a lot of the crap that is going to bog down a complete neophyte. Of course, wading through papers is going to be laborious, but the "labors" entailed will be going through the textbooks to pick up the relevant basics.

I completely agree that knowing the science is what separates a researcher from a lab rat, but that knowing the science means the papers. The literature is the actual science, before it is processed into textbooks where there is a clear thesis and ready principles and the evidence is already evaluated and ready for digestion. You will need a textbook or two (or wiki), but if youre doing science, the question being investigated won't be in the. The textbooks are a subsidiary, a reference for the literature. Your gains will be a lot quicker if you start off running, even if you trip, than if you take baby steps.

I am certainly less experienced than you as a researcher, but I can probably, by the very virtue of this, relate more to the undergraduate that doesn't know where to start.

 

[grivacobae]

mmm... I'm not going to say no, but I also wouldn't rush into it. Like I said before, you don't know what it is you don't know- i.e. you have no idea where to start. So buying a textbook (as mentioned above) may not be a bad idea, but I wouldn't start by reading it cover to cover.
Right now I'd focus on figuring out your job in the lab. Then as terms come up, go look them up and read up on those bits. Study what you need to know at the moment to understand what's being said around you.
And ask questions....always ask questions.

Alright, I'm thinking of sitting in on immuno lecture and reading along as the class goes by as a supplement, and it'll prepare me for the class later on too.

 

[sat0ri]

Alright, I'm thinking of sitting in on immuno lecture and reading along as the class goes by as a supplement, and it'll prepare me for the class later on too.

You don't seem too about this, but I suggest at least asking for some relevant review papers. It will one, paint you in a positive light, ie, as a student who actually cares about learning and not just checking the pre-med research box. Two, you'd be really surprised how much of the really fundamental basics of a topic are covered didactically in a review paper. It seems to me your a bit timid about getting your feet too wet at once, but it is really efficient to start off out of your comfort zone--you'll learn so much quicker and more efficiently that way.

This happens on the MCAT a lot too--people always want to review everything in ugrad and then start studying for the test--but this is almost ubiquitously admonished, from SDN to the review book companies.

OK, I was the same way at first, when starting to work with stem cells for the first time (I was chemistry, no bio at all). Very apprehensive, and there were all these words that I've never seen: EGF, FGF2, hemacytometry, horse radish peroxidase, etc. So even if you can't pick it up from the papers on first blush, what happens is, when you hit the textbooks/lectures, those words that are relevant to you from the papers are all of a sudden more salient in lecture/textbookds, and you're able to really zero in when combing through all the basics. So it is more efficient as you'll retain important things and see how they fit into a broad field like immunology. And then, the next time around, in the next lab, you're just that much better at picking something up directly from the science--the bleeding-edge literature--and you're just a little bit more like a real researcher.

 

[Bethany555]

Well I think we're boarding on moot, but I love moot things. So it's like saying "learn the basics of neuroscience" to work in any sort of neuro lab. Yeah, technically the "basics" does not mean "all of", but the basics usually mean the breadth of everything, but just not the depth. So I work in a few labs, one being a oxytocin/fMRI lab,. If someone told me to learn the "basics", I would have spent a third of the time learning about action potentials, and a third learning about the PNS...well you get my point: I would have wasted a lot of time going through stuff that would not have helped me directly, despite learning the fundamentals. This lab is very systems level, and not molecular, so the structure of this nonapeptide or 5HT would likely not help me. If I worked my way through their publications first, and asked for relevant papers and meta-studies, I can cut a lot of the crap that is going to bog down a complete neophyte. Of course, wading through papers is going to be laborious, but the "labors" entailed will be going through the textbooks to pick up the relevant basics.

I completely agree that knowing the science is what separates a researcher from a lab rat, but that knowing the science means the papers. The literature is the actual science, before it is processed into textbooks where there is a clear thesis and ready principles and the evidence is already evaluated and ready for digestion. You will need a textbook or two (or wiki), but if youre doing science, the question being investigated won't be in the. The textbooks are a subsidiary, a reference for the literature. Your gains will be a lot quicker if you start off running, even if you trip, than if you take baby steps.

I am certainly less experienced than you as a researcher, but I can probably, by the very virtue of this, relate more to the undergraduate that doesn't know where to start.

I'm sure it varies between labs and the individual's background, but I think a combination of both of your suggestions would be best.

Grivacobae, I would recommend opening up a review paper (written by your PI on the research you'll be doing if he has one) and figuring out what you don't understand. If you understand what's being said, read some basic science papers of his. If you don't, I'd go and review the fundamentals based on that. From your initial post, I presume you don't completely understand how PCR works. From that, I figure you haven't taken many biology/biochemistry classes. I'd watch a few videos on how PCR works and possibly learn how to design primers (someone will probably teach you the latter, it's pretty simple though).

As a personal example, when I was a freshman in college, I did nephrology research. I did not even know what the parts of the nephron were, the transporters in the kidney, any hormones (aldosterone, angiotensin, etc.), etc. Piecing together fragments of information from Wikipedia wasn't very fun or effective, so I spent a few hours watching videos on renal physiology to get a bigger picture and at least understand the basics. You don't need to go to a lecture. Just watch videos on immunology (Khan Academy Medicine, Dr. Najeeb, Armando Hasudungan) and/or read Chapter 1 of Janeway's.

 

[grivacobae]

You don't seem too about this, but I suggest at least asking for some relevant review papers. It will one paint you in a positive light, as a student who actually cares about learning and not just checking the pre-med research box. Two, you'd be really surprised how much of the really fundamental basics of a topic are covered in a review paper. It seems to me your a bit timid about getting your feet too wet at once, but it is really efficient to start off out of your comfort zone--you'll learn so much quicker and more efficiently that way.

This happens on the MCAT a lot too--people always want to review everything and then start studying--but this is almost ubiquitously admonished, from SDN to the review book companies.

OK, I was the same way at first, when starting to work with stem cells for the first time (I was chemistry, no bio at all). Very apprehensive, and there was all these words that I"ve never seen: EGF, FGF2, hemacytometry, horse radish peroxidase, etc. So even if you can't pick it up from the papers, what happens is, when you hit the books, those words that are relevenat to you are all of a sudden more salient, and you're able to really zero in when you're in lecture. So it is more effecient. And then next time around, in the next lab, you're just that much better and picking something up directly from the science, the bleeding-edge literature, and you're just a little bit more like a real researcher.

What are review papers? Are they publications, or like further summaries (more detailed) than just abstracts?

 

[grivacobae]

I'm sure it varies between labs and the individual's background, but I think a combination of both of your suggestions would be best.

Grivacobae, I would recommend opening up a review paper (written by your PI on the research you'll be doing if he has one) and figuring out what you don't understand. If you understand what's being said, read some basic science papers of his. If you don't, I'd go and review the fundamentals based on that. From your initial post, I presume you don't completely understand how PCR works. From that, I figure you haven't taken many biology/biochemistry classes. I'd watch a few videos on how PCR works and possibly learn how to design primers (someone will probably teach you the latter, it's pretty simple though).

As a personal example, when I was a freshman in college, I did nephrology research. I did not even know what the parts of the nephron were, the transporters in the kidney, any hormones (aldosterone, angiotensin, etc.), etc. Piecing together fragments of information from Wikipedia wasn't very fun or effective, so I spent a few hours watching videos on renal physiology to get a bigger picture and at least understand the basics. You don't need to go to a lecture. Just watch videos on immunology (Khan Academy Medicine, Dr. Najeeb, Armando Hasudungan) and/or read Chapter 1 of Janeway's.

That's the textbook I got, the 7th edition, and I went ahead and asked grad student what chapters to focus on and that's what I'll be focusing on. And now videos like you mentioned

 

[sat0ri]

What are review papers? Are they publications, or like further summaries (more detailed) than just abstracts?

Ok review papers: Usually there is a line of research being pursued, like using vectors as an oncolytic. So there's tons of different experiments published investigating this, from the chemistry to the biology. So a review paper sums up a whole line of research, explaining what has been done, what is the relevance of each study in the context of all these other studies, evaluates contradicting research in a field, where the research needs to go. It normally gives an overview first as well, an introduction, and explains fundamental concepts that will be needed to understand the body of work. So it might have a bit on cancer therapy, and viruses, and some basics on everything in this field (if the basics they provide don't make sense, then you hit the textbooks). Another important feature, is it is all based on past publications, so if something sounds important, like something very similar to what you do, you can find the reference and look it up.

But in short, it is just the summary of previous research on a common topic or research question.

 

[kraskadva]

Alright, I'm thinking of sitting in on immuno lecture and reading along as the class goes by as a supplement, and it'll prepare me for the class later on too.

Not a bad idea if you've got the time. If your PI teaches it, then bonus points for initiative/dedication. Def take it for credit once you can fit it in. Though other, perhaps more basic, bio classes may need to come first. Also for specific learning (i.e. what you want/need to know now) looking things up in a textbook or on google may be most effective.

What are review papers? Are they publications, or like further summaries (more detailed) than just abstracts?

A review paper is a pub that reviews the pubs written on a specific topic recently. It will say REVIEW at the top and have a reference section several pages long. Very good for general overviews and identifying pertinent literature to read through.

 

[IslandStyle808]

What are review papers? Are they publications, or like further summaries (more detailed) than just abstracts?

Ok review papers: Usually there is a line of research being pursued, like using vectors as an oncolytic. So there's tons of different experiments published investigating this, from the chemistry to the biology. So a review paper sums up a whole line of research, explaining what has been done, what is the relevance of each study in the context of all these other studies, evaluates contradicting research in a field, where the research needs to go. It normally gives an overview first as well, an introduction, and explains fundamental concepts that will be needed to understand the body of work. So it might have a bit on cancer therapy, and viruses, and some basics on everything in this field (if the basics they provide don't make sense, then you hit the textbooks). Another important feature, is it is all based on past publications, so if something sounds important, like something very similar to what you do, you can find the reference and look it up.

But in short, it is just the summary of previous research on a common topic or research question.

I concur strongly with Satori on this one. Reading research articles are definitely a necessity when working in a lab. OP you want to be doing intellectual work after some point and this means understanding similar literature t0 the research your working on. The best way to start is with a review article. The way to discern a review article from a primary article is by looking at these formats:

Primary articles (original research)
Abstract
Introduction
Materials and Methods
Results
Discussion

Review articles (literature review)
Abstract
Introduction
Body
Discussion

Review articles are a good comprehensive summary of all research related on a topic. If you want more detail of a certain sentence or paragraph, then look at the citations and find those papers. You won't understand everything, so don't worry about it. In fact, you can ask your PI or the graduate students in your lab about them if stuck. Learning is a part of the process of being proficient in the lab.