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ScienceGAF? Is there interest/presence?

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FelixOrion said:
I worked at a biomass ethanol startup's lab for a bit as an undergrad intern. One of the senior engineers made everyone take a test like that before we go to work with then. In addition to just water and checking our standard deviation, he also made us repeat it with food colored water (so we could see where we were contaminating things) and a thick gycerol-like solution (so we had to go slow and to see how we'd deal with a heavy viscosity solution). For my first time on micropipettes it was actually quite a nice crash course.
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The worst is pipetting sticky things. Glycerol at least doesn't clog up a pipette tip.
 
Smiley90 said:
The worst is pipetting sticky things. Glycerol at least doesn't clog up a pipette tip.
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I don't think I've ever had the pleasure of pipetting something that really sticks to the inside of a tip. Thebclosest thing I've had to that was re-suspending a large cell pellet, but that was entirely easier than I imagine a sticky substance would be.
 
Try to pipette pure Triton X-100 and alike :P



Do your institutes "make" you do common duties, too? As in, you can opt out of it but someone has to do it.

Like, I'm in charge to get rid of our radioactive waste. So from time to time I have to lay down my pipette, pick up an impact driver and close those big ass radioactive waste drums.
Followed by dumping them in the forest filling out the proper paperwork etc.
 
SolidusDave said:
Try to pipette pure Triton X-100 and alike :P



Do your institutes "make" you do common duties, too? As in, you can opt out of it but someone has to do it.

Like, I'm in charge to get rid of our radioactive waste. So from time to time I have to lay down my pipette, pick up an impact driver and close those big ass radioactive waste drums.
Followed by dumping them in the forest filling out the proper paperwork etc.
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Naw we have waste pickup we can order for that.

The most "common duty" thing we have to do is roll our liquid nitrogen dewer to the refill station ourselves... :p
 
SolidusDave said:
Try to pipette pure Triton X-100 and alike :P



Do your institutes "make" you do common duties, too? As in, you can opt out of it but someone has to do it.

Like, I'm in charge to get rid of our radioactive waste. So from time to time I have to lay down my pipette, pick up an impact driver and close those big ass radioactive waste drums.
Followed by dumping them in the forest filling out the proper paperwork etc.
Click to expand...

Pshhh my PI is too cheap to hire a lab tech, so I end up doing most of the duties and am technically the lab manager. Ugh it pisses me off. The worst are our inspections because a student died a couple years ago in a chemistry lab. UCLA got the shit sued out of them so now our inspections are tremendous headaches. We do simple molecular biology but for the most part, we're a microscopy lab... it's not like we even have anything too hazardous (paraformaldehyde **ohhh***).

http://whatshouldwecallgradschool.t...1755/when-my-lab-passes-a-surprise-inspection
 
Same, I'm pretty sure our most hazardous chemical is like, Ethidium Bromide. The horror.

... And a pretty strong UV lamp for mutagenesis, but who doesn't like a tan?!?


Also wait you guys have surprise inspections? Those would kill me if we had them.
 
Yeah, our surprise inspections are like "maybe we will come Thursday next week *wink* *wink*" -> suddenly everyone wears a lab coat that day :P
 
Smiley90 said:
Same, I'm pretty sure our most hazardous chemical is like, Ethidium Bromide. The horror.

... And a pretty strong UV lamp for mutagenesis, but who doesn't like a tan?!?


Also wait you guys have surprise inspections? Those would kill me if we had them.
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Same stuff as our lab. Lots of recombinant/antibiotic-resistant yeast too though I guess.

No surprise inspections that I know of...
 
totipotent.cell said:
For all great mentors out there, what do you do with a high school summer student?

I have one for the summer, which happens to be my second one for my postdoc career. Unfortunately, he seems no different than the first, which was a huge waste of time. Currently, I'm doing a lot of cloning and there is only so much RE digest, pcr, ligation, mini-prep I can show and explain, which most likely interpreted by him as me moving small volumes of liquids around.
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Yeah well, that's mostly what we do, isn't it? :p

I mean, it depends what you also want to get out of it? Potentially get some useful cloning done? Or just not expecting nothing at all?
If it's the latter, just have him clone/tag GFP or something, and then transfect cells and take "pretty" confocal pictures, or something like that. It always seems to help a bit when things aren't 100% "virtual". But yeah, such students are in the vast majority of cases helpless, and often don't give a shit to begin with...
 
Smiley90 said:
So, after there was a question addressed to biochemists yesterday and some people showed up and I randomly saw a fellow gaffer that might be able to help me with some input for my work, I was wondering if ScienceGAF is big enough to warrant a community?

I'm thinking things like

- Networking, talk to fellow Scientists outside of your lab/department/university
- Exchange of Science news (e.g. papers, new journal guidelines, etc)
- Troubleshooting help (PCR conditions, contaminated plates, you name it)
- Nerding out (omg look at this cool thing I found)
- Generally talk science (e.g. debates on what way which field might go, etc)
- Answer questions (e.g. undergrads/grads/whatever with questions that people with other specialties might be better able to solve. no "plz do my homework" though, or at least not too much of it haha.)

I have absolutely NO idea how big ScienceGAF is or how big the interest in a thread like this is, but I figured I'd put it out there. I don't get the chance to fully nerd out that much as the lab I work in isn't very big (3 people).

About myself, I've been working in a Molecular Biology lab for about 2.5 years now, finished my Undergrad in Molecular Biology and Biochemistry 3 months ago and will be starting my Master's this fall. I've been working on my own (mainly Genetics) project for about 2 years now. I have a stupid model organism. 10 bucks to whoever guesses it right. :(
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my thing is earthquakes and volcanoes
love to have threads on both
and space weather
 
The worst experimental failures are the simplest ones... I spent two months trying to conduct a successful enzymatic activity assay for a single-step reaction (pyruvate to lactate, measured by observing the change in absorbance by converting NADH to NAD). As an undergrad, I had no problem operating multi-step assays in glycolysis. I felt so feeble, but today, finally, I resolved the issues and it seems to be working closer to how we predicted.

I've never been so happy about completing a single tiny experiment. This bastard was the last little part I needed for my manuscript, a manuscript that once accepted will allow me to take my preliminary exam and get that much closer to completing my Ph.D.
 
Soka said:
The worst experimental failures are the simplest ones... I spent two months trying to conduct a successful enzymatic activity assay for a single-step reaction (pyruvate to lactate, measured by observing the change in absorbance by converting NADH to NAD). As an undergrad, I had no problem operating multi-step assays in glycolysis. I felt so feeble, but today, finally, I resolved the issues and it seems to be working closer to how we predicted.

I've never been so happy about completing a single tiny experiment. This bastard was the last little part I needed for my manuscript, a manuscript that once accepted will allow me to take my preliminary exam and get that much closer to completing my Ph.D.
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Congratz man!

I'm currently trying to figure out this PCR. I have one primer set that gives me very odd results, so I'm trying a second one. The PCR works PERFECT, like it's one of the most beautiful ones I've seen. Thick, single band.

It just doesn't give me any results. I need to find a restriction enzyme that cuts differently between my mapping strain and the strain I'm using. It cuts everything the same. I'm sad now.
 
Apparently one of my undergrad volunteers believes in Creationism and doesn't acknowledge evolution.

I'm at a loss for words
 
SourShoes said:
You know what to do.
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I can't make him get 10X water again, that only works once.

I'll go with the old and trusted "I'm gonna make you understand" technique.

1. Do you think small changes in DNA/genes might make someone's traits slightly different (duh)

2. Do you think those small changes might make an individual more or less likely to reproduce (duh)

3. Do you think that over time, if it makes someone more or less likely to reproduce, that trait will become more widespread or disappear (duh)

4. DO YOU NOW UNDERSTAND EVOLUTION

5. IF NOT, CHECK OUT HOW WE'RE BREEDING DOGS

6. I won't stop yelling until you realize you're wrong.
 
Give him an assignment comparing mitochondrial DNA to bacterial DNA. Then ask him to explain the mitochondrial replication process that takes places in every one of our cells and compare to bacterial binary fission. Then ask him to compare the same processes with chloroplasts. Why do they all follow the bacterial genetic code as well as the bacterial replication process? How did this come to be in our cells and plant cells?
 
SourShoes said:
Give him an assignment comparing mitochondrial DNA to bacterial DNA. Then ask him to explain the mitochondrial replication process that takes places in every one of our cells and compare to bacterial binary fission. Then ask him to compare the same processes with chloroplasts. Why do they all follow the bacterial genetic code as well as the bacterial replication process? How did this come to be in our cells and plant cells?
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The long con? I like it. I have to find a way to make it relate to my research, but I can probably do that. I'll think of something.
 
Goddamn I love mitochondria. They really are everything. So many people in my field are creationists/religious. I can destroy any argument with mitochondrial evidence. Very few challenge me; however, real science is a dying breed in medicine. It's utterly disgusting. Half the problem is that students were not scientists to begin with, and the other half is that people do not want to project any sort of vibe that is anti-christian in any way. It's all about marketing. It stinks up the field at every angle and is something you always have to be cognizant of. You're persecuted if you challenge beliefs. I really hate this "customer service" game that has become medical science.
 
I don't understand how you can be in science and not acknowledge Evolution. It's one of the most fundamental principles behind ANYTHING biology. And it's beautiful. And really not that hard to understand.

It's like being in physics and not acknowledging gravity.
 
Smiley90 said:
Apparently one of my undergrad volunteers believes in Creationism and doesn't acknowledge evolution.

I'm at a loss for words
Click to expand...

I am very tolerant towards anyone that holds a religious belief... But it is hard to accept someone not acknowledging evolution. Sure, if they can propose an alternative, evidence-based reason why evolution is inaccurate I am very happy to discuss that with them. Unfortunately, it sounds like this kid just denies it owed to his/her religious beliefs. That's pretty bad logic and more or less unacceptable for a scientist.

On the other hand, if the kid is helpful to you in lab, I'm not sure it is worth your time to try and change their stance.
 
Soka said:
I am very tolerant towards anyone that holds a religious belief... But it is hard to accept someone not acknowledging evolution. Sure, if they can propose an alternative, evidence-based reason why evolution is inaccurate I am very happy to discuss that with them. Unfortunately, it sounds like this kid just denies it owed to his/her religious beliefs. That's pretty bad logic and more or less unacceptable for a scientist.

On the other hand, if the kid is helpful to you in lab, I'm not sure it is worth your time to try and change their stance.
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Yah I'm ignoring it. He's super religious and I don't really care. As long as he doesn't bring it up he can stay. Just don't try to debate any of us, I don't have time for that lol.
 
Smiley90 said:
I don't understand how you can be in science and not acknowledge Evolution. It's one of the most fundamental principles behind ANYTHING biology. And it's beautiful. And really not that hard to understand.

It's like being in physics and not acknowledging gravity.
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I guess people who say it's unrealistic or something can't even begin to grasp the scale of time we're talking about here.
They are stuck with their ~5000 years ish, dinosaurs in paradise n stuff.
 
I think we should stay away from the religion/creationism derails in this thread.

Anyway, anyone know a good website/tool for promoter/regulatory elements prediction?
 
Just look at a genome map and take everything the space between the gene you're interested and the gene in front of it. There's bound to be a promoter somewhere in there.

If that doesn't work, first intron is a good second bet.
 
archnemesis said:
I don't think there is a tool that is capable of predicting different regulatory elements with high accuracy. If you're looking for PolII promoters you can use this tool.
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Yeah, I've used that one but it just gives a yes/no kind of answer, which I guess is useful if you're scanning genomic areas where you suspect an unannotated gene might be present, but that's pretty much it. In my case I just wanna scan sequences upstream of a known gene to see if there's anything fancy popping up.

I found one called MatrixCatch. Not sure how reliable/useful it is, but it does list regulatory elements with potential tissue specificity and stuff.

http://gnaweb.helmholtz-hzi.de/cgi-bin/MCatch/MatrixCatch.pl
 
We've had a power outage for like 2h now. On a Sunday. Thank god I have no life and am here. The -80 is all that is on emergency power, if it continues I'll have to move the contents of like 9 fridges and freezers myself UGH
 
Hey molecular biologists! When I was in undergrad, the hot restriction enzymes were EcoRI and BamHI. What's awesome right
now?
 
SourShoes said:
Hey molecular biologists! When I was in undergrad, the hot restriction enzymes were EcoRI and BamHI. What's awesome right
now?
Click to expand...

... Still those. :p

I work with high-GC DNA so the hot ones in my lab are MspI, HaeIII and HhaI.
 
A friend I graduated with just posted this on Facebook. It's the project he's working with. All of us that studied with him are incredibly jealous, particularly those who applied and weren't considered.
:'(

http://www.geologypage.com/2014/07/geophysicists-prep-for-massive.html

A small army of 75 geophysicists is set to converge on Mount St. Helens this weekend to begin final preparations for the equivalent of a combined ultrasound and CAT scan of the famous volcano's internal plumbing. The ambitious project, a joint undertaking by Earth scientists at Rice University, the University of Washington, the University of Texas at El Paso and other institutions, requires placing more than 3,500 active seismological sensors and 23 seismic charges around the volcano over the next few days.

...

The coming tests follow two years of detailed planning and are part of a four-year project called Imaging Magma Under St. Helens (iMUSH), which could bring improvements in volcanic monitoring and advance warning systems at Mount St. Helens and other volcanoes.

The work area for the tests extends from Mount Rainier on the north to the Columbia River on the south, and from Interstate 5 on the west to Mount Adams on the east. An advanced team of researchers has been in the area for weeks installing 70 passive seismographs. Levander said these instruments, which take several hours to set up and will be left in place for two years, are more sophisticated and sensitive than the active sensors.

"The active-source monitoring will provide very high-resolution images at a relatively shallow depth, while the passive experiment data will be at a lower resolution but will be at a much greater depth," said Kenneth Creager, a University of Washington professor of Earth and space sciences who is leading the passive monitoring.

Having both sets of monitors recording data from the active-source detonations will help scientists have a much clearer idea of how the deeper, harder-to-see structure compares with better defined shallow structure, he said.

A third technique, magnetotelluric monitoring, which produces data based on fluctuations in Earth's electromagnetic field, will also be used to image the subterranean structures.
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Best science.
 
Raist said:
Anyway, anyone know a good website/tool for promoter/regulatory elements prediction?
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Try Biobase:

http://www.biobase-international.com/product/transcription-factor-binding-sites

Searches using their latest curated database (TRANSFAC) are behind a pay wall but using their older version is free. Just have to sign up. Look for TRANSFAC public database.

Alternatively, there is another free one from SoftBerry:

http://linux1.softberry.com/berry.phtml?topic=index&group=programs&subgroup=promoter

I used the Nsite tool a couple of times and it seemed to hit all the known regulatory elements I know of present in the upstream sequences I inputted. The results were also similar (albeit not identical) to promoter analysis using the old TRANSFAC database.
 
I'm a computational physicist and my wife is a microbiologist. She is thinking of studying also some geology and expand to stuff like astrobiology. I've detoured to pedagogy the past couple of years.

I don't post very much, but it's always nice to read scienceGAF.
 
There's nothing quite like waking up to 8 emails from your PI freaking out about not understanding your data on a Monday morning

-calmly slurps coffee-
 
Anyone here have any experience crafting a manuscript (and working up the data) for a Genome Announcements publication? I'm basically teaching myself how to properly understand/prepare my sequencing results for a draft genome to publish in GenomeA and am wondering if anyone knows any great review articles that may relate to this area? I basically know nothing about this stuff, but I do have CLC Genomics Workbench access and what seems to be fairly high-quality sequencing results (as far as I can tell). Now I'm just putting it all together piece-by-piece and hoping I'm not botching something along the way.

This paper seems ideal, but perhaps there are others someone could suggest?
 
SourShoes said:
Hey molecular biologists! When I was in undergrad, the hot restriction enzymes were EcoRI and BamHI. What's awesome right
now?
Click to expand...

I made a bunch of vectors with an EcoRI/XhoI/NotI/BamHI MCS. And PmeI for blunt fun.
E/X/N is fairly popular in my institute. Cut super well, decent amount of compatible sites etc.
 
Serious question

I have 15 targets for 20 alleles we need sequenced. High GC content, the targets have some overlap.

Sanger or next-gen? 454 or Illumina? We did WGS on Illumina and got reasonable results, but because we only have one target now it might be better to go with Sanger? I'm in the process of collecting a whole bunch of quotes and feedback atm, it's fun.
 
Smiley90 said:
Serious question

I have 15 targets for 20 alleles we need sequenced. High GC content, the targets have some overlap.

Sanger or next-gen? 454 or Illumina? We did WGS on Illumina and got reasonable results, but because we only have one target now it might be better to go with Sanger? I'm in the process of collecting a whole bunch of quotes and feedback atm, it's fun.
Click to expand...

If you're doing this in-house, I assume the folks at your sequencing platform must know about this. If you're just using a 3rd party service (as in, companies other than Illumina/Roche etc providing sequencing services), they must know that too.
 
How long are your target sequences? Are they repetitive? Getting non-ambiguous data is essential for assembling the raw reads.

Edit: Yes, Raist is right. If you're not familiar with sequencing technology yourself then it's better to let the sequencing team decide the details.
 
Raist said:
If you're doing this in-house, I assume the folks at your sequencing platform must know about this. If you're just using a 3rd party service (as in, companies other than Illumina/Roche etc providing sequencing services), they must know that too.
Click to expand...

Not doing it in-house, I'm in touch with the companies yeah. Figured I'll ask here too! ;)

archnemesis said:
How long are your target sequences? Are they repetitive? Getting non-ambiguous data is essential for assembling the raw reads.

Edit: Yes, Raist is right. If you're not familiar with sequencing technology yourself then it's better to let the sequencing team decide the details.
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Atm they're PCR-products of 0.7-2.4kb, but I can digest them to make them smaller. They're rather repetitive, yeah.

I'm getting input from like 6 places, can't help to get a 7th in GAF I thought haha. I'm not exactly an expert on it, sadly.
 
Raist said:
If you're doing this in-house, I assume the folks at your sequencing platform must know about this. If you're just using a 3rd party service (as in, companies other than Illumina/Roche etc providing sequencing services), they must know that too.
Click to expand...

archnemesis said:
How long are your target sequences? Are they repetitive? Getting non-ambiguous data is essential for assembling the raw reads.

Edit: Yes, Raist is right. If you're not familiar with sequencing technology yourself then it's better to let the sequencing team decide the details.
Click to expand...

Yup. Maybe this is my own ignorance speaking, but I often just refer to each company, labmates, or on-campus facilities and then decide from all the various opinions given. I really need to (and am in the process of, as mentioned a few posts up) teach myself more about sequencing.
 
If your repeats are large you probably want to choose a platform capable of using longer read lengths so that you can get reads that can only be mapped to one position. Illumina's MiSeq platform is capable of 2x300 bp.
 
Seems like I'll have to digest them for whatever I do. 454&Sanger can do up to 700bp, MiSeq is best up to 500.

BioBasic has a 40% discount on Sanger atm... Real tempting lol.


I have to teach myself how to code for the data analysis too. I'm the do-everything guy in out lab. -sigh-

Good thing I like bioinformatics.
 
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