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Below are the 20 most recent journal entries recorded in Biology Talk's LiveJournal:

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Tuesday, March 26th, 2013
5:24 pm
[lizardphunk]
Mitochondrial disease

I'm making a student presentation on mitoochondrial disease (15 minute lecture).

As I'm sitting here reading my articles, it seems to me that a lot of the dieases are "more prevalent in Northern Europe" (be it nuclear or mitochondrial mutations affecting mitochondrial function).

Coincidentally, I am in Norway, so maybe that's why this popped out. I haven't actually sat down and mapped the prevalences of the mutations. ;)

I was wondering if any of you guys know why this might be the case? Does it suggest that a specific group of people spread into the Scandinavias? Does it have anything to do with the Sami population (I know that some native american populations have a high incidende of specific mutations).

Examples are Leber's and Kjell's optic neurpathies, also PolG mutations leading to Alper's syndrome.

Sunday, October 28th, 2012
1:05 pm
[lizardphunk]
A gel and some questions

lab2

Hi!

I wanted to discuss something - I'm working on a report where we've isolated kallikrein-4 RNA from prostate cancer cells, made cDNA, amplified by PCR, and analyzed on a 1,5% agarose gel. I pasted the results above.

Sorry about the Norwegian in the text, basically we expected a 700bp fragment for KLK4 (which we see in lane 2 from a KLK4 expressing plasmid).

In lane 5, you can see the KLK4 cDNA we amplified by PCR. Now for what I'm wondering about ... we see a lot of noise compared to the plasmid KLK4.

I'm wondering why this could be, and was hoping you guys had any idea. I'm an undergraduate with a good deal of experience with gels, but I haven't done exactly this before.

- We see another clear band other than the 700 bp fragment + some other noise

- is the other band a result of alternate splicing? I suppose the mRNA is already spliced since cDNA doesn't contain introns. Do you think the noise could be because of some cancer-specific process?

- I'm worried about the noise we see over the whole lane in well number 5 - is this simply because of PCR-byproducts?

Thanks. I just wanted to mention that I don't really need this for my report, it's somewhat extracurricular, but I'm just personally curious since this was a lot of fun. :)

Saturday, May 14th, 2011
12:04 am
[silent__dreamer]
Does anyone have access to this paper?
 Does anyone have access to this paper?

E.S. Kim, M.S. Kim and A. Moon, TGF-beta-induced upregulation of MMP-2 and MMP-9 depends on p38 MAPK, but not ERK signaling in MCF10A human breast epithelial cells, Int. J. Oncol. 25 (2004), pp. 1375–1382.

I can't seem to find the full text version anywhere.

Thanks!

My email addy is eventide_spirit@yahoo.com

Int J Oncol. 2004 Nov;25(5):1375-82.
TGF-beta-induced upregulation of MMP-2 and MMP-9 depends on p38 MAPK, but not ERK signaling in MCF10A human breast epithelial cells.
Kim ES, Kim MS, Moon A.
Source
College of Pharmacy, Duksung Women's University, Seoul 132-714, Korea.
Abstract
Transforming growth factor (TGF)-beta has been reported to exert growth inhibitory activity in normal epithelial cells whereas it induces cell proliferation and invasive phenotypes in advanced carcinomas. Our previous study showed that MCF10A, a spontaneously immortalized "normal" breast epithelial cell line, is resistant to TGF-beta-induced growth inhibition, suggesting that conversion of TGF-beta growth inhibitory signaling into an oncogenic pathway may occur at the early stage of tumor development/progression. To address this issue, we investigated the TGF-beta signaling pathway and its role in phenotypic transformation of MCF10A cells. TGF-beta treatment induced changes in the MCF10A cell morphology from cuboidal to an elongated spindle-like shape, accompanied with down-regulation of epithelial cell marker E-cadherin. TGF-beta treatment was sufficient to induce migrative and invasive phenotypes in these cells, an important phenotypic conversion during tumor progression. We also showed that TGF-beta treatment rapidly activated ERK-1/2 and p38 MAPK leading to upregulation of matrix metalloproteinase (MMP)-2 and MMP-9. Using chemical inhibitors and dominant negative mutants of MAPKs, we provide evidence that while both p38 MAPK and ERKs are required for TGF-beta-induced MCF10A cell migration and invasion, TGF-beta-induced MMP-2 and MMP-9 expression depends on p38 MAPK signaling, but is independent of ERK activity. This study demonstrates the roles of TGF-beta signaling pathways for induction of oncogenic signaling in preneoplastic human breast epithelial cells and will deepen our understanding of TGF-beta signaling in the progress of breast cancer.
Saturday, April 23rd, 2011
5:30 pm
[ugly_boy]
Actin and cell migration
I have an exam in my cell biology lab on Monday and I'm stuck on two of the items on the study guide:

Consider the leading edge of a cell. What specifically is occurring at the leading edge to push the membrane forward? Why is the band of F-actin seen at the leading edge discrete; in other words, why is it only ~1 µm in width?

I know that branched microfilaments assemble at the leading edge with the (+) end facing the plasma membrane. The actin cytoskeleton is fixed with respect to the surface that the cell resides on, I believe this is accomplished by integrins at focal adhesions, and that the growing filament therefore pushes on the membrane, extending it forward. What I'm not sure about is how and why it maintains a constant width.

Can cell crawling occur in solution or is a substrate required?

I think the answer is that substrate is required, but I want to double check. I'm aware of other mechanisms of motility, for example using flagella. Am I correct in assuming that 'cell crawling' refers specifically to this type of movement, which involves lamellipodia and requires adhesion to a surface?

Thanks. :)
Monday, April 11th, 2011
9:17 pm
[ugly_boy]
How much physics do biology students need?
How much physics do you think students should be required to take to complete an undergraduate degree in biology? Is there specific material that you think is especially useful or important for biology students? Do you think a typical year-long introductory course covering classical mechanics, thermodynamics and electricity and magnetism covers the material that is most relevant for biology students? Is it physics per se that is valuable, or the quantitative skills and systematic approaches problem solving, or both… or neither?

I would love to know what people think.
1:20 pm
[may_k]
Paper access
Dear friends,

does anyone by chance have access to the Journal of Alzheimer's Disease?
It would be great if you could help me to open the following paper:
http://www.ncbi.nlm.nih.gov/pubmed/21178287

Signaling via Amyloid Precursor-Like Proteins APLP1 and APLP2.
Orcholski ME, Zhang Q, Bredesen DE.
J Alzheimers Dis. 2011 Jan 1;23(4):689-99.

Thank you very much in advance!

Best wishes,

May K.
Friday, February 4th, 2011
5:09 pm
[million_moments]
Journal Club - Negative Results
I am going to do my labs journal club next month, and I thought I'd have a theme of negative results. I know sometimes people struggle to publish good scientific studies that have resulted in a negative results (e.g hormone x is not up regulated during disease y despite symptoms being similar to over expression of hormone x). However I have also read some negative results papers that make me question why they were published, even though they might have been scientifically sound.

I thought I would pick one journal I thought should have been published, and one whose publication seems strange to me (for example, I have an article where it is extremely unlikely any researcher would unknowingly attempt the experiment again, because the likely-hood of it working was quite far fetched in the first place). If you have any "negative" results papers (preferably ones not published because they challenge previously published data) you'd like to point me to I'd appreciate it. I know there is a Journal of Negative Results in Biomedicine and one for Pharmacy, but I don't want to group to start questioning these Journals because they are less traditional/lack official impact factors.

Thanks!

Current Mood: curious
Wednesday, October 27th, 2010
10:26 pm
[laithalshawaf]
Disgust Sensitivity Survey
 Researchers from The University of Texas at Austin are conducting an online survey to understand why people differ in their levels of disgust sensitivity. This survey takes about 15 minutes in total, and the study would benefit from your participation.

You must be 18+ years old and fluent in English to take this survey. These are the only requirements for participation. If you are interested in taking this survey, or learning some more about it, please click on this link:

http://qtrial.qualtrics.com/SE?SID=SV_3EolMi7ycaG6mlC

If you choose to participate, all of your answers will remain anonymous and confidential, and you will not be asked to provide any identifying information.

If you have any additional questions or concerns, please don’t hesitate to contact the researchers at laith.alshawaf@mail.utexas.edu. Thank you for your consideration!

Sincerely,

Laith Al-Shawaf and David M.G. Lewis
Friday, October 8th, 2010
6:03 pm
[aclarar]
petroleum help
Hello magnificent people!!!

I need some help.

Part of my PhD project is to be done here in the USA and it involves petroleum.

The thing is, I don't need a huge amount of it. I mean, a barrel is way too much petroleum for me. So I can't really go out and buy it.

I was wondering if maybe someone has access to a sample of petroleum that he/she is will to share?

I need 300ml of a low density petroleum, hopefully similar to 20 to 23 API grade and hopefully recently drilled. Any help will be greatly appreciated.

thanks in advance.



x-posted all over.
Monday, September 13th, 2010
1:35 pm
[ugly_boy]
Effect of lipids and ethanol on cells, tissues and viruses
If you immersed a cell in oil or another non-polar solvent, would the cell eventually lyse due to loss of membrane integrity? If the hydrophobic "force" is the major factor holding the cell membrane together, it seems like immersion in an oil would significantly decrease the stability of the membrane. I would predict that lower molecular weight non-polar solvents, like benzene, chloroform or n-hexane, would be even more effective at dissolving the lipid bilayer, and that some of these might also act chemically to alter the structure of the membrane. What would happen if you submerged an entire body in a non-polar environment? Would the soft tissue eventually melt away, leaving bones and a few tough, proteinaceous structures like hair? How would the effect differ for living and non-living bodies? What kind of membrane repair mechanisms do we have to combat such a scenario, and how effective are they?

I know that ethanol (as in Purel and other hand sanitizers) and isopropyl alcohol (rubbing alcohol) are small, amphiphilic molecules that are highly hygroscopic and work as disinfectants by disrupting cell membranes and causing dehydration. What would happen if you immersed an entire body in a low molecular weight alcohol or another small, amphiphilic solvent? Would it simply dessicate the body or would it break up the membranes and dissolve soft tissue? How would this compare to the body's behavior in oil, benzene or other solvents?

Finally, what is the virucidal mechanism of ethanol? Does it only work on enveloped viruses? I would not expect it to disrupt the covalently linked viral capsid, unless it acts chemically, for example on by cleaving peptide bonds. I remember hearing on NPR that ethyl alcohol is not effective against rhinovirus but that it does kill influenza and many other common viruses and most (or all?) bacteria. What about the structural or biological properties of rhinovirus accounts for this?
Tuesday, June 15th, 2010
7:25 pm
[dna_man]
I am in a jam, any chance anyone would have

Nature Reviews Microbiology 8, 171-184 (March 2010) | doi:10.1038/nrmicro2297

Molecular mechanisms of Escherichia coli pathogenicity

Matthew A. Croxen & B. Brett Finla

OR

Nature Reviews Microbiology 8, 389 (June 2010) | doi:10.1038/nrmicro2378

Bacterial pathogenesis: Opening the gates of type III secretion

Christiaan van Ooij

I feel bad for asking but I really really need these.

Thanks
Monday, May 17th, 2010
12:10 pm
[yelya]
Electronic notebooks
I was wondering if anyone has experience with using electronic notebooks? My company is looking into potentially switching to electronic notebooks, but we have nobody here who has used them before, and no information that would help us choose a particular brand. How are lab notes done at your company?

Please, help! :)
Thanks!
Wednesday, April 14th, 2010
4:16 pm
[silent__dreamer]
Biology Industry
Hey everyone, 

So I don't know very much about going into industry in biology since I'm still a graduate student and I get the sense that it's sometimes frowned upon to want to go into industry, but I was wondering what careers in industry are available for people with phDs and what industry values?  E.g. to get a good job in industry, what should you make sure you do when you are a graduate student? 
Do people usually do a short 1-2 year post doc in an academic lab first/a post doc at a company? 
Friday, February 26th, 2010
12:36 am
[puf_almighty]
Random question
You know how some frogs increase their solute levels to be able to hibernate in sub zero temps without their cells popping from the water expansion? And I guess probably other things than frogs do this too. Does that mean those frogs are physiologically pre-adapted to become salt-water frogs?
Tuesday, February 2nd, 2010
8:03 pm
[captainsavvy]
What is life?

Since September i've been working on a project. I have neglected posting about it here because i wanted to really dig in and understand it myself before i felt ready to share or debate.

Basically I want to redefine what we consider to be alive as our reasons for excluding what most consider "inanimate objects" just doesn't make sense to me and I would argue don't make sense even according to our current ideas of what is alive. It also solves the question of when did life "arise" on the planet as its always been here, just in a way that is different than what we think of as life. The earth itself is alive, so instead of there being this almost mystical change over from "inanimate matter" into "life" we have simply an evolution from one form of life to another, molecules into single cell organisms. It makes a lot more sense science usually prefers the simpler explanation.

Anway i've done a lot of writing and a lot more thinking on the subject and most of it is posted on my blog which I welcome you to read, comment on and question with me.

XPosted
Sunday, January 24th, 2010
8:52 pm
[ugly_boy]
Macromolecular components of cells
Does anyone know a resource that gives the macromolecular composition of various cells? For example the (average) percent mass that is due to proteins, lipids, carbohydrates and nucleic acid for a variety of cell types. Something in a nice, concise table with a handful of examples would be great. I do have some textbooks at the house that might have this info, in particular Campbell's Biology and Lodish's Molecular Cell Biology but I haven't had a chance to look yet and I'm not sure whether these will have what I'm looking for. This came up because I answered a question on Yahoo! Answers and now I'm exchanging e-mails with the guy; I'm all cells contain all four types of macromolecules, and I would like to have some real data to share. Also, if anyone knows of examples of (living) cells that do not contain one of the four types I would be very interested in this. I told him I did not know of any exceptions, and it's hard to imagine how a cell could get by without some of each, but of course words like "always" and "never" have to be used with caution in biology.
Friday, January 22nd, 2010
2:03 pm
[sunemai]
About Dolphins and Hair
Two quick questions:

My little brother was told by his biology teacher that all mammals have hair. He has been wondering for the past week if dolphins have hair, too. What should I tell him? Is there a species of fur covered dolphins swimming around somewhere?

I'm not sure how "hair" is defined in this case and that would be the second question. When determining (in scientific context) which creatures have hair, what is considered to be hair?


ETA: Thank you everyone, for taking the time to answer! You have been of great help. My brother can finally stop mumbling about dolphins and how he has never seen a picture of a fur-covered dolphin. :D
Wednesday, January 20th, 2010
6:26 pm
[yelya]
qPCR primer help
Hi, everyone,

I hope that you can help me (yet again!)

I am new to RT-qPCR, and I'd like to ask some questions about the primers:

1) Where do you usually order your primers? Does it matter? What level of purification do you usually order for your primers - HPLC, PAGE or just standard desalting? I am following the protocol from T. Nolan (Nature Protocols 2006, 1(3), 1559), and it says that the primers have to be either HPLC or PAGE purified, whereas a sales representative at IDT DNA told me that standard desalting is fine (although it implies that a typical primer of about 22 bases or so will contain about 17% trancation products.

2) When you are starting a new assay, how do you usually get primers? Do you design them yourself, or do you look in the primer databases or literature to see what other people used? What online programs would you recommend for primer design?

3) When looking in the primer databases, I have found separate primer sets for SYBR Green and Taqman assays. Except for the presence of the probe, how would primer design be different for these two assays? What would be the difference in primer design if I am just interested in an RT-PCR assay (semi-quantitative?) - would the amplicon length be typically bigger?

Thank you very much for your help.
(x-posted)
Monday, January 18th, 2010
7:39 pm
[wolodymyr]
Question about gametes produced by a Drosophila cross
I'm trying to put together three Drosophila crosses. I'm new at this, so I'm just getting the hang of nomenclature.

I've successfully done one. I'll use it as an example, and then, if you could, I would deeply appreciate your help figuring out the gametes of the other two.

First:
BL7018 (Bloomington stock number 7018): w[*]; noc[Sco]/CyO; P{w[+mC]=tubP-GAL80[ts]}7

there are 3 genes here. w[*] means white eyes, noc[Sco]/CyO means curly wings and stubby bristles, and the 3rd, which I'll abbreviate Gal80ts, produces a temperature-sensitive Gal80 protein.

First question: Gal80ts has a mini-white marker on it. Does [+mC] indicate that marker?

There are 4 gametes possible from the male flies:
w; ScO; Gal80ts
w; CyO; Gal80ts
y; CyO; Gal80ts
y; CyO; Gal80ts

Second question: How do I determine the males' gametes for BL 7019, w[*]; P{w[+mC]=tubP-GAL80[ts]}20; TM2/TM6B? (Where w[*] is white eyes, P{ etc is the protein as above, and TM2/TM6B are balancers, meaning they're homozygous lethal. I don't know what phenotypes the heterozygotes show.)

Are they:
w; Gal80ts; TM2
w; Gal80ts; TM6B
y; Gal80ts; TM2
y; Gal80ts; TM6B

?

Third question: Pretty much the same thing for male fly gametes for BL 7016, P{w[+mC]=tubP-GAL80[ts]}9; w[*]/FM7c, where there seem to be two genes involved.

I'm a little more confused about this one, because I'm not exactly sure how the balancer FM7c works. Does it always have the phenotype bar eyes? Is it homozygous lethal, sterile? Can males carry it?

I was given a sample cross for this that I'm finding confusing. Here it is:

Females\....Males

............\ Gal80ts...............FM7c..................Y


Gal80ts...|.Gal80/Gal80..........Gal80/FM7c............Gal80/Y


FM7c......|.Gal80/FM7c...........FM7c/FM7c.............FM7c/Y


What confuses me is that it looks like all 3 of these genes are on the same chromosome (?) - so that the results are gene/gene, not gene;gene. Is Gal80 on X, here?

Also, (questions 8-10) what are the fates of these offspring? Is FM7c/Y viable? How do I recognize Gal80/Y? Are those all the males with normal-shaped eyes? And speaking of that, back to the gametes: the cross I was given doesn't include the mutant eye color. Should it?



Any confirmation, explanation, or instruction you could provide would be hugely appreciated.
Thursday, January 7th, 2010
10:11 am
[yelya]
RT--PCR and microarrays
Guys,

I hope somebody with experience can help me with some basic questions about RT-qPCR and microarrays that I knows next to nothing about.

1) Concerning RT-PCR:

Suppose, you know that for a particular experiment you will need to run 20 RT-qPCR reactions. How much total RNA would you start with? Or, putting it another way - suppose you start your experiments with 50 ng of total RNA, then do the RT reaction, and then use it for qPCR - how many reactions would you be able to run, assuming I don't do any pre-amplification steps after cDNA synthesis?

Also, can you share your experience of isolating total RNA from cells (not tissues) - if, say, you start with 100,000 cells, how much total RNA can you isolate, and what method do you use? Have you ever tried isolating RNA from a very small amount of cells (say, 100 or 1000)? Or used something like "Cell-to-CT" kits? What, in your experience, is the minimum number of cells that can yield reliable data?

2) Concerning microarrays:

Have you done microarray experiments using universal RNA (URNA) as an internal standard? Some papers claim that using URNA provides means to compare microarray data across experimental platforms and labs. So, why isn't everyone using it? What are pros and cons?

Thank you for your help!
(x-posted to _scientists_ and lab_gripes
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