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#158941 POL launched its first scientific journal - Journal of Biological Methods

Posted by bioforum on 14 August 2013 - 03:01 PM

Dear Colleagues,
We are proud to announce that Protocol Online has just launched its first scientific journal – Journal of Biological Methods(JBM, ISSN 2326-9901)!
Since its launch in 1999, Protocol Online has received hundreds of submissions of methods and protocols from worldwide researchers. To meet the growing needs of our contributors and provide them with formal publishing opportunities, Protocol Online created this new multidisciplinary and open-access journal.   
JBM is committed to publishing high quality peer-reviewed papers on cutting-edge and innovative biological techniques, methods and protocols.
The editors of JBM invite submission of papers for its inaugural issue to be published in October 2013. Manuscripts submitted for consideration are expected to describe original research on novel biotechnology, biological methods and experimental techniques, significant optimization and modification of existing methods, development of step-by-step protocols based on proven methods and technologies, and reviews on technical aspects of a particular biological field. JBM covers all biological sciences including, but not limited to, the following areas:  Biochemistry,  Bioinformatics,  Biomedical science,  Biotechnology,  Cancer biology,  Cell biology,  Chemical biology,  Epigenetics,  Genetics and genomics,  Immunology,  Microbiology,  Model organisms,  Molecular biology,  Nanotechnology,  Neuroscience,  Physiology,  Plant biology,  Signal transduction,  Stem cells, and  Zoology.
Types of articles include Research Articles, Protocols, Reviews, and Application Notes.
JBM is also inviting applications for positions on its Editorial Board. Please see the announcement on JBM website for details. Qualified individuals should send their applications to the editor at "editor at jbmethods.org".
For further information, please check out the following links:
Information for Authors | Author guidelines | Online submission

We look forward to reviewing your submissions.

#25012 Being good at the bench

Posted by jangajarn on 23 May 2009 - 11:06 AM

Hey guys,
Being a relatively new graduate student in a big lab where people do not have time to train me, I wanted to train myself. I read this book "At the bench" by Kathy Barker and wrote down things which were important for me. But nevertheless I thought it might be useful to somebody else also. I've attached the document with this post.

Attached Files

#91190 Why God Didn't Get Tenure

Posted by rkay447 on 02 November 2010 - 11:55 AM

Why God Didn't Get Tenure

1. He had only one major publication.
2. It was in Hebrew.
3. It had no references.
4. It wasn't even published in a refereed journal.
5. Some even doubt he wrote it himself.
6. It may be true that he created the world, but what has he done since then?
7. His cooperative efforts have been quite limited.
8. The scientific community has had a hard time replicating his results.
9. He never applied to the Ethics Board for permission to use human subjects.
10. When one experiment went awry he tried to cover it up by drowning the subjects.
11. When subjects didn't behave as predicted, he deleted them from the sample.
12. He rarely came to class, just told students to read the Book.
13. Some say he had his son teach the class.
14. He expelled his first two students for learning.
15. Although there were only ten requirements, most students failed his tests.
16. His office hours were infrequent and usually held on a mountaintop.

#31939 How to find promoter sequence for methylation study

Posted by pcrman on 05 August 2009 - 07:43 PM

Many people have problem identifying or predicting the promoter sequence of a gene, or don't know how to get the actual sequence for analysis such as primer design, transcription factor binding site search, etc. Here I provide ways how I do these things.

1. How to find and retrieve promoter sequences from genome databases

Promoter sequences are usually the sequence immediately upstream the transcription start site (TSS) or first exon. If we know the TSS of a gene, we will know with confidence where the promoter is even without experimental characterization. For many organisms, such as as human, mouse, the genome is well annotated and TSS well defined. Thus promoter sequence retrieval is an easy task. There are three major genome browsers: NCBI, Ensembl and UCSC. For our purpose, Ensembl provides the most convenient interface. Here is an example:

  • go to ensembl website: http://www.ensembl.org/index.html
  • choose an organism such as human http://www.ensembl.o...iens/Info/Index
  • Search your gene such as BRCA2 http://www.ensembl.o...ns;idx=;q=brca2
  • Click the right hit on the search result page and it will bring you to the gene summary page. For example the link to BRCA2 gene is http://www.ensembl.o...ns;idx=;q=brca2
  • On the left, under "Gene Summary", click "Sequence", the sequence of the gene including 5' flanking, exons, introns and flanking region will be displayed.
  • The exons are high lighted in pink background and red text, the sequence in front of the first exon is the promoter sequence.
  • By default, 600 bp 5'-flanking sequence (promoter) is displayed. If you want to get more, click "Configure this page" in the lower left column, a popup window opens allowing to input the size of 5' Flanking sequence (upstream). You can put for example "1000" and then save the configuration.
  • Sometimes there are discrepancies between Ensembl and UCSC annotation regarding TSS. To make sure the first exon given by ensembl is right, copy the promoter sequence
  • Go to UCSC BLAT search at http://genome.ucsc.e...t?command=start and choose the right genome (eg, human), paste the sequence there. On the result page, click browse of the first hit, this will bring you to the genome browser Page. the query sequence is now aligned with UCSC genome sequence. Zoom out a bit, you will be able to determine whether the promoter sequence matches UCSC annotation. If it matches, the sequence is very likely the right one. Here is the BRCA2 promoter sequence aligned to BRAC2 gene.
  • In UCSC genome broswer, you can turn on CpG island feature, if there is CpG island in the promoter sequence, the sequence is highly likely a true promoter. In the above example (BRCA2), a CpG island is displayed in the proximal promoter.
  • Beware some genes have alternative promoters. To find those sequences, it requires extensive bioinformatics and experimental analysis.

2. How to predict promoter sequences

... to be updated

This post has been promoted to an article

#141671 Buffer in Gel

Posted by phage434 on 18 September 2012 - 05:53 AM

I may run two gels if I am doing both, after loading fresh buffer. But I do not trust the buffer left over in a gel box others have used. I even wash the gel box out after I'm done (probably the only time it ever gets washed).

#13775 Important literature for real time PCR users

Posted by tea-test on 29 January 2009 - 09:46 AM


I have gathered some important documents with many useful information regarding real time PCR.

#13566 Handbook of Biological Statistics

Posted by gebirgsziege on 28 January 2009 - 12:02 AM

I find this site quite useful!

Handbook of Biological Statistics, online version

#126268 No band in PCR

Posted by phage434 on 02 January 2012 - 05:53 AM

I went for a walk, and got lost. Thank you for any help.
Seriously, what can you possibly expect as an answer? We know nothing about what you did or want to do.

#54001 Re-using Culture flasks

Posted by bob1 on 05 January 2010 - 03:22 PM

Hi dear, you can use culture flask 4-5 times unless you devoid trypsin from it. Either wash the flask using PBS or Culture medium, then add cell B) s.

ya,we regularly reuse culture dishes upto 3 times.....there is no problem....but rinse properly

If I wash the plate well with PBS, can I reuse 6 well plates?

If you all read the above posts you will see that you are in error... re-using is a problem, if you do it you are jeopardizing you results through a number of factors including cellular damage, cell type drift (lab evolution), and general contamination issues.

Be better scientists!

#25732 Re-using Culture flasks

Posted by bob1 on 01 June 2009 - 04:34 PM

Quite right, you are selecting for cell populations that adhere strongly, meaning that expression of a wide range of genes is altered. Your cells will be undergoing laboratory selection, and drifting from the parent population (assuming that these are commercial cell lines, or other cell lines used by multiple labs) meaning that other labs may not be able to replicate your results.

#172185 the gender of computers

Posted by mdfenko on 18 December 2014 - 04:55 AM

this was posted at another forum:


A Spanish teacher was explaining to her class that in Spanish, unlike English, nouns are designated as either masculine or feminine.

'House' for instance, is feminine: 'la casa.'
'Pencil,' however, is masculine: el lapiz.'

A student asked, 'What gender is 'computer'?'

Instead of giving the answer, the teacher split the class into two groups, male and female, and asked them to decide for themselves whether computer' should be a masculine or a feminine noun. Each group was asked to give four reasons for its recommendation.

The boys’ group decided that 'computer' should definitely be of the feminine gender ('la computadora'), because:

1. No one but their creator understands their internal logic;

2. The native language they use to communicate with other computers is incomprehensible to everyone else;

3. Even the smallest mistake is stored in long term memory for possible later retrieval; and

4. As soon as you make a commitment to one, you find yourself spending half your paycheck on accessories for it.

The girls’ group, however, concluded that computers should be Masculine ('el computador'), because:

1. In order to do anything with them, you have to turn them on;

2. They have a lot of data but still can't think for themselves;

3. They are supposed to help you solve problems, but half the time they ARE the problem; and

4. As soon as you commit to one, you realize that if you had waited a little longer, you could have gotten a better model.

The girls won.

#167205 Reference gene(s) selection and validaton for qPCR

Posted by Trof on 22 April 2014 - 05:01 AM

Selecting a proper reference gene(s) for RT-qPCR is an ongoing struggle.

It's easy to "do it", but it's significantly more difficult to do it right.


I will dedicate this topic to general discussion about selecting reference (sometimes called housekeeping) genes, software/application used and so on.


A web page first.


Massively resourced but rather ugly pages concerning normalization and reference genes selection on Gene-Quantification.info site.



(often contains fulltexts of papers)


Some papers.


The need for transparency and good practices in the qPCR literature - Nature Methods 2013

Evidence Based Selection of Housekeeping Genes - PloS ONE 2007


and of course


MIQE Guidelines


Today I came accross a free web tool to select reference genes using algorithms from four currently used applications geNorm, Normfinder, BestKeeper, and the comparative ddCt method.

Since I have used only one of them and this requires to only copy Ct directly from the Excel table (!!) it's like a huge help to refgene selection (I used GeNorm for some time, I wouldn't really call it user friendly..)



But since I can't compare with the others I don't have any comments on this would be appreciated.


(I may add later some sites/papers/... I found highly relevant, post any sources regarding the topic, if you want, too)

#156947 xkcd reality hack

Posted by Trof on 26 June 2013 - 12:08 AM

Few weeks ago a new comics on xkcd site appeared that I instantly wanted to replay in real.
It took me some time thought to find a real-looking gun, but finally yesterday we did it.


Posted Image

Real version:

Posted Image

Starring: me, airsoft Beretta 93R and K562 CML-derived cell line (not a real gun, but real cancer cells Posted Image )

It was fun Posted Image

#156803 How to stop stomach cancer patient from hiccuping

Posted by doxorubicin on 21 June 2013 - 06:04 AM

For standard hiccups, this technique works well: http://www.cognitial.com/hiccups.shtml

If you want to make your father laugh, propose this cure to him: http://www.ncbi.nlm..../pubmed/2299306

#141994 Co-transfection with 2 plasmids

Posted by Trof on 21 September 2012 - 11:25 AM

Transfection, sorry.

The limiting size is not the problem here, the question is not whether it's possible to transfect with two plasmids, the question is, if he can transfect two separate plasmids, one with obviously different efficiency AND use the second plasmid to calculate the efficiency of the first.

It would be like measuring how much salt can dissolve in an amount of water by measuring how much sugar dissolves there.

#135352 Advice on thesis writing

Posted by Micro on 01 June 2012 - 03:43 PM

From my experience and comments my supervisor made whilst I was writing up. If you are working exclusively on writing and have strong writing and editing skills then 3-4 months is possible. For anyone with average writing skills at least 6 months writing will be required. Also, you will need to factor into your timing how long it takes your supervisor(s) to return draft's and if they have any upcoming leave or work commitments that may add delays.

As for recommendations on how to write:
Don't try to write the perfect document/chapter the first time. It is more important to just get thoughts and ideas onto the page. Once you have a few pages of notes/comments you will feel a lot more motivated to write than staring at a blank page.

Do your referencing as you go, even if you are just putting notes on the page. It will save you heaps of time in the later stages when you are editing. Also, use a reference manager (EndNote, ProCite, etc.)

Start writing NOW even if you experiments are not finished you can write 1/2 to 3/4 of a chapter without results and then just add the rest later.

And finally when the crushing wave of panic comes (and it happens to everyone) just breathe, step away from the computer and listen to your favourite song/ go for a walk (anything to distract you from your thesis for a few minutes, no longer than 1 hour) and then sit back down and start again. You will get there in the end.

Good luck!

#124132 Does it matter where a PhD is done?

Posted by gebirgsziege on 22 November 2011 - 11:13 PM

although the ranking of your university seems to get more important, the decisive factor usually is the quality of your supervisor - and there are excellent supervisors who are young group leaders and bad supervisors who are well established senior scientist - and vice versa. Most important is that you think you can spend 4/5 years with your supervisor and the people in the lab - because I have seen many people choosing their supervisor by reputation who did hate their PhD and who were really unhappy in the groups.
So in my eyes its supervisor/group first, then topic, and then the institution. If you like what you are doing and where you are doing it you will be more productive which will in the end define your chances.

#109390 phosphorylted protein smaller not bigger?

Posted by mdfenko on 10 May 2011 - 10:05 AM

the incorporated phosphate(s) can increase mobility, it increases negative charge on the protein. we used urea gels to visualize phosphorylated vs unphosphorylated proteins and the phosphorylated ran faster (urea enhances charge separations).

#104743 How do you use tips???

Posted by Adrian K on 25 March 2011 - 01:48 AM

Ok, something I did while waiting for my PCR....

Pito DSC02726.JPG



Hobglobin, DSC02734.JPG

mdfenko, DSC02732.JPG

phage434, DSC02733.JPG ...phage was too hard to be "tips engineered"...

Homebrew, DSC02731.JPG

And specially for Ameya

Done by,
For DSC02740v2.JPG

Vote + anyone? ^_^

#100607 final concentration

Posted by mdfenko on 14 February 2011 - 01:40 PM

if you mix 1ml of 20uM forward primer with 1ml of 20uM reverse primer then you will have 2ml of 20uM primer mix but 10uM each primer.

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