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Posted by bioforum on 14 August 2013 - 03:01 PM
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.
Posted by jangajarn on 23 May 2009 - 11:06 AM
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.
- Good_at_lab.doc 47.5KB 3181 downloads
Posted by rkay447 on 02 November 2010 - 11:55 AM
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.
Posted by pcrman on 05 August 2009 - 07:43 PM
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
Posted by phage434 on 18 September 2012 - 05:53 AM
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.
- Application_note_Understanding_Ct.pdf 2.03MB 4135 downloads
- Accurate_normalization_of_real_time_quantitative_RT_PCR_data_by_geometric_averaging_of_multiple_internal_control_genes.pdf 141.4KB 2775 downloads
- Analysis_of_Relative_Gene_Expression_Data_Using_Real_Time_Quantitative_PCR_and_the_2_deltadeltaCT_Method_.pdf 713.66KB 2939 downloads
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)
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
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)
Posted by Micro on 01 June 2012 - 03:43 PM
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.