How can you find the ancestors of a bacterial species?

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Which tools are there to find non-coding RNAs in bacterial RNA-seq data?

I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find some tools but I'm still quite lost (see link below). I've also seen this Biostar...

02 March 2014 4,167 2 View

Is it possible to have a 200 fold change miRNA?

We found a 200 fold change regulation (with good read coverages). Has anyone observed this?

02 March 2014 2,026 5 View

Can anyone help with batch predict membrane-related genes?

I need to predict membrane-related genes in a 2000 genes list. Could anyone suggest an appropriate approach? I've already filtered out the ones retrieved with GO terms, so this way has already...

01 February 2014 6,591 2 View

What is the difference between txid738 [Organism:noexp] and txid73 8[Organism:exp] filters?

What's the difference between these two filtering alternatives when looking for all proteins available for a selected organism in NCBI? I get the double of proteins in 'noexp' case!

01 February 2014 921 2 View

Locate amino acids in 3D protein structure?

Hi community, I would like to know how to locate a certain protein sequence in the whole protein 3D structure. We are trying to see if these short protein sequences are located on the surface. I...

01 February 2014 4,245 10 View

How can I identify pseudogenes in prokaryotic genomes?

I would like to perform whole genome identification of pseudogenes. Could anyone suggest a good strategy?

01 February 2014 3,084 2 View

No title

Hi, I would like to know the cDNA quantity you recommend for the mentioned PCR. It will be used to validate RNA-Seq results. Thanks, Bernardo

31 December 2013 8,033 9 View

What do you think about this correlation between qPCR and RNA-seq?

I would like to know your opinions about the correlation I obtained between qPCR and RNA-seq for 8 genes, two of them being reference genes. The r2 is good but I worry that qPCR FC are not as high...

31 December 2013 7,858 17 View

Can anybody provide me with a list of all reported bacteria, including their corresponding phylum, class, order, and family?

Basically, I'm looking for the same table than this one (http://genomesonline.org/documents/Export/gold.xls) and this one from GOLD genomes (http://genomesonline.org/cgi-bin/GOLD/index.cgi), but...

11 December 2013 9,942 5 View

How to get conservation of vaccine candidates between hundreds of bacterial strains?

Hi community, We have identified vaccine candidates via an ex-vivo RNA-seq approach. The next step would be to perform conservation of these candidates (about 20) between multiple bacterial...

11 December 2013 9,522 1 View

IHC on mouse liver hepatocytes?

Can anyone help me choose primary antibodies for mouse liver hepatocytes and also in conjunction Cd8 cells. Also Cd3 cells. I want to look at hepatocytes and adjacent immune cells in mice with...

01 March 2021 6,953 1 View

What is the exact mechanism of the antimicrobial effect of local anesthetics?

The antimicrobial effect of local anesthetics has been known for more than 50 years, but it still seems to have an unclear mechanism of action. which bacteria? which concentration? etc etc. ....

27 February 2021 4,450 2 View

Uncertianiny in using dry or wet basis in mixing a sediment with fuel oil?

Hello I'm currently working on a topic related to studying the anaerobic biodegradation of TPH in marine sediments. In this work, sediment should be mixed with fuel oil to a concentration of 20 g...

24 February 2021 9,839 3 View

Advice on growing lactobacillus species in the lab?

Hello everyone, For part of my PhD project, I'm hoping to grow some lactobacillus species in the lab so that I can create standard curves for a qPCR quantification of a faecal sample. However, I...

24 February 2021 3,157 6 View

What are the best cations for preparing competent cells, Ca2+ or Mg2+?

I have been reading various articles and most state that treatment with CaCl2 produces higher efficiency of transformation than MgCl2. Can anyone explain why Ca2+ is better than Mg2+ at...

16 February 2021 8,519 5 View

Various schools have emerged in the study of comparative literature. Mention the most prominent of them in a nutshell.?

Various schools have emerged in the study of comparative literature. Mention the most prominent of them in a nutshell. And he talked about one of them?

09 February 2021 1,099 8 View

Would using an asRNA for repressing transcription of a high expression Listeria monocytogenes non-coding RNA harbored in a plasmid be a viable option?

Hello all, I am interested in deleting a highly expressed non-coding RNA located on a Listeria monocytogenes plasmid. Currently, there are not any optimized gene deletion methods for Listeria...

09 February 2021 4,994 1 View

Review Papers regarding transcriptional regulations & promoter types/classes in Gram positive bacteria?

Dear fellow researchers, Could you please suggest me excellent review papers discussing transcriptional regulations and/or promoter classes in Gram positive bacteria? Thank you so much for your help!

08 February 2021 6,909 3 View

I am looking for a co-author specialised in decision-making/managerial studies/data science/?

I am currently working on a publication with the intention of presenting a proprietal method for a ranked comparison of incompatible features in a limited data set. I am looking for a co-author as...

08 February 2021 1,450 5 View

Flexibility of RNAseq?

When you use RNAseq I understand that it must follow certain conditions when you use it. One of them is the insertion of a polyA tail. The insertion of the polyA must include then...

05 February 2021 3,770 4 View