How can you find the ancestors of a bacterial species?

More Bernardo Bello Ortí's questions See All

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 4,293 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 2,122 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 6,681 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 1,014 2 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 3,176 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 4,349 10 View

What is the minimum RNA quantity for a 20 uL RT-qPCR ΔCt-method?

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 8,136 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 7,975 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 10,025 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 9,607 1 View

What precautions should be taken while handling S. aureus enterotoxin Type B in the lab?

I would like to understand potential safety concerns while handling SEB in the lab. Especially while working in animal house facility. Would like to know precautions for handling. Sigma MSDS...

07 August 2024 6,034 3 View

How can I inoculate a lyophilized anaerobic bacteria into the culture medium without an anaerobic chamber?

There are anaerobic gas pak jars and environment providers in the laboratory that provide anaerobic environmental conditions for the growth of anaerobic bacteria. However, there is no anaerobic...

05 August 2024 4,945 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Request for Advice: Starch Metabolism Research Project?

I am currently considering a research project focusing on a comparative analysis of starch metabolism in orchids and roses. I am particularly interested in identifying the types and quantities of...

30 July 2024 4,267 2 View

How does the Retention time effect the Biogas Production?

List down the various factors responsible and how does this effect the overall biogas production when it is related to Hydraulic retention time of the digester based on the feedstock?

27 July 2024 4,800 4 View

Question about MHB (Mycorrhiza Helper Bacteria) isolation technique??

What are the most effective isolation techniques for obtaining MHB?? Is there are best approach techniques? I keep struggling in obtaining it.

26 July 2024 7,387 0 View

Pink bacterial colonies?

I am cloning an overexpression plasmid with my protein of interest tagged with mScarlet. After transforming my ligated product into DH5α bacteria and plating on LB agar, I noticed colonies with a...

22 July 2024 5,953 6 View

What does negative readings in spectrophotometer denote. Was testing TSS content of bacterial cultures?

I was performing estimation of Total Soluble Sugar content in bacterial cultures by Anthrone method. Out of 9 samples, only one sample showed positive reading while others had a negative reading...

22 July 2024 9,576 4 View

How to prepare bacterial conditioned media to study the effect of bacterial secretome?

I would like to investigate the effect of bacterial secretome on cancer cells. How do you prepare conditioned media from bacteria?? conditions- time points - media I am looking for the best way...

17 July 2024 3,785 9 View

Is there any paper published which evaluates the effectiveness of "GaitOn running gait analysis software" ?

I am doing a comparative study in which I will check the patient's progress by assessing their gait parameter, and to do that I will be using the abovementioned software. Still, before that, I...

17 July 2024 6,552 2 View