Any software that could detect recombination in bacterial whole genome data? How far could we interpret this data?

When do we normally look at recombination in a large dataset of bacterial genomes- is this particularly important for medical pathogen? How do we normally interpret this?

08 September 2016 4,551 3 View

What are available bioinformatics tools for bacterial whole genome functional assignment/analysis (gene ontology)?

Any software pipelines that are more user-friendly for biologists to assign GO terms for bacterial whole genome data?

08 September 2016 3,187 1 View

Does evoglow plasmid work well with in vivo real-time imaging?

I am wondering if evoglow plasmid work well with animal whole body imaging as some say cyan-green fluorescent proteins do not work well in animals as they penetrate poorly. Any recommendations for...

03 April 2016 7,518 0 View

What could be the yellow pellets seen after phenol-chloroform genomic DNA extraction?

I have done nanodrop on the samples, some were detected to be phenol contamination as seen in the yellow pellets but results were not consistent at all. I suppose yellow pellets should be protein...

01 February 2016 1,827 3 View

How do I confirm/visualise the sporulation of bacteria?

I am interested in Clostridial spore formers and wondering what are the methods to confirm the bacterial sporulation besides using microscopy?

01 February 2016 8,463 3 View

Does anyone know how to identify antimicrobial peptides secreted by bacteria?

11 December 2015 4,403 6 View

Has anyone worked on IEC6 with C. perfringens (cell culture experiement)?

As IEC6 will die in anaerobic environment, C. perfringens will form spores in aerobic environment, will heat-killing method suitable in this case?

09 October 2015 6,828 1 View

How do I heat kill Clostridium spp (including C. perfringens)?

Any recommended paper or protocols? Autoclaving seems like not a good way as it might detroy the cell walls and stuff-I need intact bacterial components.

09 October 2015 5,150 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

Modeling viscosity using model of Chung?

Hello, As part of simulation of gases mixture and water, I need to calculate viscosity of the fluid components and I am using relationships proposed by Chung et al. (1988). The irony is while I...

25 February 2021 8,053 5 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

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

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

What are advantages of NELF model?

I am trying to simulate permeation of gases in polymers. For this reson normally i use the clasic models like dual sorption model but newly i foun dthe non equilibrium lattice fluid model. It...

03 February 2021 1,203 3 View

How do microbes tell the presence of an inorganic minaral in the soil?

Due to their ubiquitous nature, there is a tendency of the presence of microbes in a given mineral(s). For instance, if microorganisms that love the of pH less than 6 in the pH value, is isolated...

03 February 2021 4,630 10 View