Silvia Caprari

40 Questions 25 Answers 0 Followers

Questions related from Silvia Caprari

Can the values plotted outside the error bars be coinsidered outliers?

Hi, I plotted my data in a bar chart (I used GraphPad) showing the average values, the standard deviation error bar and the single point values. I can't understand if the points that are plotted...

06 November 2018 4,168 4 View

Reference for 0.5 McFarland standard corresponding to 0.08 to 0.13?

Hi, I have a question about the 0.5 McFarland standard. In different websites I read that the for the 0.5 McFarland standard, the absorbance at a wavelength of 625 nm should be 0.08 to 0.13. I...

21 September 2018 5,635 1 View

How to measure density with ImageJ in images that have different magnification?

Hi all, i am new in image processing and using ImageJ. I want to measure the density in areas of pictures that were originally taken at a different magnification. I attached an example that I hope...

06 June 2018 4,599 3 View

Theoretical question about western blot?

Hi, I am new with Western Blot and I need a few clarifications about the use of blocking and incubation solution. I understood that blocking is done to saturate the membrane with proteins...

06 December 2017 9,080 4 View

Preparation of sodium phosphate buffer?

Hi, I am preparing a sodium phosphate buffer solution at 0.1 M pH 7. For the preparation I am following this instruction that requires to mix 1 M Na2HPO4 and 1 M NaH2PO4 like this: 57.7 ml 1 M...

13 November 2017 9,444 3 View

How to calculate the enzyme activity from absorbance?

Hi, I have a question about how to calculate the enzyme activity from absorbance. I have absorbance values for different concentrations of my samples at different times. As far as I understood, I...

26 September 2017 6,993 3 View

Can you help me with understanding how to determine the beta lactamase activity?

Hi all, I would like to ask you a question about the data analysis in an enzymatic activity assay. It is the first time I deal with this kind of stuff. I have a kit for the beta lactamase...

25 September 2017 3,547 4 View

Don't I loose the plasmid with a new eluition in water during the miniprep?

Hi all, I made different minipreps starting from the same sample of bacterial culture because my intention was to increase the concentration of plasmid in my final plasmid preparation. Now I have...

22 June 2017 8,979 3 View

Which ratio of vector and two inserts do I need to use in the ligation reaction?

Hi all, I have a few questions about ligation 1)Could you explain to me why you need an excess of insert compared to the vector?What is the “chemical principle” of this reaction? 2)In my...

14 June 2017 8,069 6 View

In silico analysis of plasmids?

Hi, I am running PlasmidFinder on fasta files containing assembled contigs. The results seem to indicate the presence of two replicons in the same contig even if I am not completely sure of how...

24 May 2017 7,379 3 View

How can I determine where the signal peptide is in a DNA sequence?

Hi all, I was wondering.Given the DNA sequence of a protein in bacteria, how can I determine where the signal peptide is in this sequence? I found servers that predict the position of the signal...

16 March 2017 6,093 3 View

Are there more reads for a piece of sequence in the ngs process?

Hi all, I have a few questions about next generation sequencing and the generation of the reads. I did not understand some parts of the process..In particular, are there more reads generated for...

08 February 2017 5,689 3 View

Why is the MIC measured after overnight growth?

Hi, can you explain me why the minimum inhibitory concentration is measured after overnight growth of the microorganism? Actually, I thought the MIC was measured during the log phase since the...

20 January 2017 7,569 15 View

What does "2x250bp paired-end reads" means?

Hi , I am new with the Illumina sequencing and I got back the sequencing data. I am quite new with the terminology. Can you explain to me what it means that a project will be sequenced using...

10 January 2017 7,613 12 View

How do I distinguish between DNA and RNA on a gel?

Hi all, I extracted RNA from bacteria and I run an agarose gel on these samples. How do I recognize if I have RNA and not DNA? I have three bands (in attachment) and I am not sure about what they...

22 December 2016 7,988 13 View

Meaning of the formula for the normalization of the real-time PCR data ?

Hi, I can't understand well the use of the normalization for analysing reverse transcriptase real-time pcr data and why you need to use housekeeping genes. Actually my issue is that I can't...

13 December 2016 6,345 4 View

Why do I need to normalize after a real-time PCR reaction?

Hi, can you explain to me (in simple words) why i need to normalize my values after a RT-qPCR? In my case, I am studying how the expression of antibiotic resistance genes changes when the cells...

07 December 2016 3,391 6 View

Clarification about the excluded regions in Primer3?

Hi all, I am trying to design primers (I am using Primer3) for RT-qPCR on a bacterial gene (so the reaction will first do cDNA with reverse transcriptase and then qPCR). I am following a tutorial...

07 November 2016 3,361 1 View

Are LB broth and Nutrient broth minimal or complex media?

Hi all, are LB broth and Nutrient broth minimal or complex media? I am following the QIAGEN protocol for the RNA extraction from bacteria and the protocol for the preparation of lysates is...

02 November 2016 6,195 3 View

How to find antibodies for western blot?

Hi all, I am completely new in the field of Western Blot. I need antibodies directed against the bacterial gene "aac(6`)-Ib-cr" that codifies for a protein that is a fluroquinolone acetylating...

31 October 2016 3,787 4 View

Why the repeat sequences interfere with the assembly of the contigs in the sequencing?

Hi , can you explain in a very very simple way why the repeat sequences interfere with the assembly of the contigs in the sequencing? I can't figure it out. And why the pair-end sequencing helps...

19 October 2016 5,377 4 View

Where to keep bacterial overnight cultures if you don't use them immediately?

Hi all, I wanted to ask you where it is better to keep bacterial overnight cultures if you don't use them immediately. Let's say that I have overnight cultures and I want to streak them on plates...

28 September 2016 3,486 3 View

Too tick and bright bands on agarose gel?

Hi,I am trying to visualize my DNA bands run on agarose gels (stained with gel red during the gel preparation). Although I am using UV fluorescence to visualize the gel, I think some setting in my...

15 September 2016 1,243 3 View

What happens to my resistance gene?

Hi, I am studying genes for the resistance to the antibiotics in Klebsiella and I am analysing an outbreak of carbapenem-resistant isolates. The gene I am analysing is OXA-48 and it is known to...

23 August 2016 876 3 View

2 isolates with the same RAPD profile and genotype but different plasmid profile?

Hi, I am analysing some data coming from genotyping I am performing on carbapenem- resistant isolates of K.pneumoniae. The resistance genes should be carried on plasmids and I looked for the...

22 August 2016 3,528 1 View

Some help on the interpretation of this restriction digestion of plasmids?

Hi, I am trying to get plasmid profiles from clinical isolates. I extracted them and visualized them in the gel electrophoresis. I tried to cut them with a 6bp enzyme XbaI to have more ideas on...

19 August 2016 6,499 2 View

How do I determine the plasmid carrying the resistance genes?

Hi ..I run an agarose gel on a plasmidic extract and I have different bands. I don't know if they are different forms of the same plasmid or different plasmids. I want to determine if the bands...

16 August 2016 4,658 2 View

Why to test a wide range of antibiotics in the minimal inhibitory concentration tests?

Hi, I am studying the resistance to antibiotics in bacteria and I often happen to read papers where the authors report minimal inhibitory concentration tests performed on these resistant bacteria....

31 July 2016 3,648 5 View

How do I get acceptor strains suitable for bacterial conjugation?

Hi, I have to do conjugation experiments to see if the resistance is transferred by plasmids. I don't have a strain in lab to be used as acceptor for my conjugation experiments, so I have to buy...

28 July 2016 1,563 3 View

Do competent cells bought keep their high efficiency features after streaking and preparation of an own stock of competent cells?

Hi, I am considering to buy MAX Efficiency DH5 alpha Competent Cells to try to do both electroporation and heat-shock experiments with large plasmids. I don't know what procedure will be better,...

27 July 2016 9,906 6 View

What went wrong with my electroporation?

Hi all, I performed electroporation with bacterial plasmidic extract for the first time to confirm that the plasmids carry resistance genes. Nevertheless, it didn't work. I had no colonies on the...

23 July 2016 3,261 12 View

What's the cause of the resistance at low concentrations of antibiotics showed by Dh5a cells?

Hi, I am doing transformation experiments with plasmidic extract and I am using DH5a cells for the transformation..I obtained few colonies on a plate with 1 ug/ml of meropenem antibiotic. Anyway,...

19 July 2016 9,040 3 View

How do I choose the gel running conditions depending on the size of the fragments?

Hi all, I have to run a gel to separate small fragments, 50-25 bp..What are the best running gel conditions (in terms of time and voltage)? I did not understand very well how you choose the time...

12 July 2016 3,086 6 View

Faint bands on the gel?

Hi all, I run a PCR to look for an integron in different bacterial isolates to test the presence of this integron in the bacterial genome. This integron is often associated with resistance...

11 July 2016 4,275 3 View

Too diluited DNA to be seen on the gel?

Hi all, I am extracting natural plasmids from my bacteria. I don't know the size, nor the sequence. I am trying to determine plasmid profiles of the bacterial isolates I have. I have bands on...

20 June 2016 2,751 5 View

No bands after digestion with restriction enzymes?

Hi all, I am trying to extract natural plasmids from my bacterial strains. I don't know the size of plasmids, nor if different plasmids are present in the same strain. I run a gel with the...

14 June 2016 6,078 7 View

EDTA at PH 9.5?

Hi all, in your opinion is it a problem that I have an EDTA solution at 9.5 instead of 8 for plasmidic extraction? I added more NaOH to dissolve the powder because at Ph 8 there still were not...

08 June 2016 6,663 2 View

Separation plasmids on gel?

Hi all, I have to separate bacterial plasmids (after extraction) on agarose gel. Which electrophoresis conditions would you suggest me to use (in terms of hours, voltage)? Thanks

03 June 2016 6,204 5 View

How to calculate the hybridization temperature for a DNA probe?

Hi, I need to calculate the appropriate hybridization temperature for my probe (DNA probe). The equation used to calculate it requires the knowledge of the % G+C and the length of the hybrid in...

31 May 2016 6,461 3 View

How can I determine the location of a bacterial gene?

Hi all, can anyone suggest me a method-protocol to understand if a bacterial gene is on the genomic or plasmidic DNA?I have done PCR on purified DNA sample (that contains both genomic and plasmdic...

25 May 2016 7,476 4 View