Efficient primers to do qPCR for MS2 bacteriophage?

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When do you want to use full protein sequences or only conserved domains to make a phylogenetic tree?

Hi, I'd like to know what difference makes using FULL PROTEIN SEQUENCES versus PROTEIN CONSERVED DOMAIN SEQUENCES in order to make a phylogenetic tree. In my case, the goal is to put in...

03 April 2019 8,726 5 View

Model creation in GeneMarkS?

Hi all, I am trying to perform self-training with GeneMarkS to improve protein calling from virus genomes and transcripts. Could someone tell me if it is correct what I am doing? First, I...

09 October 2018 9,876 0 View

What is different in aged ferric oxide?

Hi all, I'm looking for the expert opinion from a chemist, since I am only a biologist. I have a set of samples made in the following manner: many litters of seawater were...

07 August 2018 2,807 3 View

RnaSPAdes for RNA viruses?

Hi all, would you say that rnaSPADES is a better assembler to discover RNA viruses from read datasets THAN SPADES? thanks!

06 July 2018 8,560 2 View

Conserved domain database?

Hi all, I looking for RNA viruses from datasets. I already performed a blastx of the contigs generated against the database of all reference RNA virus proteins download from GenBank. Now I'd...

05 June 2018 9,974 3 View

RP-SISPA with RNA virus isolates?

Hi all, I just did my first RP-SISPA. I extracted RNA from two virus species by different methods. One virus genome is ssRNA of 3 kb and the other virus genome is segments of dsRNA (3, 4 and 6...

03 April 2018 5,335 4 View

Low efficiency of qPCR?

Hi all, I've been having trouble increasing the efficiency of a couple of primers using a standard curve. - The standard curve is built with log10 dilutions of plasmid into which the amplicon...

02 March 2018 9,513 7 View

What are the bioinformatic tools for collecting RNA viruses from metagenomic data?

Hi all, I wondering about bioinformatic tools to capture "RNA viruses" from environmental sequence datasets. dsDNA phages are pretty abundant and have relatively conserved hallmark genes....

02 March 2018 6,879 6 View

Precipitation after autoclaving?

Hi all, I know this is a typical phenomenon, but after reading I'm not getting a convincing explanation. I prepared 4 L of a buffer containing 10 mM KH2PO4 and 1 mM MgSO4*7H2O. This time I...

31 December 2017 2,583 4 View

Iron ions mediated nucleic acids degradation?

Hi all, I looking for literature evidence for this phenomenon. Apparently, RNA (I'm not sure if also DNA) is cleavaged in a non-enzymatic manner by iron. I would need some theory to support...

31 December 2017 7,341 3 View

In PRIMER, is it possible to downweight certain taxa in multivariate community datasets to reflect uncertainty around identification??

I have a dataset with about 80 different species. As usual, some species are very easy to identify with certainty whereas others are more difficult, which means that I am less certain of my...

03 March 2021 8,066 4 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

How to calculate the annealing temperature of a primer pair?

I have to amplify a gene and my primers just reached. The Tm for Forward primer is 64.2, and that of reverse primer is 65.5. Can some one suggest how to get the best annealing temperature? Thanks...

01 March 2021 360 7 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Anybody with an idea on how do design specific primers for detecting tomato resistance genes tm-1, TM-2 and Tm2^2?

I am trying to identify these 3 genes among some tomato cultivar collections and after aligning some sequences from NCBI, I couldn't find unique sequences to target for specific primers. There...

28 February 2021 606 3 View

What is the ideal efficiency for a qPCR?

hello everyone, I need to do standard curves for my qPCR, what is the ideal efficiency range? I tried a primer (Mglu2 receptor) that gave an efficiency of 90.2%. Is it accepted?

28 February 2021 1,254 3 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

The reason that the culture of white fungi Contamination with green mold(Trichoderma), the culture autoclave at121 for 15 min. What is it?

Is the period to autoclave not enough? The inoculation in a hood and flame and UV and alcohol.

27 February 2021 9,356 3 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View