How to make Principal Coordinate Analysis Plot from DNA sequence data?

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I have a time series data of some biochemical studies ( DNA and Chromosomal damage) which I intend to use to further predict into future ?

I have a time series data of some biochemical studies ( DNA and Chromosomal damage) which I intend to use to further predict into future without necessarily conducting the assay for an extended...

23 February 2021 7,842 1 View

No mRNA increase in PCR after successful transfection in ARPE-19 cells ?

Hello, i am a bit curious about my results. I transfected the human cell Line ARPE-19 with a Plasmid containing a GFP tagged p53 (p53-GFP, Plasmid #11770). After 24h i checked under the...

18 February 2021 3,811 7 View

Do there exist stand-alone permanently in-ground soil-moisture sensors with an installed GSM module, for outdoor use?

Am searching for a stand-alone permanently in-ground soil-moisture sensor with an installed GSM module, for outdoor use. The idea is for the sensor to send a moisture reading via a cellphone text...

04 February 2021 2,047 4 View

What is the easiest way to remove the water from organic solvents?

Hello everyone! I have one question. I have couple of solvents and all of them were pure when they were bought but after some months or years of storage after opening I am not 100% sure about...

03 February 2021 2,154 8 View

Virus neutralization assay in BSL2 lab?

Hi I want to set up a virus neutralisation assay such as PRNT or FRNT at my lab (BSL2), but im uncertain of the bio safety requirements that has to be fulfilled in order to work with...

01 February 2021 5,626 3 View

Using LINK11 to Apply force in ANSYS APDL?

I'm trying to use LINK11 to apply a force as if it was a cable pulling a structure twowards a point in ANSYS APDL. When I solve the model, the deformation of the overall structure is far too...

30 January 2021 7,919 1 View

Cytoflex Flowcytometer, clotting issues and cleaning procedures?

We have been having clotting issues with our Cytoflex S from Beckman Coulter. Back in December 2020, we had to have the tubing system and sample needles replaced, but we are beginning to observe...

28 January 2021 6,897 2 View

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View

What excamples do you know wasting unused contents of "empty" packaged products?

Most of us use tooth paste more times a day. The empty tube we throw away. I wondered how empty the tube really is. This does not sound being Research? I began to collect empty tubes...

19 January 2021 808 3 View

What is the largest disadvantage in using of face masks at present? What would you like to be improved?

We all use face masks many hours a day. I wonder what are your items you like to be improved. We have the opportunity to write an application for support to a sponsor. Your answers will help us a...

18 January 2021 1,311 4 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 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

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

What might be the reason for obtaining two bands in plant genomic DNA extraction?

I got a thin band and a thick band i guess it would be the genomic DNA and the 260/280 ratio is 3.

21 February 2021 6,523 6 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Ayoob Obaid Alfalahi

Dear Peter...

The best way is to calculate matrix of dissimilarity indexes (MEGA6 may be helpful), then use outputs to conduct Coordination Analysis with aid of PAST software.

Best Luck.

Subham Dasgupta

You can use R for PCA.

https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html

Although I have never used this.

Elizabeth Suter

We have used this website for advice when doing multivariate analyses with ecological data. It gives guidance on using R:

http://mb3is.megx.net/gustame

And here is the reference

Article A Guide to Statistical Analysis in Microbial Ecology: a comm...