Is there multiple-alignment tool which would not neccassarily align all sequences together?

When I get results from sequencing, they often overlap only partly or not at all. In such case it's easier to align them with the "parental" sequence (of what I expect), to see where they align....

01 February 2020 8,336 3 View

A simple method for quantitative separation of apoplast and plant cells?

Hello everybody, I wish to separate apoplast from the rest of the plant (i.e. intact cells) to see whether the compound I treat the plants with goes inside or stays outside. When I mentioned this...

07 August 2019 2,886 3 View

How to make a dot plot?

How do I make a dot plot like in this paper Show the data, don't conceal them in Figure 1? All I'm finding on the Internet are only this type of dot plots:...

05 June 2019 2,092 5 View

How can I improve binding to chitin beads?

I express my protein in pTYB12 vector as fusion with intein and then try to purify on chitin beads. Typically, I load overnight at low flowrates (something like 0.3 ml/min). The loading buffer is...

04 May 2019 2,589 7 View

How to determine mode of action of a certain compound?

I'm working with plant hormones cytokinins - derivatives of adenine with a side chain at the N6-group. They are mostly active as free bases (with no modification on the adenine core), or maximally...

02 March 2019 3,322 11 View

I have two questions regarding adenine conjugates at N9 position /?

My first question concerns lupinic acid - conjugate of adenine derivative with alanine https://commons.wikimedia.org/wiki/File:Lupinic_acid.svg The question: What type of bond is it between the...

08 September 2018 8,949 0 View

Is the cell lysis efficiency by ultrasound affected by cell density and/or the volume?

Hi everybody, I'm currently expressing proteins in and extracting from bacteria. The procedure is that I pellet the bacteria from bioreactor, resuspend in buffer (50 mM Tris/HCl, pH 8.0; 1M NaCl;...

07 August 2018 2,453 9 View

I have a few questions about growing E. coli in bioreactor - and the obligatory question mark?

Hello everybody, I'm currently growing E. coli in bioreactor and I have experience only with P. pastoris in bioreactor, so I'm not sure, how should it behave. With Pichia, one can try hard to...

02 March 2018 9,364 4 View

Does ligand have affinity towards protein or vice versa?

In the texts, it's often written, that the ligand has affinity towards a protein (with appropriate affinity constant). However, to me it always occurred that the protein binds the ligand and...

09 October 2017 6,994 0 View

How common is substitution at position 7 of adenine ring?

Some old papers (from the 70s) claim, that the substitution at position 7 is rare in the nature https://www.ncbi.nlm.nih.gov/pubmed/486500https://www.ncbi.nlm.nih.gov/pubmed/4640371 However, that...

09 October 2017 7,784 2 View

Standard curve shifting over time. How do I stabilise the ELISA?

24 February 2021 1,365 3 View

How to calculate the fraction metabolized of a drug by an enzyme using clearance(ml/min) values of the metabolite formed?

I am trying to find the fraction metabolized of a drug by CYP and UGT enzymes. I am unable to get the values of fraction metabolized (Fm) directly from the literature. Can we calculate the Fm of a...

21 February 2021 5,379 2 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

Kinetics of Enzyme production in Recombinant E Coli?

Hello, I am trying to find kinetic information (such as rate of enzyme production etc.) on the expression of taq polymerase in E-Coli after inserting a recombinant plasmid. Any help would be...

12 February 2021 1,386 3 View

No title

Hello! I want to determine the activity of my in house Reverse Transcriptase enzyme. For this, I have used Thermo's Enzcheck Reverse Transcriptase assay kit. I used commercial Thermo RT enzyme to...

08 February 2021 7,285 1 View

How define one baker unit(BU) is the amount of hydrogen peroxide catalase ?

07 February 2021 2,006 1 View

Does DNA A-tailing survive after agarose gel electrophoresis and purification?

Hi everyone, I need to clone in pGEM-T vector the result of amplifying a metagenomic library by PCR with a high fidelity polymerase but I only want to clone the fragments of an specific size...

04 February 2021 6,051 8 View

What are the conflicts between EIA and environmental engineers and lawyers?

Environmental Impact Assessment (EIA) does not live up to the expectation of environmental lawyers and environmental engineers. In your own opinion, how can the EIA process therefore be made more...

03 February 2021 1,329 6 View

What is the maximum storage time for samples used in soil enzyme assays?

01 February 2021 4,616 3 View

What are some common oxidants used to oxidize iron sulfur clusters in proteins for techniques like EPR?

I have used potassium ferricyanide (which is likely the most common) extensively in the past, but I am curious to know if there are other oxidants that work well. I need to generate the oxidized...

29 January 2021 9,803 4 View