Science with J

Represent carbon atoms labeled in metabolic pathways If you've ever wondered how to create those metabolic maps that show the number of atoms labeled by a carbon isotope ( e.g., C-13 ), we'll show you how. But before you begin, you need to know a few important details. Examples of labeled metabolic flow diagrams  ( Labbé, K. et al., 2024 ). What is the Exchange Rate? The Exchange Rate is a parameter that indicates the number of atoms exchanged between the uniformly carbon-labeled molecule to which your cells were initially exposed and the remaining fully or partially labeled metabolites detected in the Isotopic Profiling experiment, also called Isotopic Trace Analysis . In articles, the Average Exchange Rate is often represented in diagrams with filled or empty balls, with the filled balls representing the average number of labeled carbon atoms in the metabolite in question and the empty balls representing the average number of unlabeled carbon atoms for the same metabolite...

History of Scientific Conferences The development of scientific conferences has been a constant in scientific history since the emergence of the first Philosophy universities. While initially based on long lectures in enormous halls where the most prominent figures in the field of study gathered, today they constitute an academic and social event that sometimes falls far short of fostering proactive and respectful debate among leaders in the field. Any opinion that deviates from what is politically and scientifically accepted is subject to censorship, cancellation, and ridicule. The True Objective of Participating in Scientific Conferences Today Furthermore, their goal is often to train young researchers struggling for stable employment. These researchers are subject to public scrutiny every time they give a talk, in order to obtain a certificate that, vaguely, will help them improve their scientific resumes in an increasingly competitive world. And those who innovate in their discours...

How to create a DOI code for your PhD thesis report If you have completed a PhD, you know that having a higher number of citations is important for your research CV.  In the world of citations, everything counts (everything that is citable in indexed scientific publications, of course). Let's start by creating your article library where you are the author The first thing to do is to k eep your  ORCID  profile up to date . This platform allows you to officially compile all of your publications in which you are the author (first author or author in any other position). In addition, if a publication has not been automatically included in your profile thanks to cross-references, you can add it yourself manually. Logo of the entity that maintains the DOI codes. Make your PhD thesis citable Although your university has probably already provided you with a reference code in its reposito ry (for example, URI), this is not typically the code used for international bibliographic re...

Convert RPM to RCF easily Can your centrifuge only be programmed in RPM? Here's a quick solution to find out its equivalent in RCF (also called g). What is RCF? If you're used to reading scientific papers, you'll have noticed that the typical way of expressing the speed at which you should set a centrifuge is " RCF " or " g ". This is because it's a standardized way of referring to the speed at which a centrifuge's rotor spins. Image of a centrifuge. What is special about this way of expressing rotational speed? What makes RCF the most accurate way to express the speed at which the centrifuge is set is that this value does not depend on the distance of the tube from the rotor axis, whereas RPM does. That is why we say that RCF is a standardized or normalized parameter. And what is the impact of the RCF being a standardized unit? By using RCF instead of RPM, you ensure that the centrifugal force you apply to your sample tubes is the same across al...

Do you need an expression plasmid that is not commercially available (e.g. a mutated variant)? Whether you want the plasmid to contain a mutated gene or a wild-type coding sequence , here is a quick step-by-step guide. First: Find the sequence The first thing is to find the coding sequence of the wild gene that expresses the protein you want. To do this, go to  https://www.ncbi.nlm.nih.gov/ and search the name of your interest gene using the Nucleotide search. Then click on the desired organism and select  mRNA . Choose the best entry for your query according to your requirement, and select the CDS  (and the protein sequence will appear on the right, a.k.a., translation ) .   Next,  copy-paste both FASTA text codes into a Word file . We will need them later. Graphic representation of a DNA molecule. Second: If you only want to express the wild-type protein... Paste the CDS directly into the corresponding ORF item from the supplier (e.g.  VectorBuilder ...

Systematic reviews:  The advice that nobody taught you 👂 If you are about to embark on the world of systematic reviews, you will probably have flooded your mind with information from courses that are not at all practical. This is because nothing can replace better learning how to conduct a systematic review than getting down to business. The PICO question If you follow the traditional method of analysis, you will have to keep trying and failing with your search algorithm , until you get a number of articles that are feasible for you or your team to analyze . To do this, start by asking yourself an unexplored PICO ( P atient/Population; I ntervention; C omparison; O utcomes)  question , and perform a search in one or more databases, using linked terms following the guidelines of boolean logic (AND, OR...) and parentheses. Artistic representation of a flowchart  (Poklepović Peričić T. and Tanveer S., 2019). But I've gotten thousands of results!😯 After your boolean sear...

You have amplified and measured the Ct of your serial cDNA dilutions... Now what? To validate your primer couple  (i.e., to measure their efficiency) , you have probably been recommended the serial dilution method. What does the serial dilution method for validating primers entail? This method involves making dilutions of your typical control sample (e.g., 1 in 4 , 1 in 16 , 1 in 64 , 1 in 256 , 1 in 1024 ) and mixing it with your typical Master mix and your favorite primer concentration.  This way you can confirm in silico whether the amplification pattern of your primers in successively diluted samples fits a trend line. DNA strand on which the PCR reaction is carried out. How to measure the efficiency of your primer couple using the serial dilution method If you measured Ct values ​​from at least 3 replicates of each dilution, calculate the Ct average of the 3 replicates for each dilution . Consider your 1 in 4  sample as a hypothetical cDNA concentration value of 10...