Molecular Analysis - Science topic

Do you have access to a Qbit or nano drop + gel electrophoresis? That's what folks typically use to measure the concentration, quality, and determine if the RNA is intact or degraded.

I've never heard of an RNA positive control as an extraction comparison.

I would move to another researchers area (in case yours is contaminated) and set up using their pipettes and plasticware and as many of their pcr reagents as possible. Run assays with 5 NTCs and one positive control only. If this works clean then introduce one feature at a time until the contaminations shows up. While doing this strip your pipettes down completely and clean them inside and out. Often pcr product gets into the barrel of the pipette and dries there and this dried material can fall into the assay reagents or tubes. I think that dust in a contaminated working area ( from pening tubes/aerosols or spillage of electrophoresis buffer (used) and internal pipette barrel contamination are the most common reasons for contamination

Yes, there are several partner labs and companies in Europe that specialize in molecular sexing from feathers. One notable company is TARGAN, which has launched an automated feather sex identification system in Europe that uses AI-powered advanced imaging technology. Additionally, the European Molecular Biology Laboratory (EMBL) is a prominent institution with multiple locations across Europe that conducts extensive research in molecular biology, including molecular sexing of birds. Another relevant source is Surescreen Scientifics, which offers DNA-based bird sexing services using feather samples.

Hello Lucas Hassib

It seems that your DNA samples and ladder are fine, but there might be a problem in the agarose gel preparation. Are you sure you have used 1X TAE buffer while preparing you gel and run the gel in 1X TAE buffer? I think the gel is made with water or run against water. TAE buffer provides ions that conduct electricity, which is essential for the DNA to migrate through the gel. This poor migration of DNA samples and and "smileys" are typical sign of low buffer capacity.

Best wishes.

Yes, this is a very solvable investigation.

Step 1: read what is already known. There is no substitute for doing your own deep dive into the literature.

Step 2: Talk with your mentor! They can assist you in outlining a plan.

Step 3: Decide how you will analyze your data BEFORE you collect any data. Trust me on this one.

Step 4: Start small. Test out one or two markers with a good set of controls. Don't scale up until you are certain that your assay is working.

This is going to take a big chunk of your time. As my research mentor said "You can't rush quality". And there are no shortcuts. You are going to have to create your own research plan.

Good luck!

I would do both. One is mitochondrial, the other nuclear, which is nice. Both work well on Cone Snails and Mammals. CO1 is great for most anything.

Coating a microplate with viruses for a whole-virus enzyme-linked immunosorbent assay (ELISA) requires precision and adherence to a standardized protocol to ensure reproducibility and accuracy. Here is a detailed, step-by-step guide on how to coat a microplate with viruses for this purpose:

By following these detailed steps, you ensure that the virus is properly adhered to the microplate, maximizing the sensitivity and specificity of your whole-virus ELISA. Each step, from the preparation of the virus to the final storage of coated plates, is designed to maintain the functional integrity of the viral antigens and provide reliable, reproducible assay results.

Check out this protocol list; it might provide additional insights for resolving the issue.

Hi Arbesu, I am wondering such RNA concentration of 15-20 ng/uL is enough to do cDNA Reverse Transcription? And from your experience, what ratio of A280/260 were you getting from Nanodrop of the platelet RNA sample? I appreciate any replies from you!

Well, the process of Agro infiltration itself is going to change gene expression in the short-term in your plants. Are you trying for stable or transient transformation of your plants?

There are a few things you can try to parse out bacterial vs plant contributions.

1. add some negative controls. I would suggest a buffer only control (no bacteria) that will show any changes due to the infiltration process in general. I would also suggest an Agro with an empty vector control.

2. you can use polyA-specific RT analysis for the gene expression (use oligo dT for mRNA to cDNA RT). The bacterial gene transcripts will lack the polyA tail so you won't have any showing up.

3. For DNA analysis, it really depends on what you are trying to detect. You could use Agro-specific gene primers to see if the cells are still present in your plant (they probably are, at least in the short-term).

Hope this helps and good luck!

Actually, I have worked on PEC and have also generated them. However, the thing is, in polyatomic molecules, we need to consider molecular dynamics. Once we scan a particular bond, the other bonds do not remain the same. So my worry is how we can incorporate this effect to obtain accurate PEC curves...

Can you clarify the roles of the variables you mentioned? If one of them is a dependent variable, for example, which one is it? Thanks for clarifying.

Please clarify too what "a trait with continuous variables" means. Perhaps if you just said what the trait is (and what the continuous variables are), it would help readers to understand better. Thanks.

In Portugal:

The chromatogram quality is not so good, but I can detect a small peak (in black) corresponding to G at this location.

This is a confusing question. The molecular phylogenetic literature on plants surely must have many papers that discuss the relative utility of various genes with evolutionary rates suitable for your project. The choice depends entirely on the organisms you study and approximately when you think the various OTUS may have separated: e.g. 40 mya and 4 mya would require different markers.

Hello,

The following article might help you.

https://doi.org/10.1007/s10404-021-02455-6

Hi Daniel,

In addition to molecular dynamics, DFT can simulate the solvation dynamics of various polymers, including but not limited to DMSO, ETHANOL, METHANOL, and WATER. Examples of software cover Gaussian 09 and Biovia Material Studio. For molecular dynamics, you may use LAMMPS or BIOVIA Biovia Material Studio; please be advised that Material Studio software includes many modules that cover both quantum mechanics (e.g., DFT, HF). Quantum mechanics can predict potential and kinetic energies, but I am unsure about temperature, while molecular dynamics can provide them all.

Both approaches do have pros and cons, as well as challenges. Molecular dynamics can speed up the computations, but its accuracy is a function of many other parameters, such as the selection of the size of the unit cell representing the reaction and the full understanding of the reaction sequence and kinetics. Whereas simulation based on quantum mechanics is relatively slower, the reaction size can not exceed a hundred atoms at max – recall that molecular dynamics can have hundreds of thousands of atoms.

I did several computational modelling and simulation for ionic liquids and used both quantum mechanics and molecular dynamics to increase calculation repeatability and reproducibility. You can find in the literature many papers explaining the use of each, but I found a hybrid-based approach can predict results close to experimental results.

In my opinion, kit tubes should be fine. If adherence is the problem, you can short-spin it after adequate tap mixing.

Hope, it helps.

Yes, there are multiple options for designing positive controls for RT-PCR in virus detection. MEGA software is primarily used for phylogenetic analysis and may not be the best option for designing positive controls. However, you can design positive controls for RT-PCR in virus detection using the following methods:

To design positive controls using MEGA software, you need to obtain the nucleotide sequence of the virus of interest. Once you have the sequence, you can use MEGA software to design primers that can amplify the virus-specific sequence. However, MEGA software does not directly design positive controls. Instead, it can be used to design primers that can be used to amplify a specific virus sequence that can serve as a positive control.

These video playlists might be helpful to you:

In freezer I think.

I believe the issue here is that you are not normally going to reach 100% hybridization in an experiment even if the DNA was 100% identical. So it is an experimental constraint.

It surely depends on what type and range of organisms you are studying. The diversity we observe in HIV-1 in one single infected individual over ten years is greater than the diversity we observe between different species of insects or mammals over millions of years. The diversity between viruses today in the global SARS-CoV-2 pandemic varies with time, depending on whether two major lineages such as Delta and Omicron are co-circulating or Omicron has taken over and delta died out.

The diversity in insect or birds or shellfish is different than the diversity in mammals. You should compare the values you have in your organism to the values from other similar organisms.

Hi,

The supplier claims that their "sample release reagent" (nucleic acid release technology), can lyse pathogens at room temperature very fast, with no need to heating, centrifuging or replacing tubes, the sample DNA/RNA can be extracted quickly through simple operations. The reagent is applied for the pretreatment of nucleic acid molecules, to release them from specimens, then the released nucleic acids can be used for clinical in vitro diagnosis or for the detection through appropriate apparatus.

The algorithm for CLUSTALW works by calculating the similarity scores as the number of k-tuple matches between two sequences, accounting for a set penalty for gaps. The more similar the sequences, the higher the score, the more divergent, the lower the scores. While The MUSCLE algorithm proceeds in three stages: the draft progressive, improved progressive, and refinement stage. In this first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy. This step begins by computing the k-mer distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a progressive alignment is constructed. The 2nd and 3rd stage is focused on obtaining a more optimal tree by calculating the Kimura distance for each pair of input sequences using the multiple sequence alignment obtained in Stage one, and creates a second distance matrix. UPGMA clusters this distance matrix to obtain a second binary tree. A progressive alignment is performed to obtain a multiple sequence alignment like in 1st Stage , but it is optimized by only computing alignments in subtrees whose branching orders have changed from the first binary tree, resulting in a more accurate alignment.

Further, in terms of accuracy both MUSCLE and CLUSTALW show greater accuracy in alignment of multiple sequences but MUSCLE is advantageous in handling more complex dataset and sequence length greater than 1000 bp.

We also had a problem and after consulting with the experts of Kiagene Fanavar Company, who are based in our university, we finally decided to buy a MIC machine. I will send you the company link and email, maybe they can help you

I find a lot of people don't realise quite how dilute cDNA can afford to be.

cDNA synthesis buffer itself is inhibitory to PCR (it contains DTT, for example), and you can also inhibit your reaction by saturating the system with too much target (or too much non-specific target).

In almost all cases, cDNA should be diluted prior to qPCR.

I typically dilute all my cDNA 1/20 (so for a 20ul prep I add 380ul water, giving me 400ul of final cDNA), and using 2ul of this per reaction is _plenty_: it allows me to reliably detect even low abundance genes.

For reference I use ~1600ng of RNA in a 20ul cDNA synthesis reaction, so 2ul of diluted stock is ~8ng of cDNA, assuming 1:1 conversion.

In your case it may be nothing to do with the lipids and everything to do with just...generally using too much cDNA.

When running dilution curves of cDNA historically, I expect the extremes at either end to be unreliable: with too much cDNA you have all the issues noted above, and with too little cDNA you have stochastic effects and thus highly variable data. This is FINE. The whole point of a dilution series of cDNA is to establish the range over which your reaction is linear and trustworthy.

Find that range, use it, don't worry about the extremes.

Before studying any ligand binding profile to and target, you must first establish and validate a docking procedure. To do so, if your target has a co-crystalized ligand in its binding pocket, you can extract and re-dock in the same binding pocket. Then, by taking the initial structure as reference, you can superimpose the docked structure and compute the RMSD. If this value is lower than 2 Å for almost the 10 or more conformer with highest docking score, you can consider your docking procedure good. Further, you can also perform MD simulations to investigate the stability of the interactions between the re-dock complex. By looking the RMSD and visualizing the structure from the production stage, you can be further convince for the accuracy of your docking procedure (this verification is not an obligation, the first one is enough). After validating your docking procedure, you can use it to dock your compounds and perform post-docking process such as free energy perturbations analysis, MM-PBSA/GBSA, MD simulations analyses an so on. Several popular softwares for these studies are Schrodinger, MOE, AMBER, GROMACS, Chimera an so on.

Hi, you can convert 2D or 1D (SMILES) molecule file into 3D molecular structures using different ways, such as:

1. Using OpenBabel as a standalone tool, https://sourceforge.net/projects/openbabel/

2. OpenBabel as web-server, http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html (Comparatively easier approach)

3. Using ChemDraw/ MarvinSketch etc.

For energy minimization, you may use

1. Avogadro, https://avogadro.cc/

2. If you perform docking using PyRx/ Glide or some other sophisticated software, they have options for energy minimization before docking.

Watch some YouTube tutorials to get more insights about the tools.

How about your positive and negative control? Is that valid?

If Beta-actin also didn't amplified, it is either there is inhibitor in the master mix or samples or there is no cDNA inside the sample.

Beware of ethanol or alcohol, which can serve as the source of inhibition. If your positive also without amplification, it might be the problem of master mix or qPCR protocol.

Interesting

Dear Suzanne,

If you are confident about your statistics, one or more assumptions behind the Hardy-Weinberg equilibrium must be false. It is most likely that your sampling of patients is not random and does not reflect the real population structure that they belong to.

There are two interesting possibilities.

First, their might be something unique about your group of patients which is linked to the alleles you have been investigating; i.e., the patients, because they all have the same type of medical condition may mean that the alleles you measured (which somehow underlies the medical condition), will be in disequilibrium. You could test this (perhaps) by looking at a second set of alleles that have nothing to do with the medical condition, and these we would expect to be in equilibrium.

Second, all of your patients may be from a population of people in which the alleles you are investigating are in disequilibrium (and the alleles are not directly linked to the medical condition they may all have). This might be the case if all of the patients were in a regional hospital serving an area which had little migration and mixing, but less likely if they were in a metropolitan hospital that serves a diverse city. You could test this by looking at other alleles not linked to the medical condition, and in this case we would expect them to be in disequilibrium too.

Regards, Andrew

Hi, shruti. GAPDH, beta-actin and 18s are well-established housekeeping genes. Coming to your question, 18s is endogenous in eukaryotes. Hence in case you are working with eukaryotic ones, it is highly recommended to use either GAPDH, Beta-actin or 18 s to perform qPCR from cDNA samples. (based on the reference levels). However, 16s rRNA is highly used for prokaryotes.

Thats good:

hello,

Primarily we should get to know that for what purpose we are carrying out molecular studies and based on that analysis can be done. like,

Stat tools:- ArleQin, GenAlEx, Molkiv, Power marker, NTSYS, STRUCTURE, MEGA and Darwin.

*If you are using genic SSRs-

Stat Tools: - Windows QTL Cartographer, TASEL.

all the best

Check https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/04._Reactions_in_Aqueous_Solution/4.5%3A_Concentration_of_Solutions

In that case Jessica Little the handbook on that page suggests 10exp8 cells should produce between 25 and 70ug RNA depending on the growth medium used so it looks like you can count cells,spin them down,decant most of the supenatant and then make up to a small convenient volume and add rnaprotect. You might contact the company making the rna for you and check with their tech support how and in what volume they want their samples sent. They will have a lot of expertise in converting various sample types and volumes to RNA

thank you, dear Shin Murakami for your sugession

```r

nc <- ncol(dat)

out <- matrix(0, nrow = nc, ncol = nc, dimnames = list(colnames(dat), colnames(dat)))

Jaccard <- function(x, y) {

i_len <- length(intersect(x, y))

u_len <- length(union(x, y))

return(i_len/u_len)

}

for (i in seq_len(nc)) {

for (j in i:nc) {

out[i, j] <- Jaccard(dat[, i], dat[, j])

}

}

pheatmap::pheatmap(out)

```

Stomach cancer is cancer that may affect any part of the stomach and extend to the esophagus or small intestine, and it causes the death of nearly one million people annually. It is more prevalent in Korea, Japan, England and South America. It is more prevalent among men than women. It is associated with eating too much salt, smoking, and also low intake of fruits and vegetables. Therefore, it is believed that its spread in countries such as Korea and Japan is due to the consumption of salted fish mainly by Koreans and Japanese, as well as the use of canned food and food preservatives. Mucosal colonization of H. pylori is believed to be the main risk factor in about 80% of stomach cancers

Stomach cancer is diagnosed through an endoscopic examination that allows a biopsy to be extracted from the affected tissue, and then analyzed to confirm the presence of a tumor. Dr. Riccardo Rosati, a specialist in gastroenterology at San Raffaele Hospital in Milan, says, "Before undergoing treatment, the patient needs to do a series of other ultrasound and other examinations to check the areas, glands and organs covered by the disease, in order to determine the degree of its progression.

As a researcher, I believe that stomach cancer cells do not send messages to the brain due to the lack of associated neurons

Check https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338555/

Hi Dr Gaurav Kumar . I think this can be done by methods such as co-immunoprecipitation (co-IP), pull-down assays, crosslinking, label transfer, and far–western blot analysis is critical to understand protein function and the biology of the cell. See the link: https://www.thermofisher.com/uk/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-protein-interaction-analysis.html

Dear Abhay Vincent

I would say that it largely depends on what you want to do. For example, do you want to perturb the system or to drive a near-equilibrium transformation?

This being said, looking for previous works done in the same field is quite mandatory to see what has been done, what constants have been used and so on. If you want to unfold a protein, you will need to use force constants large enough to actually unfold it, and not play a tug-of-war with the intra-protein forces of the system. On the other hand, if you want to drag a solute/permeant through a membrane/a protein channel/a nanotube/etc. you may want to not perturb/disrupt the bilayer, or you may want to sample the interaction along the protein channel therefore you need slow velocities to let the permeant interact with its surroundings.

Overall, apart from the limits intrinsic to the software you are using and to the artifact you can introduce, it greatly depends on the theory you are applying. Does it depend on the velocity/k constants? Are you sampling states which need equilibrium conditions, and therefore must perturb the system the least possible? Or does it depend on fast dragging with ensembles of out-of-equilibium trajectories? Does it depend on any approximation, like stiff-spring which maybe would work better with constraints rather than restraints? Or maybe are you trying to reproduce a pulling AFM experiment, and therefore can get some insights from the experimental work?

In a way, it is always a matter of trial and error and checking was has already been done.

Hope this helps,

Nicola

Dear Dr Mohammed,

I also suggest you to read these recent articles:

Best regards,

Pr Hambaba

Check https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596854/

we have contacted qiagen and they have proposed us the PRO version of the kit. Of course the results with the normal kit and the PRO are not comparable, that's why we would like to run all the samples with the same type of kit for DNA extraction. Anyway thanks for checking in your lab. if you had some of them

Best regards

I assume you do mean "molecular magnet" rather than the more common ferrofluid, right? DIY ferrofluids are doable at home, and make a lot of sense for science demonstrations. There also seems to be a lot of recipes for those.

I am not sure of whether any single-molecule magnet is doable in a home lab, but in any case they won't do any good since one needs specialized equipment and cooling well below liquid nitrogen. I do know that only a few molecules present magnetic hysteresis at or near liquid nitrogen temperatures, and their synthesis is very challenging.

In case you mean "molecule-based magnets" (something like this ), then the question is legitimately hard but maybe possible. I am not familiar enough with this to provide a good answer though.

Indeed, this is a fact, the number of infections increases after holidays, when people do not adhere to health guidelines, and this is clearly visible in our countries as well ... The risk lies not only in the high rates of infections but also in the possibility that the virus may be subjected to new mutations that may produce new strains of it that are faster widespread and more lethal to humans ... My sincere gratitude to everyone.

I would choose the last updated one, ARS-UCD1.2. There are quite important differences sometimes with previous assemblies, e.g. position of DGAT1 in ARS-UCD1.2 and in UMD3.1.1. If I would be the Reviewer I would ask for the most accurate/recent reference genome

Probably the latest version does not match with the hardware of your system.

You can use GelJ software, it is java-based, free, and user friendly, which can draw different dendrogram with different analysis.

I use 96% ethanol as a fixative, DNA can be isolated, even with long-term storage

Information about primers, concentrations and volumes are provided in user manual.

Patricio Hernáez Tu relato no solo es increíble, si no inadmisible, la naturaleza de GB es precisamente acceso abierto para el uso científico de datos, ello permite la replicabilidad, incluso la curaduría molecular de las mismas seciuencias ya publicadas. Soy autor que hago uso frecuente de NCBI y además editor en dos revistas de biodiversidad, taxonomía y sistemática donde evaluamos artículos constantemente con evidencia molecular generada y obtenida de GB.

Creo que aquí la reflexión de la supuesta falta a la ética no esta precisamente en los autores.

Thank you both for your responses.

Professor Grabowski, I read the three papers you cited here. The first paper is from 2013 and therefore and these more novel technologies for CTC capture had not been developed at this time. This paper specifically refers to EpCAM-based enrichment of CTCs using CellSearch. It also states:

"Our understanding of biological characteristics of

This is why I'm wondering if these more novel techniques perhaps provide this opportunity. It concludes asking:

The second paper is from 2019 and asks whether CTC usage is ready for clinical practice. It states that:

"At present, it is not clear how this knowledge can be transferred to a prediction of therapy response and an improved clinical outcome. The STIC CTC trial showed the first data for a positive effect of a CTC-based decision in a subgroup with a high count of CTCs before starting treatment. Thus, CTCs might represent a helpful early treatment monitoring tool and can be used in situations with uncertain therapy response."

However, I note all the studies included in this paper (SWOG S0500, CirCe01, STIC CTC, CirCe T-DM1, DETECT use the CellSearch EpCAM based system and do not examine the more novel technologies for CTC capture.

The final article cited here mentions the newer techniques of isolating CTCs using not just protein expression (eg. epCAM) to detect cells but also physical properties. It states that:

It would appear to me therefore that these more novel technologies are indeed useful for CTC capture and may complement existing techniques?

It appears evidence is still outstanding on how these technologies be able to predict response to treatment in the near future? Are there any trials ongoing that provides fresh information?

Thank you Dr Anu for your response. Why is CTC limited to lung cancer with EGFR and have CTCs enabled treatment based on EGFR expression in these cancers? Do you think this will progress to other cancers such as breast and prostate? What does CHIP refer to in this context? I understand that tumour DNA shedding is unpredictable so perhaps this will limit the utility of ctDNA and CTC usage in clinical practice unless these techniques can be refined?

Regards,

Cormac Mullins

As a general rule, you should not correct ambiguities without referring to the chromatogram, unless you have multiple reads and can create a consensus.

Using an existing sequence as a template for correction is scientifically suspect as it can easily lead to confirmation bias. If an ambiguous sequence leads to an ambiguous identification, then that is the right result.

You may find that you need to replace ambiguity codes with 'N' in order to get comparison to work properly. Some programs, e.g. BLAST, treat the ambiguity codes as if they were nucleotides and search for a perfect character-for-character match.

Mr. Solis,

To perform 'literature research' is part of your training at the University, (presumably.) So, ask your professors how to do this. They receive salaries, namely, for your training.

About 1,or 2 ml blood is need

Khudeja Salim

Storing blood for dna is trouble free because the first stages of purification of dna involve RBC lysis steps and the dna is protected against nucleases but RNA is much more susceptible to rapid rnase degradation.

Some possibilities are rapid freezing and storage at -80c or using RNA protective kits like Paxgene ( quiagen). Tempus blood rna tubes ( ABI/life technologies/thermo) or Rnalater for blood from Ambion/life technologies

For protein the storage depends on what protein you are analysing and whether it is necessary to separate the plasma or serum or if you can just add glycerol and freeze before analysis. The discussion at

https://www.researchgate.net/post/How_do_we_prepare_purified_proteins_for_long_term_storage#:~:text=widely%20used%20methods%3A%201%29%20freezing%20samples%20in%20liquid,liequid%20nitrogen%20and%20then%20store%20them%20at%20-80%C2%B0C.

is helpful

For EBV transformation I prefer to separate WBC on Ficoll or Percoll and store the wbc in DMSO at

-80 for months or in liquid nitrogen for years although there are methods online for transforming from whole blood samples

Pre-heat your thermal cycler to 95 degree C and then load your samples. Reduce your primer concentration. Reduce your annealing step duration. Use gradient function of our thermal cycler to obtain the optimum annealing temperature. Limit to 35-40 PCR cycles to prevent unnecessary non-specific amplifications.

Yes, you can use these datasets for research work equivalent to a PhD thesis. As a reference, you can check the publications by TCGA and other groups which utilized TCGA data. A series of these publications have been published by Cell Press as TCGA-Pan Cancer Atlas.

You can see, just in silico work published in the Cell Press journals. But, before thinking of that extend i.e., to entirely rely on these datasets, think what novel question you can address. If you have a highly relevant question, you can go for it. Otherwise, a simple and safe plan can be using hypothesis generation by datasets followed by validation using in vitro studies or vice-versa. This type of combinational work is regularly published and will be more acceptable to most universities and individuals. All the best.

You can check our papers also where we have used simple tools to analyze TCGA data.

Neha Paserkar Have you solve the problem? I have same problem right now.

On "electropherogram" drop down menu, select "show sizes"

In general - and if results of otheres (50% reduced viability") are reliable - WB will not be an adequate compensation for mising viability data. However, you could perform alternative viablility assays, such as Calcein AM assay, or poptosis testing (AVPI staining), or analyses og Bcl-2 vs BAX expression etc. to determine viability, apoptosis and/or surcival of cells. This depends on the functions you want to determine, such as cell proliferation (MTT or CFSE staining), cell viability (calcein AM assay), apoptosis/survival (expression Bcl2/BAX or better AVPI assay (FACS method)).

Better to ask your supervisor / colleague. Those terms are all easily definable with google or a dictionary, however the EXACT context will be entirely dependent upon the systems and sciences you are describing / working with.

Hi, Gustavo Yasser Lorente González,

Thanks for contacting me. I also copy this answer to your RG email.

Several reports have shown that lyophilized plant materials are not idea for some enzyme activities assay. For example, in this article, "Effects of storage time and freeze-drying on the activity of antioxidant enzymes in sugarcane leaves", it claimed that "the freeze-drying technique should not be used to preserve samples for further analysis of antioxidant enzymes."

Hello

through: http://bisearch.enzim.hu/

Section: Primer search, ePCR

You can use our recently published paper for genome-wide mapping of N7meG and N3meA, but not O6meG. Link: https://genome.cshlp.org/content/early/2017/09/14/gr.225771.117.abstract

Hope it is helpful for you!

Thank you so much Fei Guo and Marcela Krutova

Dear Nicholas

High temperature leads to a decrease of pollen viability which is directly correlated with a loss of fruit production. The reduction in pollen viability is associated with changes in the level and composition of several (groups of) metabolites, which play an important role in pollen development, for example by contributing to pollen nutrition or by providing protection to environmental stresses. This review will give an overview of the current state of the art on the role of various pollen metabolites in pollen homeostasis and thermo-tolerance. Their possible use as metabolic markers to assist breeding programs for plant thermo-tolerance will be discussed.

Hi! Haven't been on this platform for a while. Back then I did contact Roche technical service. It's a software bug.

Yes, I agree, but i would want to know some experience before to pay for all the reactants necessaries!!! (you know are very expensive!).

Thank you professor, nice to meet you.

You may like to use mirDIP (http://ophid.utoronto.ca/mirDIP/), which is the tool developed in our lab. In its recent version mirDIP integrates miRNA-target computational predictions obtained across 30 original resources. It stores nearly 152 million predictions, while covering 2,586 human mature miRNAs and 34,010 human genes. If you have any question regarding its use, please feel free to contact me.

Angstrom.

SybrSAFE is dreadful. It costs more than EtBr, doesn't stain well, and gives too much background fluorescence in your gels. I had to use it once in a teaching lab and I'd never use it again.

Honestly, I'd rather use EtBr. Just practice good safety habits (gloves, goggles, etc.) and dispose of it properly.

hope this link is useful

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039391/

regards

you may also try https://biit.cs.ut.ee/gprofiler/

and GOsummaries http://bioconductor.org/packages/release/bioc/html/GOsummaries.html

Word cloud summaries of GO enrichment analysis .

I concur with Abhijeet: No.

It will not express embryonal, or tissue-specific genes (Except of course those from the specific differentiation state these cells are in). And of course some genes are only expressed upon stimuli (radiation, virus infection, IFN, LPS) if you are looking for a broad source of expressed genes, I would probably recommend whole mouse embryos (and even there......(see above)). However at VERY low levels you might find almost every gene in almost every tissue (And I mean V E R Y low)

Thomas :-)