Science topic

Molecular Markers - Science topic

A forum for debate and questions regarding molecular markers.
Questions related to Molecular Markers
  • asked a question related to Molecular Markers
Question
2 answers
Dear Professor/Researcher, I am pleased to inform you that we are currently editing a 6-volume book on Plant Genome Editing for potential publication by Springer. We aim to gather contributions from a diverse array of international authors, including esteemed scientists such as yourself. Given your expertise in the field, we invite you to submit a chapter on a topic from the provided list of titles or propose an alternative topic that aligns with the book's theme without duplicating existing titles. Please confirm your interest in participating within a week. Send a provisional title, a rough outline or abstract, and a list of potential co-authors after confirmation, as these details can be tentative at this stage. We eagerly await your confirmation email and, ultimately, your manuscript. Thank you very much for your interest in writing a book chapter for our book series Genome Editing for Sustainable Agriculture Book Series Volumes 1 through 11 (Springer)". The series consists of 11 volumes, and you are welcome to choose any of them to contribute a chapter. Please note that I have not yet updated the list. So you can select more than one chapter per volume. Volume 1 13Genome editing in plants via CRISPR/Cas9 21Plant Genome Editing examination of technological developments and difficulties 22Plant genome editing: Prospects, Progress, Implications, and Cautions 17Perspectives on social, ethical, policy, and governance issues for CRISPR-edited plants’ Volume 2 still has the following available chapters: 8  Plant genome editing without PAM by utilizing a CRISPR-SpRY toolkit 13 An extensible vector toolkit and parts library for advanced engineering of plant genomes Volume 3 still has the following available chapters: 6  Quantifying on and off-target plant genome editing 7   Quantitative assessment of genome editing 8 Deep learning improves the prediction of plant genome editing. 11  Plant breeding using orthogonal genome editing and transcriptional activation facilitated by CRISPR-Combo 16    Monitoring footprints CRISPR-mediated genome editing Volume 4 still has the following available chapters: 2   Genome editing translational research in plants 4 Genome editing patents worldwide 8 Genome editing in dicot: opportunities and challenges 14 Risk of off-target plant genome editing 15 Using CRISPR-TSKO technology for tissue specific Plant genome editing 19 Commercialization of technology for genome editing Plant Genome editing and future prospects of molecular marker Volume 5 still has the following available chapters: 7 Genome editing for toxicity 8 Genome editing for flooding 9 Genome editing for radiation 10  Genome editing for natural disaster Volume 6 still has the following available chapters: 7 Genome editing for toxicity 8 Genome editing for flooding 9 Genome editing for radiation 10 Genome editing for natural disaster Genome editing for pollution Kind regards Khaled
Relevant answer
Answer
Response to the Discussion:
Subject: Chapter Contribution Inquiry – Genome Editing for Sustainable Agriculture Book Series
Dear Khaled F M Salem,
Thank you for sharing this exciting opportunity to contribute to the Genome Editing for Sustainable Agriculture Book Series by Springer. The scope of this project is inspiring, and I appreciate your consideration of my expertise for participation.
I am very interested in contributing a chapter to the series. After reviewing the available topics, I would like to propose a chapter titled: "Deep Learning Enhances Prediction of Plant Genome Editing: Challenges and Opportunities" (Volume 3, Chapter 8).
This chapter will explore the integration of machine learning, particularly deep learning, to improve predictive accuracy for plant genome editing, addressing challenges like off-target effects, model scalability, and integration with CRISPR-based technologies.
Alternatively, I am also interested in contributing to "Genome Editing for Pollution" (Volume 6), given its relevance to sustainable agriculture and environmental protection.
I will provide a detailed abstract, outline, and a list of potential co-authors upon confirmation. Please let me know if these topics align with the book’s vision or if adjustments are needed.
Thank you again for this opportunity, and I look forward to your response.
Best regards,
Invitation to Join Dailyplanet.Club:
In addition, I would like to invite you to join Dailyplanet.Club, a platform for researchers and innovators dedicated to fostering collaboration on groundbreaking topics such as genome editing and sustainable agriculture.
As a member, you can:
  • Connect with experts in agriculture, genome editing, and environmental sustainability.
  • Share and discuss your work with a global audience.
  • Support technological advancements and collaborative research projects.
Membership is just £5 per year, supporting the platform’s mission to build a global hub for knowledge-sharing and innovation. Visit www.Dailyplanet.Club to join and explore its benefits.
Looking forward to collaborating with you!
Best regards, James Henderson Mitchell CEO, MJ HSA Ltd
  • asked a question related to Molecular Markers
Question
4 answers
MOLECULAR MARKER
Relevant answer
Answer
The use of SSR in the short and long arm of the chromosome
  • asked a question related to Molecular Markers
Question
1 answer
Good afternoon. Please tell me, are there molecular markers of zeina genes for the purpose of genotyping lines and varieties? There are Asid-PAGE and SDS-PAGE methods for studying the polymorphism of zein-coding loci in maize. But I have not yet been able to find molecular markers based on the PCR reaction (ISSSR, SSR, etc.)
Relevant answer
Answer
@Vladimir Vasipov as per your question regarding the zein genes in maize (corn), which are significant because they encode storage proteins in maize kernels, several studies have utilized molecular markers for genotyping. Below are some examples:
ISSR Markers:
  • Example Study: Maize Diversity Analysis Using ISSR Markers Reference: Reddy, M.P., Sarla, N., & Siddiq, E.A. (2002). "Inter Simple Sequence Repeat (ISSR) polymorphism and its application in plant breeding." Euphytica, 128(1), 9-18. Application: This study used ISSR markers to analyze the genetic diversity in maize lines, including those with different zein gene profiles. SSR Markers:
  • Example Study 1: SSR markers associated with zein genes Reference: Senior, M.L., & Heun, M. (1993). "Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer." Maize Genetics Cooperation Newsletter, 67, 56-62. Application: SSR markers were used to map regions in the maize genome, including those associated with zein genes.
  • Example Study 2: Genetic Diversity of Zein Genes using SSR Reference: Vigouroux, Y., Jaqueth, J.S., Matsuoka, Y., Smith, O.S., Beavis, W.D., Smith, J.S.C., & Doebley, J. (2002). "Rate and pattern of mutation at microsatellite loci in maize." Molecular Biology and Evolution, 19(8), 1251-1260. Application: This research utilized SSR markers to assess the mutation rate and diversity of microsatellite loci associated with zein genes in maize. I hope it helps you
  • asked a question related to Molecular Markers
Question
3 answers
I have isolated granulosa cells from mice ovary using puncture method. Cells are healthy and growing in DMEM. Their morphology is same as granulosa cells. However I would like to use a molecular markers or Immunohistochemistry method to authenticate them further, before downstream use. Can anyone suggest the best methods and markers for the same ?
Relevant answer
Answer
Dear Dr. Khare,
I had flow in mind too. When it is between ICC vs flow cytometry, you should opt for flow cytometry as per your requirement.
Best.
  • asked a question related to Molecular Markers
Question
4 answers
I have been observing double bands for protein molecular marker(especially 15 kDa band) every time I am doing SDS-PAGE. Sometimes even the samples appear to have a double band. These are 12.5% handmade gels and sample running voltage is 160 V. Can anyone suggest how to resolve this issue.
Thank you for your answers.
Relevant answer
Answer
Thank you all for the valuable suggestions.
Meera J. Patel I haven't tried the titration or the gradient gel approach as I just need to check the purity of the sample before moving on to the next step of the experiments. To answer your third point; Yes, I too had the same thing in mind. So I ordered a new ladder; but I am still getting the double band.
Sara Kishta Mohamed The size of the protein of interest is ~14 kDa. So, I and not using low % gels. But, Yes I will probably try lower volt to Run the gels.
  • asked a question related to Molecular Markers
Question
3 answers
Molecular markers are specific DNA sequences that can be used to identify and track particular genes or genetic traits of interest in plant breeding programs. These markers serve as tools to assist breeders in selecting plants with desired traits more efficiently and accurately. Molecular markers can be used to determine genetic relatedness, assess genetic diversity within populations, identify specific genes responsible for traits, and facilitate marker-assisted selection (MAS) or marker-assisted breeding (MAB) techniques.
Relevant answer
Answer
Molecular markers are commonly used to assess genetic variation in agronomic germplasm, analyze population structure, localize quantitative traits (QTL), or linkage mapping for gene mapping. The most interesting application of molecular markers is marker-assisted selection (MAS). Molecular marker technology enables plant breeders to select individual plants based on their marker pattern (genotype) rather than their observable traits (phenotype). This process is called marker assisted selection (MAS) or marker assisted breeding (MAB). Compared with traditional breeding programs, molecular markers can increase the efficiency and effectiveness of breeding programs. Molecular markers in the construction of linkage maps, they have numerous applications in plant breeding such as assessing the genetic variations within cultivars and germplasms. Molecular markers are one of the most powerful tools for studying genetic diversity. They are used in the study of phylogenetic relationships, selection of superior plants, and the study of similarities or differences between different specimens. Molecular markers are also used in germplasm management and marker-assisted selection (MAS) to increase the efficiency of germplasm breeding.
  • asked a question related to Molecular Markers
Question
3 answers
I am testing molecular marker association (different combinations) with a trait. How can we apply this test on SPSS for different molecular marker interactions? Any kind of contribution is welcome.
Relevant answer
Answer
There is no such thing as a Kruskal-Wallis test for the interaction.
  • asked a question related to Molecular Markers
Question
2 answers
Could you please recommend some molecular markers for identifying the genes for disease resistance such as blast (Pita, Ph-k, Piz), bacterial leaf blight (Xa12, Xa7, xa5, etc...), brown plant hopper (BPH17, BPH18, BPH37, etc,...). Thanks!
Relevant answer
Answer
Dear Sir Kalisa Alain. Thank you very much for your recommendation!
  • asked a question related to Molecular Markers
Question
3 answers
To breed rice for drought tolerance, is it feasible to start selection in the F2 by picking out offspring harbouring certain molecular markers, given that it is expected that these QTLs will continue segregating in the subsequent generations? Or is it better to keep selfing a hybrid population until the F5 or F6 and then start selection?
Relevant answer
Answer
Thank you Hoan and Adamu. Your help is appreciated.
  • asked a question related to Molecular Markers
Question
3 answers
There are different plant barcoding regions present in plants like RbcL which stands for Ribulose 1,5-biphosphate carboxylase and MatK which is Maturase K.
So what are these regions stands for which include; trnH-psbA, trn L, rpoC1, rpoC2, rpoB, accD, psb k1 and atpF-F?
Relevant answer
Answer
Did you check https://www.wikigenes.org/ ? It also provides specific references for each gene
  • asked a question related to Molecular Markers
Question
5 answers
I run my gene specific primer PCR product on 2.5% Agarose it did not show any amplification only primer dimer was seen
But the same product I used in 8% PAGE gel (with silver staining process) it shown the amplification result
What is the reason behind it...
Relevant answer
Answer
My only guess is that the silver stain is just extremely sensitive compared to your agarose gel. Are you using ethidium bromide or something similar for the agarose? The detection limit of this usually falls off hard below 25-50 ng while the silver stain is much better than that so it can see what the agarose gel cannot.
  • asked a question related to Molecular Markers
Question
2 answers
We need to sequence markers to perform phylogenetic analysis of a snake but the only material we currently have available is a dried blood sample. I would like to know if it is feasible or possible to obtain information from this type of sample.
Thank you.
Relevant answer
Answer
Quality and Quantity of DNA will also depend on time and conditions of storage (UV light, etc). Extraction is key, so I suggest to carefully consider your options and chose the best extraction method available.
We had success with dried blood samples using Blood&Tissue Kit from qiagen (maybe enhancing the initial volumne depeding on the support medium) but also precipitation based methods (dissolving the dried blood in buffer medium).
  • asked a question related to Molecular Markers
Question
4 answers
if samples are limited, e.g., less than 10 samples per population, which molecular markers are suitable(Microsatellites or SNPs generated by RAD-seq)? If you can provide some references for your opinion, it would be better. Thank you for your attention!
Relevant answer
Answer
I will go for microsatellites
  • asked a question related to Molecular Markers
Question
9 answers
I got my fragment analysis results of Microsatellite markers designed using haploid species. I am using a gene marker to analyze the peaks. I read that since it is haploid, i should see only one peak (means one allele per locus?). But i see many for types of markers ( di, tri , ...) . I want to select polymorphic markers and want to score them for population analysis.
Also, gene marker has the option only to analyze plant dinucleotide and plant fragments. So i am not sure what settings should i select for fungal species?
i would appreciate if someone could clear my doubts?
Relevant answer
Answer
Dear @Chiti Agarwal I refer your statement:
......since it is haploid, i should see only one peak (means one allele per locus?).
Is it true for all haploids? Haploids of polyploids have more than one allele per locus.
  • asked a question related to Molecular Markers
Question
4 answers
We have SSR marker (150) based genotypic data of 190 rice landraces. Want to prepare a research article. Which kind of analysis may be performed with these data? Kindly give your opinion and suggestions.
Regards
Parmeshwar
Relevant answer
Answer
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,
  1. for genotypic characterization:- Basic genetic parameter analysis like hetertozygotes level, allelic frerquency, PIC value etc.,
  2. for genetic variability studies:- AMoVA
  3. for ancestry studies: - phylogenetic analysis OR dendrogram studies.
  4. for genetic distance studies:- PCA, Genetic distance matrices.
  5. for population studies: - STRUCTURE.
Stat tools:- ArleQin, GenAlEx, Molkiv, Power marker, NTSYS, STRUCTURE, MEGA and Darwin.
*If you are using genic SSRs-
  1. trait identification studies
  2. QTL analysis.
Stat Tools: - Windows QTL Cartographer, TASEL.
all the best
  • asked a question related to Molecular Markers
Question
12 answers
Large germplasm collections may have several duplicates which need to be removed from the set. DUS characterization based on morphological traits are the best way to differentiate them. But it is very tough to DUS characters in large germplasm lines. Is there any method in molecular breeding to identify the duplicates in huge germplasm collections of rice? Kindly give your opinion and suggestions.
Relevant answer
Answer
You could use SNP, PCR, molecular markers, and other molecular methods to differentiate the DUS Characteristics in large germplasm lines.
  • asked a question related to Molecular Markers
Question
11 answers
As SSR are most widely used markers in major cereals. They are highly reliable (i.e. reproducible), co-dominant in inheritance, relatively simple and cheap to use and generally highly polymorphic. What other factors can affect polymorphism in case of SSR markers?
Relevant answer
Answer
The polymorphism at DNA level depends on several factors of which genetic divergence of the parents or the genotypes under study is one of the most important one. Secondly, as very rightly mentioned by Ricardo Julian Licea-Moreno sir, it requires detailed information about the genotypes and the markers you are using because it is possible that many of those markers may belong to the same region of a specific chromosome.
  • asked a question related to Molecular Markers
Question
6 answers
In case of morphological markers are also not available
Relevant answer
Answer
Dear Divya - S. Yes, one can identitfy a hybrid without molecular markers. It is well established that a hybrid exhibits "hybrid vigour". By growing the parents of the hybrids side by side, and making record for a number of traits including growth of radicle, plumule, early vigour, and stress tolerance. Moreover, there may be a number of morphological markers, dominance relations of which can provide a clue to identify a true "hybrid". I have attached two PDFs; hope, these two will be useful to you.
  • asked a question related to Molecular Markers
Question
7 answers
I want to visualize EOMES, a transcription factor, in CD8 T cells. I am planning to perform an immunofluorescence test and I was wondering what kind of stain or chemicals I can use to enable the visualization of internal markers of a cell.
Relevant answer
Answer
Fa Ro , that does make this quite a bit more complicated.
Fluorescently-conjugated small peptides (i.e. phalloidin) can be used to visualize some intracellular targets in live cells (actin filaments in the case of phalloidin), but this does not apply to most proteins. Unfortunately the size of normal antibodies prevents their entry into live cells, but a few different approaches for labeling intracellular targets in live cells (e.g. quantum dots and nanobodies) have been published. Unfortunately, none of these systems are in widespread use.
The most common approach for live cell visualization of a specific protein is constructing a fluorescent fusion protein. This can be done with transient transfection or through generation of stable cell lines. However, there is no guarantee that the fusion proteins will behave in the same manner as the wild-type due to steric hindrance.
One group has already reported a GFP-Eomes fusion protein in mice: . They used TALENs to insert the GFP into the first exon of Eomes, but you should be able to reconstruct this in a plasmid.
  • asked a question related to Molecular Markers
Question
4 answers
As I have started a new research work, I am looking into the circadian rythm and genes that controll it in mammal models. In order to do this experimentally I need to find consistent molecular indicators for when the Night and Day genes are activated respectively.
Which would you consider relevant?
Do you know about any molecular markers in bronchial cell lines that indicate the expression of Night/Day genes?
Relevant answer
Answer
Dear Daniel Garcia sir, Per (Period) and Cryptochrome (Cry) genes are responsible to maintain the circadian rhythm of mammals. (3 Per genes- Per1,2,3 and 2 Cry genes- Cry1,2). During the day, these genes are activated after the binding of BMAL+CLOCK combined activators to the promoter region and produce Per and Cry proteins then translocate into the cytoplasm. Those proteins can't exist alone therefore have to be made dimers per-per or per-cry dimers. Another molecule/CKε1 enzyme plays a key role in manipulating these dimers. It has 3 functions
1 Phosphorylation of alone per proteins and degrade them, this helps to reduce the formation/accumulation of per-per and per-cry dimers quickly (maintain a considerable dimer formation rate until night)
2 Translocation of dimers into the nucleus
3 Turn over the inhibitory complex
During the night those dimer negative factors interact with BMAL+CLOCK complex and inactivate the genes
Again at the morning the concentration of inhibitory dimers become lower in the nucleus compared to the BMAL and CLOCK. BMAL+CLOCK bind to the promoter to activate the genes again.
Mutations of CKε1affect on the circadian rhythm for an example poor phosphorylation make quick accumulation of dimers then negative feedback starts earlier....
Activation/Deactivation of these genes affect on the body physiological processes- Hormone secretions, Body Temperature, Sleep wake cycle etc.
Photoreception of our eye sends the signals to the brain. These genes are prominent in some structures(SCN-suprachiasmatic nucleus or nuclei is a tiny region of the brain in the hypothalamus in the brain). recognize day and night then activate or deactivate that genes that genes. send signals to the Pineal gland if it is activated to secrete melatonin.
melatonin is a predetermining molecule of other secretions such as thyroxin hormone (in the metamorphosis/growth)
I think Melatonin, Thyroxin or CKε1 levels can be used as measurements in your research.
Best regards!
Lahiru
  • asked a question related to Molecular Markers
Question
3 answers
I am differentiating bone-marrow cells into bone marrow-derived macrophages (BMDM) using M-CSF.
What is a reliable specific gene marker for bone marrow Common Myeloid Progenitors that is lost or downregulated during differentiation into monocyte and then macrophage?
Thanks,
J
Relevant answer
Answer
I may tell you surface markers to differentiate CMP vs Monocytes vs Macrophages, which may be used for flowcytometry.
For CMP: CD34+, CD38+, CD45RA-, CD61-, CD71-, CD123+
For Monocytes: CD34- CD45+, CD14+, CD33+
For Macrophages: HLADR++, CD80/86
  • asked a question related to Molecular Markers
Question
5 answers
Most of the current existing plants are the result of an adaptation of plants to various factors, especially the environment, of course, there are small portions of species or cultivar plants produced by humans. This evolutionary and adaptation process results in various species of plants growing only in certain geographic environments, where could be owned by certain countries based on the territory. A country where certain plants have grown may claim that this particular endemic plant belongs to the concerned country. Please give an opinion, whether this claim can be justified or not? Is DNA barcoding needed to be legal evidence to support the claim concerning those certain plants?
Relevant answer
Answer
It is a very important step, if implemented in India. There are more duplicacy in the variety exist in the country.
  • asked a question related to Molecular Markers
Question
6 answers
The polymerase chain reaction (PCR) technique has created new ways of revealing DNA polymorphisms among closely related genotypes.Molecular markers which have been applied to Colletotrichum sp. diversity studies include internal transcribed spacer (ITS) regions, restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers.
Relevant answer
Answer
All the markers may be effective but use combination of different marker systems. Like u can use about three different markers to get more reliable results.
  • asked a question related to Molecular Markers
Question
7 answers
I'm doing my postgraduate studies and I am developing my research on the taxonomy of polyclads (Platyhelminthes: Polycladida). In addition, I am doing molecular taxonomy, so I am interested about knowing the best molecular marker for this taxa.
I thank in advance for your help and support.
Kind regards
Relevant answer
Answer
I agree with Fred R. Opperdoes with his answer.
  • asked a question related to Molecular Markers
Question
3 answers
Turmeric is a polyploid and vegetatively propagated crop. Usually, F1 populations are used to identify QTLs. As this crop generally has no viable seed, what is the best approach to genarate QTLs.
Relevant answer
Answer
An F1 clonal propagated population should work fine for qtl mapping.
  • asked a question related to Molecular Markers
Question
2 answers
Which mapping function is preferred for linkage map construction; Haldane's or Kosambi mapping function?
What are the effects of each one on the resulted linkage groups?
  • asked a question related to Molecular Markers
Question
5 answers
Hi everyone I am running Structure version 2.3.4 programme smoothly.But now I am facing problem that in Result folder I am getting only one file although I am setting k=2 to k=10 and iterations 5 with admixture model format. Earlier there was not any problem.
Relevant answer
Answer
If it worked before I'm asuming your input file is ok, so my recomendation will go in another direction... Maybe you could try setting the folder that will gather the results in a way that its name is not too long. I have experienced problems with STRUCTURE and TESS if I have folders inside folders inside folders... the name of the result files just get too long.
Try creating a folder in your desktop just to run STRUCTURE, then you can move it into wherever you want.
  • asked a question related to Molecular Markers
Question
6 answers
Hello everyone,
I am looking at markers that I can use for qPCR to check the phenotype of microglia after primary microglia culture. I found a protocol to prepare microglia from pups but I would like to check their phenotype after culture to be sure to have microglia before starting assays on these cells.
Can you help me ?
Audrey
Relevant answer
Answer
PCR
  • asked a question related to Molecular Markers
Question
4 answers
I have target sequences that I want to blast and then extract from all Glires reference genomes on NCBI along with 500bps upstream and downstream of each top match for a few hundred sequences. Does anyone have any suggestions on a good automated way of doing this? All I want are the sequences so that I can add them to the aligns I have made.
Thank you for any guidance.
Relevant answer
Answer
Max R. Bangs I know that you already know most of this, but I am going to put in some details for others reading this thread who have not already gone as far as you have.
From the BLAST results, you can download all hit sequences. But you want the hist sequences plus 500 bases beyond each end. You can also download a "hit table of text" and from that you can extract the accession number, begin match and end match coordinates. You can then subtract 500 from each hit-begin and add 500 to each hit-end value to get the database call for each sequence.
DQ648857: 13022 18018
DQ412043: 13019 18015
KJ473814: 12936 17932
JX993987: 12908 17903
KJ473812: 12733 17729
MK211375: 13007 18002
KY417147: 13006 18001
MK211377: 13004 17999
KY417148: 13006 18001
DQ648856: 12989 17985
KJ473816: 12771 17766
KY417145: 13006 18001
KY417152: 13006 18001
MK211376: 13005 18000
KY417143: 13006 18001
KY417142: 13006 18001
MK211378: 13006 18001
KJ473813: 12756 17752
KT444582: 13006 18001
...
for example in the table is then converted into the database call for each:
But you don't want to paste a URL like that into your browser for each sequence, and then have to click "file: save as" on each entry, one at a time. So you go to the NCBI help page:
How to: Download a large, custom set of records from NCBI
and you follow those intstructions.
  • asked a question related to Molecular Markers
Question
7 answers
The true composition of soil organic matter and soil carbon processes are very complex. Accurately distinguishing carbon components in soil is the bottleneck of current research. Molecular markers with certain specificity and stability can be used as an important methods to distinguish different carbon pools, e.g., amino sugars, phospholipid fatty acids and lignin. Apart from these, What other molecular markers do you know?
Relevant answer
Answer
Dear Xingde Xu, please have look into a review published by Prof. Wulf Amelung and his colleagues a couple of years ago:
Best regards
Nils
  • asked a question related to Molecular Markers
Question
5 answers
Hi all
I am working on markers assisted selection and I wish to know the sequence of primer of this marker(MahSe2) linked to resistance of cowpea to Striga.
Best regards
Relevant answer
Answer
Mahse2 is different from C42-2B.
  • asked a question related to Molecular Markers
Question
2 answers
I would like to know if there is any literature on the genes that are considered the best molecular markers for phylogenetic analysis on the Metazoa scale.
Relevant answer
Answer
Thank you Mohammed!
  • asked a question related to Molecular Markers
Question
5 answers
After doing a selective neutrality test of the molecular markers I worked with, it turned out that 30% of the markers are subject to selection and the remaining 70% are neutral, should I do my study with those who are neutral only or should i use all of them?
Relevant answer
Answer
As a clarification: I am assuming that you mean 30% of your SSRs had statistically significant evidence of departures from neutrality, correct? Unless you have a genome and know they are from known region, you don't "know" they are under selection, just that the statistical test indicates they might be. Thus, immediately removing them from the dataset would be an over-reaction. Those tests are prone to Type I errors.
It depends on the analysis you want to perform. Some measures of genetic differentiation (e.g Fst, Bayesian clustering) assume markers are neutral. Others (such as a PCA) do not. Some are robust to departures of neutrality: check the assumptions first.
Depending on how many markers you have, run the analyses with the full suite, just those "under selection", and those presumably neutral: see if you get a different answer.
Hope this helps.
  • asked a question related to Molecular Markers
Question
4 answers
I am going to start DNA molecular markers using DAMD and SSR on the confirmation of true-to-type cloned plants in plant tissue culture.
I came across that many genetical statistics had been used such as PCA.
How am I going to apply PCA on my study?
Is it something like:
I have plenty primers for DAMD and SSR, after running the gel eletrophoresis and calculated similarity index, I run PCA on the similarity index...then I group the primers up, and redo the grouped primers??
Relevant answer
Answer
you can applying PCA method in quantifying genetic diversity or measuring Intarpopulation genetic diversity
  • asked a question related to Molecular Markers
Question
4 answers
I was hoping someone might be able to provide some insight into what could be causing our issues with protein SDS-PAGE. We are using the BioRad mini-PROTEAN tetra cell. If anyone recognizes any of the symptoms of our issues, please share your expertise and help us diagnose the problem!
I have also attached some images for consideration.
Here is a brief summary of our issues:
- Our separation is taking significantly longer than it should; some times it can take ~1.5-2 hours @120V, we also had an instance where @110V the dye front did not migrate more than an inch after 3 hours
- gels are separating at the wrong %; for instance, we have been making 8 and 10% gels that separate as if they were 12 or 15%
- our BioRad dual color pre-stained ladder will begin to disappear around the 75kDa marker; this effect will then permeate the molecular markers above it and slowly disappear also. The weird thing is you can see a pink/blue tinge throughout that lane, so it is almost like the ladder is not migrating at a specific front, but is instead just diffusing throughout the lane
- some of our gels will also show uneven migration with one side of the gel migrating faster than the other
- the dye front runs uneven
One of the frustrating issues is that this is apparently random. Sometimes one SDS-PAGE run will work fine, other times only 1 of 4 gels might be affected by something, and they generally only show one problem when there is a problem at all.
These will then translate over into issues with our Western where there is noticeable unevenness in the protein signal especially in the middle lanes. Interestingly, when our ladder begins to disappear, our protein signals below 75kDa are completely fine, signals near 75kDa are entirely uneven and splotchy, and signals ~100kDa and above will begin to show signs of issues depending on the severity of the disappeared ladder.
The random nature of the issue has made it very difficult to trouble shoot.
These are things we have tried to troubleshoot so far:
- Remade all of our buffers
- purchased new acrylamide
- purchased pre-casted gels
- changed out our old power system for a brand new one
- tried different pre-stained ladders
- used other labs to make all of our materials
None of this has helped. One of the only promising things we have tried was using another labs SDS-PAGE equipment. These were definitely running noticeably quicker with no obvious errors. We have also used other labs equipment with our reagents and it has seemed fine.
I have narrowed the issue down to either being our power packs or our power outlets. I find it hard to believe it is the power pack as we have issues whether we use an old one, or one that is new and has only been used maybe a dozen times. I am also not sure if it might be a power supply issue as plugging another labs power pack into the same outlet showed improvement.
At this point, we are completely at a loss. If anyone has any insight, I would really appreciate it.
Relevant answer
Answer
It looks like a buffering problem to me. Check very carefully your buffers.
  • asked a question related to Molecular Markers
Question
2 answers
Mutant 195 mice treated with iso stimulation showed upregulation of all molecular markers in amles and down regulation with emfales ??
Any explanation ? I did only suggest a protective effect (antihypertrophy of estrogenes )
Thank you
Relevant answer
Answer
I understand..thank you for your reply
  • asked a question related to Molecular Markers
Question
7 answers
My question is about how to distinguish two Phytophthora species infecting the same host and is responsible for causing the same disease. Which molecular marker can I use to distinguish between the two species of Phytophthora.
Morphologicaly these two species cannot be distinguished from one another, so we have to rely on molecular markers. Can any body enlighten me on which molecular markers are to be used for solving the particular problem.
Relevant answer
Answer
Microsatellite markers are the best choice available for such problems.
  • asked a question related to Molecular Markers
Question
7 answers
I didnt add any molecular marker in sample. moreover light bands are seen.
My protein is showing proteolytic activity and fibrinolytic activity too.
But bands are very light .
please tell me what can i do for proper bands.
Relevant answer
Answer
Also you have to use fresh sample buffer with adjusted components for degradation of the protein
  • asked a question related to Molecular Markers
Question
4 answers
Hello everyone, I would be very grateful if you could give me guidance on the use of transcription factors as molecular markers. I am studying senescence in fruits through the analysis of transcriptome and I´m looking for genes of interest that serve to explain the differences between the different varieties of fruits.
I´m interested in the transcription factors associated with the metabolic pathways that lead to the senescence of the fruit , but I'm not sure if studying it that way is the right thing to do, since many similar studies only focus on one metabolic pathway or one specific gene within the same pathway. I feel that it would be more interesting to study the transcription factor because it is capable of modulating multiple routes, so it can be a marker that defines whether a fruit has a more rapid maturation than another. I hope you understand my question, thank you very much to those who comment.
Success to all.
Relevant answer
Answer
Please have a look of the following papers describing significance of TFs based molecular markers. These suggested articles will give you some basic information of TFGMS and their utility for improving crops.
  • asked a question related to Molecular Markers
Question
5 answers
It is well known fact that Indian aquaculture is mostly confined to carp farming. Most of the carp hatcheries do not maintain data on pedigree. It is not sure that how many times brooders are changed in the hatcheries. It is said that declining productivity is observed in the carp farming due to inbreeding happening in the hatcheries. Therefore, I wish to know that molecular markers can be useful to estimate the inbreeding accurately. It yes, the result would be the same that of classical method.
Relevant answer
Answer
Thank you Shaheb
  • asked a question related to Molecular Markers
Question
3 answers
pcr, upland cotton
Relevant answer
Answer
You could use GBS based SNP markers
  • asked a question related to Molecular Markers
Question
11 answers
Dear my professors and colleagues,
I prepare a review about use biotechnology and molecular marker at poultry breeding.
I want your help.
Relevant answer
Answer
Hello Dr. Esteftah
I recommend for you the following chapter
"Selection Methods in Poultry Breeding: From Genetics to Genomics"
Good Luck
  • asked a question related to Molecular Markers
Question
3 answers
I am trying to use the molecular marker information to estimate the additive and residual genetic variances in multi-location trial dataset and wonder any suggestion on best software or package to construct a genomic relationship matrix
Relevant answer
Answer
Abdel Rahman Mohammad Al Tawaha stop spamming here. I HAVE REPORTED YOU.
  • asked a question related to Molecular Markers
Question
3 answers
Is there any reports that Hydrogen peroxide (H2O2) pre-treatment in seeds can cause changes in genome sequence?
Can H2O2 works as mutagen?
Relevant answer
Answer
above a normal level in cell, can cause changes and damage the DNA.
  • asked a question related to Molecular Markers
Question
10 answers
I have isolated DNA from 382 plants without running them on gel . I thought i will run them together after one month of completed extraction i found a long band of smear on my gel for all of my samle . I want to run SSR marker for these sample what i dont know is this possible or not . Nanodrop conc. of all of my sample is ranging from 500- 2000 ng/microlitre with A260/A280 ratio of 1.8 -2.02. lease tell me what should i do ,i cant perfom dna ext6raction of this much sample again . My gel images are attached below
Relevant answer
Answer
ther is rna present and also degradation of the dna but so long as many of the degraded dna fragments are longer than your expected pcr amplimers I would expect pcr to work well on these samples. People are amplifying ancient ( m0re than 6000year old) and cell free circulating dna both of which are broken up into small fragments and are successful
  • asked a question related to Molecular Markers
Question
5 answers
I am interested in molecular markers study of cordyline spp. there is no literature available on ISSR ,SSR or even RAPD of cordylines. Can anyone help that how to select best primers?
Relevant answer
Answer
Dear Colleague, here are only two examples (there are many!) where you can see that you can get quite easily good results with PCR primer designed for SSR motives (i.e. GATCGATCGATCGATC) Many of these primers should also work in your new species.
  • asked a question related to Molecular Markers
Question
2 answers
I reconstructed a Bayesian phylogeny using MrBayes in CIPRES for further study in BayesTraits, but BayesTreesConverter returns an error because there are no branch lengths in the posterior sample of trees.
Checking the parameters in CIPRES, I specified 'yes' for savebrlens.
Is this normal? Could it be the large size of the alignment, 4 molecular markers for 1280 taxa?
Relevant answer
Did you try to use the sump and sumt commands? When these commands are used MrBayes automatically generates a consensus tree with branch length. In other hand, if you do the consensus from other software, the consensus tree usually is a cladogram, without branch length information.
  • asked a question related to Molecular Markers
Question
4 answers
How genetic diversity in a plant species can be corelated with molecular marker
Relevant answer
Answer
A nice example from narrow-leafed lupins can be found in the recent literature, which shows molecular markers are associated with collection site data and demographics in the Mediterranean region. Mousavi-Derazmahalleh et al TAG 131:887 (2018) attached.
  • asked a question related to Molecular Markers
Question
8 answers
I would like to know what is the best methodological approach to align non coding sequences. In the other hand, I'm using ITS molecular marker (nrDNA in plants), this marker has secondary structure and it has been suggested that it could be used to improve alignment. I don't know which tool could perform an alignment of ITS sequences using information from the secondary structure. Thank you in advance!
Relevant answer
Answer
Thank you Abhijeet and Richard, I was a little bit confused about alignment of noncoding sequences.
  • asked a question related to Molecular Markers
Question
3 answers
My question is that how it can be ensured that methyl jasmonate treatment works well? How we can demonstrate the activation of methyl jasmonate response at morphological, physiological and molecular level in treated plants?
Relevant answer
Answer
There are many JA-responsive gene markers, such as AOS (JA biosynthesis gene) among others, which are activated upon MeJA treatment trough a positive feeback loop. Consequently, you could test the expression of AOS using qRT-PCR and you would expect to see induced transcript level(s).
Depending on the MeJA concentration and treatment duration used, as well as the plant you work on, simple physiological observations such as anthocyanin production (pink-ish colouring of petioles) could be made. At least this is usually the case in Arabidopsis thaliana.
  • asked a question related to Molecular Markers
Question
3 answers
I am investigating the feasibility of validating my IHC-based protein expression analysis in FFPET samples using TaqMan protein assays. I wonder if anyone has any experience with these assays?
I am interested in their accuracy when using protein extracted from FFPET, the ease of creating protein-specific probes with user-supplied antibodies and the difficulty in identifying suitable controls?
Relevant answer
Answer
I was also thinking about it. Sharing experience would be greatly helpful for beginner.
  • asked a question related to Molecular Markers
Question
6 answers
Is there a study on the molecular diversity of Lepidium or other Brassicaceae plants using Start Codon Targetted Polymorphism (SCoT) marker?
Can the SCoT primers used for other plants be used for Lepidium?
Relevant answer
Answer
Hello,
I do not know any paper on Lepidium sp. in which authors used SCoT markers. However, this is a universal method for DNA fingerprinting (applied so far on many plant species) so I am sure that you can use it in your studies.
Best wishes
Piotr
  • asked a question related to Molecular Markers
Question
4 answers
Using data from ITS massive parallel sequencing, is it possible to do an silico functional inference similarly to what is it done to 16S rRNA gene using PICRUSt or Piphillin?
These softwares are used for bacterial functional inference, IS there available any similiar software for fungi molecular markers?
Thank you in adavance!
Relevant answer
Answer
Hi Marta,
FUNGuild is a free, user-friendly tool that can be used to assign fungal OTUs to their ecological guild (ectomycorrhiza, saprobe, pathogen, etc). Although it doesn’t predict the metagenome as the PICRUSt, you can use it to find functional traits based on ITS high-throughput sequencing data.
Hope this helps you.
Diogo
  • asked a question related to Molecular Markers
Question
9 answers
Variety of markers like RAPD, ISSR, SNP, etc. used in plants, among them which one is best to solve the taxonomic problems in plants?
Relevant answer
Answer
Dear Raj,
Please keep in mind that each marker has its own nature, which might not be suitable for all applications, but generally speaking, markers can be either used for inter or intra specific variation assessment. The RAPD and ISSR of markers you have mentioned are mostly used for within (intra) species variation, the RAPD is to be excluded (due to serious technical problems) and I strongly advice against it for solving taxonomical issues. While SNPs markers detected by using fingerprinting techniques (e.g. AFLP) or Sanger sequencing are the most recommended, due to several reasons, one of which is the ability to apply several phylogenentic approches, and estimate several evolutionary and population parameters, which definitly are the key to resolve most of the taxnomical issues.
In a short answer, using DNA sequencing, will save you effort and money, and the outputs for your taxnomical problem is highly probable to be solved than applying the other markers you mentioned.
Several literature can be found, but beware, genetic variation within a population (intra) is one thing while between species (inter) is another thing!
Best wishes!
  • asked a question related to Molecular Markers
Question
2 answers
HeLa is an immortal cell line used in scientific research. It is the oldest and most commonly used human cell line. The line was derived from cervical cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of cancer on October 4, 1951.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome.
Relevant answer
Answer
Because cancer cells are quite divergent in term of chromosomal "patterns" compared to "normal" cell lines, they were not used in the efforts in the 1980's to late 900s to map genetic loci on human chromosomes. Instead people used what are called "somatic cell hybrids": these are cell lines that are hybrids of two cell lines: for human gene mapping the preferred system was to create hybrids of rodent cell lines (mostly mouse and hamster) with human cell lines. This process is well described in:
Best
Amos
  • asked a question related to Molecular Markers
Question
5 answers
I'm currently trying to isolate pET28a via alkaline lysis. This has worked once but only resulted in around 20ng of product (I assume due to the low copy no.) which is not enough for consequent steps. Today both myself and professor repeated this (x4 to try and retrieve more product) with separate solutions but NO bands appeared on the gel - the molecular marker was clear so it doesn't appear to be an issue with running the gel itself.
The colony was incubated in LB treated with Kan (80µl in 80ml). Is this too low an amount of antibiotic? Can the antibiotic degrade and so this is why it hasn't worked with the repeats? Any advice would be appreciated.
Relevant answer
Answer
How long did you incubate your colony and what was the final density ?
Using plasmid isolation kit is a good idea and gives nice amount of product.
  • asked a question related to Molecular Markers
Question
4 answers
When I perform western blot experiments I often get inconsistent results post transfer.
What I mean is that when I look at my PVDF membrane after the transfer step I can often see the molecular marker has transfered to the PVDF membrane, I can see the colours of the dye forming a ladder. The rest of the PVDF membrane is sometimes a perfect and single colour of white. Sometimes it appears to be a uniform white that has patches/blotches of a different colour white and sometimes parts of the gel appear to be a shiny and translucent colour. Sometimes it seems as if I can even see what appears to be the protein bands marked out in this fashion or sometimes the edges of the lanes of the gel. The western blot often works no problem regardess of what I see, and normally after being soaked in the blocking buffer in an hour any of these different patches go away and become uniformly white again. Sometimes my blots do fail however and I wonder if this has any contribution.
I cant find any information on this phenomen. How unusual is this?
I always activate the PVDF membrane in methanol for at least a minute, before soaking it in thransfer buffer for ten minutes (I soak the gel in transfer buffer for the same time) before assembling the transfer sandwich and doing a semi dry transfer.
Just to be clear I am talking about the appearance of the PVDF membrane straight after the transfer step. No antibodies have been applied and the blot has not been developed.
Relevant answer
Answer
I agree that it's a good idea to stain the filter with Ponceau S after transfer. From the patterns of the bands you can have an idea of how the transfer has worked: it should be uniformly for the entire gel; and the quality of the protein samples. You may notice patches of different colors of the filter after transfer, but as long as this does not affect your western blot results, you probably don't need to worry about. It's always advisable to carry out the gel electrophoresis and transfer carefully as @Nurul and Jean-Francois suggested.
  • asked a question related to Molecular Markers
Question
4 answers
This is a question on statistical methods used in DNA research
Lately, many plant species are changing from species, genera, or even families due to studies in molecular makers. For example, teak and gmelina tree species were changed from Verbenaceae to Lamiaceae. The old Bombacopsis quinatum was changed first to Pachira quinata and now to Pochota fendlery. In the case of Orchids, the species of the genera Cattleya, Laelia, Schomburkia, and Sophronitis are suffering continuous changes in the classification of the various species within these genera. How sound are statistical techniques used to ensure these are real differences. What is the sampling method used?
Relevant answer
Answer
Dear Dr. Jerez,
Perhaps you are familiar with the term DNA Barcoding. This method is not an alternative for classical taxonomy but rather a addon to increase the stringency of taxonomic study. With the advent and use of this technology it has been seen that many plant/ animal species although have tremendous physiological similarity, but they represent two far off families genetically. And the exact opposite phenomenon has also been seen. Huge amount of work in this field is going on across the globe, which you can find out online.
  • asked a question related to Molecular Markers
Question
11 answers
There are a number of molecular markers such as RAPD, RFLP etc.. Why are SSR markers gaining popularity and attention as the markers of choice?
Relevant answer
Answer
It also have a large number of alleles per locus. This means that with a relatively small number of markers 7 (at least), a great diversity of studies, populations, reproductive ecology, conservation, germ-plasm banks, etc. It is important to select markers that segregate independently.
  • asked a question related to Molecular Markers
Question
3 answers
Hello,
I am starting a new project with DNA barcoding and I am not sure how to codify sequence DNA. In this project we are using the following molecular markers: rps16-trnk, rpl32-trnl and trnl-trnf (chloroplast).
Relevant answer
Answer
When I asked this question maybe I was not so clear. I was referring to the correct way of dealing with the DNA sequence to identify barcode. For example, how to deal with insertions, deletions, duplicated regions and microsatellites.
  • asked a question related to Molecular Markers
Question
1 answer
Can anyone suggest me about-
We did MALDI- TOF/MS analysis for 15 protein spots in different time intervals and idetified both downregulated and upregulated proteins. Now how do we conclude those proteins were molecular markers for copper metal stress?
Relevant answer
Answer
Both the up/down regulated sets of proteins may serve as molecular markers but requires validation in copper stress models through immunoblots/ degree of expression variation along with the different exposure durations to copper stress.
  • asked a question related to Molecular Markers
Question
4 answers
CURRENTLY AM DOING A RESEARCH FOCUSING ON TEA BREEDING USING MOLECULAR MARKERS FOR SPECIFIC TRAITS, I ALSO DO SAMPLE COLLECTION AND DNA EXTRACTION ON THE SAME
Relevant answer
Answer
Dear Shareef
It is depending on the tools and traits you desire. Good progress has been made in identifying molecular markers for various purposes in tea that range from diversity studies to the search for molecular markers associated with different agronomic traits. For instance, identification RAPD markers that may associate with seven important traits in tea; identification of a RAPD marker for drought tolerance; identification of quantitative trait loci associated with yield; identification of 112 novel tea unigene-derived microsatellites and sequencing of the tea transcriptome that has revealed a number of unigenes for tea and increased the coverage over the tea genome. I hope the attached articles can be useful to you.
  • asked a question related to Molecular Markers
Question
7 answers
Cancer drug hobbled by diagnostic-test confusion
A landmark cancer drug was approved last year to target tumours with specific mutations, no matter where in the body the cancer first took root. Yet physicians are struggling to identify which patients are likely to respond to the treatment, because of limitations in diagnostic tests to pick out molecular markers that indicate susceptible tumours.
Relevant answer
Answer
Decision making regarding therpeutic strategies in cancer patients is complicated. How you can identify the mutations, how much you rely on the results, heterogeneity of tumoral cells, cost benefit of the treatment, insurance coverage, patient cooperation and many other factors.
  • asked a question related to Molecular Markers
Question
5 answers
Please suggest inflammatory markers, in particular.
Relevant answer
Answer
I dont think there should be a specific molecular marker. However, a battery of various molecular moieties may serve as a guiding light. To this effect Bhaskar has given you a fairly good list. I would suggest to evaluate their expression. The big problem, however, is that the test can be carried in blood which may not be the actual representative surrogate of the ocular tissues.
  • asked a question related to Molecular Markers
Question
6 answers
Dear Friends, Please suggest me , how i can calculate resolving power and allele frequency of a molecular marker (RAPD/ISSR). Is there any software to calculate these parameters?
Relevant answer
Answer
Dear Sonu
Resolving power (Rp) which shows the ability of the most informative primers to differentiate between the genotypes was assessed according to Prevost and Wilkinson, (1999) using:
Rp = ∑ Ib
where Ib is the band informativeness with Ib= 1 - [2 x (0.5-p)]
and where p is the proportion of clones containing the band. The resolving power is based on the distribution of detected bands within the sampled genotypes.
  • asked a question related to Molecular Markers
Question
5 answers
Its to write a paper on sex differentiation of a population.
Relevant answer
Answer
It is not a question of the species you work on, different markersystems have advantages and disadvantages, no matter what you are working on. RAPDS have a bad reproduceability and RFLPs are much to expensive.
You should take a sequence specific marker that is inherited codominant, for a system you have in your lab. SSRs (also not the cheapest system, but highly polymorphic), SNP (if you have a detection system for this) or SCAR-marker.
It is more a question of the poymorphism you find between the sex chromosomes, this determines the markersystem you must use to detect it.
  • asked a question related to Molecular Markers
Question
3 answers
Hey, So i have a 39kDa Membrane Protein, cloned into pRSET C and transformed into C43, sequenced to makes sure everything is there and made a glycerol stock of.
From that glycerol stock i start a culture overnight, next day i pellet it, resuspend in fresh LB and inoculate a culture and let it grow to OD 0.6-0.7 where i add 1mM IPTG and let it grow for 4 more hours for induced and without iptg for uninduced. all at 37C. All standard stuff.
I tried lysis in about 500ul of 2 different buffers for 4ml cell cultures:
Buffer A: 25 mM TRIS-Cl, 2 mM EDTA, pH 7.6. 5mg/ml lysozyme
Buffer B: 40mM Na2HPO4, 300mM NaCl, 10mM Imidazole. ph 8. 1mg/ml lysozyme
Incubated at RT for about an hour( checked cells under phase microscope and i did see a bit of lysis but most of the cells were still intact with both buffers even tho the lysis was more with the EDTA but i observed the E coli aggregating into huge clusters in that buffer)
So lysozyme alone isn't working for lysis for me, EDTA or no EDTA
*Worth saying cell suspension turbidity was obervable higher for uninduced samples, i'll bring this up again later.
Sonicated both solution until turbidity was gone.
Centrifuged at 20000g for 20min
Separated into supernatant and pellet
Supernatant stored at 4C till next day, Pellet incubated in 8M Urea in respective buffers overnight.
Next day i run 12% SDS-Page and ive attached a picture. my protein is about 39KDa
Lane M , Molecular markers, Lane 1 supernatant uninduced Buffer B, Lane 2 supernatant induced Buffer B, Lane 3 supernatant uninduced Buffer A, Lane 4 supernatant induced Buffer A, Lane 5 pellet uninduced Buffer B, Lane 6 pellet induced Buffer B, Lane 7 Pellet uninduced Buffer A, Lane 8 pellet induced Buffer A
Could it be the basal expression is toxic? and like i mentioned uninduced cells also grew much more turbid. Could it be plasmid containing cells are dying upon induction?
I will try 1% glucose before induction to see if that will resolve the issue or at least give me a difference between induced and uninduced. Also will run an empty plasmid transformed cell.
Will Also try to Ni purify the pellet , in case the arrow ive indicated might be my protein. but i doubt it.
Is it possible they aren't toxic and just aren't being expressed, or solubilized by 8M Urea?
Western is not an option if you will recommend it.
PS Should i just go for a cell free system such as
PURExpress supplemented with liposomes?
Relevant answer
Answer
You need to sonicate the cells. Being a membrane protein I will guess the protein will be in inclusion bodies. You can find several protocol online.
Good luck
  • asked a question related to Molecular Markers
Question
3 answers
I would like to put my cells in ATP depletion condition (10 mM NaN3, 6 mM 2-Deoxy-D-glucose) for 30 min to see the effect on the mobility of nuclear protein.
What would be good readout of ATP depletion in cell culture? Any molecular marker I get check by qPCR or Western Blotting?
Thank you
Relevant answer
Answer
Dear Seaho, do you have tried CellTiter Glo 2.0?   Does your ATP depletion condition work?
  • asked a question related to Molecular Markers
Question
1 answer
I have quantified astrocytes with GFAP in a series of westerns. I would like to know if the lower level of GFAP I am seeing is because it is non-reactive due to a healthy environment or non-reactive due to inability to signal an inflammatory response and therefore, pathological. I would not like to do a morphological analysis at this point. I was more looking for a molecular marker.
Thanks in advance! 
Relevant answer
Answer
Neoplastic astrocytes in diffuse low grade gliomas frequently express IDH1. 
  • asked a question related to Molecular Markers
Question
4 answers
The date palm is one of the most important fruit tree in Iraq and other parts of the Middle East. detecting seedling  sex early is important. various techniques are used to do so ,one of which is molecular markers,
Relevant answer
Answer
See:Genetic map page in "Date palm Molecular Marker Database" ‫‪http://dpmmd.easyomics.org‬‬
  • asked a question related to Molecular Markers
Question
3 answers
I recently stumbled across MCLab's alternative size standards, which appear to be very similar to ABI's LIZ and ROX 500 size standards.  Has anyone used these for fragment analysis with ABI sequencers (eg 3130 or 3730)?  They seem like the same thing for half the price.  Any obvious drawbacks I'm overlooking?  Thanks!
Relevant answer
Answer
I liked the paper. compliments to you
  • asked a question related to Molecular Markers
Question
4 answers
 I am working on cancer and molecular markers. I tried to find out which was the first marker identified for cancer, who discovered it and where was it published?
Relevant answer
Answer
Hi Sangeet,
The first genetic cancer marker identified was t(9;22)(q34.1;q11.2). Publication date is 1960 by Peter Nowell and David Hungerford.  Science. 132 (3438): 1497. This is the Philadelphia chromosome, diagnostic for chronic myelogenous leukemia.
The first oncogene discovered was src in 1970 but not named src till later.  Martin GS. (1970). Nature, 227, 1021–1023
Hope this is helpful.
  • asked a question related to Molecular Markers
Question
5 answers
I am doing an in situ hybridization and have localised my expression to the developing zebrafish eye. I would like to have some kind of positive control, but am not too familiar with eye development in the first 5 dpf. Is there a gene that is expressed symmetrically during zebrafish eye development?
Thank you!
Relevant answer
Answer
Dear Monica, You can also try  with cadm3, atoh7, cdkn1ca and ccnd1 .
Good luck
  • asked a question related to Molecular Markers
Question
6 answers
How to improve the inheritance of pigeons, selection or crossbreeding? 
whats most important traits we study? Can we use molecular markers in enhancement? What is the suitably markers we use?
Relevant answer
Answer
Dear Dr Esteftah ElKomy,
greetings, many thanks for your question. It is interesting to answer for your question from breeders "plant breeding" point of view.
I think if you have a wide population you can select first individuals "selection"
Then try make wide crosses between them and neglect the self crossing as make inbreeding depression "you will face low yield and growth" 
and try select for economic traits that important for consumers 
DNA markers is the best tools and you need to select the MAS marker assisted selection i.e,. SSRs, SNPs, ESTs
for enhancement the DNA markers I think you could find that in previous work.
with best regards
Khaled
  • asked a question related to Molecular Markers
Question
3 answers
how these molecular markers work ,  what is the procedure for generating  these markers 
Relevant answer
Answer
Hi! 
SPAR (single primer amplification reaction)
DAMD (directed amplification of minisatellite DNA)
Pandian explained already. These techniques/methods used to find the genetic diversity among the species.
The same primer act as Reverse and Forward like how RAPD works. I answered many questions on RAPD in the beginning. Check patiently my answers link your doubts will be cleared or any doubts write/msg. me. 
Check the following links you get good information
Single primer amplification reaction methods reveal exotic and indigenous mulberry varieties are similarly diverse
(