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  • Philip Lyons added an answer in MiSeq:
    What is an acceptable sequencing depth for microbiome analysis?

    I am undertaking 16S amplicon microbiome characterization of fish gut using MiSeq. Just wondering if anybody has any similar experience in figuring out a required sequencing depth to achieve this goal. The Illumina protocol recommends over 100,000 reads per sample as acceptable?

    Philip Lyons · University of Stirling

    Thank you very much Thomas for your detailed and helpful answer to my question. I will analyze the V3/V4 region of the 16S gene, and  the amplicon length is 292bp with the current primer set

  • Silvia Matesanz asked a question in Variance:
    What does it mean when heritability is larger than 1?

    I have a half-sibling design with a partly selfing but mainly outcrosser plant. My design includes families within populations and I measured several functional traits. I calculate heritability as 4Vf/PV, where Vf is family variance and PV is phenotypic variance. In some instances, I obtain heritabilities that are larger than 1.

    Is this due to maternal effects or to selfing (or both)? Most importantly, what can be done?

    Thank you.

  • Julie Frouard added an answer in Ficoll:
    Can anyone help me to isolate PBMCs from buffy coat ?


    I am trying to find a solution for my problem during the isolation of PBMCs from buffy coat. I am currently using ficoll gradient to isolate PBMCs.

    My steps are :

    - dilution of buffy coat at 1/2 in PBS (without Ca and Mg)
    - put 13mL of ficoll in falcon and add slowly 17mL of diluted buffy coat
    - centrifugation during 30 minutes at 400g (1500 rmp) with no brake
    - get the ring of leucocytes and proceed 2 washes in PBS (without Mg and Ca) (centrifugation at 200g and 160g)
    - proceed to count cells

    At this step I have a lot of very small components, probably platelets with my PBMCs.

    Then, I isolate monocytes with negative selection (using Monocyte Isolation Kit II). After isolation, I put monocytes in culture but I still have lot of very small components...

    Has anyone ever had this problem? How do you prevent it?

    Thank you.

    Julie Frouard · Université de Rennes 1

    Thank you Dafna, I will try to remove the plasma after my first centrifugation and I will increase wash volume.
    I hope my problem will be solved :)

  • Is an electron larger than Planck length?

    An electron is usually assumed to be either a point particle or a Planck length vibrating string which is virtually a point particle. While these models work well for some mathematical analysis, there are also numerous difficulties. For example, renormalization is often required when the electron’s size becomes part of the calculation. This implies that a rigorous extension of the starting assumptions gives infinity – the wrong answer. Also, if an electron has a radius equal to or less than Planck length, the energy in the electron’s electric field would exceed the electron’s measured energy by a factor of at least 1020 times . The small size also makes it impossible to explain spin as physical angular momentum.

           Collision experiments have been interpreted as implying the radius of an electron must be less than 10-18 m. On the other hand, the very successful Dirac equation implies that an isolated electron has a radius on the order of its reduced Compton wavelength which is about 10-13 m. I have proposed a wave-based model of an electron (see link below) that has a radius in isolation equal to the electron’s reduced Compton wavelength but reduces its wavelength (radius) in energetic collisions. This is one example of an electron model which permits an isolated electron to have a relatively large radius. In your opinion, are electrons and other fundamental particles virtually point particles or do they have size larger than Planck length? Do they have internal structure that will eventually permit their physical properties to be calculated and conceptually understood?

    The electron becomes more point-like as energy scale increases. If you consider the field to be part of it’s structure, then it becomes a localized entity or excitation of Planck-scale structure. For example, the Dirac equation is actually tracking two points in the case of an orbiting electron; the classical position of the electron (uncertainty principle) and a (family of) point(s) along its spin plane. At the reduced Compton wavelength, the magnetic dipole moment becomes twice the Bohr magneton before relativistic corrections. Thus the application of mass in the Dirac equation or QED is related to spin rather than something more fundamental like an invariant scalar field and the origin of mass; e.g. Higgs field.

    Think in terms of the double slit experiment and wave-particle duality. As the energy of a particle increases, its final distribution becomes more concentrated. For a massive particle with v -> c the diffraction pattern would become point-like, although this is not achievable in nature (also note that at v = c, the particle’s field would no longer be spinning).

  • Are there specific cell markers to identify metastatic cancer cells?
    Does a primary tumor contain specific cancer cells that can leave the tumor and cause metastasis? Or are these changes triggered by the tumor microenvironment after the cancer cell has left the tumor?
    Serguei N Skatchkov · Central University of the Caribbean

    The question of Josef Kas was: Is there are Markers of Metastatic Cancer Cells?


    (i) we observed (published now) some strange phenomenon of protein translocation or mislocalization (for example OCT-3 transporter from cancer cell membrane to nucleus membrane/surface) and

    (ii) it seems general phenomenon, because other researchers reported on glial Kir4.1 translocation from membrane to nucleus),

    (iii) we visualized that this phenomenon occurs only in cancer cells starting migration from brain tumor (seems metastatic process), but not in the cells inside the tumor!

    So, if you/we ask what is a marker for metastasis I suggest to include this translocation phenomenon.

    Is it a right way?

  • Nadia Mohd Fadzli added an answer in ChIP Assay:
    Does anybody know a protocol to perform Native Chip using mild conditions of lysis?

    Hello everybody,

    I am trying to immunoprecipitate a protein that localise at DNA Damage foci to perform Mass Spectrometry analysis and identify interactors. I am not sure which procedure to use to solubilize chromatin complexes before to perform the IP.

    One option could be isolate the nuclei and then freeze them directly in liquid nitrogen drop by drop. Then cryogenic lysis with Mill Ball followed by Benzonase digestion. It looks to me a harsh protocol for protein complexes as the proteins are frozen and than thawed before the IP. I was thinking to use 10 % glycerol and 0.1 mM DTT to the lysis buffer that I use to resuspend the nuclei before freezing them. Glycerol to protect the complexes from the freezing and thawing and DTT to prevent the oxidation as the protein grindates are exposed to air during the procedure. Are Glycerol and DTT deleterious for protein interactions?

    It would also great if you could suggest protocols with milder lysis conditions. This brings me to another question. To isolate the nuclei from the cytoplasmic fraction, I would like to avoid the use of Hypotonic buffers (e.g. 10 mM NaCl) to break the cells with a dounce homogenizer with a lose pestle. Indeed I am not sure if the fact that nuclei will be in hypotonic buffer could affect the nuclear homeostasis and thus protein interactions that are occurring during the purification procedure. So, have you ever tried to dounce in isotonic buffer to break cytoplasmic membranes? I was thinking to use 10 mM Hepes, 100 mM K acetate, 1.5 mM MgCl2, protease and phosphatase inhibitor and 0.1 % NP40. Do 5-10 strokes with loose pestle, centrifugation of nuclei, resuspend the nuclei in the same buffer and do 15-20 strokes with tight pestle.

    Thanks in advance,


    Nadia Mohd Fadzli · The University of Sheffield

    Hi, I don't know if this would help but I use the sub-cellular fractionation method by Mendez and Stillman (2000) to extract the chromatin bound protein of my interest. 

  • Dimiter Vakarelov added an answer in Set Theory:
    Are the following two statements equivalent in ZF?

    The following statement is well known in distributive lattices (D, 0, 1, ., +):
    (1) Let F be a filter disjoint from an ideal I. Then there exists a prime filter F’ extending F and disjoint from I.
    Usually the proof of (1) follows by an application of Zorn Lemma. But then the proof yields a stronger version:
    (2) Let F be a filter disjoint from an ideal I. Then there exists a prime filter F’ extending F and disjoint from I and for every x not in F’ there exists y in F’ such that x.y is in I.

    I am interested if (1) and (2) are equivalent (or not ) in ZF. Any references?

    Dimiter Vakarelov · Sofia University "St. Kliment Ohridski", Sofia, Bulgaria, faculty of mathematics and informatics

    Dear Professor Ramiro De la Vega,

    thanks for your short and clear answer. Do you know some references for (2) in order to use it without proof in a paper? Because I want to mention that (2) is equivalent to the axiom of choice, may I mention that I obtained this information from you?

  • Shiv Shanker Gautam added an answer in MIC:
    Are C. albicans considered a positive control during the anti-fungal activity tests?

    During the anti-fungal activity test, Fluconazole didn't show MIC value for C. albicans

    Shiv Shanker Gautam · Gurukula Kangri Vishwavidyalaya

    Dear Suresh,

    As you have mentioned that fluconazole doesn't show any MIC. So, can you give the standard antimycobial dose value for Candida albicans obtained in your results. 

  • Ved Prakash added an answer in Reishi:
    How do I obtain a fine powder from Ganoderma lucidum (Reishi or Lingzhi) 's fruit bodies?

    I am trying to obtain a very fine powder from the dried fungus, putting in an industrial spice grinder, but I get only a very fluffy and corky coarse powder.The literature advises to dry the fresh G. lucidum  in oven for 48 hours at 40 C, which I also did, but in the end I obtained the same results.

    I would appreciate any advice as soon as possible.

    thank you.

    Giusy Montalbano

    Ved Prakash · Madhav Institute of Technology & Science Gwalior

    You can use lyophilizer to obtain fine powder of fruting body.

  • Lawrence Margulies added an answer in Scattering:
    What type of vial or bottle should be used to avoid absorption and scattering for an x-ray experiment with a liquid?

    I need to conduct an experiment using x-rays. The test sample is in the form of a liquid and I need to use a small vial or bottle; but what exactly should the material be to avoid not only absorption but scattering from the vial or bottle?

    In other words, the vial is just facilitating keeping my liquid in front of the x-ray window.

    Lawrence Margulies · University of Guelph

    I would not use quartz. The amorphous scattering will overlap heavily with the liquid scattering. Quartz (and all glasses) give the most scattering at low angles, not high angles. Even Kapton is better than quartz since it is much thinner that any capillary. You will most likely get more scatter from the quartz than from your liquid since the quartz is some much denser. Definitely not quartz!

  • Judy Spross added an answer in Forensic Nursing:
    Can someone offering forensic nursing at post basic level recommend what the programme should include?

    I wish to start a forensic nursing program post basic degree in my institution. I am aware of SANE programs and wish to have an advanced program.

    Judy Spross · University of Southern Maine

    there is a journal of Forensic Nursing and Lynda Benak is a US expert in forensic nursing and has taught courses. She should be able to direct you to a well-defined curriculum You should be able to do a search and find her. Here is an organization that should also be useful:


  • Parth Shah asked a question in GUI:
    How can I generate a 3D model of human foot which can be modified according to patient data to replicate patients foot condition. How can I do it?

    I am trying to develop a 3D model of human foot from acquiring minimal data basically foot length, width, navicular height and foot outline. How can I do that? Which software should I use? Which software should i use to make GUI where the patient data can be inserted? Please help.

  • Madhulika Dixit added an answer in Quantification:
    Which method should be used to quantitate endothelial tube formation?

    In one of the experiments using an endothelial tube formation assay, I can see a very clear difference in that the treated vs control group showed differential tube formation in terms of number, thickness, size etc.

    Now, I would like to have that data in the form of numbers so they can be plotted on a scale.

    Any ideas or methods that help me in quantification of tube numbers, size, thickness etc, or overall tube formation would be helpful.


    Madhulika Dixit · Indian Institute of Technology Madras

    Image J, Matlab or Angioquant.

  • How can I read the file IAEA.phsp ​​in the MCNPX code?
    Despite the IAEA document to recommend the disclosure of IAEA.phsp ​​files and it is not clear how this is done in different codes for existing Monte Carlo, I am especially interested in the MCNPX code.
    Giuseppe Prestopino · University of Rome Tor Vergata

    dear all, I am using FLUKA Monte Carlo code to perform simulations of response of solid state detectors under radiotherapy photon beams. Is there a way to use phsp IAEA files with FLUKA? is there a tool to convert in ascii format such files?

    Thank you a lot,


  • Stephane Panier added an answer in Abaqus:
    What is the expression for torsion vibration of thin plates?

    I want to calculate shear modulus 'G' through the vibration method. Once I get natural frequency corresponding to torsional mode then I'll use it for the expression in order to find G.

    Stephane Panier · Ecole des Mines de Douai

    Hi Prakash

    The first pulsation for a cylindrical cantilever beam is [pi^2*G/(4*L^2*rho)]^(1/2) with L the length and rho the density (kg/m^3)

    Best regards


  • Mahmoud Omid added an answer in Energy Efficiency:
    What are the ways to reduce energy intensity?

    By definition Energy Intensity (EI) is a measure of the energy efficiency of a nation's economy. It is calculated as units of energy per unit of GDP. High EIs indicate a high price or cost of converting energy into GDP. Low EI indicates a lower price or cost of converting energy into GDP.
    Current energy trends of the world are obviously unsustainable, socially, environmentally and economically. EI in Iran’s industry sector is more than 4.6 times greater than world average! (See the attached Chart). Yet, the share of industry sector in Iran is 21%, while the world average is 30%! What scenario would you recommend for her? What infrastructure would be necessary to reduce energy consumption? How your country is dealing with EI?

    Mahmoud Omid · University of Tehran

    Thank you @Lobana for your contribution. To get a decline in waste enery higher efficiency and structural changes in the economy are needed  So this may be achieved by finding more efficient means of energy use and eliminating wasted energy we would be able to reduce EI as well as helping green growth goals

  • Alessio Bosio added an answer in Sputtering:
    Can Al droplets ~20µm diameter appear from a sputtering process?

    We're struggling with regularly getting droplets of Al, typically 5-7µm but sometimes up to 20µm in diameter, on the substrates during sputtering. They're dense, pure Al, and the grain structure and droplet form have led us to the conclusion that the Al have been close to melting.

    It's hard to believe that such large particles can originate from the target and sputter process. Local arcing have been suggested, so we changed the power supply in case the arc supression circuit was damaged. Not much effect it seems. So it's more likely that the droplet originates from dust particles that get to the substrate and get heated by the plasma, although I find it hard to understand how this might happen.

    The tool is an MRC643, horizontal sputter, with clamped targets (insets). The benefit of this is that particles generated should fall down and not hit the substrate.

    Any thoughts on this is appreciated!

    Alessio Bosio · Università degli studi di Parma

    Is it possible to measure the substrate temperature during the deposition?

    Please, consider that the surface of the growing film (the first monolayer) melts at temperature 30% below the melting point typical of the bulk material. This is known as Quasi-Rehotaxy Effect.

    In these conditions, the surface mobility of the depositing Al atoms is similar to that of the liquid Al. The film does not melt completely because it tends to thermalize with the substrate. These effects are more evident when the substrate temperature is too high and/or the the sputtering power density is high enough to heat the substrate by means of an excessive deposition rate.

  • Does anyone know of a recent paleogeographic reconstruction of South America?

    In a recent paper (>5-6 years ago), I remember seeing a paleogeographic reconstruction of South America (it looked something like the attached link, but for South America) during the period it was isolated from other land masses (either the Eocene, Oligocene, or Miocene). However, when I went to try to find the figure again, I could not locate it. All of the paleogeographic maps of South America I have seen either focus on the northwestern corner of the continent or Patagonia. I was wondering if anyone knew of any papers that had presented similar maps of South America during this time period.

    Christopher Robert Scotese · PALEOMAP Project

    I have posted an Atlas of Neogene paleographic maps at my ResearchGate webpage.I will be posting a Paleogene atlas tomorrow (10/31).  They will have the maps you need.

    I would be happy to answer any questions you might have.

    Chris Scotese, Director, PALEOMAP Project

  • Sarwan Kumar Dubey added an answer in Nationalism:
    What may account for students ignoring punctuation marks in their writing nowadays? How can the practice be checked?

    Has someone also noted that students of today ignore punctuation marks in their writing? For the past eight years, I have observed that students, most often ignore punctuation marks in their written works. In a recent assignment, I asked students to answer five question eliciting information about their uncle. Out of the 540 students who participated, 510 (representing 94%) wrote their answers without a full stop at the end of each of the five sentences. The students are of sixteen different nationalities with this common problem. The international dimension of the problem is what is quite worrying. What could be responsible for this kind of behaviour? Lack of or inappropriate use of punctuation marks has always been penalized as part of grammar errors when marking students’ exercises but this has not minimized the problem. How can this problem be tackled?

    Writing; behaviour, evaluating

    Sarwan Kumar Dubey · Central Soil and Water Conservation Research and Training Institute

    I feel that the texting message is also a big cause for poor grammar. Now they are trying to create a new dictionary of words which have meaning of a sentence. Who knows that some day the may form even new rules of grammar for short and quick writing. After all every thing is changing fast in this world. 

  • Guru Moorthy asked a question in Books:
    Need to know information about Hermite cubics. Can anyone knows?

    Regarding my research work, I need to know about hermite cubics in Fem. Can any one suggest a book regarding this? 

  • What would you do if you received a report from the reviewer of your paper asking for a major revision, with which you completely disagree?
    What would be your response? Would you appeal to the editor by asking him/her to make the final decision, would you be weak and amend what you believe is right, would you argue back with facts, would you re-submit the paper to another journal?
    Shanker Lal Shrivastava · IIT Kharagpur

    I would definitely respond pointing out the flaws in comments and explaining relevant portion of my paper. I wont be changing my version of paper in case I feel it is right. If the reviewers don't agree, I would suggest the Editor to use his jurisdiction and his final decision making authority to make a rational unbiased judgement. In fact, I have been doing exactly all this whenever needed.

  • Paul R. Yarnold added an answer in Time Series:
    Is this time series random or nonrandom?

    In binary classification of time series what is the accepted margin for measuring accuracy of classification or prediction that permit us to conclude that time series is not accidental, or vice versa?

    Or. for example, if accuracy of classification or prediction of one event was a very near accident, 50/50 for example, 51% classified true and 49% false (or even 50.1% correct and 49.9 wrong), is it random or not (this time series consists of a succession of random steps or vice versa)? And how many times should we repeat that test?

    Paul R. Yarnold · Optimal Data Analysis LLC

    Random is a pretty specific terminology in some technical areas in physics that study random processes, in computer science applications that study random number generators, etc. If I correctly understand your question, it might be potentially less confusing if you described the finding in your application in terms of the inability of the model to accurately classify (predict) the binary outcome in your sample, without making reference to the distribution of the underlying phenomenon as reflecting a random process or series. For example, perhaps relevant predictors weren't included in the model, and the phenomenon would be classified better than 50/50 had those predictors been included.

  • Why does hydrostatic pressure modulate the effective mass of an electron confined in crystal lattice?

    Dear colleagues,

    We know that the electron under the influence of the potential of a lattice ions responds to an electric field as if it had some effective mass, which is different from its true mass. So, what happen when the crystal is taken under hydrostatic pressure? How  this pressure does fabricate the effective mass of the electron?

    Lawrence Margulies · University of Guelph

    I think the question you need to answer first is how hydrostatic pressure changes the potential.

  • How can I individually dispersed a gold nanoplate on HOPG?

    I want to study Gold nanoplates by STM and I need to individually disperse on conductive substrate similar to HOPG.
    How can I dispersed gold on HOPG?

    Tanya Dahms · University of Regina

    I have not worked with gold nanoplates, but fold nanoparticles tend to cluster if you simply drop them onto a substrate as determined by aFM. However we have had success using a dilute suspension (empirical determination by serial dilution) of gold NPs in nanopure water on mica and glass (see Ma et al., 2005). You also have the option of spin coating. It will depend on their tendency to self assemble versus their tendency to interact with the substrate, in your case HOPG. I hope this helps!

  • How can I compare performance and emissions of 2 different rated DI and IDI diesel engines with same biofuel application?

    DI Diesel engines have different ratings, IDI Engine have different ratings but I have to work on both the engines with same biofuel and I have to compare performance and emissions. How can I compare both the engines with same biofuel?

    Maddali V S Murali Krishna · Chaitanya Bharathi Institute of Technology

    Generally, all performance and emissios curves are drawn taking brake power on X axis and other paramter like BSFC, EGT, VE, PM, NOx on Y-axis. But when we are comparing different engines with different sizes and combustion chambers  with same fuel, BMEP (defined as as specific torque, or torgue per unt volume) is  to be taken on X- axis in stead of BP. (volume is made 1cc in case of BMEP, where BP depends on size of the engine) . However, speed of the engines must be same as it affects the friction power. 

    When the perforamance of two engines fuelled with same fuel is compared, then BSFC is important paramter to evaluate the performance of the engine ratther than BTE.  

    Hence all the performance paramters and exhaust emissions can be evaluated for  engines  wth different combustion chambers with respect to BMEP at same speed.  


  • Hélène Plamondon added an answer in Hippocampus:
    What is the benefit of 0.2 M sucrose solution used on the filter paper during hippocampal dissection ?

    During hippocampus related research, the brain was removed immediately from the skull, and placed on a filter paper containing 0.2 M sucrose solution, over a glass plate filled with crushed ice. 

    What is the benefit of 0.2 M sucrose solution used on the filter paper during hippocampal dissection ?

    Hélène Plamondon · University of Ottawa

    Dissection will be made on your filter paper usually wet with PBS. As mentioned, your preparation should be maintained cool and to do so you can use ice covered with a petri dish cover on which you will place your wet filter paper. We use sucrose for enhancing tissue preservation and quality when performing perfusion after the PFA step we soak the brain in sucrose but we do not use sucrose for fresh tissue dissection.

  • Robert D Kirkcaldy added an answer in Geriatrics:
    Does anyone know about the natural history of Trichomonas infections in older adults?
    Does it always have to be an STD? I would like to assess the social and medical impact of diagnosing STDs on family members of patients with dementia. Looking for specific evidence in the area.
    Robert D Kirkcaldy · Centers for Disease Control and Prevention

    The other thing to consider is that diagnosis of T vaginalis may not represent incident infection.  Particularly if asymptomatic, the infection may have been present for quite some time. 

  • Does anyone has experience with the Lenti-Tet-One System linked below?

    It is a quite expensive tool and I just wanted to know if someone has experience with that or maybe could suggest a similiar one.