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  • How can i differentiate large size plasmids from genomic DNA ?

    I have a wild type bacteria culture and want to check the presence of plasmids in it. I follwed the normal plasmid isolation proceedure and got a small pellet. in gel electrophoresis a less intensity band also visualized. the problem is its size is similar to the genomic DNA when they run parallay on the same gel. Gel was 0.7% agarose gel in 0.5x TBE buffer. I did restriction digestion with Not1, BamH1, Hind111. but could not resolve visualize clear bands on the gel. 

    Abdolmajid Ghasemian · Tarbiat Modares University

    Do you know the size of plasmids? If yes, you can run on the gel electerophoresis and also use a large sized ladder to detect the size of plasmids. you probably need to prepare low density agarose. also using probe for the specific plasmid gene may be useful. 

  • What are the best conceptual model simulation tools based on your experience?

    Is it an open source tool?

    What modeling language/method/diagrams does it use?

    What type of simulation is that, e.g. symbolic animation, prototyping, ...?

    Research methodologies/publications behind?

    Pau Fonseca i Casas · Polytechnic University of Catalonia

    The conceptualization of a simulation model is a key issue that often are misunderstanding and forgotten in a simulation project. The conceptualization have, among other benefits the capability to represent all the relations, the structure and the behavior of the constitutive elements of the model, allowing a complete and unambiguous understanding of the model prior any implementation. Some of the common formal languages for computer simulation also have the capabilities to understand and analyze some model properties prior any implementation, like the reachability of certain model states. This possibilities to perform a validation over the conceptual model.

    The final implementation of the simulation model depends on several aspects that often are independent of the problem itself (often not always); this implies that it is needed to distinguish between the model and the implementation of the model (that may use a specific simulation tool to accelerate this implementation, but thisis not a must).

    Hence it is important that the formal languages must be independent of the tool that must be used for the implementation. In that sense I can recommend a book recently we publish that summarizes some of the most widely used formal languages to be used on simulation projects. Just to mention that the selection of the appropriate formal language to represent the model depends on the people involved on the project, his background and his personal preferences; mainly the first goal of this is to share among all the modelers the knowledge of how the model behaves.

    In the framework of our research center (http://inlab.fib.upc.edu) we widely use Specification and Description Language (SDL) (great for his graphical capabilities and support tools that understand and helps in the syntactic and semantic validation of the model), Petri Nets (great for the capability of perform some analysis like reachability and coberability trees) or Discrete Event System Specification (DEVS) (great for its capability to synthetize the key elements of the simulation model); please, this is not, in any sense a description of the capabilities of these formal languages, I suggest that if you want a better description reefer tot he book I suggest on the link. Also there are other great formal languages that can be used on the frame of simulation like SysML or others. The key element here is to use a formal language to represent the model and obtain the great benefits of use it.

    Regarding the tools to accelerate the representation of the models, they obviously depends on the language finally selected, but more and more simulation tools allows to use a formal representation of the model to allow an automatic implementation (or execution) of the model.

  • Tomasz Kolerski added an answer in Hydrodynamics:
    Does any body know any thing about SPM and CEM methods and their usage in marine hydrodynamic?

    does any body know any thing about SPM and CEM methods and their usage in marine hydrodynamic?

    Tomasz Kolerski · Gdansk University of Technology

    Do you mean smoothed particle hydrodynamics (SPH)? If so there is number of papers talking about this method applications to hydrodynamics and wave dynamics (i.e. Staroszczyk, Simulation of Solitary Wave Mechanics by a Corrected Smoothed Particle Hydrodymamics Method, Archives of Hydro-Engineering and Environmental Mechanics, Vol. 58 (2011), No. 1–4, pp. 23–45), If you interested in SPH please contact me to my email.

  • Piyush Srivastava added an answer in Yeasts:
    Is there any other way to induce the GAL1 promoter in yeast PJ69-4A without using raffinose?

    I actually inserted my target DNA in pYES2/NT B vector and transformed in yeast PJ69-4A, and want to express my target protein in yeast PJ69-4A. 

    I still haven't received a satisfactory result.

    Piyush Srivastava · Central Drug Research Institute

    Thanx, Curt, for ur an expert suggestion...........

  • How can the phases of TiO2 be seen?

    As in XRD we can get the pattern of different phases but how the different phases of TiO2 can be seen?

    Suresh Doke · Dr. Reddy's Laboratories

    Refer JCPDS database for phase confirmation through by XTD

    JCPDS card no. 21-1272 (anatase TiO2)

    JCPDS card no. 21-1276 (rutile TiO2)

  • Ed Buijsman added an answer in PM2.5:
    Which are the best long term passive sampler methods for outdoor air pollutants (Gaseous & PM)?

    We need to monitor air quality in term of SOX, NOX, PM2.5, PM10 and total VOCs pollutants for 2 years with seasonal resolution.In your opinion what is the best feasible option for passive monitoring seasonal concentration (3 month continuous measurement) of SOX, NOX, PM2.5, PM10 and total VOCs?

    Ed Buijsman · Retired from Netherlands Environmental Assessment Agency

    Gradko in the UK offers a wide range of passive samplers (see: http://www.gradko.com).

  • Mehdi Hedayati added an answer in Malondialdehyde:
    What are the markers other than MDA to measure lipid peroxidation?

    Are there any bio-markers we can check in addition to malondialdehyde in order to measure the extent of lipid peroxidation?

    Mehdi Hedayati · Research Institute for Endocrine Sciences

    Dear Zewdneh,

    For lipid peroxidation you can measure oxidation products such as malondialdehyde (MDA), 4-hydroxynonenal (4-HNE), Oxidized LDL (Ox-LDL), Acrolein, glyoxal and methylglyoxal.



  • J.L. Gómez de la Fuente added an answer in Slurry:
    Why do my electrodes burn during RDE measurements?

    This problem occurs during RDE measurement on a catalyst.  After measurement, it became burned. Then I polished it by abrasive paper to smooth its surface and then 0.5 um Al slurry. But the measurement was not successful, it was again burned? What cause it? Is there any electric conduct problem? Please give me comments.

    J.L. Gómez de la Fuente · IBERCAT, S. L.

    Connections also measurements. Which range potential are you using?

    If has any electric contact wrong, with a multimeter you will observe. 

    I guess your electrode is GC. For polishing, Depends how much destroy it is, I use sand paper, with minor grain (the lowest as I have), Alumina (1um)-Nylon cloth, Alumina (0.05 um)-fabrique cloth, sequentially, and check by CVs.


  • Which branch of mathematics is now active in economics?

    I am interested in mathematics and its applications to economics. I want to know if there is a wide capacity to work on this area. Also, if you can, please guide me for some references.

    Konstantinos Konstantakis · National Technical University of Athens

    I would add, on top of the aforementioned fields, the field of Input-Output analysis and its non-linear applications.

  • Dolores Modic added an answer in Patents:
    How can I know whether a patent is granted at a national or international level?

    I have a research idea, I think this is not have been done by anyone before. How can I confirm it?

    Dolores Modic · Faculty of Information Studies in Novo mesto

    Hi Shubham,

    since I am unsure if you are asking if the patent is a patent that has been granted at your home patent office - and if that could be the case - i would suggest to start your search using your national patent database search engine (they are usually pretty easy to navigate).One other possible simple clue is if the patent starts with letters - they usually inicate the origing of the patent office, where it was granted (though this would in your case probably be more of a "lucky shot")

    Otherwise I concur with other colleague"s advices - and also warn that there is no "international patent" no PCT patent and no (till now) European patent (the latter is coming now). In terms of databases I would suggest to start with WIPO"s Patentscope (http://patentscope.wipo.int/search/en/search.jsf) - which is also one of the options presented to you by Ankush.

    Hope you have a successful search,


  • Henrik Rasmus Andersen added an answer in Diamines:
    Why light red wine type color is observed after treating with adsorbent in chromium solution ?

    what is the main reason of getting  light red wine color type, after treating the chromium (VI) solution with amine (ethylene diamine functionalized iron nanoparticles doped carbon) in batch mode ? Usually with decrease in Cr(VI) concentration, the yellow color disappeared and solution became clear. Although, the solution pH was found 8-9 after adsorption. I also checked the iron and chromium conc after adsorption it was below 0.2 ppm for Fe. Chromium also decreases more than 95% as confirmed from ICPMS, AAS analysis and also from DPC methods.

    Henrik Rasmus Andersen · Technical University of Denmark

    I think it will create this comples, but I don't know if the color intensity is enough to be visible. Since you have the chemcials you could add increasing concentrations of ethylene diamine to a Fe(III) solution to see the color.

  • Cheng Wei asked a question in Gas Flow:
    How to define and extract the side-blown jet penetration depth ?

    in the side-blown flowing process, with the increasing of gas flow, the gas flow regime will be jet flow, the jet flow is shown in figure 1. however,  how to define and extract the side-blown jet penetration depth?

  • Ruslan Kozhemiakin added an answer in MATLAB:
    Why Gaussian image noise obtained using MATLAB's imnoise function is different?

    Dear friends, I have seen many a times in results of research articles that, Gaussian noise present in an image with particular variance are much different from that obtained using MATLAB's imnoise function.

    Ruslan Kozhemiakin · KhAI - Aerospace university

    Because the image is first normalized to the range 0-1 and only then noised with the chosen variance value. Therefore obvious that the variance value should be much less than 1 for an adequate noise present.

  • What is the use of Hessian in computational chemistry?

    Couldn't figure out the use of the Hessian matrix in computational chemistry.

    Naiwrit Karmodak · Indian Institute of Science

    Hessian matrix is the double derivative of the energy functional. The algorithm used for geometry optimization in gaussian is based on Hessian matrix. It is known that for finding roots of a function the first derivative of the function has to be zero at those points and if the double derivative of the function is positive, then the roots corresponds to the points where the function attains its minimum value. Likewise, when the algorithm in gaussian searches for the minimum energy structures along the potential surface, the Hessian matrix provides a good direction since it is the double derivative of the energy functional. 

  • Any recent research examining the relationship of personality disorder to the therapeutic relationship?

    Any research on patient personality disorder as it impacts patient-therapist interactions or the therapeutic alliance since 2010.

    For example: Tufekclioglu, S., Muran, J.C., Safran, J.D., & Winston, A. (2013). Personality disorder and early therapeutic alliance in two time-limited therapies. Psychotherapy Research. 

    Vittorio Lingiardi · Sapienza University of Rome

    Hi Chris, and thanks to Adriano for indicating my paper.

    Happy New Year,


  • Ali Doryab asked a question in Bioreactors:
    What are the on-line monitoring methods in cellular bioreactors?

    Esp. Tissue engineering bioreactors

  • Charles Konan Kouakou added an answer in Striga:
    Does anyone has information concerning a quantification of yield loss due to Striga in recent years?

    Dear colleagues,

    The economic loss attributable to the parasitic weed Striga has been estimated to US $7 billion per annum (M’boob, 1986). Does anyone has information concerning a quantification of yield loss due to Striga in recent years?

    Best regards,

    Charles Konan Kouakou · National Centre for Agricultural Research

    Dear Dr Hassan,

    Many thanks for your answer and for the article that I found very interesting.

    Best regards

  • Can I explore the association between two continuous variables using simple regression?

    Is it fine to explore the association by applying simple linear regression as I could visualize the positive association on regression line using scatter-plot? Also, this analysis would help me to treat one variable as a predictor and another as an outcome variable, it would also help to demonstrate how much variance is explained in the latter by the former. I have rarely encountered this way of analyzing the relationship between two variables, most scholars employ correlation analysis.

    Abhay Tiwari · The ICFAI University, Dehradun

    If you want to see only strength and direction of association ship you can apply correlation anlysis, if yor objective is measure the changes in dependent variable along with relationship, you should apply regression analysis. basically there are four assumptions in regression analysis.

    1.variables should normally distributed

    2.Linear relationship between dependent and Independent variables

    3.variables are measured without error

    4. variance of error is the same across all the leveles of independent variables (HOMOSCEDASTICITY)

  • Dr A. Kumar added an answer in Perovskites:
    Can anyone explain the negative conductivity of the materials?

    I am working on rare earth perovskites. When I measure the electrical conductivity (dc) of my samples at low temperatures (below room temperature) it is linearly increases (upto 1.0 S.cm-1@280K) with respect to temperature. After a particular temperature (Nearly RT), the material shows negative value of conductivity (i.e. -1.3 S.cm-1@RT) again it follows the same trend. Actually I don't know how to interpret this behavior. I have used Broad band Dielectric Spectrometer (BDS) Make:  NOVOCONTROL Technologies GmbH & Co. Model : Concept 80.  The temperature range is from 120 K to 473 K and the frequency range up to 5MHz.  So can anyone explain why I am suddenly getting negative values in conductivity at RT and above?  I am awaiting your valuable suggestions.


    Dr A. Kumar · Harcourt Butler Technological Institute

    Dear Dr. Satyamurthi,

    I suggest you to run some other dummy sample and check whether you get the same type of sign reversal. If not, your set up is o.k. If yes, then you have to worry about the vacuum, electrical contacts and measuring set up as I pointed out in my previous answer. Good luck.

  • Does the concentratrion of hydrogen peroxide affect the TOC (Total Organic carbon) values ? or stabilizers plays any role in the TOC value ?

    Using heterogeneous fenton catalyst, we are degrading the organic content in the water. when we increase the concentration of hydrogen peroxide, we found that there is a rise in TOC values than the initial value. Hydrogen peroxide alone gives around 130 ppm without any prior dilution. (TOC - L shimadzu both NPOC and TOC method) 

    Henrik Rasmus Andersen · Technical University of Denmark

    I see I misunderstood your question slightly. In fact most hydrogen peroxide contain one or more stabilizers of which several of the most common are organic. You can read more in the link.

    I have had problems in my experiments from interference of stabilizers. It is very difficult to get the identity of the exact chemicals added from the suppliers.

  • Ana-Maria Ciobotaru added an answer in Predators:
    Any studies on wolf (Canis lupus) distribution within countries or regions?
    I am studying wolves in Finland. One important issue I need to take into account is the distribution (population density variations) of animals within the country. The idea is to compare other relevant data on a municipality to province scale to where the animals are, rather than just considering the country as a single cell with "n" animals.

    I was wondering if there is some resource or publications on similar distributions in other countries? Could be Canada, US, Italy, Romania, Russia, India, etc. Anything, something I could compare the data to. Other apex predator distributions might be interesting too.

    I acknowledge that the method of identifying the distribution is crucial - making a map using radio collar data from individuals may not be comparable to a map done using sighting abundances.
    Ana-Maria Ciobotaru · University of Bucharest
    1. Eric Marboutin; Marie Pruszek; Clément Calenge; Christophe Duchamp  - On the effects of grid size and shape when mapping the distribution range of a recolonising wolf (Canis lupus) population
    2. Yuji Ishii; Tatsuya Takizawa; Hiroshi Iwasaki; Yukihiro Fujita; Masaru Murakami; Jay C. Groppe; Kazuaki Tanaka  - Nucleotide Polymorphisms in the Canine Noggin Gene and Their Distribution Among Dog (Canis lupus familiaris) Breeds
    3. Włodzimierz Jȩdrzejewski; Magdalena Niedziałkowska; Sabina Nowak; Bogumiła Jȩdrzejewska  ---  Habitat variables associated with wolf (Canis lupus) distribution and abundance in northern Poland
    4. M. Singh; H. N. Kumara  - Distribution, status and conservation of Indian gray wolf (Canis lupus pallipes) in Karnataka, India
    5. Juan Carlos Blanco; Santiago Reig; Luis de la Cuesta - Distribution, status and conservation problems of the wolf Canis lupus in Spain

    I have attached also all the article in this zip archive. Merry Christmas and a Happy New Year. 

  • Antoine Bonnet added an answer in Income Tax:
    Does anybody know of an internationally accepted measure of personal income tax progressivity?

    What I have in mind is a numeric (preferably continuous) measure of personal income tax progressivity that allows to compare countries in a consistent manner.

    Antoine Bonnet · University of Lausanne

    If you have micro-data on pre- and after-tax incomes, you can use a measure inspired by Bénabou (2002), Econometrica (see link below, page 485). Basically the measure of tax progressivity is here the elasticity of after-tax income with respect to pre-tax income (plus one).

  • Ahmad Zaidi Tani added an answer in Ferritins:
    How can I identify a genomic DNA sequence from mRNA (Bread wheat)?

    I request your kind help, regarding the identification of a genomic sequence from a mRNA sequence. I had identified a mRNA sequence for Ferritin in wheat (EU143671).Now I want to identify the genomic DNA sequence (including both exons and introns) for particular mRNA (query sequence) in wheat. How can I identify it? Please help me in this regard.

    Ahmad Zaidi Tani · Universiti Malaysia Sabah (UMS)

    do you have the whole genome the organism? if not what i can suggest is that remapped the gene back to close relative plant genome from there you can try design primer and amplified your wheat and do sequencing from there you can target the expected intron and exon  

  • Ali Doryab asked a question in Bioreactors:
    What are the On-line monitoring methods in Cellular bioreactor?

    Esp. Tissue engineering bioreactor

  • Zinal Patel added an answer in Microstrip Antenna:
    How can I optimize the parameters of a microstrip antenna in ADS?

    I simulated a microstrip antenna in ADS, I want to know how the optimization of the antenna parameters is done in ADS?

    Zinal Patel · Nirma University


    You can find many videos on it on YouTube.


  • D. V. Reddy added an answer in Hydrogeology:
    How many distances from the shoreline the Ghyben-Herzberg equation is valid?


    D. V. Reddy · National Geophysical Research Institute

    It is a very important question,  Pl. see our recent study in coastal sandy aquifer (Hydrological Science Journal 59(12) 2014), though the groundwater levels are going down to 4 to 5 m below mean sea level, still the aquifer is producing the very fresh water. Hence, I feel that the Ghyben-Herzberg equation works only in certain conditions.

  • Ajay Kumar added an answer in Cell Culture:
    Should I centrifuge the cells after thawing them in order to remove the DMSO from the medium?

    All we know, centrifuging the cell is harmful right after thawing the cell. But in the other hand, remaining the DMSO in the medium can hit the cells, too. So shall I remove the DMSO or it's better to avoid the centrifuge?

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    @Vladimir- Dear DMSO is toxic even at a 2-3ul volume/100ul for cancer cell lines and this is evident from MTT assay as I have done that lots of times( a little cell death is there in HepG2 cells) so you can guess that how detrimental can be a 100ul DMSO. and I am also dealing with primary culture of stem cells, so trust me, even stem cells dont encounter any cell death after the specified centrigugation

    @Fatemah- Dear 2000rpm for 2 minutes is sufficient to get a good pellet and you need to minimise the centrifugation time so you can try for 2 minutes. We are working on nearly 20s of cell lines and primary cultures and it always yield a good pellet after centrifugation at recommended settings..Hope it helps.!

  • It is clear that Bitcoin can be used as money."-says US district court. What do you think? Does Bitcoin have legal world wide future?
    Should we be worried?
    Masa Radulovic, MSc · University of Novi Sad

    Dear Adam, 

    thank you, that is why I asked this question. As the time goes by I get more and more exciting answers....

    Best of luck, and happy holidays 


  • Anatoly Belonoshko added an answer in Oxygen:
    What will happen if we simulate gases at low temperature?

    I tried simulation of liquid oxygen at 70 K but after NVE simulation temperature is rising to 80-90 K. which is the boiling point of oxygen. I wanted to simulate liquid oxygen. Is it possible to do by MD simulation.

    Anatoly Belonoshko · KTH Royal Institute of Technology

    When you start an MD simulation, your system, as a rule, is not at equilibrium. Therefore, it takes some time to equilibrate it and, during the equilibration period, the temperature can rise. One needs to scale temperature to the desirable one during the equilibration period or control T in some way. In the case of oxygen there is a possibility that the internal (vibrational) degree of freedom will contribute to the rising of T and it might take quite some time to equilibrate translational and vibrational degrees of freedom. Also, please consider that you are dealing not with oxygen but rather with a model of oxygen. And the model of oxygen can have very much diffferent boiling point as compard to the experimental one. It depends on the quality of the model. The determination of the boiling point is a problem in itself.