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  • Noémie Jelly added an answer in DNA Elution :
    Can I use Agencourt Ampure XP for genomic DNA purification?

    I have genomic DNA eluted in TE buffer, and am planning to sequence them. Unfortunately, EDTA should be avoided for Nextera library preparation.

    I am thus planning to purify my gDNA again, using Agencourt Ampure XP, in order not to lose too much material and elute it in water or 10 mM Tris (without EDTA of course).

    In the protocol, it is said I should use 1,8 volume of beads for PCR purification. But what about total gDNA? Can't I use less? If I understood well, lower volumes of beads allow larger size selection?

    Noémie Jelly · University of Strasbourg

    Thank you for your answers. I agree with you Richard, it would have been better to simply dilute our samples (only 2.5 ng/µL is needed), but the problem is that the concentrations of our gDNAs are so low that it's not possible, we actually also need to concentrate them! That was our idea behind: getting rid of EDTA because we can not simply dilute them (concentrations ranging frome 3 to 15 ng/µL).

  • Mourad Attouchi added an answer in Shimadzu:
    Why the Moisture values differs from GC/MS and proximate analysis results?

    Experiments on Co pyrolysis of low rank coal and rice husk in Py-GC/MS. The GC/MS i was using is PY-2020iD, Frontier Lab, Japan GC/MS, Shimadzu GC-2010 and QP2010. My m/z range is 10-400. This is what the values i'm getting 50% GC/Ms, 6% Proximate analysis. Why this happen?

    Mourad Attouchi · National Institute of Marine Sciences and Technologies

    I agree with Mr. Fegade, at 500°C several reactions must deliver H2O

  • David Riedl added an answer in Psychotherapy:
    What is the cut-off Score for the German Childhood Trauma Questionnaire?

    Hello,

    does anyone know whether specific cut-off scores for the German CTQ have been defined? As far as I am informed in Bernstein & Fink (1998) cutoff scores for "none to low", "low to moderate", "moderate to severe", and "severe to extreme" exposure are provided for each scale of the Englisch version (Van de Eede et al. 2012).

    I have already checked these publications, but no cutoff scores were included for the German CTQ

    Klinitzke, G., Romppel, M., Häuser, W., Brähler, E., & Glaesmer, H. (2012). Die deutsche Version des Childhood Trauma Questionnaire (CTQ) - psychometrische Eigenschaften in einer bevölkerungsrepräsentativen Stichprobe. Psychotherapie, Psychosomatik, Medizinische Psychologie, 62(2), 47-51. doi:10.1055/s-0031-1295495

    Wingenfeld, K., Spitzer, C., Mensebach, C., Grabe, H. J., Hill, A., Gast, U., & ... Driessen, M. (2010). Die deutsche Version des Childhood Trauma Questionnaire (CTQ): Erste Befunde zu den psychometrischen Kennwerten. Psychotherapie, Psychosomatik, Medizinische Psychologie, 60(11), 442-450. doi:10.1055/s-0030-1247564

    Bader K, Hänny C, Schäfer V, Neuckel A, Kuhl C. Childhood Trauma Questionnaire - Psychometrische Eigenschaften einer deutschsprachigen Version. Zeitschrift Für Klinische Psychologie Und Psychotherapie [serial online]. 2009;38(4):223-230. Available from: PSYNDEX: Literature and Audiovisual Media with PSYNDEX Tests, Ipswich, MA. Accessed March 25, 2015.

    Thank you very much for your help!

    Bernstein D, Fink L. Childhood Trauma Questionnaire: A Retrospective Self-
    Report Questionnaire and Manual. San Antonio, TX: Psychological Corp; 1998.

    Van Den Eede, F., Haccuria, T., De Venter, M., & Moorkens, G. (2012). Childhood sexual abuse and chronic fatigue syndrome. The British Journal Of Psychiatry, 200(2), 164-165. doi:10.1192/bjp.200.2.164a

    David Riedl · Medical University of Innsbruck

    Thank you both!

  • Giovanni Colonna added an answer in Receptor:
    Why are ligand molecules coming out of protein ones we define solvation ?

    I was performing MD simulation for receptor ligand complex and once define simulation box and solvating ligand receptor complex ligand is coming out.

    What could be the possible reasons?

    Giovanni Colonna · Second University of Naples, Naples, Italy

    If the system under MD, once at equilibrium, is not stable may also mean that the modeling of some part was not adequate. Of course, I assume that the MD was performed in water, at neutral pH and 20 - 37 °C. is that so?

  • What should I test for in a biometric fingerprint encryption algorithm?

    Other than testing for efficiency, reliability and speeds in a biometric encryption algorithm. What else should I test for?

    Ramón Santana Fernández · University of Information Sciences

    sou should test also cryptographic security and revocability

  • Gaetano Zuccaro added an answer in Biodiesel:
    How can I detect lipids producing by fungi?

    I would like to produce biodiesel from fungi, therefore I would like to detect lipids producing from fungi, what is a suitable technique for detecting lipids?

    Gaetano Zuccaro · University of Naples Federico II

    We use Bligh and Dyer, Smedes or Folch method, but we can trying to use organic green solvents. You can read this article:
    Pulsed Electric Field (PEF) as an Intensification Pretreatment for Greener Solvent Lipid Extraction From Microalgae (Zbinden et al., 2013).

  • Dr Murugesan Muthu added an answer in Juice:
    How to measure protein in fruit juice?

    measurement with folin reagent

    Dr Murugesan Muthu · Imperial College London

    REFER

     Measurement of Protein Content in Fruit Juices, Wine and Plant Extracts in the Presence of Endogenous Organic Compounds, Lebensm.-Wiss. u.-Technol., 30, 778–785 (1997) http://www.sciencedirect.com/science/article/pii/S002364389790267X#

    http://www.gbiosciences.com/PDF/Protocol/402L_Lowry_Protein_Assay_TEACHER.pdf

  • Muddsair Sharif added an answer in Free Software:
    Pricipal component analysis, free software?

    I am looking for a Statistical Software "free" that is able to perform Principal component analysis, Discriminant analysis, and cluster analysis. This program should be easy to use and with a clear graphic results visualization. R is too complex for me!

    thanks a lot

    Sara

    Muddsair Sharif · Daimler

    HI,

          i am also agreed with above all and i am also fan of R. i have been involve in it since 3 years and found very good but you will have also option for Rapid-miner and Weka. you can also used them if you are interested!

    Regards

    Muddsair

  • Gábor Hollandi asked a question in Brain Slice:
    What may couse the facilitation in the fEPSP amplitude in a Haas type interface chamber?

    I’m working with a new Haas type interface chamber, called BSC-HT Brain Slice Chamber System Haas Top (Harvard Apparatus). The problem I encountered is as follows: after calibrating the perfusion, the slice doesn’t look dry, yet the fEPSP amplitudes facilitate during the recording (increases by about 400 uV in an hour).

    The ACSF is saturated with carbogen and is at room temperature, carbogen is also directly flown into the chamber to produce carbogen-steam. I tried different perfusion speeds (1-4 ml/min), but it didn’t make significant difference. I previously worked with a similar Haas type chamber, and managed to overcome similar difficulties.

    I wonder what may couse the facilitation in the fEPSP amplitude - any suggestion is welcome.

    Thanks in advance.

  • Andrés Méndez-Lucas added an answer in PPAR alpha:
    Anyone knows circadian change of PPAR-alpha in liver?

    Does anyone know the profile of circadian change of PPAR-alpha in mRNA and protein level? Thank you!

    Andrés Méndez-Lucas · MRC National Institute for Medical Research

    http://www.jbc.org/content/271/3/1764.long

    Fig 4, C and D.

    I hope that helps.

  • Tapan Barman asked a question in Photovoltaics:
    How the open circuit voltage of a photovaltaic device changes with intensity of incident light?

    In what factors the open circuit voltage of photovoltaic depends? How the open circuit voltage of a photovaltaic device changes with intensity of incident light?

  • Gonzalo Sanchez added an answer in Normality Test:
    Can I use a two way ANOVA for repeated measurements with discrete data?


    I am making a behavioral research about social interaction in rats, I count contacts over time. It often happens that there is no contact between the rats , so the range of the data goes from 0 to 20 approx. I made a normality test and one of the treatments that decrease social interaction does not fit normality, I guess because the increase in the number of zeros . The problem is that there is no non parametric test equivalent to 2 way ANOVA with repeated measurements.

    Actually, they just ejected my paper for this reason.

    Gonzalo Sanchez · Linköping University

    Hi Pablo!

    My advice: go ahead and use it, then if everything goes well just play the "marcha peronista" and everybody will be happy.

    Best regards,

    Gonzalo

  • Ni Ge added an answer in Special Relativity:
    Special relativity: a big Heisenberg's uncertainty principle?

    If you know the coordinates for one referential, you can only know the speed of the other. If this is true, are the Lorentz transformations incomplete? Or do they resolve the Heisenberg's uncertainty principle?

    https://www.researchgate.net/publication/274138940_Relativity

    Dear Andrew,

    When I read Joel article, it seems that relativistic quantum mechanics solve the observables problems by the concept of "localization" (not included in Galilean).

  • Does anyone have suggestions for developing a course ecological recovery potential screening tool, to address multiple ecosystems across a landscape?

    The location is a corridor from the Florida panhandle, westward to east Texas. Longleaf pine is a significant component of this landscape but riparian, wetland, seepage bogs, and other fragmented ecosystems need to be addressed simultaneously within this landscape. Developing a course tool to prioritize connectivity and where ecological restoration should/can occur is needed. 

    Joanna B. Whittier · University of Missouri

    You might consider these tools: Marxan (http://www.uq.edu.au/marxan/) Corridor Designer Evaluation Tools (http://www.jennessent.com/arcgis/corridor.htm), and Land Facet Corridor Analysis (http://www.jennessent.com/arcgis/land_facets.htm) to help address your questions.

  • Yao Zhou asked a question in Polymer Nanocomposites:
    Could anyone give me some suggestions on surface modification of nanoparticles using silane coupling agent?

    I would like to prepare polymer nanocomposites for dielectric applications. In order to ensure good dispersion of the nanoparticles, surface treatment of the nanoparticle with silane coupling agent is needed, but I do not how to do it in details. Could anyone give me some suggestions in detail? 

  • Mark Farman added an answer in Primer Sequences:
    How do I sequence PCR products?

    Greeting Guys,

    I am in need of sequencing my PCR products. My supervisor asked me that please take care that the forward and reverse primer sequence should match with the output sequence result. But, as far as I know the capillary sequencer will read the product from the 30 - 40 base pairs away. If this so, then I couldn't match the forward and reverse primer to that of the output sequence.

    Could sumone suggest me a lab or third party research labs who carrying out the outsourcing samples

    Thanks in advance

    Mark Farman · University of Kentucky

    If the PCR product is short (<800 bp), you should get the reverse complement of the "opposite" primer's sequence at the end of each read.  If, it's too long, then use Heba's suggestion.

  • Brennan Murphy added an answer in Organic Synthesis:
    How to make synthesis for Aminorhodanine ?

    Aminorhodanine

    I have reference inform about the method of synthesis but it is so sad that the paper now is offline so I cant get the paper please Scientists here who are expert in Organic Synthesis Please Suggest design to method of synthesis with the available reagents and solvents mentioned in the attached image of reaction.and please every one here tell about the amounts of reagents suggested and if one have experience with the same conditions for another reactions tell about ur experience.

    thanks in advance

    Brennan Murphy · Brock University

    If I were you, I'd use the following orgsyn procedure, but substitute ammonia with hydrazine.

    http://orgsyn.org/Content/pdfs/procedures/CV3P0763.pdf

    Though this may not work, as you may have a competing ring closure to the 6 membered heterocycle.

  • Humberto O Cisale added an answer in Semen:
    What can we estimate from sperm pellet?

    After separating seminal plasma from bovine semen, which type of parameters/biochemical tests can be performed from sediment/spermatozoal pellet?

    Humberto O Cisale · University of Buenos Aires

    It depends on wath equipement you have access. You can write me and I´ll send you some tips in order of the equipment you have.

  • Wendy Burpee added an answer in Urbanization:
    What drives diet changes in urbanization?

    Hello colleagues

    Are there any studies on what drives diet changes in the case of urbanization? Meat and wheat (bread) are up in Dakar and Dar Es Salaam compared with rural areas, but what is the driver? Higher average income? Is the fact that bread is just bought from a shop (most of the time) and does not require any preparation (such as cooking) a factor? What is the situation outside of Africa, e.g. Thailand, India? Is there any reason to suspect that increasing urbanization rates in China (65% projected for China) will be accompanied by an increase of bread consumption?

    Also about recent changes in India:

    http://in.reuters.com/article/2015/03/30/india-beef-slaughter-idINKBN0MQ0LG20150330

  • Michael Reinartz added an answer in GraphPad Prism:
    How can I determine if apparent biased agonism is significant?

    I have a number of agonists for which i have dose-reponse data in 2 or more systems. I'm using Graphpad prism to calculate bias, in this case using the equiactive approach as discussed in Rajagopal (2011). Calculating the "bias factor" from EC50s and Emax is simple enough, but I can't figure out how to get error estimates & determine significance. I have SEM for Emax and pEC50 for each ligand in each pathway but not sure how to sum these to give a total error for the calculated bias factor. Anyone have an easy step by step guide to or know where to find a suitable prism template? 

    Thanks

    Michael Reinartz · Hannover Medical School

    Maybe the Appendix of Westhuizen et al 2014 will help you to tackle this question (it did in my case of bias analysis).

    You could add weighted error propagation (simply by an coefficient), if you performed (very) different n-counts / replica per system.


  • How can I prepare E. coli control for TEM analysis?

    I'm trying to analyse E. coli with TEM, attached file is what I've done, the control sample without any treatment. It shows empty part in the cells.

    I've tried 1.changing fixatives' concentration (glutraldahyde and OsO4), 2. varying E. coli incubation time, and 3. different protocols, but still can't get the satisfying result. 

    Which step would be critical for this experiment?

    Ask some advice from any experts.

    Wolfgang H. Muss · Paracelsus Medical University Salzburg

    Your image [ultrathin section, ?nm thickness?, staining?] shows bacteria (E.coli) with an artificial morphology after "classical" fixation and perhaps processing (the latter we have no information so far, therefore one only can guess...about the causes of artifacts)  as this is displayed mostly in bacterial specs. processed without some special treatment*).

    Special treatment could be: PLT-embedding (progressive lowering temperature embedding in lowicryls HM20 or K4M), Use of microwave fixation and embedding, additives to your primary fixative, Processing by initial HPF-technol, and others. IMHO there are two major parameters influencing "ultrastructural preservation" after >>>chemical fixation:

    i) elution of bacterial core components (e.g. also due to damage of bacterial wall) by fixative and/or processing chemicals

    ii) non-preservation of bacterial core components due to bacterial wall permeation hindrance to fixative(s) and processing chemicals.

    Also one should not forget the temperature maintained during all processing.

    There are a lot of methods/articles on bacteria ultrastructure preservation out in the wild waiting to be found by eager young researchers... 

    (to  name only some of some hundred articles  cf: e.g. 

    http://onlinelibrary.wiley.com/doi/10.1042/BC20070106/full, http://jb.asm.org/content/174/20/6508.full.pdf;  or also  www.researchgate.net/.../09e4150ab035d7de05000000.pdf,  && )

  • N.F Mthembu added an answer in Vegetation:
    Does anyone know what AFRI vegitation index does and what does it stand for?

    I want to know what AFRI vegetation index is. I am working with different indices and AFRI is one of them.

    N.F Mthembu · University of KwaZulu-Natal

    Thank you Heath for your answer.

  • Dominique Liger added an answer in Elution:
    How to purify protein with 27 KDa from GST ?

    Dear colleagues, i am trying to purify a protein with 26 kDa size that is expressed as a GST fusion protein. When i have done  on column GST cleavage in the flow through both GST and my protein of interest coming together. Even i tried Superdex 200 SEC there also proteins are co-eluting. My protein pI is 4.54 and GST pI is 6.09 so i did ion exchange (mono q) with buffer pH 6.5 i eluted by gradient elution with 1M NaCl but here also both the protein coming together. Please suggest some idea to purify the protein. I need this protein for crystallization and structural studies.

    the image i have given is MONOQ profile in 18% SDS gel 

    Dominique Liger · Université Paris-Sud 11

    Hi there,

    Pass your eluate containing the mix of proteins onto Glutathion-agarose column again to trap the free GST. Hopefully your protein of interest will be in the flow through.

  • Emeline Maufroy added an answer in Imagination:
    What is the practical procedure for a mapping of the frequency-scaled curvature?

    Lets imagine we have a DEM. How I map curvature for a changing curvature baseline length (h in questioned paper)?

    I guess, that the best description is the list of the steps, like:

    Step 1. Mapping of curvature from DEM with pixel size 20 m

    Step2. ?????

    How should I map frequency-scaled curvature for h=60 m, 100 m, 320 m, etc.? 

    Emeline Maufroy · University Joseph Fourier - Grenoble 1

    Dear Almaz,
    I'm not sure that you can simply take the average of the curvature values in the baseline length. I never tried that, so I don't know if it is equivalent or not.
    The procedure that we describe in our paper is totally equivalent to the ArcGis procedure, so I advice you to closely follow it as this procedure is commonly used by people in geomorphology and hydrology.
    Best regards,
    Emeline Maufroy

  • Samir Qasim added an answer in Sport:
    Motivations in Martial and Non-Martial Sports?

    I would like to measure behavioral regulations (motivation) in Martial sports, by comparison with Non-Martial Sports.
    I am curious to receive either published or unpublished research in this area.
    Any help would be appreciated.

    Samir Qasim · The University of Edinburgh

    Dear Behzad,

    Below are two studies that reported motivation for practicing martial arts.

    Jones, G. W., Mackay, K. S., & Peters, D. M. (2006). Participation motivation in martial artists in the west midlands region of England. Journal of Sports Science and Medicine, Combat Sports Special Issue, 28-34.

    Zaggelidis, G., Martinidis, K., & Zaggelidis, S. (2004). Comparative study of factors-motivates in beginning practicing judo and karate. Physical Training: Fitness for Combatives, May, 1-8.

    Hope this helps

    Samir

  • Alvaro D Garcia added an answer in Forage:
    What feeds should be added to a ration based around sprouted barley fodder?

    When working with a dairy cow that is either approaching or at peak lactation, what other feeds should be incorporated into a total mixed ration to meet her energy needs? Also, what could be limiting her highest production level?

    Alvaro D Garcia · South Dakota State University

    Dana,

    it is just one more feed to be included in the diet. One needs to look at it's composition and that of the rest of the feeds and balance the ration accordingly.  I've used it in the past in dairy cow diets and animal performance was good.

    Regards,

    Alvaro

  • Taqee Syed asked a question in Egg Shell:
    FTIR analysis for rubber samples?

    I have a couple of Rubber samples which are basically natural rubber derivatives with and without bio-fillers. The bio-fillers used are Palm fibre, egg shells and an amalgamation of the two. I want to know if it is quite possible to conduct an FTIR analysis for a rubber sample? I am pretty sure it is possible. What i am confused about is the method of sample preparation. I have tried immersing the rubber sample in liquid nitrogen to freeze it so i could grind it into a powder for the analysis. 

  • Are these Taeniidae eggs found in feces from Neotropical Otter (Lontra longicaudis)?

    These eggs were found in feces from Neotropical Otter (Lontra longicaudis)

    Narayanaperumal Jeyathilakan · Veterinary College and Research Institute (TANUVAS), Orathanadu, Thanjavur, Tamil Nadu, India

    I agree with Hudson. Taenid eggs must have hexacanth embryo. Hence it seems an artifact.

  • Martina Gaisch added an answer in Grounded Theory:
    What is the best way to operationalize grounded theory?

    Since many conceptual thoughts are embedded in memos ( which -according to Charmaz- remain private and unshared), I wonder how to best operationalize the steps taken before the Integration of the abstract analyses in the grounded theory?

    Martina Gaisch · Fachhochschule Oberösterreich

    Does anybody know of any GT research (preferably a PhD thesis) where memos were incorporated and represented an integral part of the conceptual trail?

  • Why would cooling a polycrystalline material down cause differences in peak intensity in powder XRD?

    I have run a sample at various temperatures with out removing / rotating the sample or changing the diffractometer, it was locked in the machine the whole time. There are definitely  diffrences in peak intensity that are monotonic with temperature and reversible...I'm not sure how to explain it.

    Any ideas?

    Marijan Marciuš · Ruder Boskovic Institute

    As Dominique has explained in great detail the temperature effects on crystal structure, there is also another possibility. Without any more details about your experimental setup, regarding the cooling of the sample, one possible effect might be condensation of moisture and other atmospheric fluids on the surface of your sample (if unprotected) during the cooling phase, that might interfere with intensity of your diffraction peaks.