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  • Michael Snyderman added an answer in DNA:
    How to detect retrovirus by NGS (murine leukemia viruses)?

    I can obtain RNA NGS on peripheral blood mononuclear cells from the SUNY @ Buffalo center but can't analyze the data. What I want to do is detect the presence of murine leukemia retroviral sequences. The retroviruses integrate copies of their DNA into the nuclear DNA of monocytes and T-lymphocytes and this "proviral DNA" codes for DNA primed RNA synthesis.  The viruses have known sequences that could be aligned against the NGS sequences.  I have no background in informatics and am at a loss as how to go forward with this. 

    Michael Snyderman · University at Buffalo, The State University of New York

    I have two questions. First, Pathseq and SURPI: appear to subtract the human genome from the NGS to allow identification of none-self sequences. As HERV-H and HERV-W have MLV-like sequences, won't that make it impossible to identify and exogenous MLV? Second,  Kraken appears to require an exact fit which is a problem with retrovirus because of poor fidelity of replication and therefore some sequence variation.

    Are these questions a real concern?

    Michael Snyderman

  • Anna Git added an answer in Touchdown PCR:
    What annealing T range to set in Touchdown PCR?


    I'm trying to amplify a DNA fragment using primers with Tm: 79.3℃ and 63.4℃. I have tried T gradients between 54-68℃. There's always a loylt of unspecific bands. Ithink that a touchdown PCR could work fine. What do you think?

    Could this program be fine?:

    95℃  5'

    10 times:

    94℃  1'

    72℃  1'


    72℃  1'

    29 times:

    94℃  1'

    58℃  1'

    Anna Git · University of Cambridge

    The primer Tm is very high indeed.

    If the high Tm comes from adding terminal sequences to gene-specific primers, try two rounds of PCR. In the first one, use only the gene-specific primers with no added sequences (Tm ~50-60oC) for ~16 cycles. Then use a 1/100 of this PCR product as a template for a second PCR which adds the tags/restriction sites/etc.

    If that fails, I can warmly recommend trying to play with Mg (go lower if possible), DMSO (add to decrease non specific priming) and betaine (magical ingredient, honestly.) rather than annealing temperature alone.

    Other suggestions: you do not mention the length of the amplicon or your template, but if it is short-ish, try to find restriction enzymes that do not cut it, and pre-digest the template DNA to reduce the probability of off-target amplification?

    Good luck!

  • Ahmed Mubarak asked a question in Channel Estimation:
    What is the first point for channel estimation studying (recommended steps)?

    What is the first point for channel estimation studying (recommended steps)?

  • Yurij Tynkevich added an answer in Cloning:
    Can anyone please help to find out how we can calculate the cloning efficiency (CE) of Petri dishes instead of plates for HPRT Mutation assay?

    Please Note: To calculate the cloning efficiency (CE) of plates I follow the formula below:

    CE= (In number of negative wells/total wells scored)/ number of cells plated per well)

    Calculate of Mutation Frequency (MF)

    MF= CE+6-TG/CE-6-TG


    Yurij Tynkevich · Chernivtsi National University

    May be: "CE= N of colony per plate / N of cells per plate x 100%" ?

  • Sarwan Kumar Dubey added an answer in Academic:
    Could you please name necessary steps for developing a more innovative organization?

    Academic knowledge and managerial experience is first built on what others have said, done or written. What are the capabilities organizations must develop
    if they want to grow and compete in innovation-intensive environments. 

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

    Dear All, I feel not only in innovation intensive environment but in all possible environment knowledge is prime key than management. Regards

  • Hamza Kheddar added an answer in ns-3:
    Are you interested to attend the workshop on ns-3?

    Kindly fill up the survey form that is available on given link. Workshop will be conducted by famous experts. Venue is Gujarat, India. More information is given into the form.

    Hamza Kheddar · University of Science and Technology Houari Boumediene

    i'm from algeria, how can i atted? it must be sponsored by the university i'm belonging to?

  • Mehraj Ahmad Bhat asked a question in Kurtosis:
    What should be the expected value of Skewness and Kurtosis to check normality of the data?

    To check the normality of the data what should be the expected value of Skewness and Kurtosis. Please send any references for supporting the answer. 

  • Kris Joseph Mahoney added an answer in Water Stress:
    If there is any relationship between disease incidence and stress and early post emergent herbicide?

    I am working with ragi (Eleusine coracana) and its associated weed species with three herbicides. among that Nomine gold (early post emergent herbicide) treated plots at 15 days after transplanting showing severe blast symptoms, susceptible to water stress. So if any body have related field please provide me the reason.

    Kris Joseph Mahoney · University of Guelph

    Could you provide the active ingredient for the herbicide?

  • Gordon Ade-ojo added an answer in Workplace:
    Is anyone aware of an instrument that measures perceptions of workplace monitoring?

    I am looking for an instrument that captures individual perceptions of being monitored in the workplace. One that captures personality differences would be particularly useful.  Thank you.

    Gordon Ade-ojo · University of Greenwich



  • BK Punia asked a question in Esteem:
    Knowledge and Wisdom ?

    There have been debates overtime on knowledge and wisdom. Some people are of the view that knowledge comes first and then it transformed into wisdom. Whereas some other believe that wise people i.e. people with wisdom breeds knowledge. I would like to have the scholarly opinion of my esteemed RG fraternity. 

  • Sanit Sichukhiet asked a question in Books:
    How to deal with the price variables in Rating-Based Conjoint ?

    Dear all kindly professors and specialists 

        I'm doing my dissertation by using conjoint technique. Now I have a problem to design levels of price variable. The point is that I have decided to use 4 price levels in my study. However, my friend from economics field has claimed that price should be more varying than 4 levels because price is seen as a continuous variable rather than categorical one. The problem is expected that when I apply more price levels, my orthogonal profiles will increase to burden respondent's task. ........ Later, I found from the book "Applied Conjoint Analysis by Vithala R. Rao" that continuous variable can be randomly assigned but the deep details are not provided in the book. This following explanation is what I understand.......For example,

    I have 4 attributes including price variable. Firstly, I create the orthogonal profiles from the first 3 attributes (supposed that there were 16 profiles). For 10 respondents, we need to manage 160 profiles in an arrangement. Then, I have determined, for example, 6 levels of price (e.g., the price of this store is 0% more than average price at other stores, 2%, 4%, 6%, 8%, 10%). Then, we have to assign those 6 price levels randomly to "all 160 profiles."

    I have no idea if my understanding is right. Any suggestions or helps .... kindly please ^_^ 

    Thank you very much    

  • Liubov Lebedintseva asked a question in Professions:
    Who is inerested in sociology of occupation and professions?

    Studying profession in sociological field

  • What is the physical meaning of fractional differential equations??

    for example in dynamics firs derivative is rate or velocity: dx/dt

    or the second derivative is acceleration: d2x/dt2

    but in some cases we see fractional differential equations such as( d^0.8x/dt^0.8). I mean the order is fractional and 0.8 can be another fractional number. in mathematics there is no problem with this but what is the physical meaning? this equations are frequently used in anomalous diffusion.

    Paul Louangrath · Bangkok University

    The attached article is a thesis. It explains quite well, beginning on page 51---application of fractional differential equation in 4 cases. Cheers.

  • Is there anyone here doing research focused on the use of ontological model to represent academic curriculum?

    The challenge is to use an ontological model of academic curriculum as a reference to a process of teaching and learning focused on the adaptive learning.

    Michael Brückner · Naresuan University

    In March, we are going to publish a paper using an ontology for curriculum comparison ("A Semantic Similarity Assessment Tool for Computer Science Subjects Using Extended Wu & Palmer’s Algorithm and Ontology"). If you're interested, contact me via private mail from RG.

  • Avijit Pramanik added an answer in Antibiotics:
    How to design narrow spectrum antibiotics to improve therapy?

    We need better antibiotics! we need better therapy to eliminate those pathogens rather than commensal bacteria.


    Avijit Pramanik · DAV University

    rather than thinking of killing a broad group of bacteria all together, we can just target virulence factors and develop molecules that can interrupt action of specific virulence factor used by the target pathogenic bacteria. that'll likely slow down the spread and multiplication of the target pathogenic bacteria inside the human host. immune system can take care of the elimination of those target pathogens from the host body.

  • Can anyone recommend some helpful books, manuals and/or guides covering microbiology, bacteriology and methods?

    Something I can keep for a quick reference to pull off the shelf while I'm learning labortory techniques and methods for working with bacteria.  Research is focused on Paracoccus denitificans (gram-negative facultative anerobe).

  • What is your experience in using SF-36 health-related quality of life (HR-QOL) in children with chronic diseases?

    SF-36  health-related quality of life (HR-QOL) in children with chronic diseases.

  • Md. Siddiqur Rahman added an answer in Forestry:
    How can the contribution of the forestry sector of any country be measured towards GDP calculation accurately?

    Forestry sector contributing toward national GDP has always been underestimated in the tropics due to many reasons. Ranging from environmental to educational, and widening between infrastructural and methodological approaches adopted; how best forest assests and liabilities could be accounted using GAAP (Generally Accepted Accounting Principles)?

    Md. Siddiqur Rahman · University of Chittagong

    Dear Mr. Dhaval

    Thank you for your contribution. Your accountability for NPV of forest ecosystem services were admissible.

    One point should be noted that, there are some disturbances those may hamper accounting of GDP which I call environmental dis-economies, like disasters caused with great losses to the forest resources.

    You may also have to include any subsidies or grant provided to the forest dwellers with any special consideration while calculating ecosystem services of the forests.

    Thank you.

  • Why social inequality persists?

    “Beliefs which serve privilege, elitism and inequality infect our minds
    like computer viruses. But now Dorling provides the brain-cleaning software we need to begin creating a happier society.”
    Richard Wilkinson, Emeritus Professor of Social Epidemiology and au-
    thor of The Spirit Level

    Marwan M. Obeidat · Hashemite University

    There is no equality on earth! Equality is heavenly. Inequality is mundane and human!

  • Abdelrahim Sayied added an answer in Fish Ecology:
    Are there recent studies on the Sanriku Coasts struck by the 2011 Tsunami and Earthquake (flora and fauna, fish habitats, fishing activities, ..)?

    flora and fauna, fish habitats, fishing activities, ..

    Abdelrahim Sayied · University of Bahri

    No, thanks for your question

  • Ayaz Ahmad added an answer in Homology Modeling:
    Will different force-fields effect the structure and function of homology model and docking of ligands with that model?

    I am using MOE for homology modelling of an enzyme but the model contain too many outliers. So I applied different force-fields which minimized outliers. My question is on whether applying different force-fields on a homology model will effect the structure and function of that enzyme and also whether it will further effect the docking of ligands/drugs?

    Ayaz Ahmad · Abdul Wali Khan University Mardan

    did you minimize energy of your model? check after E minimization.

  • How can we derive real parameters with physical meaning from imaginary data using electrochemical impedance spectroscopy?

    I always use electrochemical impedance spectroscopy in my studies. In nyquist plot one axis is the imaginary part. If we don't use it we couldn't calculate the physical parameters such as double layer capacitance, charge transfer resistance etc., but the imaginary part doesn't have physical meaning and we use it to calculate physical parameters! How can I explain this for someone who doesn't know about impedance but nevertheless is a professional physicist?

    Ahmad Sharifi-viand · Khaje Nasir Toosi University of Technology

    Thank you for your time and consideration dear Dr. Peter Viscor.

  • Why high level of fat in diet (more than 6%) increases the incidence of aortic repture and how can we reduce this incidence?

    Is there any relationship between this incidence and methionine or other methyl donor compounds?

    Robert Michael Davidson · PhyNet Inc

    With regard to medium chain saturated fatty acids, lauric and capric acid, there are published reports of antiinflammatory benefit. I suspect that this benefit derives from their amphiphilicity, membrane stabilization, increase in zeta potential (to more negative values), increase in protein-water interfacial tension, and increase in microvascular perfusion. Further, I suggest that well-controlled prospective in vivo studies, would validate my speculation. A major part of the antiinflammatory, pleiotropic properties of ascorbic acid, are likely to be based on similar considerations.

  • Abdelrahim Sayied added an answer in Marine Ecology:
    Has anyone experimented with the hormones involved in the regulation of gametogenesis and nutrient storage in the gonads of sea urchin?
    Two processes that are continuously evolving in the gonads are known to be regulated by temperature and light, as well as other environmental factors, what is known about hormonal regulations?
    Abdelrahim Sayied · University of Bahri

    My work emphasizing on Synchronization's of oestrus and study the breeding cycle of Dorcas gzazelles  

  • Will making more than two mismatches in primer (mutated) cause a problem?

    When designing a mutated primer with two or four mismatches, and when its Tm is less or around 70 degrees C, and its GC% is less than 40% (may be 38%). Will all these affect the succession of the mutation in a gene (in case of using Quick change site- directed mutagenesis kit)?

    Daniel Lerda · Catholic University of Córdoba

    Dear Hero Akrayi,

    My suggestion for you is:

    17 cycles instead use 12

    Screen for clones (~ 15 clones for sequencing)

  • How can oil and tween 80 in emulsion technique be sterilized?

    In the emulsion technique, a small volume of cell-polymer suspension (discontinuous phase) is added to a large volume of a vegetable oil (continuous phase) such as soybean oil, sunflower oil, canola oil or corn oil. In some studies, white light paraffin oil (Rao et al. 1989) and mineral oil (Groboillot et al. 1993) have been used. The mixture is homogenized to form a water-in-oil (w/o) emulsion. In some cases emulsifiers are added to form more stable emulsions, since these agents lower the surface tension of droplets leading to smaller spheres. The most common emulsifier used is Tween 80 at low concentrations. Once the emulsion is formed, solidification occurs after the addition of an adequate solidifying agent to the emulsion. In the emulsion procedure, adjustment of agitation speed and phase ratio enables production of the targeted bead size. The size of the beads can vary between 25 mm and 2 mm.

    Mohammad Ali Khosravi Zanjani · Islamic Azad University

    Thank for your valuable and constructive comments.

    It is important to note that, the aim of sterilization of tween 80 and vegetable oil (corn oil) is to microencapsulation of probiotic bacteria via emulsion technique in order to work in sterile condition.  

  • Gordon Ade-ojo added an answer in Atlas.ti:
    Qualitative research tools like ATLAS.ti, Nvivo etc. have appeared and more are likely to appear. How good are these tools?

    Despite its popularity increasing, the analysis of qualitative data is cumbersome. Coding, theme development etc. manually consumes lot of time though quite a number of researchers are still using manual methods.  New tools are being developed and the existing ones are getting updated but its diffusion among the researchers are low. Lot of training and practicing is needed before researchers become conversant with these.

    Gordon Ade-ojo · University of Greenwich

    I am familiar with and have used NVIVO. IN MY VIEW, IT IS A LOT OF WORK FOR NO CONCRETE OUTCOME. NVIVO for instance, is simply finding a way to quantitatively represent qualitative data. I think sometimes, the drivers behind all of this are: standardisation, potential adherence to the impact of new technology, which almost boarders on political correctness and the inevitable economic factor. What is wrong with our old tested and trusted human controlled methods of qualitative analysis?

  • Prasanta K Ray added an answer in Cancer Biology:
    Why are immune cells not able to kill or destroy cancer stem cells?

    Though we know that abnormal cells like tumors must have some flag on surface. Does the cell biomass in tumor evade stem cells from killing?

    Prasanta K Ray · Centre for Applied Science and Technology (CAST)

    The moment a cell assumes the properties of a cancer stem cell or full-fledged cancer cell,it also achieve several properties along with that protects it from the attack of immune cells of the body. Among these are specific cell membrane cover that does not allow the body's immune cells to recognize the tumor cells as 'foreign', cell surface negativity of an increasing order on cancer cells may repel the immune cells having negative charges, mimicking the cell membrane as that of normal cells may be a mechanism that cancer cells develop at least initially until it assumes certain mass when it comes under the law of mass action phenomena and cancer cells thrive because of the balance in its favour.

  • Abdelrahim Sayied added an answer in Snail:
    What is the moisture content of Elimia snails?

    Need to do a dry weight conversion.

    Abdelrahim Sayied · University of Bahri

    My specialization in captive wild mammals