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- What would happen if one forgot to start PCR after putting samples in it?
Hi, I put my PCR tubes in and forgot to press enter in order to start it. After 1 hour when I was expecting that it would be finished I went and checked that it was never started. Has anyone made the same mistake? If so what did you observe?
Add taq. pol into it and run the samples again. it will be definitely amplify.
I have done this and get good amplification.Following
- Is there any evidence to subcellularly localize of plant aquaporin in cytosol?
If there are any evidence please give me the references.
Dear Leszek sir,
I already read this paper, but there are some plant aquaporin homologs according to our in silico prediction are localized on cytosol, So I am looking for experimental evidence that is it possible plant AQPs localized in cytosol?
Thank you sir!!Following
- How do I compute the quality score for dermatological images? What are the criteria that I should include in a dermatological image's quality score? How do you classify them as good or bad quality?
Hi Mr. Belattar,
thanks for your fast response. I will check on it as soon as possible.
And your aim is to remove the artifacts or a quantitative analysis of the images?
Sincerely, Dominik LenzFollowing
- Does anybody know economic debubbling systems for ship underway continuous optical measurements? As above.
Thanks Emmanuel! I'll have a look at the options you suggest.Following
- Are electrical sources elements with "static negative impedance"? If so, is there any benefit from this concept?
The negative impedance concept is so attractive that some authors try to bring it on even the most basic electrical elements as voltage and current sources. See as an example the work of this Wikipedian (although it seems his own creation, it is assembled entirely by else's thoughts extracted from reputable sources):
Also, this viewpoint was presented by Simone Orcioni in the question below:
As far as I understand, this "negative resistance viewpoint at voltage sources" is the following. A voltage source is connected to a load (a resistor)... so the voltage V (VG in he Simone's figure) across them and the current I through them are the same... and therefore the ratio V/I (the resistance) for each element is the same (see the first attached picture below)... Thus the resistor has a resistance RL = V/I and the voltage source has a "negative resistance" RS = V/-I = -RL... so the sum of the two resistances (voltages, according to KVL) is zero... It sounds temptingly simple but...
In this arrangement, there is only one "main" voltage source and one resistor (the load)... and this is the possibly simplest electric circuit still from 19-th century - a source driving a load. But the popular belief is that "negative resistance" is a "supplemental" concept... It implies another (supplemental, "helping") voltage source (BH in the second attached picture)... and this is not an ordinary constant but "dynamic" voltage source whose voltage is proportional to the current flowing through it (a 2-terminal current-to voltage converter)... and so it will act as a negative resistor with resistance -Ri. This negative resistance compensates another positive resistance Ri (e.g., the source internal resistance or the line resistance) thus giving as a result zero total resistance between the main source VIN and the load RL... and this 4-component circuit is reduced to the Simone's initial 2-component circuit (source and load)... The sense of this "trick" is that the unwanted resistance Ri (the voltage drop across it) is neutralized by an equivalent voltage:
If this supplemental voltage source was an ordinary constant voltage source, it would still compensate the voltage drop across Ri... but only for one value of the current; maybe because of that they name this kind of "negative resistance" with the name "static negative resistance". Really, it can compensate also the relatively steady voltage drop across a constant-voltage nonlinear resistor (diode, LED, Zener diode, etc)... but this is just another special case...
Note that, in contrast with an ordinary source, this exotic voltage source will not independently produce voltage if there is no input voltage VIN; it starts acting after the main (input) voltage source begins increasing its voltage from zero.
IMO the word "resistor"/"negative resistor" has the meaning of something that resists/"helps" the current flowing through it... so it implies some initial current produced by another (main, input) voltage source... Therefore, this main source is simply a source, not a negative resistor... and maybe this viewpoint is just a misconseption as many others in the field of negative impedance phenomena?
I would add here also the questions asked by Lutz Wangenheim: "Does it make sense to interpret this scenario as a connection of a positive and a negative resistance of the same value? More than that, are voltage and current directions of the voltage source in accordance with the DEFINIONS of a negative resistance? If this would be true, we could treat each voltage source in each circuit as a negative resistance, couldn´t we?"
....and this is the case.....
Really? Can you justify it?Following
- Can I use two different dilutions (one for reference genes, and one for GOIs) if I am using the deltadeltaCT calculation?
I have two reference genes that have been previously verified for level expression under biotic stress (specifically pathogen inoculation, which is what I am doing).
I also have two genes (homologs) that I would like to compare the expression of.
There is 3 different genotypes, and there are treated, and untreated within each genotype. (replicated 3 times)
The catch is: my genes of interest are expressed at a low level, to the point that I cannot dilute the cDNA more than 1:10 before it gets too close to the NTC (I already tried everything known to man to reduce the NTC signal, and it is not possible: 35-40CT on it.)
So, I have settled on using a PCR product extracted from a gel, and diluted to a reasonable series for my standard curve for the GOI. However, for my reference genes, I am using cDNA diluted.
Bottom line is: Can I use two different dilutions (one for reference genes, and one for GOIs) if I am using the deltadeltaCT calculation?
Also: Do I simply average the two reference gene CTs to use in the formula?
Thanks in advance, and if there is any clarification needed, let me know.
1. When you use the Livak method (ΔΔCt) it is better to study the expression with one housekeeping gene each time. Theoritically, if these genes are not affected, you must obtain the same results. However, it is not recomended to use the average of them, as it affect the data the most of the times.
2. Usuallt the Ct>35 means unspecific product. You may observe the curve in your qPCR experiments, but it might be another product. You should first check with melting curve, and even better perform an electrophorsis of you product.
3. The dilution of cDNA is performed, as the use of high amount of cDNA can inhibit the PCR reaction. There is no problem to use different amounts of DNA, as you use the ΔCt which is Cthousekeeping-Ct GOI.
4. You can try to amplify the RNA you receive. There are a lot of kits, that can amplify the whole RNA and specially mRNA, in increase the amount of cDNA and then to reduce the Ct.
- Can anyone help with item reduction of an adopted scale?
For my study I am going to adopt three scale a total of 101 items and want to reduce items based on pilot study please guide me the steps to be followed for the same as there are many items that are intended to measuring same. From pilot study I have generated 50 responses and respondents also commented that questions are repeating but sample size is small to go for principal component analysis I am confused how to eliminate these items.
The literature points to an acceptable sample size of between 5-20 participants per item, so for your 101 Qs, you would want a min of 505-2020 participants to make reasonable use of PCA. However, depending on who you are getting feedback from you may be able to accept their establishment of similar face validity for multiple questions as a criteria to consider getting rid of a few of those questions.
If you are using established measures, valid and reliable, then the authors of these measures will hopefully have published somewhere the dimensions and factor loading etc for each of these measures. You can then compare each measures respective data and if they are measuring a similar construct/phenomenon and you can find similar dimensions being measured for said construct within each measure then you may be able to eliminate redundancy by comparing this information. That would be my first step.Following
- Specific questions about chemical protocols to detect and quantify secondary metabolites in seeds
I would like stay in contact with people working to detect and quantify secondary metabolites (tannins and alkaloids) in seeds.
I am using protocols published in previous articles but I have several questions about details of the procedures.
I am following these articles:
Steele et al. 1993. Tannins as partial consumption of acorns: implications for dispersal of oaks by seed predators. Am. Midl. Nat. 130:229-238. [To extract tannnins].
Schultz et al. 1981. Hemoglobin as a Binding Substrate in the Quantitative Analysis of Plant Tannins. J. Agric. Food Chem. 29: 823826. [To quantify tannins].Following
- Transfection problems - can anyone help?
I'm trying to transfect BxPC-3 (human pancreatic cancer cell line) with siRNAs or DNA from a while but I had a very low transfection efficiency (To date I used lipo2000 and electroporation). Can anyone give me a tip about this? Thanks
I am working with 'tank' cell line which is really hard to transfect and kill. after using Lipofectamine2000, jetPEI, homemade PEI and transfection efficiency less than 1% I tried Magnetofectamine. The approach is very logical (you're bringing DNA to the bottom of the plate using metal particles in the lipofectant bubles and a magnet under the plate), the protocol is simple and fast. First you have to buy the whole starting kit to get the magnetic plate. afterwards you can buy CombiMag separately and use homemade PEI instead of expensive Lipofectamine - that makes your transfections very cheap :) it worked for me very well.Following
- Does anyone have knowledge on the dilution of primers?
The commercial primers which I have ordered come labelled as: 4.37 OD, 20.91 nmol. How do I dilute before the addition to the PCR mixture?
Simply add 20.91 uL water to the lyophilized primer to get a 1nmol/uL soln. Tap to dissolve and spin down. This is your primer stock solution. Now dilute it 100 times to have a 10 pmol/ uL working solution.Following
- Can anyone help with learning strategies for creating autonomous learners?
So far I am reading Rebecca Oxford. Need guidance on what to read for effective learning strategies in order to make my learners autonomous.
When working with adults don't use pedagogical methodologies convert to Andragogical Methods. Look up Malcom Knowles. I did my research on what motivates an adult learners.
You are probably asking: what do you mean by Andragogy?
Knowles identified the six principles. I outlined them below:
Adults are internally motivated and self-directed
Adults bring life experiences and knowledge to learning experiences
Adults are goal oriented
Adults are relevancy oriented
Adults are practical
Adult learners like to be respected
Let me know if you need more information because I did my dissertation on him.
Call me: 210-313-7739 Dr. Cathy CokerFollowing
- How can we purify Algae from Bacteria that may grow with Algae during the incubation period? We are investigating the metabolic profile for different type of Algae using NMR and MS-based metabolomics approaches. We wonder how can we purify Algae from Bacteria that may grow during the incubation period ?
Thank you so much for your help, This great
- What are the main concerns and challenges as regards information management in Healthcare?
There is an increased requirement both in ethics and law for the preservation of patients's confidential information. The various theories underpinning ethics-Kantian, Consequentialism, Virtue ethics and Communitarianism uphold the need to maintain confidentiality to a different varying degree. Fidelity to the absolute need to preserve confidentiality is advocated by Kantian. This level of adherence is largely consistent with the Hippocratic Oath; although ancient, the Oath continues to provide an overarching umbrella on national and international codes of practice. The Oath contains succinct but strong statement as regards confidentiality. However, Hippocratic medicine was a one-one consultation without the involvement of other professionals; health insurance and electronic transmission of information. Information disclosure for the overall benefit of the society was almost unknown.
Particularly in our case, Malawi. I find that one of the main concern is lack of skill and motivation of the operational health staff to collect and feed the systems with the data appropriately. This in turn leads to senior management not having enough data to make their decisions on. This of course could be a problem at senior levels as I have a doubt on the abilities of senior managers in querying the database enough to get deep knowledge the data may have.Following
- For biofilm assay in gram negative bacteria, which approach should I follow? In Burkholderia spp.
I use 96 well plate CV assay to quantify monospecies and multispecies gram negative biofilms for static conditions and flow cell system followed by fluorescence or confocal microscopy for dynamic coinditions.
I attach a general paper about CV assays and a Legionella specific one for CV and flow cell assays.Following
- How can I measure body length and width of Scenedesmus acuminatus?
In Scenedesmus acuminatus since the cell are arranged zigzag and terminal cells are curved outward, I am finding it difficult to measure width. Kindly help me out.
Is this just to calculate the cell volume or are you interested in the morphology? in the former case, I would go for a volume-displacement cell counter.
Alternatively, there are cheap shape-recognition softwares that may help youFollowing
- Can anyone suggest a good book, tutorial, or papers on Percolation Theory? In mathematics, percolation theory describes the behavior of connected clusters in a random graph. I would like know this theory in detail.
The concept of percolation is extremely wide! The books or papers you might be interested in reading would strongly vary depending on the specific application you are working on. I would agree with the books proposed, they as known for giving a good introduction. The one from M. Sahimi "Application of Percolation Theory" published at Taylor and Francis is also very good. There are also many lectures, papers, PhD thesis available on the web.Following
- Are there online tools to find mouse exon sequences? I am planning to use the CRISPR-Cas system to make a new mouse cell line. I need to design an sgRNA that targets the end of the last exon. In order to do this, I am hoping to find a mouse genome browsing tool that clearly marks exons and allows me to check out their sequences. Is there such a tool available? I know how to find the FAFTA sequences of the entire transcript, but I want to know where a specific exon lies on that transcript.
Was recommended this site earlier today (made close to you!) but haven't tried it yet:
- Can anyone help with software for gaze-contingent eye tracking research?
I'm looking for software to program an SMI Red eyetracking system for a gaze-contingent reading study (using Rayner's "boundary technique"). Unfortunately, it isn't part of SMI's reading package. I have come across OpenSesame and PyGaze, but I don't have much coding experience, so I would really appreciate code I could use either directly (adding text files) or as a template. Thanks.
@Russel: I look forward to your email!Following
- Is your country at a risk from transboundary pollution?
Transboundary pollution (pollution that crosses the boundaries of a nation) is the pollution that originates in one country but is able to cause damage in another country’s environment, by crossing borders. Pollutants can travel through pathways such as wind, dust particles, flow of rivers, ocean currents, and via seabirds. The long-range transport of air pollution has been recognized as an important factor affecting health of ecosystems and human. Transboundary flows of pollutants occur between states of a country, between closest neighbouring countries, as well as between continents.
Persistent organic pollutants (POPs) (e.g. dioxins, furans, PCBs, and some organochlorine pesticides) can be transported over long distances in the atmosphere, resulting in widespread distribution across the earth, including regions where they have never been used. Coal-fired and oil-fired power stations, and mobile sources, such as cars, ships and aircraft emit a complex mixture of pollutants, including sulphur dioxide and nitrogen oxides (the precursors to acid rain). These air pollutants can also be transported over hundreds or even thousands of kilometres, for example, it is reported that much of the pollution emitted in the UK travels across the North Sea and is deposited in Scandinavia (as acid rain). The Arctic is supposed to be a pristine environment, however, in recent years; several types of contamination have been found in the arctic (e.g. heavy metals, POPs, radioactive) which are transported to the Arctic by winds, rivers and ocean currents. Smoke haze (dust, smoke and other dry particles) due to land clearing and ‘slash and burn’ agricultural practices in Indonesia has been a perennial problem in the southern ASEAN region causing much environmental damage in Singapore, Malaysia, Brunei, and Southern Thailand.
Owing to their toxicity, the POPs can pose a threat to humans and the environment (POPs bioaccumulate in human and animal tissue, in food chains, also an endocrine disruptors). Acid rain causes acidification of lakes and streams and contributes to the damage of trees at high elevations and many sensitive forest soils. Acid rain accelerates the decay of building materials and paints, including irreplaceable buildings, statues, and sculptures that are part of nation's cultural heritage. Sulfur dioxide and nitrogen oxide and their particulate matter derivatives—sulfates and nitrates—contribute to visibility degradation and harm public health. Air pollution from open burning can cause serious health problems and damage the environment. Children, the elderly and those with existing health problems are particularly vulnerable to smoke from open burning.
To control the spread of transboundary pollution the United Nations Economic Commission for Europe (UNECE) implemented the Convention on Long-Range Transboundary Pollution (1979).The Minamata Convention on Mercury is an international treaty designed to protect human health and the environment from anthropogenic emissions and releases of mercury and mercury compounds. The Stockholm Convention on Persistent Organic Pollutants is an international environmental treaty, signed in 2001 and effective from May 2004, that aims to eliminate or restrict the production and use of persistent organic pollutants (POPs).The ASEAN Agreement on Transboundary Haze Pollution is a legally binding environmental agreement signed in 2002 by all ASEAN nations to reduce haze in south-East Asia
Question: Is your country at a risk from transboundary pollution?
(Any weblinks or references relevant to transboundary pollution or any regional or international treaties to reduce transboundary pollution would be much appreciated)
I noted that greenhouse gases and other pollutants (from power plants) emitted from India may impact Malaysia and Singapore. Thanks for the weblins which would be helpful!
Transboundary Pollution is difficult to control because the damage from the pollution occurs in a locality that has no authority over the generator of the pollution.Following
- Does anyone have experience with docking analysis?
How can I count the Hydrogen Bond after docking by Autodock Vina through visualizing by PyMOL? Ligand consists of Oxygen, Nitrogen, Carbon and so on. Oxygen of Ligand binds with the amino acids of protein. How can I confirm that Oxygen binds with the hydrogen of amino acids. Expecting experts comments.
PyMol : right panel > A > preset > ligans sites
- Do numerical solutions explain the origin of turbulence? Has the Navier-Stokes equation explained the origin of turbulence?
@Andrea Di Vita: OK, you're surely right, I was not precise enough. I wished to underline the granularity (intermittency) which structures the fluid with respect to scalar properties. Generally much denpends on the problem configuration. If you have a steady state or flow equilibrium, then your are 100% right. But the situation is different in an initial-value problem where mixing still needs to set up LTE along its a way down the Richardson cascade. I am not sure that we may always assume LTE in such a case. Besides, your Max-Min entropy pager is quite nice and really readable! Only for curiosity, did you ever hear the name Max Steenbeck?Following
- Can one do Parallel Computing coding in MATLAB ?
Can one do Parallel Computing coding in MATLAB ?
I want to implement some parallel algorithm in MATLAB.
To be more specific, I want to implement the parallel maximum weight bipartite matching algorithm (Hungarian method), and for that I am thinking to implement it in MATLAB.
To Mark Hahn,
With reference to the my above comment; the page http://www.netlib.org/utk/lsi/pcwLSI/text/node223.html is working now.Following
- What is the best free software for QSAR and molecular docking? Apart from ArgusLab
i am working on 3d qsar through sybyl..
u shared a link bt dts not opening is there any other free software for 4D QSAR??
or any other free online software for 3D QSAR???
send me details on my mail ID : firstname.lastname@example.org
- Failed DNA sequencing reaction
I sent my PCR products for sequencing. Unfortunately all of them have noise. After post PCR gel electrophoresis I had very sharp bands without any unspecific bands or dimer primer. What could be the cause of this? What can I do with these noises to interpret the results?
I attached one sample of the results.
As stated by Yoav, cloning is the best way to solve this. However, I am aware that this can take some time. Are you sequencing with the same primer(s) you used for amplification? If so, you could try a nested primer. Same question as above- did you do a clean-up or just use the PCR product directly?Following
- Can anyone explain to me the molecular signalling for plant microbe interactions in potatoes?
I need to determine correlations between plant-rhizobacteria interactions in field conditions and molecular analysis in leaves and tubers for potatoes. We have made some field experiments last year and in 2014 will have to plant the same treatments inoculated with Bacillus sp. in pots at greenhouse.
Thanks a lot, for all the friends that help me in this; I need to precise that the kind of interactions are related to SAR (plant inmune system) and agronomical performance as affected by Bacillus sp., Azotobacter and Pantoea sp. The hypothesis is that inoculation for tuber seed is a sustainable technology and could be use for potato small farmers.... I will read carefully your answers to the question to respond everyone. Thanks again!Following
- Do you have information about national projects of LIDAR and photogrammetric missions in your country? I am looking for data description, links to data browsers including data collected by national institutions in other countries over the worlds. What are their parameters? How often they are collected usually? Is there any official data browser? For example, in Poland, LIDAR of whole country with an average density of 4p/m2 and 12 p/m2 (for big cities) has been almost collected (90%). Link to the availability of data (DSM, DTM, LAS datasets) http://skorowidze.codgik.gov.pl/nmt/ Aerial photos are obtained every 2-3 years for whole country with a resolution of 10 cm (for big cities) and 25 cm or 50 cm for agricultural regions (depending on the size of real-estates) Link: http://skorowidze.codgik.gov.pl/foto/ I'll be grateful for the assistance and support information about situation in your countries.
Data of this nature is in the Public Domain at the U.S. Geological Survey (USGS). Major data center for topographic information, aerial photography coverage, LIDAR, etc. is at the USGS EROS Data Center in Sioux Falls, South Dakota. Furthermore, the American Society for Photogrammetry and Remote Sensing has recently published Guidelines for LIDAR projects at: www.ASPRS.org. (That's also where my column is published every month on the Grids and Datums of a different country every month ... including on the Czech Republic back in January 2000.)Following
- Which stain can I use for Mycobacterial FtsZ protein in Fluorescence microscopy?
I would like to track the Mycobacterial cell division by using the polymerization of the FtsZ protein as a starting point.
You will need to find antisera that recognizes mycobacterial FtsZ and a secondary antibody conjugated to a fluorophore. For the former I would contact a lab working on FtsZ in mycobacteria. For the latter, I would order it from a supply company like Jackson Immunoresearch. Make sure the secondary antibody is raised against the immunoglobulin from the animal the primary was raised in (e.g. if the primary is from rabbit, the secondary should be from anti-rabbit antisera).Following
- Can you help me identify this creeping plant?
Very small leaves over creeping main branch. No adequate water supply required (mostly I observed this plant growing in soil deposits between the small cuts and grooves of a rock or stone). Upon cut of brownish stem a white latex like liquid oozes out. Leaves are not thick and stem has a little stretching capability not like rubber.
I think it is Euphorbia prostrata (unless it is from Europe in which case I suppose it would be E. chamaesyce unless there is a publication I haven't seen (see Rhodora 1966 pg. 155-166)). In E. thymifolia, the capsule is not fully exerted from the cyathium (these are (I saw this by right clicking on the opened picture and clicking open in a new tab)), or to put it a different way, the gynophore is short in this species. E. maculata has more oblong leaves and the hair is generally longer. It also usually has a red "splotch" on the leaves. E. stictospora (a similar looking plant) generally has longer, more dense hairs all over the plant. For identification, I strongly suggest Wheeler's paper about the group found in Rhodora 1941 pg. 97-154, 168-205, 223-286. It is not perfect as there was some confusion over the type specimen for a few (all summarized under Rhodora 1966 pg. 155-166), but the illustrations are remarkable and it gives most of the species (at least the common species) in the US (excluding Florida). The journal Rhodora can be found online at the Biodiversity Heritage Library (link: http://www.biodiversitylibrary.org/bibliography/721#/summary).
These used to be in the genus Chamaesyce but is considered under Paul Berry and Ya Yang to be under Euphorbia subg. Chamaesyce sect. Anisophyllum (link: http://www.amjbot.org/content/98/9/1486.full.pdf+html). I still find the genus Chamaesyce more useful and find myself using it often because it is the easiest way to make the distinction between this group of Euphorbia and the other groups. Saying Euphorbia doesn't give the distinction and saying Euphorbia subg. Chamaesyce sect. Anisophyllum not only gets tiresome but also seems to make it more difficult to communicate with people (it seems to just complicate things).Following
- How can I predict the insilico ADMET (toxicity) of a new drug?
We are designing new drugs using online molinspiration program for that we want check the ADMET in silico. What are the standards for ADMET of a designed drug. Are there any software's online/offline modules are available to know the ADMET?
If it is an actual approved drug in the US, you can get the toxicity data from the FDA review from the FDA web site (drugs@FDA). Otherwise, predicting anything beyond genetic toxicity in silico is unlikely to be accurate.Following