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15

You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject. Yes It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you should do in collaboration with the person who is going to be helping you analyze your data. To address a couple points: You'll see all ...


15

The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and that it could not have arisen by natural selection. This is theoretically falsifiable, but the ...


13

Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different filters on your microscope for the various fluorophores. For morphological assessments, perhaps a ...


10

In order to calculate power, you need to know the variance of the data being collected. You can only estimate this prior to actually gathering the data itself, so any a priori power calculation is itself just an estimate. This is why sometimes you will see small studies being conducted as pilot studies (for example, see (1)), which enable variance to be ...


9

Wow that can vary from a couple of months and a few thousand dollars to a lifetime and millions of dollars. I can give a couple of examples, but this is an extremely broad question. Wet science is not cheap might be the message here. Gene Ontology terms are meant to cover all biological roles known for genes. Terms are added and retire regularly. They ...


7

The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies. Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expression should be a measure of the protein. If a gene ...


7

You may be interested in this paper and a video that summarizes it. It seems to be made quite clear that 1) effectively all of the parts of the flagellum are not original to it, and 2) there is a reasonable evolutionary path (one involving only increment/refine steps) that could have been responsible for it. The video mentions but doesn't describe ...


7

You could do different things: First you could, as you say yourself, sequence the complete genomes of the strains from a biofilm and compare these with some, which do not form biofilms. This may give you an idea which genes are involved when they are present in the "biofilm genome" but not in the other. The proof would be to disrupt these genes either by ...


6

The main problem with what you are asking is that you want to show effects on vigilance and memory in vitro. That is just not possible: if you want vigilance and memory you need a live animal, there is no way around it. Next point: you have an audience of non scientists, so you can lose them very quickly if you start speaking about NMDA, LTP or similar ...


5

I would be very surprised if the time of day made a difference. I've personally never heard mention of such a phenomenon in discussions with intensive care practitioners (where of course HR and BP are measured constantly). However this is only the case during rest, this paper (on horses) suggests that there is some difference in HR and BP after exercise ...


5

the devil is in the details here - the logic is okay, but there is no experiment here. Too many unanswered questions. Are you doing anything specific to see optimize RT activity? How are you preventing your GFP mRNA from being turned into protein, producing much larger signal than you will ever see from RT activity? Once its integrated into the ...


4

The instrument you are looking for is probably an UV-meter.


4

Due to my own woeful ignorance on the subject, I have been reading up on statistical methods recently. From what (little) I understand, the real answer to this question is: Yes, but only if you are doing Neyman-Pearson hypothesis testing and Absolutely not, if you are using Fisher p-values That is, the question isn't formulated correctly, because power ...


4

I'm with @Mad Scientist. Save yourself the trouble and do this in an in vitro system. At the moment, you don't even know if the HIV-RT will express or will be active in E .coli. Rather, express mutated HIV-RT in T-Cells or Rabbit Lysate. Purify. Add in a RNA template with the appropriate primer. Hydrolyze your RNA Detect your cDNA.


4

There is evidence that copper pots have antibacterial effects when used for storing drinking water (Sudha, et al. 2012), so the copper coins will probably have a similar effect. The easiest way to test this at home would probably be to buy a test kit from an online vendor - these are relatively inexpensive. Some Googling produced this website ...


4

I would first like to address a couple of your underlying assumptions: 1) Most "copper" looking coins (in North America anyway) are actually a bronze alloy, reflecting a change from ~95% Cu to ~95% steel. As a result, I don't think that there would be much antimicrobial effect from the coins. Now, if you did really have copper in the water (like copper ...


4

There are several reasons why a lab might choose to get DNA from lymphocytes instead of whole blood. Generating genomic DNA from whole blood is not necessarily the best idea, as all the excess protein (mainly hemoglobin from RBCs) needs to be gotten rid of at some point. By narrowing down your input to just include cells that have DNA, you lessen the amount ...


4

Addition to Chris' answer. If you do not have a strain that doesn't produce biofilm then you would have to screen for the genes that are involved in biofilm production (this goes for any phenotype). In earlier times people used to do this by random mutagenesis with mutagens such as EMS (Ethyl Methanesulphonate) or UV. Nowadays it is possible to build a ...


3

My personal favourite is OpenWetWare. Think wikipedia for scientific protocols and an open access lab notebook. There's a problem with this things. Despite the common stereotype of scientist being open and good at sharing, my experience is the opposite. Many laboratories are not good at all in sharing their techniques/secrets. They will share the basic ...


3

There is also protocol online, but without tags, only sorted by category. It could nevertheless be interesting.


3

There's Benchfly, which is a video-based protocol library: http://www.benchfly.com/video-protocols.php There's also JOVE, which is a peer-reviewed video journal that sometimes covers protocols: http://www.jove.com/


3

I like that you are considering a simple and standardized approach. However, there are a number of potential pitfalls to consider with this proposal. First of all, what specific RT activity are you trying to quantify? Is the the transcription speed or accuracy, or are you trying to characterize something else entirely? If you are measuring speed, how and ...


3

In the Bgee database, you can look at gene expression and anatomy of various model species, e.g. Drosophila. This doesn't give you the full anatomy, but at least an ontology of tissues and cell types.


3

[I'm answering my own question, but this seems too important not to include as an answer.] A long-term E. coli evolution experiment (Wikipedia) was begun in February 1988 by Richard Lenski. He took 12 initially identical populations of Escherichia coli, and let them grow, having now completed over 50,000 generations. One striking observation made through ...


3

I think you might be better advised to try plating out samples of the water and counting bacterial colonies. There has been some good advice on doing basic microbiology at home elsewhere on this site.


3

Depending on the exact goal of the experiment, the researchers may back-cross both to smooth out genetic variation between individuals and to potentially normalize expression of a transgene, although once you get past the chimeric stage gene expression should be fairly stable. In my experience, back-crossing allows you to generate a genetically-altered mouse ...


2

Reporter genes are also used when the experiment is trying to distinguish the effect of that gene that the scientist introduces (exogenous) and the same gene that the cell already has (endogenous). Ideally, one would like to choose a cell system that does not contain endogenous genes of interest because of this confounding effect, but it is not always ...


2

First you should decide whether you want to design an shRNA or use siRNAs. If you want to use shRNA you should look at the rules that "Mad Scientist" mentioned. You can insert mismatches but make sure not to disrupt the secondary structure. You can use RNAFold to verify. shRNA always has issues and you have to optimize your design, test it by realtime ...


2

Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two ...


2

Supplementary information from the Comments from the first answer: I have perhaps found @terdon's reference? Not sure if this is it, but by measuring transcription events in individual cells, Taniguchi et al. certainly make the case that there is no correlation between protein and mRNA levels. However microarray data (and most rnaSeq and qPCR ...



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