Posts Tagged ‘research methodology’

How Scientific Sharing Equals Scientific Caring

 :: Posted by American Biotechnologist on 08-05-2013

Over the past few weeks, we have explored the question of what constitutes scientific success and several important “comandments” for achieving this holy grail. In this post, we will discuss a presentation given by a young scientist at Delft University of Technology, who has expressed frustration with the common use of publication rate for defining scientific achievement. The presentation is especially noteworthy as it comes from a young scientist, Guenevere Prawiroatmodjo, who has yet to been tainted by years of politicking to climb the academic ladder. Nonetheless she is clearly bothered by the importance that is attached to an end-result that doesn’t pay tribute to, or encourage sharing of the entire scientific process. Not just results.

As Dr. Richard Feynmen so eloquently stated:

There isn’t any place to publish what you actually did in order to get to do the work

Richard Feynman

So what is Dr. Prawiroatmodjo’s solution to this problem? To create more openness and to share more parts of the scientific process. Furthermore, she postulates that it is critical to stimulate scientific motivation by encouraging entrepreneurship and commercialization.

In this vein, Dr. Prawiroatmodjo has come up with the “p” index which ranks scientific success as the number of times a scientist’s techniques or scientific tools have been used by the scientific community. In other words, if the “h” index ranks scientists by the number of citations their publication has received in the scientific literature, the “p” index ranks scientists by the impact their scientific methodology has had on the scientific community.

A New Way to Generate iPS Cells from Fibroblasts

 :: Posted by American Biotechnologist on 04-02-2013

A team of New York Stem Cell Foundation (NYSCF) Research Institute scientists led by David Kahler, PhD, NYSCF Director of Laboratory Automation, have developed a new way to generate induced pluripotent stem (iPS) cell lines from human fibroblasts, acquired from both healthy and diseased donors. Reported in PLOS ONE, this cell-sorting method consistently selects the highest quality, standardized iPS cells, representing a major step forward for drug discovery and the development of cell therapies.

Read more…

Keeping it constant: A lesson in protein transfer

 :: Posted by American Biotechnologist on 05-22-2012

Power supplies that are used for electrophoresis hold one parameter constant (either voltage, current, or power). The PowerPacâ„¢ HC and PowerPac Universal power supplies also have an automatic crossover capability that allows the power supply to switch over to a variable parameter if a set output limit is reached. This helps prevent damage to the transfer cell.
During transfer, if the resistance in the system decreases as a result of Joule heating, the consequences are different and depend on which parameter is held constant.

Transfers Under Constant Voltage
If the voltage is held constant throughout a transfer, the current in most transfer systems increases as the resistance drops due to heating (the exception is most semi-dry systems, where current actually drops as a result of buffer depletion). Therefore, the overall power increases during transfer, and more heating occurs. Despite the increased risk of heating, a constant voltage ensures that field strength remains constant, providing the most efficient transfer possible for tank blotting methods. Use of the cooling elements available with the various tank blotting systems should prevent problems with heating.

Transfers Under Constant Current
If the current is held constant during a run, a decrease in resistance results in a decrease in voltage and power over time. Though heating is minimized, proteins are transferred more slowly due to decreased field strength.

Transfers Under Constant Power
If the power is held constant during a transfer, changes in resistance result in increases in current, but to a lesser degree than when voltage is held constant. Constant power is an alternative to constant current for regulating heat production during transfer.

The above information was adapted from Bio-Rad’s protein blotting guide. For more great information, be sure to download the Protein Blotting Guide from Bio-Rad Laboratories.

Top 8 reasons for high background noise on your western blot

 :: Posted by American Biotechnologist on 05-02-2012

The following are the top 8 causes for overall high background on your western blot and potential solutions:

  1. Blocking was incomplete
    • Increase the concentration of blocker
    • Increase the duration of the blocking step
    • Use a different blocking agent
  2. Blocker was impure
    • Use a pure protein such as BSA or casein as a blocker
  3. Wash protocols were insufficient
    • Increase the number, duration, or stringency of the washes
    • Include progressively stronger detergents in the washes; for example, SDS is stronger than Nonidet P-40 (NP-40), which is stronger than Tween 20
    • Include Tween 20 in the antibody dilution buffers to reduce nonspecific binding
  4. The blot was left in the enzyme substrate too long (colorimetric detection)
    • Remove the blot from the substrate solution when the signal-to-noise level is acceptable, and immerse in diH2O
  5. Contamination occurred during electrophoresis or transfer
    • Discard and prepare fresh gels and transfer solutions
    • Replace or thoroughly clean contaminated foam pads if a tank blotter was used
  6. Excessive amounts of protein were loadedon the gel or too much SDS was used inthe transfer buffer. Proteins can pass through the membrane without binding and recirculate through a tank blotting system.
    • Reduce the amount of protein on the gel or SDS in the transfer buffer
    • Add a second sheet of membrane to bind excess protein
  7. The primary or secondary antibody was too concentrated
    • Increase antibody dilutions
    • Perform a dot-blot experiment to optimize working antibody concentration
  8. Incubation trays were contaminated
    • Clean the trays or use disposable trays

For more great information, download the protein blotting guide from Bio-Rad Laboratories.

Low-income dads support breastfeeding…so what?!?

 :: Posted by American Biotechnologist on 10-18-2011

I just saw the following news release out of the American Academy of Pediatrics and I am not sure what to make of it. From what I see, the study has an n of 10 and tries to pull “accurate” information from a group of fathers who were interviewed in a focus group setting.

I know that this is preliminary data out of an AAP presentation and that my critisism may be unjustified. Nonetheless have a look at the press release and let me know your thoughts.

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