Friday, June 27, 2014

Fun fact: LEGO bricks used to study plants

LEGO bricks
by Priwo

A group of scientists at the Iowa State University were seeking to find a frugal alternative that would allow
them to hold soil substitutes for germinating and growing plants. They wanted something that was modular, scalable, and capable of housing simultaneous experiments.


They found what they were looking for with LEGO blocks, which despite being a toy, are made of high quality plastic, held to very precise standards. And, of course, you can build things with them! Which they did! Their results are reported in the PLoS ONE paper entitled : LEGO Bricks as Building Blocks for Centimeter-Scale Biological Environments: The Case of Plants.




Some information for this post obtained from the Science Direct article: LEGO bricks turned into scientific tool to study plant growth

Thursday, June 26, 2014

Application: Monitoring hydrogen peroxide production in cell monolayers

Hydrogen peroxide (H2O2) has been characterized for its role in a wide variety of biological process. Some beneficial, such as regulation of immune system function, and others viewed detrimental, such as involvement in aging. Therefore, there are many instances where understanding the cellular level of H2O2 would be useful. Application note 252, recently added to BMG LABTECH's website describes the use of the PHERAstar FS to detect a genetically encoded redox probe specifically designed for H2O2 detection.

Lung adenocarcinoma H1975 cells expressing the cytosolic
roGFP2-Orp1 probe. Cells were exposed to hydrogen 
peroxide as indicated, and the probe response followed using 
the PHERAstar FS
This note entitled: 'Real-time monitoring of genetically encoded redox probes in mammalian cell monolayers' describes a very useful tool that can be used to monitor cellular redox changes. This note employs biosensors based on redox sensitive green fluorescent protein (roGFP). RoGFPs are GFPs that have had 2 surface exposed residues changed to cysteines. These cysteines are in appropriate positions to form a disulfide bond. In the oxidized state this bond is strained and the protein contains localized structural changes which are believed to be responsible for the spectral changes of roGFP that change the excitation maxima from 485 nm to 400 nm. Furthermore, roGFP can be engineered to respond to specific redox species. In this case,  fusion to the thiol peroxidase Orp1 generates a H2O2 sensitive roGFP.

The PHERAstar FS proved to be an excellent tool for detecting changes in H2O2 using this biosensor. To find out more please visit the Applications Page on BMG LABTECH's website.

Application note: #252 Real-time monitoring of genetically encoded redox probes in mammalian cell monolayers

Wednesday, June 25, 2014

Did you know your microbiome can be detected on your phone?

Structure and shape of E. coli 70S
ribosome. For the 30S subunit, the
16S rRNA (dark blue) is shown.
by Vossman


According to a study published recently in Peer J. the bacteria that are present on a cell phone closely resembles that which was sampled from the owners fingers. The analysis, performed by University of Oregon scientists, was a proof of concept experiment that used short-read 16S sequencing to categorize the whole microbial community.

This type of sequencing refers to sequencing of the gene for the 16S ribosomal RNA component of a subunit of the prokaryotic ribosome. Previous work has indicated that this gene is highly conserved in bacteria species and thus can be used in phylogenetic studies such as this.

While it may not be surprising that the bacteria that reside on our hands can also be found on our phones, the authors propose that the phones could be used as a non-invasive way to monitor our health. The uses of this screening could include real-time assessment of possible exposure to pathogens that could be carried into and out of a medical facility.

Some information was obtained from the Science Direct article:  Cell phones reflect our personal microbiome

Original article: J.F. Meadows et al Mobile phones carry the personal microbiome of their owners. Peer J, 2014

Thursday, June 19, 2014

How well do we understand water?

Water is all around us and inside us, it is essential for life as we know it.

It's chemical formula is one that nearly everyone knows regardless of their background. Water has a very simplistic structure as well so what else can we learn about water?

It turns out there is still a lot we can learn about water as was exhibited by two papers that were published in a recent issue of the journal Nature.

Image of the electron localization of water
by JVertrees
One aspect of water which we still can't fully explain is why it floats when it freezes. This characteristic is unlike other molecular substances. Without this characteristic marine life could not survive as lakes, rivers and oceans could freeze solid. To investigate the properties of water as it freezes, scientists at Princeton University used computer modeling. Their results indicate that at very cold temperatures and above a certain pressure water actually splits into two different liquid phases. This finding supports the 'liquid-liquid transition' proposed by Eugene Stanley in 1992. The authors propose that these two liquid phases may be responsible for the areas of low and high density that are known to exist in forming ice. As ice solidifies the low density regions predominate leading to a solid form that is less dense than the liquid form. If this dual nature can be observed in experiments it could improve the predictive ability of our weather and climate models.

The second paper could go a long way toward providing the experimental evidence necessary to study water under different conditions. In this paper scientists at the Stanford Linear Accelerator Center used the Linac Coherent Light Source X-ray laser to collect rapid-fire snapshots of waters molecular structure in the instant before it freezes.

For their experiments the researchers produced a steady stream of very pure water droplets in a vacuum that were directed toward a laser that was pulsing with a femtosecond shutter speed. As the water traveled towards the laser beam some of the liquid evaporated supercooling the remaining water to temperatures below minus 42 F ( -41 C). Their results showed the molecular structure of water is continuously transforming just before freezing and further cooling dramatically accelerates the structural changes observed. It is hoped that by pushing these experiments into colder regions closer to the transition to a solid that they will be able to identity the theories that best explain waters behavior.

Some information for this post was obtained from the Science Daily articles:

Familiar yet strange: Water's split personality revealed by computer model

Scientist take first dip into water's mysterious 'no man's land'

Original articles are:

J.C. Palmer et al Metastable liquid–liquid transition in a molecular model of waterNature, 2014; 510 (7505): 385 

J.A. Sellberg et al  Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperatureNature, 2014; 510 (7505): 381 

Thursday, June 5, 2014

Applications: HTRF Epigenetic Assays using the PHERAstar FS


Epigenetics remains a hot topic in the biological scientific community due to its role in cancer and autoimmune diseases. This field describes how the regulation of gene activity and expression are not solely dependent on genetic sequence but can be influenced by DNA methylation and histone modification.

Enzyme inhibition curves for three G9a compounds

In this application note we verify the performance of a Cisbio HTRF® assay that allows you to detect the activity of the histone methyltransferase G9a. G9a is a member of a class of enzymes that mediate the methylation of histone H3 and is an excellent epigenetic target due to its reported role in embryogenesis and cancer cell proliferation.

The use of laser excitation, HTRF® optimized optic module and matched PMT’s dedicated for TRF detection make the PHERAstar FS an excellent choice to perform this assay. Combined with BMG LABTECH’s MARS data analysis software you will be able to perform enzyme inhibition curve analysis quickly and easily with high quality data.


For more information please visit the Applications Page on BMG’s website or access the application note at the following web address:

Monday, June 2, 2014

Experimental drug could be useful MERS treatment

MERS virus 3-D image
by Scinceside
MERS (Middle Eastern Respiratory Syndrome) has been featured in the news of late due to the spread of the disease globally.

 The virus that causes MERS belongs to a group called coronaviruses. Currently, no treatment for coronaviruses exists. However, a chemical called K22 was recently shown to inhibit the growth of various strains of coronavirus, including those that cause MERS.



The results are reported in the PLOS pathogens article entitled:'Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus.' The work is a collaborative effort of scientist at a number of European Universities and describes how K22 inhibits viral RNA synthesis and the formation of double membrane vesicles. Therefore, K22 halts viral replication at a very early stage. The authors propose that the recruitment of cellular membranes for viral replication represents a druggable target for antiviral treatment and expect to be able to exploit this to develop new drugs to combat viral infections!

 The original article can be found at:

http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004166