Thursday, October 31, 2013

Review details potential role of epigenetic targets in cancer therapy

Scientist from Boston University School of Medicine recently published a review article in the International Journal of Molecular Sciences entitled: Cancer Development, Progression and Therapy: An Epigenetic Overview. In this article they propose that epigenetic and other changes mediate the development of cancer progenitor cells. Based on the acknowledgement of the key role of epigenetic changes in cancer progression they hope that better epigenetic drugs will become available.

Epigenetics refers to external modifications made to DNA and proteins associated with DNA. These modifications turn genes on or off but do not affect the DNA sequence. Epigenetic regulation is an important part of normal cell development and cell fate determination but when dysregulation of epigenetic mechanisms occur the results can be detrimental. The dysregulation of these epigenetic mechanisms may be in response to internal and external, or environmental, factors.

DNA molecule that is methylated on both strands on cytosine
by Christoph Bock
The importance of epigenetics is clearly on the rise and there are a number of different assays available to study modulators of epigenetic enzymes. At BMG LABTECH we have multiple microplate reader platforms that are capable of detecting these epigenetic enzyme assays. Please visit our website to see the capabilities of all of our instruments: www.bmglabtech.com

Wednesday, October 30, 2013

Three new vertebrate species found in Australia

Cape Melville, Cape York, Queensland, Australia
Cape Melville in Australia contains a rugged mountain range that consists of large black granite boulders stacked high. The unique nature of this mountain range has allowed surveys of the base of the mountain but restricted access to the rainforest that sits atop a plateau. Now, a National Geographic expedition finally made it there, with the help of a helicopter to fly them in. Within several days of their arrival the scientists and film crew were surprised to find 3 new vertebrate species! The new species were named and described by Dr. Conrad Hoskins from James Cook University.

One of the species is especially unique, the Cape Melville Leaf-tailed Gecko, which, as its name suggests, has a broad flat tail at the end of its 20 cm body. The other species are the Cape Melville Shade Skink which is golden in color and the Blotched Boulder-frog whose range is completely restricted to the boulder fields at Cape Melville.

It is very surprising to find three new species anywhere, let alone in Australia which was thought to have been thoroughly explored.

Information for this blog was obtained from Science Daily

Friday, October 25, 2013

Three-dimesional structure of RNA polymerase I solved

Diagram of the essential subunit of
human RNA polymerase I, II, III
by Nevit Dilmen

Three different RNA polymerases are employed in order to make all of the different types of RNA required for normal cell function. The structure of RNA polymerase II, which makes mRNA, has been known for over 10 years but the structure of RNA polymerase I, which is responsible for making RNA which will form ribosomes has been elusive, until now. Details of the structure of RNA polymerase I may be found in a recent publication in the journal Nature. The report is a collaboration between German and Spanish scientists entitled:  'Crystal structure of the 14-subunit RNA polymerase I.'



One aspect that had previously confounded the study of RNA polymerase I is its size, which is much larger than RNA polymerase II. The results of the 3-D structure indicate that some of the larger size is the result of additional modules that are very similar in structure to proteins that assist RNA polymerase II function. Having these modules constantly attached may, in part, explain why RNA polymerase I produces RNA faster than RNA polymerase II. However, the permanent association provides the cell with fewer means of regulating RNA polymerase II function.

To find out more about this discovery you can read the ScienceDaily entry: Bigger, Better, Faster: 3D Structure Reveals Protein's Swiss-Army Knife Strategy

Thursday, October 24, 2013

Recently added: BMG application notes on DLR, protein concentration and nephelometry.

BMG LABTECH recently added three new application notes two are on topics that are quite familiar to most biological scientists and one that is....not so much.

Representative DLR data.


Dual luciferase reporter (DLR) assays and using absorbance at 280 nm for protein detection are assays that many are very familiar with. DLR is the popular technique from Promega that uses two reporter constructs that allow users to monitor the regulation of gene transcription and normalize with an internal control. Since other BMG LABTECH instruments like CLARIOstar and Omega Series have been previously certified as DLR ready it was not surprising that the PHERAstar FS was also capable of passing this certification, which is described in AN #243.

BMG's LVis plate
The other common assay, protein quantification by UV absorbance at 280 nm is described in AN #242. The detection was performed using the LVis plate. The LVis plate allows the user to perform low volume detection of samples while reading up to 16 samples. In this application note the performance of the LVis plate was validated over a wide range of protein concentrations. The LVis plate is compatible with any BMG microplate reader that is equipped with our ultra-fast UV/Vis spectrophotometer such as the SPECTROstar Nano, PHERAstar FS, CLARIOstar and Omega Series of readers.


Finally we have the not so familiar. AN#238 employs an approach called nephelometry. Nephelometry is a specialized detection method that measures the amount of laser light that is scattered dependent on the size/shape of particles in a solution. The NEPHELOstar from BMG LABTECH is the only microplate reader available that employs this detection technology. In this application note the NEPHELOstar was used to monitor the amount of calcification that occurs in serum samples. When calcification takes place in blood vessels it can lead to cardiovascular disease.

These applications show that whether or your assay is usual or unusual BMG LABTECH has a microplate reader that will suit your needs.

Tuesday, October 22, 2013

RTQuIC at Expanding Prion Horizons

As the Expanding Prion Horizons Symposium wrapped up last week we at BMG LABTECH were happy that we could sponsor such a stimulating meeting. All the talks and posters were excellent and generated lively discussion. BMG LABTECH is pleased to see the Real Time Quacking Induced Conversion (RT-QuIC) assay is being used extensively and we are glad that a plate reader like the FLUOstar Omega can contribute to the prion research field. As reported at this meeting the high sensitivity RT-QuIC is capable of detecting disease prions where western blots and immunoassays can’t, such as higher through put cell culture studies where prion protein expression is low. Furthermore, its sensitivity is at least comparable to ELISA and IHC in detecting Chronic Wasting Disease (CWD) in a variety of cervid species.

Representative data from BMG application note # 232


The RT-QuIC assay is being considered for use in the early detection of prion diseases. CWD can now be detected in deer saliva in as little as 6 months, which is at least one year before deer exhibit clinical symptoms. Among the prion diseases CWD appears to be unique in the amount of disease prion that is externalized. Therefore, another study used RT-QuIC to look at which tissues are affected by prions. Finally, a more wide spread early detection application may be a blood test. Indeed, a blood test was described that is a modification of RT-QuIC and is capable of detecting prion infection at the midpoint between infection and onset of symptoms.


RT-QuIC is also being used to study routes of prion transmission. One study looked at the ability of bovine spongiform encephalopathy (BSE aka ‘mad’ cow disease) prions to infect deer and CWD prions to infect cows. Another investigated the possibility of prion transmission from mother to offspring. Clearly RT-QuIC can be used in a variety of ways and the FLUOstar Omega from BMG is an excellent tool to perform this assay.

Friday, October 18, 2013

Conference Report: Expanding Prion Horizons - Day 1

Characteristics of Alzheimer's disease
We at BMG LABTECH are happy to be able to sponsor this weeks Expanding Prion Horizons meeting at Colorado State University. The first day was certainly a success with excellent talks and stimulating discussion.

Nobel laureate Stanley Prusiner got the day started with an excellent key note speech in which he stated his hypothesis that all neurodegenerative disease can also be considered prion diseases. This includes chronic traumatic encephalopathy (CTE) which has been in the news recently due to the concerns over head trauma in football in the United States.

The morning had a number of excellent talks that discussed the various ways that protein misfolding can lead to human disease while the afternoon focused on the biology and pathology of prion diseases. One talk that BMG took particular notice of was by Martin Margittai discussing fibril growth of Tau which results in neurofibrillary tangles in Alzheimer's Disease. His talk was interesting due to the experimental approach he presented which can be used to monitor Tau filament growth. After labeling Tau monomers they were able to monitor filament growth using fluorescence spectroscopy in which they excited at a wavelength of 344 nm then performed an emission scan from 360 to 600 nm. As the Tau filament grows the emission peak shifts so they can now use this assay to test for filament growth efficiency.This approach could be easily adapted for higher throughput using the new CLARIOstar from BMG LABTECH which features an Advanced LVF Monochromator.

Tuesday, October 15, 2013

How can non-coding mutations affect disease states?

Recent advances have made it easier to sequence the genome of an individual. With this information in hand it now becomes important to be able to use this information to make predictions about the effect that genetic mutations have on the chance that an individual will be affected by a disease. If a mutation occurs in a gene it is fairly straight forward to predict the effect that this alteration will have on the function of the protein encoded by the gene and subsequently the propensity to acquire a disease. However, genome wide studies that investigate the association of mutations with disease reveals that only 12% of the disease associated mutations occur in coding regions of the DNA. It, therefore, stands to reason that the remainder of these mutations will occur in regulatory elements, regions of DNA that bind transcription factors in order to control when and how strongly a gene is expressed. However, the mechanisms for genetic variation to affect regulation of transcription are incompletely understood.

Cartoon representation of the molecular structure of
transcription factor PU.1 residues 171-259 interacting with
a strand of DNA

by Jawahar Swaminathan





With this in mind scientists at the University of California-San Diego sought to characterize transcription factor binding across a genome. The results of their study are presented in the recent Nature article entitled: 'Effect of natural genetic variation on enhancer selection and function.' They used macrophage cells from two different mice strains and compared about 4 million DNA sequence differences. They chose the DNA sequences to analyze based on their binding to transcription factors using a technique called ChIP-Seq. This approach allows you to isolate the chromatin (DNA) which is bound to a protein by immune-precipitating the protein then perform sequencing of the DNA that is bound by the protein and therefore co-precipitates with the protein. Based on this they believe they have genomic data for lineage-determining transcription factor binding sites that can be used to study disease-associated variations in the DNA sequence.

Friday, October 11, 2013

Upcoming BMG LABTECH Events

Representative RT-QuIC data from BMG application note #232
Next week BMG LABTECH is proud to sponsor the Expanding Prion Horizons 2013 meeting at Colorado State University. Our involvement in prion research is due to the utility of the FLUOstar Omega in performing real time quaking induced conversion (RT-QuIC) assays. This fluorescence based assay monitors the accumulation of misfolded protein that is the hallmark of prion diseases. The RT-QuIC assay exhibits sensitivity equal to bio-assays that are much more time consuming and expensive.

Please stop by and meet one of the BMG LABTECH representatives during the meeting to find out more about the RT-QuIC assay and the performance of the FLUOstar Omega and other BMG LABTECH microplate readers.

For more information on this and other events which BMG will attend please visit the Events Page on the BMG LABTECH website: http://www.bmglabtech.com/events/BMG-Labtech-Events.cfm

Thursday, October 10, 2013

Key Molecule Involved in Cell Division Could be a Novel Therapeutic Target

Regulation of cell division is essential for developing organisms but can lead to harmful tumor growth when the process is dysregulated. Our expanding knowledge of how this process is regulated has lead to novel therapeutic targets based on the blockade of cell division or mitosis. A paper in the current issue of The Proceedings of the National Academy of Sciences describes the collaborative efforts of Spanish and French scientists to decipher the role of the protein Greatwall in mammalian cell division.

Cell in prometaphase
by Roy van Heesbeen

Previous to this report, Greatwall was shown to regulate cell division in invertebrates such as the Drosophilla melanogaster fly and its biochemistry has been characterized in Xenopus. The current work describes the generation of the first mammalian genetic model of this protein using mice. The authors found that cells lacking Greatwall are not capable of adequately dividing themselves even though they enter mitosis with normal kinetics. The deviation from normal cell division occurs after the nuclear envelope breaks down exposing nuclear components such as chromosomes to the cytoplasm and the enzyme activities localized there. Without Greatwall the DNA does not condense to form the correct structures and cell division is halted at prometaphase.



The potential therapeutic capacity of Greatwall is enhanced because it acts by blocking the function of PP2A, a frequently altered tumor suppressor. Therefore, inhibition of Greatwall could slow down cell division and reactivate a tumor suppressor that has been shown to be capable of inhibiting many oncogenic pathways involved in the development of cancer. The search now begins for compounds capable of inhibiting Greatwall and understanding which types of cancer would most benefit from treatment with a Greatwall inhibitor.

The title of the PNAS article is: 'Greatwall is essential to prevent mitotic collapse after nuclear envelope breakdown in mammals'


Wednesday, October 9, 2013

Three Nobel Laureates Share the 2013 Nobel Prize in Chemistry

The Royal Swedish Academy of Sciences announced today that the Nobel Prize in Chemistry for 2013 would be shared by Dr.'s Martin Karplus, Michael Levitt and Arieh Warshel 'for the development of multiscale models for complex chemical systems.' The three receive the award based on their collaborative efforts to design a computer program to reveal how chemical processes proceed.







Under normal conditions chemical reactions occur very quickly as electrons move between atomic nuclei. This makes it virtually impossible for every step in the process to be mapped experimentally. When the 3 Nobel Laureates began their collaboration in the 1970's suitable computer programs were being developed based on classical Newtonian physics, which were useful in showing how atoms are positioned in a large molecule, such as a protein, and  programs based on quantum physics which were useful for simulating chemical reactions. The work that earned Karplus, Levitt and Warshel the Nobel Prize was the program they developed that allowed these two fundamentally different types of physics to work side by side. They used quantum theoretical calculations to describe the interface between a protein and its smaller substrate while the rest of the large protein was simulated using classical physics. Their breakthrough made the computer just as important to chemists as traditional experiments.

Information for this blog was obtained from:

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/press.html


Tuesday, October 8, 2013

2013 Nobel Prize in Physics Awarded Today

The Royal Academy of Sciences gave the Nobel Prize in Physics jointly to Dr.'s François Englert and Peter W. Higgs “for the theoretical discovery of a mechanism that contributes to our understanding of the origin of mass of subatomic particles, and which recently was confirmed through the discovery of the predicted fundamental particle, by the ATLAS and CMS experiments at CERN’s Large Hadron Collider”. The Noble Laureates independently proposed the theory for how particles acquire mass in 1964 and saw their ideas confirmed last year with the discovery of the Higgs particle.

This represents the Standard model of elementary particles:
You can see representations for 12 fundamental particles
that make up matter (orange and green boxes) and
4 fundamental force carriers (purple boxes).

Dr.'s Higgs and Englert are both Professors Emeritus at University of Edinburgh, UK and Université Libre de Bruxelles, Belgium respectively. Their theory is central to the Standard Model of particle physics which describes the construction of the world based on the interaction between matter particles and force particles. The Standard Model relies on the existence of the Higgs particle which originates from an invisible field. The theory for which Higgs and Englert received this award describes the process where particles acquire mass when they interact with the invisible field.

Congratulations Dr. François Englert and Dr. Peter W. Higgs! Thank you for your contribution to our understanding of the physical world!



Information for this blog was obtained from:

 http://www.nobelprize.org/nobel_prizes/physics/laureates/2013/press.html

Monday, October 7, 2013

Winners of The 2013 Nobel Prize in Physiology or Medicine Announced.

The Nobel Assembly decided to jointly award the 2013 Nobel prize in Physiology or Medicine to Dr.'s James E. Rothman, Randy W. Scheckman and Thomas C. Südhof 'for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells'. Vesicles are the sub-cellular packages surrounded by membranes that are responsible moving molecules, such as hormones, enzymes or neurotransmitters which are produced by cells, from their site of production to the their eventual release either inside of outside of the cell. Each of the Nobel Laureates was instrumental in uncovering the molecular principles that govern the appropriate delivery of these packages.

Exocytosis, one of the possible endpoints of vesicular
trafficking,  is the process by which a cell directs secretory
vesicles to the cell membrane. These membrane-bound
vesicles contain soluble proteins to be secreted to the
extracellular environment, as well as membrane proteins
and lipids that are sent to become components of the
cell membrane.
by Mariana Ruiz
Dr. Südhof, a German born scientist, currently a Howard Hughes investigator and Professor at Stanford University, revealed how signals precisely regulate the release of cargo from vesicles. Dr Scheckman, is also a Howard Hughes and is a Professor at University of California at Berkley. His contribution was the discovery of a set of genes that are required for the cargo carrying vesicles to move through the cell. Meanwhile, Dr. Rothman, currently a Professor and Chariman of the Department of Biology at Yale, discovered the protein-protein interactions necessary for vesicles to fuse with their correct targets.

Without the appropriate function of vesicle transport a variety of physiological processes can be disrupted such as the release of hormones and cytokines. The result of these disruptions are a variety of disease states such as diabetes as well as neurological and immunological disorders. The contributions of these scientists have expanded our understanding of a vital process and are clearly worthy of the honor that is The Noble Prize!

Information from this blog was obtained from:
http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/press.html


Friday, October 4, 2013

New Small-Molecule Catalyst Could Greatly Speed Therapeutic Discovery Process

To create new therapeutics scientists identify lead compounds which have the desired effect. In order to make these compounds more efficacious, modifying this lead compound is often desirable to improve biological function. Currently, this usually involves either a long synthetic process or engineering an enzyme that is specific to that molecule. However, a recent report in the Journal of the American Chemical Society describes the work of University of Illinois chemists that shows the utility of a human-made catalyst that is an 'enzyme-mimic'.

Ball-and-stick model of the camphoric acid molecule,
 an oxidation product of camphor.

(Black: Carbon(C), White: Hydrogen(H), Red: Oxygen (O)
Unlike enzymes which are large proteins that act on only select molecular targets the new catalyst can oxidize specific carbon hydrogen (C-H) bonds on many different targets. The hope is that catalysts like this new one (called iron CF-3 PDP) and a previously reported catalyst (called iron PDP) will represent a new tool-box that will allow therapeutic designers to alter any C-H bond on any molecule quickly and efficiently.

If these catalysts realize their potential it will allow new therapeutics to be made in less than an hour rather than weeks. The new compounds can then be used in high throughput screening, something at which the PHERAstar FS from BMG LABTECH excels.

The original article from JACS is entitled: Catalyst-Controlled Aliphatic C–H Oxidations with a Predictive Model for Site-Selectivity.

Tuesday, October 1, 2013

New High-Throughput Screen for Hepatitis C inhibitors


Simplified diagram of the structure of Hepatitis C virus
by Graham Colm
RNA-dependent RNA polymerases (RdRp) play an essential role in replication of hepatitis C virus (HCV). As such it is a key target for novel antiviral therapies and inhibitors are in clinical trials for HCV genotype 1 (G1). However there are 6 distinct genotypes and the inhibitors for G1 exhibit a poor efficacy for non-G1 genotypes.

It was because of this scenario that a group from Australia sought to identify potential inhibitors for genotype 3a. The result of their work is described in the recent JBS article entitled: 'A Fluorescence-BasedHigh-Throughput Screen to Identify Small Compound Inhibitors of the Genotype 3aHepatitis C Virus RNA Polymerase’.

Their assay design was quite straight-forward in that they sought to assess RdRp activity by detecting synthesis of double-stranded RNA from a single-stranded template. To do this they took advantage of the fact that the commercially available fluorescent dye PicoGreen binds double stranded RNA preferentially over single-stranded RNA. Production of double-stranded RNA was quantified by measuring fluorescence intensity on a POLARstar Omega microplate reader from BMG LABTECH.


We at BMG LABTECH are happy that we can contribute in some small way to the assay development and performance of HTS necessary for drug discovery such as that described in this JBS article. Our new CLARIOstar provides even more flexibility when designing a FI based assay due to its Advanced Linear Variable Filter Monochromator. Furthermore, the PHERAstar FS continues to be an excellent choice for HTS. Whatever your microplate reader needs, BMG LABTECH has a product that will help you make the most of your application.