Author: Sara Klink

The Black Death: World Traveler or Persistent Homebody?

Posted on by Sara Klink

Spread of the Black Death. By Timemaps (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL , via Wikimedia Commons.
In the last six years, researchers have untangled the origins of devastating human plagues, sequenced the genome of a Yersinia pestis strain responsible for the Black Death and explored how long this bacterium has been with humans. However, the information arising from this research begs more questions. How many variations of Y. pestis occurred during the 14–17th centuries, the second pandemic that began with the Black Death? Did these differences reflect the location in which the Y. pestis-positive skeletons were found? What were the geographic source or sources of these plagues? A recent PLOS ONE article examined Y. pestis found in German remains separated by 500km and 300 years to answer to some of these questions. Continue reading “The Black Death: World Traveler or Persistent Homebody?”

A Better GTPase Assay for Drug Development

Posted on by Sara Klink
Cover of October Issue of Assay and Drug Development Technologies featuring GTPase-Glo™ Assay.

The path to drug development is strewn with obstacles: Identifying targets; configuring assays to help identify targets or drugs; uncovering the right compound to affect the selected target without off-target effects and screening multiple compounds to eliminate or identify potential drugs. Without the right tools, compounds or target, identifying potential disease therapies becomes nearly impossible.

When it comes to a drug target for cancer, the Ras protein family is at the top of the list because the proteins are expressed ubiquitiously and found mutated in many types of cancer. Because Ras proteins are involved in transducing signals from the surface of cells, many of the resulting mutations produce an activated Ras, inducing uncontrolled expression of the genes that Ras controls. Ras proteins are small GTPases (20–25kDa) that comprise a larger superfamily of proteins divided into five subfamilies: Ras, Rho, Rab, Arf, and Ran. These proteins control diverse cellular activities, including cellular differentiation, proliferation, cell division, nuclear import and export, and vesicle transport. GTPases are guanosine-nucleotide-binding proteins with affinity for GDP or GTP and are able to hydrolyze GTP. When bound to GTP, GTPases are active (turned on) and interact with downstream proteins in the signaling cascade. When GTPases are bound to GDP, the proteins are inactivated (turned off) and no longer transduce signals.

Continue reading “A Better GTPase Assay for Drug Development”

Yersinia pestis Reveals More Secrets From the Grave

Posted on by Sara Klink
Yersinia pestis. By A.Myasnikov for Wiki (Self made work) [CC0], via Wikimedia Commons

Fridays are generally reserved for fun posts to share prior to the weekend. As we all know, fun is relative and to me, the latest news about how long Yersinia pestis has been entwined with human history is intriguing. I enjoy writing about the latest historical finding of Y. pestis even if I do earn a black reputation among my blogging colleagues (pun intended). Therefore, as soon as I saw the Cell article about Y. pestis found in Bronze age human teeth, I knew my blog topic was at hand.

Y. pestis has long been suspected in several plagues that occurred in the last two millennia. Publications in 2011 and 2013 used DNA extracted from teeth of human remains dated to the 14th century Black Death and 6th century Plague of Justinian to confirm Y. pestis was the causative agent in those devastating plagues. These results beg the question: How long has Y. pestis been infecting humans? The phylogenic trees generated from recent studies suggested Y. pestis has been with humans for as little as 2,600 years and as long as and 28,000 years. Equipped with these DNA-based tools, Rasmussen et al. asked if they could find evidence of Y. pestis in older human remains.

Continue reading “Yersinia pestis Reveals More Secrets From the Grave”

A Potential Single-Tube Multiplex Assay for Detecting Dengue Virus in the Field

Posted on by Sara Klink

In areas of the world where the electricity is intermittent, resources are limited and transporting bulky equipment and reagents that are sensitive to temperature fluctuations is difficult, diagnosis of viruses like dengue can be challenging. If you could reduce or eliminate the need for electricity dependent equipment for diagnostic assays without sacrificing sensitivity or specificity, it would be a boon to field workers. An article published in PLOS ONE describes how researchers developed a multiplex isothermal amplification method that could assess a potential dengue infection with a visual real-time or endpoint detection in a single tube.

Countries affected by dengue. By Percherie (Distribution de la dengue sur Commons) [GFDL ), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.5-2.0-1.0 , via Wikimedia Commons
Continue reading “A Potential Single-Tube Multiplex Assay for Detecting Dengue Virus in the Field”

Friday Cartoon Fun: Is It Drawn or Is It Real?

Posted on by Sara Klink

I always enjoy Ed Himelblau’s cartoons, but one that makes me chuckle every time I see it is the following:

Copyright Ed Himelblau.

I am sure our readers that enjoy coffee can empathize.

Recently, our Swiss branch had fun with a number of the cartoons from our Cartoon Lab archive and recreated the cartoon in real life:
Real-life recreation of Ed Himelblau's cartoon.
What do you think?

All You Need is Pla (for Pneumonic Plague)

Posted on by Sara Klink

Yersinia pestis. By Mrs Robinson at bg.wikipedia (Transferred from bg.wikipedia) [Public domain], from Wikimedia Commons.
Writing about Yersinia pestis or the Black Death, has earned me a reputation among Promega Connections bloggers. I am interested in what researchers have been able to piece together about the causative agent of ancient plagues, what modern research shows about how Y. pestis spreads in the body and the continuing reservoirs in modern times, resulting in publication of eight blog posts on the subject. Understanding Y. pestis bacterium is of continuing interest to researchers. How did Yersinia pestis evolve from the humble Yersinia pseudotuberculosis, a pathogen that causes gastrointestinal distress, into a virulent pneumonic plague that is a global killer? One strategy for answering this question is to look at the genomic tree of Y. pestis and trace which strains had what characteristics. In a recent Nature Communications article, Zimbler et al. explored the role of the plasmid pPCP1 in Y. pestis evolution and the signature protease Pla it expresses. Continue reading “All You Need is Pla (for Pneumonic Plague)”

Friday Cartoon Post: Do You See the Assays Glowing?

Posted on by Sara Klink

As a tribute to the fireflies lighting up the night during July evenings in Wisconsin and the reporter gene assays they inspire, I wanted to share a special Ed Himelblau cartoon:

Cartoon Copyright by Ed Himelblau
Cartoon Copyright by Ed Himelblau

Developing a Model System to Test Ketamine Toxicity

Posted on by Sara Klink

Figure 2. Ketamine induced morphological changes in neurons derived from iPSCs. Cells were treated with 0μM (Panel A), 20μM (Panel B), 100μM (Panel C) or 500μM (Panel D) ketamine for 24 hours. doi:10.1371/journal.pone.0128445.g002
Ketamine induced morphological changes in neurons derived from iPSCs.
Cells were treated with 0μM (Panel A), 20μM (Panel B), 100μM (Panel C) or 500μM (Panel D) ketamine for 24 hours. Scale bar = 50μm. From Ito, H., Uchida, T. and Makita, K. (2015) Ketamine causes mitochondrial dysfunction in human induced pluripotent stem cell-derived neurons. PLOS ONE 10, e0128445.
doi:10.1371/journal.pone.0128445.g002
When I consider that major surgery was performed long before anesthetics were developed, I am grateful to be alive in the anesthesia era. Just the thought of being subjected to various cutting and retracting instruments without general anesthesia calls to mind a phrase: The cure is worse than the disease. Despite the advantages of unconsciousness during surgery, anesthesia can have side effects. Studies in neonatal nonhuman primates have demonstrated that the anesthetic ketamine has toxic effects. However, the differences between humans and nonhuman primates mean the outcome in one species is not the same in another. In an article recently published in PLOS ONE, scientists were interested in creating an experimental model of developing human neurons and using the model to better understand the toxic effects of ketamine on human cells. Continue reading “Developing a Model System to Test Ketamine Toxicity”

Cancer Detection on a Chip?

Posted on by Sara Klink

Figure 5 shows typical scanned images of bead-array for analyzing adjacent normal tissue and tumor tissue. Huang et al. (2015) Digital Detection of Multiple Minority Mutants and Expression Levels of Multiple Colorectal Cancer-Related Genes Using Digital-PCR Coupled with Bead-Array. PLOS ONE 10(4):e0123420. doi:10.1371/journal.pone.0123420.g005
Figure 5 shows typical scanned images of bead-array for analyzing adjacent normal tissue and tumor tissue. Huang et al. (2015) Digital Detection of Multiple Minority Mutants and Expression Levels of Multiple Colorectal Cancer-Related Genes Using Digital-PCR Coupled with Bead-Array. PLOS ONE 10(4):e0123420. doi:10.1371/journal.pone.0123420.g005
The ideal cancer detection method would involve giving a sample of blood or tissue and using DNA or RNA analysis to determine if there were any gene sequence or gene expression changes that are known hallmarks of cancer. Unfortunately, most current screening methods used are not so precise and in some cases are invasive. However useful tests for colon cancer may be, many people do not subject themselves to the standard colonoscopy. What if there was an easier, noninvasive method that could be used to screen for cancer and detect changes at the early, easily treatable stages of cancer? A recent article in PLOS ONE describes just such a mutation detection method for colorectal cancer using purified nucleic acid with a method that involves emulsion PCR, bead arrays and fluorescent probes. Continue reading “Cancer Detection on a Chip?”

Cloning Tips for Restriction Enzyme-Digested Vectors and Inserts

Posted on by Sara Klink

Cartoon created and owned by Ed Himelblau
While T-vector cloning is commonly used for PCR-amplified inserts, restriction enzymes still have their uses. For example, you can ensure directional cloning if you digest a vector with the same two enzymes like BamHI and EcoRI that are used to digest your insert. This way, the insert can only be cloned in one direction. However, there are other cloning techniques that can be used to modify the end of vectors and inserts after restriction enzyme digestion and prior to ligation. Continue reading “Cloning Tips for Restriction Enzyme-Digested Vectors and Inserts”