Author: Kari Kenefick

To Meditate Perchance to Dream

Posted on by Kari Kenefick

First the disclosure: this blog is of course about Me.

But it’s also about You. And yours. Because as you know, we’ve become a culture that does not sleep.

Why don’t we sleep? I like to think that it is an evolutionary adaptation; not sleeping, after all, allows us more time for Facebook.

Or Etsy for you makers. Or Amazon for you shoppers. And let’s not forget our middle, high school and college students. Do they even have classrooms anymore, or are lectures all online (on screens)?

One tired pony. By Rachel C from Scotland (Flickr) [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
One tired pony. By Rachel C from Scotland (Flickr) [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
Honestly, the evolutionary adaptation idea comes from how we live and work today. And no, this is not another rant/lecture on the color of light emitted by whatever non-cathode ray tubes are in our phones or tablet-like devices.

It’s just that just working in our very busy online/wired world, jumping from web page to project management software, to big-screens in meetings has us adapted to being  on: capital “O” capital “N”.

This multi-multitasking has grown (for me) a new type of neurons that are not happy unless they are gleaning new information from a screen, all the time. And these neurons don’t stop working when the screen is gone; no, they continue seeking and trying to process. For me, if there’s no screen to look at, the neurons ping-pong around behind my eyeballs, looking and searching, as if to say, “Input missing! Input missing!”

The result can be hours in bed sans sleep; it seems the racket these neurons make keeps all the other neurons up. Continue reading “To Meditate Perchance to Dream”

Studying Mitochondrial Fission with NanoBiT Complementation Assay

Posted on by Kari Kenefick
3D depiction of NanoBiT Protein Complementation

Updated February 15, 2021

If you’re interrogating two proteins to understand the conditions under which they interact, a complementation system enables you to tag each protein. Interaction of the tagged proteins facilitates the complementation of the subunits, resulting in a signal. Here we discuss the NanoBiT complementation assay and describe its use to study mitochondrial fission.

Continue reading “Studying Mitochondrial Fission with NanoBiT Complementation Assay”

How Fruit Flies (and maybe Pigeons?) Navigate; A New Report

Posted on by Kari Kenefick
A rock dove, similar in plumage to a pigeon.
A rock dove, similar in plumage to a pigeon.

Several years ago an intriguing story of successful navigation in complex situation, by pigeons, the birds most often compared to rats, caught my eye.

Our backyard once had a coop full of pigeons, so I’m not a total stranger to their navigation abilities (nor am I a pigeon expert). My favorites were the tumbling pigeons.

But it didn’t take much time researching that article from 2012, to learn that one of the more hotly debated how-do-they-do-it topics is animal navigation, in particular, the ability of pigeons to navigate back to home/point A when released at point B.

So when it appeared online today, in Nature Materials, the story “A Magnetic Protein Biocompass” caught my eye.

Continue reading “How Fruit Flies (and maybe Pigeons?) Navigate; A New Report”

About the Development of an Improved BRET Assay: NanoBRET

Posted on by Kari Kenefick

"Protein BRD4 PDB 2oss" by Emw - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Protein_BRD4_PDB_2oss.png#/media/File:Protein_BRD4_PDB_2oss.png
“Protein BRD4 PDB 2oss” by Emw – Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:Protein_BRD4_PDB_2oss.png#/media/File:Protein_BRD4_PDB_2oss.png

One of the more exciting reporter molecules technologies available came online in the past year, with the launch of the Promega NanoBRET™ technology. While it’s easy for me, a science writer at Promega, to brag, seriously, this is a very cool protein interactions tool.

A few of the challenges facing protein-protein interactions researchers include:

  • The ability to quantitatively characterize protein-protein interactions
  • Ability to examine protein-protein interactions in situ, in the context of the living cell

A goal of the NanoBRET™ developers was to improve the sensitivity and dynamic range of traditional BRET technology, in order to address these challenges.

In May 2015 these researchers published an article outlining their efforts to create NanoBRET technology in ACS Chemical Biology, in an article entitled, “NanoBRET—A Novel BRET Platform for the Analysis of Protein-Protein Interactions”. Here is a brief look at their work.

Continue reading “About the Development of an Improved BRET Assay: NanoBRET”

Sequencing the Octopus Genome: Invertebrate Intelligence Explained?

Posted on by Kari Kenefick

In a Letter in Nature magazine last week (August 13, 2015), researchers published surprising findings from a genome analysis of the octopus. As a result, we now know that this invertebrate has more than just behavioral oddities with which to amaze.

In their publication, C. Albertin et al. report the results of genome sequencing of the California two-spot octopus, Octopus bimaculoides. They did not find the predicted whole-genome duplication, but rather an unexpectedly large genome with many rearrangements, and two gene family expansions that were previously thought to exist only in vertebrates.

Califonia two spot octopus. Image by Jeremy S. Taken at Santa Monica Aquarium. Used via Creative Commons license, Wikimedia.
Califonia two spot octopus. Image by Jeremy S. Taken at Santa Monica Aquarium. Used via Creative Commons license, Wikimedia.

The Research
Albertin et al. sequenced the O. bimaculoides genome using a whole-genome shotgun approach, and then annotated it using extensive transcriptome sequences from 12 tissues. They estimate that the genome assembly incorporated 97% of protein-coding sequences, and 83% of the entire 2.7gigabase genome. The remaining sequence was composed largely of repetitive elements. Continue reading “Sequencing the Octopus Genome: Invertebrate Intelligence Explained?”

A Reason for Ribonuclease: From Laboratory Nuisance to Cancer Therapeutic

Posted on by Kari Kenefick

"RNase A". Licensed under CC BY-SA 2.5 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:RNase_A.png#/media/File:RNase_A.png
“RNase A”. Licensed under CC BY-SA 2.5 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:RNase_A.png#/media/File:RNase_A.png

RNase, back in the early 1990s, posed a serious threat to laboratories working with RNA isolation. My graduate work involved isolating RNA from the tissues of Lyme disease-infected mice and hamsters. We struggled to DEPC-treat glass and plasticware, or autoclave anything that could be autoclaved, kept tissues cold during RNA harvest and held our breaths (truly, as aerosol could be another source of ribonuclease) until PAGE proved us successful in RNA isolation.

Ribonuclease (RNase) was omnipresent and the arch rival of our work, across several species, due to its RNA destroying abilities.

Now, a July 13, 2015 publication by researchers at the University of Wisconsin-Madison provided both a catch-up for this former lab rat on modern day research with and knowledge of RNase, as well as an exciting look at what may be a real purpose for this RNA-destroying molecule: RNase has moved to clinical trials due to the discovery of it’s cytotoxicity for cancer cells.

Raines’ group in the Department of Chemistry at UWI-Madison published in ACS Central Science their findings on the ligand that RNase 1 uses to attach to human cancer cells, in the article, “Human Cancer Antigen Globo H is a Cell-Surface Ligand for Human Ribonuclease 1”. Continue reading “A Reason for Ribonuclease: From Laboratory Nuisance to Cancer Therapeutic”

Your Health has a Season

Posted on by Kari Kenefick

Photo of pasque flowers
Pasque flowers in a northern hemisphere garden in spring.

As the seasons change so does the general state of health for many of us. The further from the equator we live, the more pronounced these effects are. For instance, did you know that blood pressure elevation for many people increases with the distance they live from the equator, an effect most pronounced during the low sunlight season (winter in the northern hemisphere)?

A report published online in Nature Communications May 12, shows evidence of changes in cellular physiology with the seasons. Todd et al. published a study entitled: “Widespread seasonal gene expression reveals annual differences in human immunity and physiology”, where they note,

“Here we find more than 4,000 protein-coding mRNAs in white blood cells and adipose tissue to have seasonal expression profiles, with inverted patterns observed between Europe and Oceania.”

Let’s Take a Look at the Research

Todd et al. looked at ethnically and geographically distinct populations, including subjects from Australia, The Gambia (Africa), Germany, the UK and Iceland. Individuals from the various studies were infants, adults with type 1 diabetes and asthmatics in the range of 18-83 years of age. The authors analyzed RNA from peripheral blood mononuclear cells and subcutaneous adipose tissue biopsies, as well as examining peripheral blood cell counts and circulating levels of proinflammatory cytokines. Continue reading “Your Health has a Season”

Immune Checkpoint Inhibitors: Has Cancer Met its Match?

Posted on by Kari Kenefick
The cover of S. Mukerjee's book, The Emporer of All Maladies: The Biology of Cancer. Used courtesy of Wikimedia and WLU.
The cover of S. Mukerjee’s book, The Emporer of All Maladies: The Biology of Cancer. Used courtesy of Wikimedia and WLU.

Dr. Drew M. Pardoll, Johns Hopkins University School of Medicine in Baltimore, in his 2012 review, “The blockade of immune checkpoints in cancer immunotherapy” published in Nature Reviews Cancer (1) writes:

“The myriad of genetic and epigenetic alterations that are characteristic of all cancers provide a diverse set of antigens that the immune system can use to distinguish tumour cells from their normal counterparts.”

Tumors have antigens, so we should be able to address/attack these antigens with our immune system, right?

Various immune mediators as therapeutic agents against cancer have entered and mostly flopped in clinical trials over the past 30 or more years. As a graduate student in the 1980s I remember IL-2 and interferon raising many hopes. More recently, drugs against chronic myeloid leukemia and CLL have shown early promise. However, so far cancer cells have mostly won against these therapies. Yet recent news points to some exciting new therapeutic agents, that over the past 15 years or so, and in and out of clinical trials, are getting a leg up in the cancer battle. These drugs are immune checkpoint inhibitors.

Continue reading “Immune Checkpoint Inhibitors: Has Cancer Met its Match?”

Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection

Posted on by Kari Kenefick

http://upload.wikimedia.org/wikipedia/commons/6/65/Blausen_0012_AdiposeTissue.png
Cross-section of skin and adipose tissue enlargement. Used courtesy of Wikimedia Commons, Blausen.

A basic tenet of immunology is that antibodies produced by B cells are very important and specific immunoprotective agents, released in response to infection.

However, antibodies do not supply immediate protection. The invading organism needs to get into the host, meet up with T cells and then B cells, in order for antibody production to occur. If the host has seen this particular pathogen previously, the antibody response occurs somewhat more quickly, but we’re still talking about days. If the invading organism is a bacterium, it can multiply and double in numbers in just hours. Thus an infection could potentially gain a foothold in a body prior to an antibody response.

Fortunately we have a more rapid, first line of defense to invading pathogens, a cellular response. In the case of a puncture or skin wound, epithelial cells, mast cells and leukocytes are activated quickly in response to pathogens. Neutrophils and monocytes also aid the cellular response.

Now a recently published report demonstrates that fat cells also play a part in the cellular response to invading bacteria. R. Gallo et al. published a study on Jan. 2 in Science, providing more in depth information on the role of adipocytes in the host response to the bacterium Staphylococcus aureus (S. aureus). Continue reading “Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection”

Insights into the Function of P7C3 Compounds in Neuroprotection

Posted on by Kari Kenefick

The multiple Lombardi trophies won by Pittsburgh Steelers. Image used under Wikimedia Creative Commons, and attributed to daveynin.
The multiple Lombardi trophies won by Pittsburgh Steelers. Image used under Wikimedia Creative Commons, and attributed to daveynin.

It is fall and the season for American football. For this football fan, watching the game is a bit less enjoyable than it used to be, as more and more information is available about the serious and permanent brain injuries suffered by football players.

In the introduction to a recent paper in the journal Cell, “P7C3 Neuroprotective Chemicals Function by Activating the Rate-Limiting Enzyme in NAD Salvage”, not a word about American football is mentioned.

However, the paper begins, “No substantive therapeutics are available for the treatment of almost any form of disease entailing nerve death” (1). The authors list a range of neurodegenerative disorders such as Huntington’s, Alzheimers and Parkinson’s diseases, as well as ALS  or Lou Gherig’s disease. They also note that there are currently no effective treatments for trauma to the brain or peripheral nervous system.

The authors note that a chemical treatment that could interfere with nerve cell death would have a “transformative impact in modern medicine”. Continue reading “Insights into the Function of P7C3 Compounds in Neuroprotection”