Author: Sara Klink

microRNA: The Small Molecule with a Big Story

Posted on by Sara Klink

Introduction

miR-34 precursor secondary structure. The colors indicate evolutionary conservation. Ppgardne [GFDL (http://www.gnu.org/copyleft/fdl.html)

RNA molecules have become a hot topic of research. While I was taught about messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA), many more varieties have come into the nomenclature after I graduated with my science degrees. Even more interesting, these RNAs do not code for a protein, but instead have a role in regulating gene expression. From long non-coding RNA (lncRNA) to short interfering RNA (siRNA), microRNA (miRNA) and small nucleolar RNA (snoRNA), these classes of RNAs affect protein translation, whether by hindering ribosomal binding, targeting mRNA for degradation or even modifying DNA (e.g., methylation). This post will cover the topic of microRNAs, explaining what they are, how researchers understand their function and role in metabolism, cancer and cardiovascular disease, and some of the challenges in miRNA research.

What are microRNAs? MicroRNAs (miRNAs) are short noncoding RNAs 19–25 nucleotides long that play a role in protein expression by regulating translation initiation and degrading mRNA. miRNAs are coded as genes in DNA and transcribed by RNA polymerase as a primary transcript (pri-miRNA) that is hundreds or thousands of nucleotides long. After processing with a double-stranded RNA-specific nuclease, a 70–100 nucleotide hairpin RNA precursor (pre-miRNA) is generated and transported from the nucleus into the cytoplasm. Once in the cytoplasm, the pre-miRNA is cleaved into an 18- to 24-nucleotide duplex by ribonuclease III (Dicer). This cleaved duplex associates with the RNA-induced silencing complex (RISC), and one strand of the miRNA duplex remains with RISC to become the mature miRNA.

Continue reading “microRNA: The Small Molecule with a Big Story”

How Do Agricultural Landscapes Affect Bee Health?

Posted on by Sara Klink

Honey bee carrying pollen.Honey bees are hard-working insects. Their pollination services are in such demand, humans tow hundreds of hives carrying millions of bees around in the back of semitrucks to bring honey bees to various locations such as California almond groves. Humans are also quite partial to the bee colony winter energy storage also known as honey. So while honey bees work hard to collect pollen and nectar from blooming plants and trees and store honey for the winter, humans insist on robbing the colony’s store of delicious sweetener for their own uses. Recent reports of high mortality in honey bee colonies has caused concern in many beekeepers who manage European honey bee apiaries for honey production and pollination services. These severe depletion of honey bee colonies have been attributed to the parasitic mite Varroa destructor in the colony, not only feeding off the larvae and pupae brooding in the colony but also transmitting viruses carried by the mite. Bee nutrition is important for the pollinators especially when overwintering in the hive. Without adequate nutrition, a colony may become weak and succumb to parasite or disease pressure, unable to survive until nectar and pollen are available in the spring. A study was recently published in PLOS ONE that examined how the landscape around Midwestern honeybee hives affected the ability of bees to overwinter and assessed their health by measuring levels of Varroa mites and honey bee viruses. Continue reading “How Do Agricultural Landscapes Affect Bee Health?”

Finding a Connection Between Glucose Metabolism and Macrophage Activation

Posted on by Sara Klink

Introduction to Glucose Metabolism

Macrophages. By NIAID (https://www.flickr.com/photos/niaid/17380707492/) [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
Many think of glucose as something diabetics have to test each day using a blood monitor, or a quick energy boost for someone exercising intensely. However, the simple sugar glucose, a monosaccharide, fuels most of the cells in our bodies. Disaccharides that contain glucose (e.g., sucrose is comprised of glucose and fructose) and glucose polymers (e.g., starch and glycogen) are carbohydrates that are consumed by organisms from bacteria to humans to produce energy. These carbohydrates are broken down into component monosaccharides like glucose and lactose. The process of glycolysis generates the energy currency of cells, ATP, as well as precursor molecules for nucleotides, lipids and amino acids. Because glucose is the cell fuel source, the uptake of glucose and its subsequent metabolism is increased by cells that divide rapidly like cancer cells. The more energy and precursor molecules the cancer cell can create for itself, the more rapidly the tumor can grow.

Because glucose metabolism is central to cellular functioning, changes that decrease glucose uptake or increase glycolysis have a widespread effect on on both the cells and organism. How does a simple sugar molecule create such broad effects on health? For example, diabetes results from the inability to store glucose because of a lack of insulin, a hormone that draws glucose from the blood and stores it as glycogen in the liver, muscles and adipose tissue. High levels of sugar in the blood negatively affect the body over the long term, damaging blood vessels and eyesight, making the kidneys work harder to excrete the excess sugar and increasing the risk of stroke and coronary artery disease. Because cancer cells have such a high metabolic demand for glucose, many of the mutations in cancers affect pathways that regulate glucose uptake and glucose breakdown, allowing the cancer cells to survive and grow, crowding out nearby normal cells.

Glucose metabolism is altered by processes other than mutations or an reduced production of a hormone. Throughout its life cycle, a cell will vary its requirements for glucose. For example, the cells that comprise our innate immune response are typically in a quiescent or steady state. However, when these immune cells encounter an foreign invader, they become activated and increase their demand for glucose. To respond to a potential pathogen, the activated cells need glucose to fuel cell proliferation and the production of cytokines, chemicals that activate other immune cells and initiate an inflammatory response. The typical signs of inflammation are red inflamed area that may be painful to the touch, such as a cut that becomes infected. Most inflammation resolves when the infection is eliminated, leaving behind whole skin in the instance of a cut, and the activated immune cells become quiescent again.

An Interesting Observation about Glucose Metabolism in M2 Macrophages

Glucose uptake, immunity and metabolism are cellular pathways that are intertwined such that understanding how glucose is utilized in macrophages illuminates gene induction and regulation in activated macrophages. In a recently published eLife article, Covarrubias et al. studied how activation of murine bone marrow-derived macrophages (BMDMs) by interleukin-4 (IL-4), a signaling cytokine, altered glucose metabolism in the cells and regulated a subset of genes involved in macrophage activation. Continue reading “Finding a Connection Between Glucose Metabolism and Macrophage Activation”

Analyzing the Effects of Yersinia pestis Infection on Gene Expression

Posted on by Sara Klink

Yersinia pestis. See page for author [Public domain], via Wikimedia Commons
While scientists using ancient DNA analysis are learning how Yersinia pestis developed over time into the causative agent of three worldwide pandemics, there is still much to learn about the early hours and days of an organism infected with the plague. Y. pestis still infects humans so any insight into disease progression is useful for determining treatment timing and even developing novel treatments to supplement or replace antibiotics. A 2012 study observed how Y. pestis injected into mice spread throughout the body using bioluminescent imaging to track the infection. More recent research reported in PLOS ONE used a more real-world route of infection by introducing an aerosolized Y. pestis to a nonhuman primate model and tracking the transcripts altered during the first 42 hours of infection. Continue reading “Analyzing the Effects of Yersinia pestis Infection on Gene Expression”

Friday Cartoon Fun: Entertaining Yourself Between Incubations

Posted on by Sara Klink

Occasionally, time in the lab passes slowly. There is a two-hour incubation and nothing can be done until the timer goes off. Our science cartoonist Ed Himelblau has illustrated what some creative lab members may have done to fill this time, but is not advised to do:

Copyright Ed Himelblau

To see additional lab shenanigans, peruse the collection of humorous cartoons in our Cartoon Lab.

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 (http://www.gnu.org/copyleft/fdl.html)], 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 (http://www.gnu.org/copyleft/fdl.html), 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”

Serious Science Earns (Irreverent) Honors

Posted on by Sara Klink

Last night, scientists were agog with anticipation as the Ig Noble awards, now in its 25th year, were presented to ten new winners. The purpose of the awards was to highlight “Research that makes people LAUGH and then THINK”. Last year, my favorite was the award given for research showing cured pork could be used to stop nosebleeds. I enjoy injecting that fact in conversation just add to the mystique that is bacon and salt pork. Not only is it delicious but good for you too! So what did 2015 bring to the table?

There was information on basic bodily functions (nearly every mammal takes about 21 seconds to urinate regardless of size), answer age-old questions (yes, you can [partially] unboil an egg but no word about which came first chicken or egg), medical diagnostic techniques (take a potential appendicitis case, drive them over a bumpy road and see how much pain results), the Jurassic era (chickens are induced to “walk like a dinosaur” with the addition of toilet plunger on its rear end), language edification (“huh?” is a universal word), economic solutions (pay police officers more not to take bribes), business risk taking (business leaders take more risks after experiencing natural disasters that don’t personally affect them), reproductive curiosity (could one historical man have fathered 888 children in his lifetime?), pain threshold exploration (one group of researchers created an insect sting pain index while one individual challenged himself to experience a bee sting on 25 different parts of his tender body) and the benefits of kissing (yes, someone studied the consequences of “intimate interpersonal activities”).

These awards encompass quite a range of research. The ceremony itself involved paper plane throwing, but only at designated times, an opera focused on the year’s theme of Life, and previous Nobel and Ig Noble winners in the audience. Award winners joined in the fun too as one of the winners came on stage wearing a toilet seat on his head. Can you guess what was the focus of his research? And of course, livestreaming video of the ceremony and live tweeting from @Improbresearch for those who could not make it.

You can read all about the award winners with links to their research at Improbable Research.

As for picking a favorite from 2015 award winners, I am debating between the induced dino-chicken and the appendicitis diagnosis method. Which was your favorite?