Archive for the ‘Science education’ Category

Illustration from David Macaluay's "The Way We Work", showing visitors throwing paper airplanes down air passages through the trachea.

Illustration from David Macaluay’s “The Way We Work”, showing visitors throwing paper airplanes down air passages through the trachea.

I woke up this Monday feeling sore, with a bad cough. Tuesday I barely had the energy to drag myself to a laptop to write this. It’s a familiar story for a lot of people around the United States right now, if the map at the top of this article is to be believed.

Yep, flu season is upon us in full swing, and in order to explain to my eight-year-old son what this means, I turned to that most awesome of all my medical reference books: David Macaulay’s The Way We Work. As you can probably guess from the title, this book provides a tour through all the major systems – circulatory, gastrointestinal, nervous, etc – that make up a human being, and contains several additional sections on health and disease. Like other David Macaulay books, including its more famous predecessor, The Way Things Work, David has meticulously illustrated the entire text with his colorful and quirky style. Diagrams of cross sections of tissue are visited by tiny tourists on observation platforms, schematics of biological systems are represented as bustling factories and conveyor belts, and sometimes even disembodied skeletons or diagrams of circulatory systems converse wryly with one another. My son eats all this up, and that’s good, as Macaulay’s light and humorous style comes with a serving of serious and well-presented content. I’ve always had a thing for the marriage of art and science, and this book is as good an example of this happy union as I can think of. (more…)

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Epigenetics is an increasingly big deal in biological discovery. We are regularly reading about the influence of actions peripheral to DNA in regulating DNA transcription and translation. We are learning that mice may fear what grandparent mice feared (Kelly’s blog ), due to heritable changes in DNA. In term of one of several mechanisms of epigenetic change, we are learning much about histone deacetylases and their role in gene regulation, as well as disease (Isobel’s blog ). In this blog, let’s take a step back and look at histones, and how they are influenced by acetylation/deacetylation.

The Role of Histones
Histones are proteins found in the nucleus of eukaryotic cells, where they package DNA into nucleosomes. Histones make up the main protein component of chromatin, acting as spool-like structures around which DNA wraps.

There are five major histone classes,three of these are core histones, the other two are called linker histones. Core histones comprise the core of the nucleosome, around which DNA is wrapped, while the linker histones bind at the entrance and exit sites of the DNA, so as to lock it into place. The linker histones also enable a higher order of structure. If you hold both ends of a rubber band, and twist one end, you’ll see that the rubber band twists and folds over itself; the end being held steady enables this twisting and folding: this is how the linker histones work. Histone-DNA structure is frequently represented as a beaded chain-type image (see figure).

DNA wrapping around histones in a bead and chain-like fashion.

DNA wrapping around histones in a bead and chain-like fashion.

Histone and DNA: Charged Interactions
Histone tails normally carry a positive charge due to amine groups present on their lysines and arginines. This positive charge is the means by which histone tails interact with and bind to the negatively-charged phosphate groups on the DNA backbone.

Histones are subject to post-translational modifications, primarily on their N-terminal tails, by enzymes. Such modifications include methylation, citrullination, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation. Such modifications can affect histone function in gene regulation. Acetylation is one of the most common post-translational modifications of histones (1). (more…)

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Shattered pitch with hammerA career as a scientist is many things: it is fascinating, ever-evolving, intense. Whatever images came to your mind when reading those words are probably nothing like the images a scientist would paint for you about his/her work day. Along with investigation and discovery, one of the major themes in a scientific career is patience. Some experiments are faster than other, e.g. one assay to measure enzyme kinetics can take less than seconds to achieve results (not including prep time), whereas it may take months to observe a mouse phenotype that may or may not change following a gene mutation. No matter what the experiment, scientists spend a considerable portion of their careers waiting.

However, no amount of waiting I have experienced in my scientific career can quite compare to the waiting that must be endured by the scientists monitoring the Pitch Drop Experiment in progress at the University of Queensland in Australia. Pitch, which is a derivative of tar, appears to be a solid and even brittle at room temperature. In 1927, scientist Thomas Parnell decided to create a demonstration to show that things are not always what they seem.  He heated up some pitch and placed it in a glass funnel with the bottom fused so it could not leak through. Professor Parnell let the pitch settle into its new formation for a full three years (!) at which point he cut the bottom of the funnel stem and the experiment began to prove that pitch is a highly viscous liquid. Now here is an important lesson about patience and perseverance: the first drop did not fall from the funnel until 1938- a full eight years after the stem was cut! 86 years after the Pitch Drop Experiment began, only eight drops have fallen from that funnel, about one drop each decade. A record and proposal for modeling pitch drops can be found here: http://www.physics.uq.edu.au/physics_museum/pitchdrop.shtml

Professor Mainstone with Pitch Drop experiment

Professor Mainstone with Pitch Drop experiment

Professor John Mainstone began supervising Queensland’s Pitch Drop Experiment in 1961. He missed drop seven by about five minutes when he stepped out for a refreshment. Although a camera was set up to capture the eighth drop fall in 2000, equipment malfunctioned while Professor Mainstone was overseas and the data were lost. Sadly, Professor Mainstone passed away in August of 2013 without ever witnessing a drop fall.

No one has ever witnessed the drop of pitch actually fall from the funnel, but you could be the first! In, perhaps, the best way to help non-scientists understand the excitement of waiting, there is a live webcam recording “The Ninth Drop” as it descends into the beaker below. It was expected to fall in late 2013 (13 years after drop 8), but is still hanging on.  If you want to be part of history, be sure to register on the website!

Researchers in Dublin, who began a similar pitch drop experiment in 1944, scooped the Queensland scientists. They first witnessed a drop of pitch fall from their funnel in July of 2013 collecting the first official evidence that pitch is, indeed, a liquid. You can catch a time lapse video of the drop falling below.

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weather blog

Gone are the days when the phrase “educational TV” would inevitably send shudders of dread through kids and teens. Quite the contrary, many of today’s educational programs are fast-paced, expertly narrated and full of surprising, fun, and visually engaging facts and science trivia. But while no doubt entertaining, are these programs still any good at their core function, namely teaching the kids actual concepts useful for understanding modern science?

The long-running PBS educational series, NOVA, aims to satisfy this goal by providing not only standard teachers’ notes and lesson plans to accompany its shows, but also by investing in extensive and realistic online laboratories in which students can explore actual scientific datasets. A good example of this approach is provided by the NOVA Cloud Lab, which is actually far more exciting than it sounds, as one of its main sections concerns the formation and study of storms. (more…)

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4621CAIt’s a question I’m asked probably once a week. “What wavelength do I select on my luminometer when performing a luciferase assay?” The question is a good and not altogether unexpected one, especially for those unfamiliar or new to bioluminescent assays. The answer is that in most cases, you don’t and in fact shouldn’t select a wavelength (the exception to this rule is if you’re measuring light emitted in two simultaneous luciferase reactions). To understand why requires a bit of an explanation of absorbance, fluorescence, and luminescence assays, and the differences among them.

Absorbance, fluorescence, and luminescence assays are all means to quantify something of interest, be that a genetic reporter, cell viability, cytotoxicity, apoptosis, or other markers. In principle, they are all similar. For example, a genetic reporter assay is an indicator of gene expression. The promoter of a gene of interest can be cloned upstream of a reporter such as β-galactosidase, GFP, or firefly luciferase. The amount of each of these reporters that is transcribed into mRNA and translated into protein by the cell is indicative of the endogenous expression of the gene of interest. (more…)

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