CauseScience Friday!! February 6th #science #selfie

psgurel – I’ve just spent most of my morning in lab meeting, and will spend my afternoon going to a few lectures.  Presenting work and getting feedback is a critical part of science.  Lab meetings are somewhat more informal sessions where the entire lab can get together and discuss specific details on members’ projects. It’s helpful for all involved in terms of troubleshooting, fine tuning direction of the research project, etc.  It’s fun, but can also be somewhat tiring.  Here’s my post lab meeting selfie 🙂

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crestwind24 – This morning I came into lab very early to make sure I got all of my experiments done before heading to Philadelphia in the afternoon. One of the things I needed to do was run 4 PCR reactions and then image the products of the reactions using gel electrophoresis. Or more simply, I needed to make specific fragments of DNA from the C. elegans genome, and then make sure I made the correct DNA by looking at its size. When I visualized the PCR reactions separated by size on an agarose gel (top panel), I did not see the size DNA I was making with the PCR. Instead I saw a bunch of randomly sized bands and smears (hence my grumpy face when sitting at the gel imager, bottom left). Luckily, since I was in lab so early, I redid the PCR at a different temperature and got nice crisp bands at the exact size I expected (right bottom panel)!!! I love when molecular biology works!!!

If you missed them, be sure to check out previous CauseScience Fridays!!

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Amazing video of immune cells attacking worm #science @JExpMed

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JEM

A very cool report published in the Journal of Experimental Medicine out of UCSF provides dazzling images and videos of immune cells in action! More info and abstract here at Pubmed, and links to actual video on Facebook here. Gif credit: CauseScience.

The immune system in action! This 11-second video shows how white blood cells (eosinophils) attack a parasitic worm in 80 mins.
Watch more fascinating videos from Steven Rosen and colleagues [UC San Francisco (UCSF)] in their recent JEM study on the immune response to parasites.

Also, shout out to the nematode C elegans! But for future reference, C elegans are not a parasitic worm in humans. Very cool to see an academic journal spreading cool science images on social media! Way to go JEM!!

[tweet https://twitter.com/JExpMed/status/477524844159193089]

November 7th CauseScience Friday! #science

psgurel – I’ve spent most of this week turning in my thesis and preparing for my defense next week. But today, I’m taking a break from all of that and repeating an experiment!  Oftentimes, we must repeat experiments to prove that we are confident in our results.  While it may not be thrilling to do the same experiment again, it is awesome when a result is reproducible! Today, I’m doing a similar kinetic experiment as I did on Sept 19th. Woohoo!

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crestwind24 – Today one of the graduate students in my lab is defending her PhD. I love going to PhD talks, it is always fun and interesting to see the story that has developed with the training of a new scientist!! Last night and this morning I spent a bunch of time baking a cake for her in the form of a C. elegans. It is a chocolate cake with cream cheese pudding frosting! The green dots and lines represent the two neurons that she has studied in her thesis! Good Luck and Congrats to Dr. Pat!!

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Past CauseScience Friday posts! 

Alison Woollard explains how worms might be the key to the fountain of youth! @ConversationUK

What the humble worm might tell us about doubling our lifespan

By Alison Woollard, University of Oxford

Nothing is more certain in life than death. As we age, we become much more susceptible to major diseases like cancer and heart disease because the mechanisms that help prevent them earlier in life start to fail. We wear out, become much less mobile as our muscles and joints stop working properly, and lose cognitive function as our nervous systems deteriorate. Put simply, ageing is the single biggest risk factor for death.

The process of ageing is also a relentless march towards our ultimate decline, with frailty and illness leading to a poor quality of later life for many older people. This has tremendous social and economic consequences. Who cannot be touched by the poignancy of the older person who loses their memory – the very essence of who they are – or shocked by the fact that the last five years of life cost more to the health service than the whole of the rest of the life put together?

Different animal species have wildly different lifespans, from a matter of hours to several centuries. All the characteristics common to a particular species, such as body pattern, reproductive capacity, brain size and so on, are genetically programmed. In other words, such features are defined by the genome – the sum total of all an organism’s DNA. So lifespan, like any other characteristic, must also be genetically programmed.

But which genes control lifespan? Biological ageing is extremely complex, so is it possible to single out particular genes as being causative? Well yes it is. In humans, some of the best genetic studies of ageing come from an analysis of premature ageing (progeroid) syndromes like Werner Syndrome (WS). Because of mutations in just a single gene, WS patients exhibit a wide range of age-related changes (from greying hair to cardiovascular disease and cancer) highly prematurely, with an average age of death of around 47.

Fascinating and important though the study of progeroid syndromes are, the problem is that such syndromes are very rare and, for obvious reasons, it is impossible to experiment and probe the function of individual human genes in a systematic way. It is perfectly feasible to study human cells in culture, but this cannot address gene function within a whole organism where effects on multiple cell and tissue types and whole organ systems can be monitored.

Looking at mutations

A bit like you.
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So what is the alternative? How about the nematode worm Caenorhabditis elegans? C. elegans is a 1mm long soil-dwelling nematode composed of only 1,000 cells. It has a lifespan of about three weeks, but crucially these nematodes age in ways that are biochemically and physiologically very similar to our own.

Like other so-called model organisms used in biomedical research, C. elegans is also strikingly similar to humans at a genetic level, with counterparts of 60-80% of human genes and more than a third of genes recognised as “orthologues” (derived from the same gene in their last common ancestor). C. elegans has been used for 40 years to illuminate a staggering collection of biological processes, from neuro-transmission to programmed cell death.

The strength of using C. elegans as a model system is its amenability to genetic analysis. Animals are exposed to DNA damaging agents (mutagens) and the resulting mutant animals are screened using simple observation or more sophisticated biological investigations, to select those showing characteristics that illuminate interesting biological processes.

Researchers who are interested in the genetic basis of development, for example would select mutants displaying developmental abnormalities. Muscle cells might be in the wrong place or intestinal cells could be replaced by neurons. These mutants would thus define genes that are crucial for normal development – when they go wrong there are problems.

The next trick is to work out which gene that is crucial for this process is defective in each mutant strain. Once its identity is known, the researcher could then go on to investigate how that gene worked at the molecular level.

Doubling healthy lifespan

Twenty years ago this wonderfully simple experimental approach was applied to ageing – and a crucial step was the isolation of mutants with extended lifespan. Short lifespan could be attributed to an animal that was simply “sick”, but lifespan extension must mean the genetic programme controlling it had been interfered with in some fundamental way.

The most important mutant to be isolated was the daf-2 gene. C.elegans with this mutation live twice as long as normal worms. This would be like us living up to 200 years. But not only that, the animals were found to be healthier for much longer.

By tweaking one gene, age-related diseases were all postponed in these longer-lived animals. This led researchers to postulate that animals must have the latent potential to live much longer than they normally do, turning ideas about the passive, entropic nature of ageing – caused by molecular changes and accumulation of waste products – completely on their head. Daf-2 must normally accelerate ageing in some way and so the mutant characteristic is extended lifespan.

Making hay while the sun shines

Daf-2 turned out to encode a hormone receptor similar to the insulin/insulin-like growth factor (IGF) receptor in humans, which is a protein found on cell membranes that transmits signals into the cell. When daf-2 isn’t working properly, theses signals change. Many knock-on effects on other genes act cumulatively to have large effects on ageing, and these effects were also found to be mediated by another gene called daf-16/FOXO.

The daf-2/daf-16 pathway has now, through years of detailed genetic analysis, been joined by many other genetic players and complex pathways, feedbacks and interactions have emerged.

If one were to postulate an over-arching mechanism of ageing, it would be based on the observation that many mutations that extend lifespan affect stress-response genes – those that help cells cope with stresses such as a change in temperature, or those that sense nutrients. When food is plentiful and stress levels low, these genes make hay while the sun shines by supporting growth and reproduction. But under difficult conditions they take a “things can only get better” attitude – their activities change, sparking a whole physiological shift towards cell protection and maintenance. This shift extends lifespan, a state that can be mimicked (or triggered) by mutations in genes like daf-2, which sense environmental conditions.

Put another way, daf-2 and daf-16 are part of the machinery that takes stock of prevailing environmental conditions and sets the appropriate course, either a “live fast die young” or “try to stay alive to see if things improve” approach. In daf-2 mutants the latter programme appears to be the default state, even in the absence of stress.

Human effects

Do similar genes regulate lifespan in humans? It looks like they do: mutations in the insulin receptor gene are associated with longevity in a Japanese cohort; those that impair IGF-1 receptor function are commonly seen in a populations of Ashkenazi Jewish centenarians; and FOXO genetic variants have also been linked to longevity in several populations around the world.

And going back the other way – we now know that the worm WS gene counterpart reduces worm lifespan when inactivated, just as it does in humans.

Thus the humble C. elegans worm leads the way in ageing research, just as it does by revealing secrets for so many other avenues of biological investigation. We just have to assemble the jigsaw pieces to expose the big picture.

Could this research one day be translated into drugs that slow down the ageing process? Or more importantly, could the diseases of old age be prevented, extending our healthspan? It is certainly reasonable to speculate that drugs that mimic the effects of insulin/IGF and FOXO mutations, for example, could have this effect. But there is still much left to learn about the basic biology of ageing if we are to “treat” old age.

The Conversation

Alison Woollard receives funding from AgeUK, Worldwide Cancer Research, BBSRC and the Wellcome Trust.

This article was originally published on The Conversation.
Read the original article.

September 5th CauseScience Friday! #science #scienceselfie

crestwind24: This morning I will spend a lot of time at my dissecting microscope (second picture is what I am looking at! with arrows pointing to worms!). I have to sort and pick a bunch of different worm strains (C. elegans) for experiments I will do next week. Maintaining my worm strains can be tedious, but is way easier than taking care of cells, mice, or humans for experiments.

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psgurel: On the other hand, I am hanging out with my homie G’s today… G forces that is.  I’m using analytical ultracentrifugation to determine if the proteins I’m working with are forming larger complexes. In lab, Centrifugation is basically a fancy term for spinning things down REALLY fast.  For example, today I’m spinning my proteins at a speed where the centrifugal (or spinning) force on my samples is 50,000x the force of gravity (50,000xg).  In comparison, Astronauts typically experience 3xg during a shuttle launch.  When the centrifugal force is applied to my proteins, they will begin to sediment with heavier/larger complexes  faster, and smaller/lighter complexes sedimenting slower.  By monitoring how they sediment, I can determine what size complexes I have.  On the left, you’ll see the rotor and I’m holding a cell which contains my proteins.  On the right is the ultracentrifuge!

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See last week’s CauseScience Friday post here!

#Science Quotable: Mark Gerstein on genetic model organisms!

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“One way to describe and understand the human genome is through comparative genomics and studying model organisms. The special thing about the worm and fly is that they are very distant from humans evolutionarily, so finding something conserved across all three – human, fly and worm – tells us it is a very ancient, fundamental process.” – Mark Gerstein on genetic model organisms, and the modENCODE and ENCODE projects.

Read more at: http://phys.org/news/2014-08-scientists-human-worm-genomes-biology.html#jCp

Spineless National Zoo has closed its Invertebrate Exhibit

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The Invertebrate Exhibit at the National Zoo is no more (so sad, this was one of my favorite exhibits at the zoo). This Sunday the exhibit closed its doors according to an article in NPR by Bill Chappelle.

The zoo says its exhibit of cuttlefish, butterflies, spiders, and other spineless animals, which first opened in 1987, needs $5 million in upgrades, along with $1 million annually. But officials say their fundraising priorities lie elsewhere, including a renovation of the zoo’s Bird House.

The exhibit of spineless animals “is not included in the zoo’s five-year strategic plan or its 20-year master plan,” the AP said Monday. “Plans call for a future Hall of Biodiversity, including invertebrates.”

Invertebrates lack a spinal cord and make up ~97 percent of all animals. Common invertebrates include worms, insects, clams, crabs (crustaceans), octopuses, cuttle fish, starfish, and snails.

Two of the most popular and important genetic model organisms are invertebrates, the fruit fly (Drosophila melanogaster) and the nematode (Caenorhabditis elegans). The use of these animal models by biomedical researchers has lead to huge discoveries in many biomedical research fields, including neuroscience, genetics, and biochemistry. These models have also been extensively used to study the genetics and molecular mechanisms underlying many human diseases. Both of these animal models have also been involved in research that led to scientists winning the Nobel Prize.