Monday, October 31, 2016

Boo! Zombies are real!

512px-placid_deathWith Halloween just around the corner, how about a little creepy science for the season?

Zombies are real.

Yes, you read that one right. The undead do exist, and not just in fiction…but maybe I should clarify before you dive right back behind the sofa. Relax; it’s not a whole-body reanimated dead-to-alive apocalypse, just a finding from a group of researchers who saw that in death, a whole series of genes come to life.


Researchers Peter Noble, Alex Pozhitkov and colleagues at the University of Washington found that for a short period after death, certain cell activities seemed to rev up—a surprise since death usually means the biological end for an organism. In both mice and zebra fish, they noted an increase in gene transcription that continued in some cases for up to 48 hours. Going public in a preprint published ahead of peer review in journal bioRxiv (pronounced “bio-archive”), the authors express their surprise at the findings. Using a car running out of gas as an analogy for death, they note “one would not expect window wipers to suddenly turn on and the horn to honk several days after running out of gas.”


So how did they find this out? The research team focused on the genetic information within cells in certain tissues. They theorized that perhaps at death, since the animal was no longer alive, then activities like gene transcription would also stop.

As you know, DNA encodes our genes, which in turn code for peptides that make up the proteins required for a whole host of cellular activities. Activating the genes by transcription into RNA is followed by translation of messenger RNA (mRNA) into peptides. Peptides then aggregate into proteins (cough! reviewed here in this excellent blog post on how amazing proteins are).

As a marker of genetic activity, Noble and Pozhitkov measured mRNA transcript abundances. Once they noticed that some mRNA levels increased in the 48 hours following death, they took a closer look to find out which genes were sparking to life.

Not unsurprisingly perhaps, they found that stress response genes that help cells cope with low oxygen levels (hypoxia) or heat stress activated in the period following death. Other reanimations included those responsible for immunity and inflammation, but the team also found activation of genes normally active only in embryonic development and also some involved in cancer.


So, apart from the very loose connection with Halloween, why does this matter? Furthermore, isn’t this just for fish and mice?

First, it’s not just fish and mice; zombie genes have been reported in humans too. Taking biofluids from human cadavers, González-Herrera et al. noticed in 2013 that expression of genes for three proteins—MYL3, MMP9 and VEGFA—actually rose at 12 hours following death.

Where these results could deliver the most impact is transplant medicine. Depending on how rapidly activation occurs, an organ for transplantation could contain activated genes normally seen only during development or even those associated with transformation to cancer.

Supporting organs between harvest and transplant, using approaches based on the types of genes activated following death, might increase success and may even cut down on rates of cancer in transplant recipients following treatment.

Another area explored by the research team and published in a separate bioRxiv paper looked at using the gene activation data in forensic science. The researchers found that since the activated genes sparked to life at different times after death, their abundance could predict the postmortem interval. Grouping genes together improved the predictions, as shown by linear regression analysis and examining the fit of the data sets to predicted and actual time of death.

However, Noble, Pozhitkov and colleagues do ponder over bringing cells back to life, asking, “what would happen if we arrested the process of dying by providing nutrients and oxygen to tissues?” … Hmm…maybe zombies do know after all!

The post Boo! Zombies are real! appeared first on Talk Science to Me.

from Amanda – Talk Science to Me

Thursday, October 27, 2016

In the Beginning: Biobanking Strategy and Study Design for Chronic Obstructive Pulmonary Disease Research

via Inside Biobanking

Call for Applications: 3rd Annual TMT Research Award

via Accelerating Proteomics

from Accelerating Proteomics

Wednesday, October 26, 2016

Transmembrane Electrophoresis Automates Sodium Dodecyl Sulfate Depletion

via Accelerating Proteomics

from Accelerating Proteomics

Tuesday, October 25, 2016

Listeria – The Science of Adhesion and Food Safety

via Examining Food

Monday, October 24, 2016

daily snapshot: October 24, 2016 at 02:51PM

I had a lovely evening making these felt beads at @pdacoquitlam last week, courtesy of a @vancouver_mom blogger event. Place des Arts is running several Christmas felting classes for children, adults and families so head on over to their website (link in their profile) to sign up :)
from instagram

Tuesday, October 18, 2016

Scanning Big Data for Rapid Response in Foodborne Disease Outbreaks

via Examining Food

Wednesday, October 12, 2016

Proteome Localization within the Arabidopsis Endosomal System

via Accelerating Proteomics

from Accelerating Proteomics

Tuesday, October 11, 2016

Paving the way for Ada: Mary Fairfax Somerville

Mary Somerville's entry record at Kirkcaldy Gallery and Museum, Fife, ScotlandWe’ve covered Ada Lovelace Day on the Talk Science blog for the last couple of years. By now, dear reader, you should know all about the “Enchantress of Numbers,” as Charles Babbage referred to her, and why her achievements are so remarkable even today.

But who came before her—who paved the way?

And this is where I launch into another of my favourite themes: coincidences. It turns out that one of Ada’s teachers grew up only a few miles away from my childhood home, 200 years before me.

Meet Mary Fairfax Somerville (1780–1872), a fellow Scotswoman who grew up in Burntisland on the south coast of Fife. As Mary was a girl growing up in the late 18th century, her education was limited to only what was appropriate for her gender: needlework, social skills and very little else, since otherwise would have been wasteful.

geograph-2371106-by-kim-traynorHowever, Mary had other ideas. After a disastrous year at a boarding school for young ladies, she set out to educate herself, learning Latin and mathematics on the fly by reading every single book in the house. When the family moved to Edinburgh, her art teacher, Alexander Nasmyth, let slip that in addition to being a great reference for understanding perspective in paintings, Euclid’s Elements of Geometry was also a way in to astronomy and science in general.  Her two brothers received a full grounding in science and mathematics, so Mary managed to convince their tutors to help her in her studies too.

Her first marriage lasted three years and was to a man who was not interested in the idea of women educating themselves or maintaining an interest in science. Her second was more supportive; during this time, Mary sharpened her mathematics skills, holding discourse with the day’s experts and publishing papers on astronomy and physics. In addition to predicting the presence of Neptune through its influence on the orbital path of Uranus, Mary taught mathematics to the Baroness Wentworth’s daughter, Ada Lovelace, and eventually introduced her to computing pioneer Charles Babbage.

And the rest, as they say, is history, with Ada Lovelace Day rolling around each year to encourage women and girls that the STEM life is attainable regardless of gender.

Although science was not completely the norm for girls while I was in high school, I certainly wasn’t discouraged in the way that Mary was growing up, and I had many more role models to inspire me. While I’m not sure entirely who inspired me to go into science, the coincidence of Mary Somerville growing up in the next village along the coast would have been meaningful—if I had known about her. I only found out her about when visiting the local museum. Women in science history are mostly invisible. For example, Fanny Hesse. Without her contribution, microbiology would struggle.

This is an issue currently being addressed by Emily Temple-Wood, who is meeting another discrimination that women in STEM face with proactive editing. For every offensive tweet or email she receives, she creates a Wikipedia entry for another woman in science. Since women who dare to voice an online presence get a disproportionate amount of hate, threats and sexual abuse directed at them, Temple-Wood is very busy. Check out the Women Scientists WikiProject page for details, and if you’d like to hack in good company, search out one of the many edit-a-thons for Ada Lovelace Day, like this one at the University of Edinburgh, my alma mater.

And this is probably as good a reason as any for the continuation of Ada Lovelace Day—promoting women’s place in science, past, present and future. Maybe I would have found out about Mary Fairfax Somerville a little sooner if women scientists were more revered throughout history.

Finally, another coincidence: translation.

According to her Wikipedia entry, Mary Somerville described her work as translation: “I translated Laplace’s work from algebra into common language.” In addition to our childhood homes, it’s something else we share and gives me inspiration in hindsight. For me, translating science into easily accessible nuggets is a common theme running through my science career and is the reason why I now proudly call myself a science writer.

The post Paving the way for Ada: Mary Fairfax Somerville appeared first on Talk Science to Me.

from Amanda – Talk Science to Me

Does Bio-objectification Affect Clinical Care and Research Management?

via Inside Biobanking

Sunday, October 09, 2016

daily snapshot: October 09, 2016 at 08:43PM

Happy Thanksgiving from us to you xx
from instagram

Thursday, October 06, 2016

daily snapshot: October 06, 2016 at 04:04PM

No, not ughs - rocket dogs, and perfect as indoor wear for the freelance writer :)
from instagram

No Need to Boil or Bake: Non-Thermal Food Preservation

via Examining Food

Wednesday, October 05, 2016

daily snapshot: October 05, 2016 at 03:18PM

Feeling like a real urban cyclist now that I've pinned a beat up karrimor pannier to my frame
from instagram

Tuesday, October 04, 2016

daily snapshot: October 04, 2016 at 09:16PM

Such a lovely holiday
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