daily snapshot: December 28, 2016 at 11:01AM

Guesses, no spoilers? #drwho
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daily snapshot: December 26, 2016 at 11:37AM

Rosco's why aren't we moving? face. We're not moving cos I can't get round the full walk this morning. The Cold struck yesterday afternoon, a gift from the mister who went down with it Dec 23. It's hammered my chest, my abdomen with the aches and knocked my balance right off. Luckily it has snowed so this morning's falls have been into the softish stuff rather than last night's ice. Rosco is appreciating slower walks in zigzag direction. Merry Christmas
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Differential Protein Quantitation at the Peptide Level

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Differential Protein Quantitation at the Peptide Level

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Obese and Healthy? Proteomic Biomarkers Give Clues

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daily snapshot: December 23, 2016 at 12:10PM

The season's festive cake; Christmas is underway
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Obese and Healthy? Proteomic Biomarkers Give Clues

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LC-HRMS Multi-Allergen Detection of Nuts Contamination

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LC-HRMS Multi-Allergen Detection of Nuts Contamination

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Food Authentication with Proteomic Analysis

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Deep Proteome Characterization Highlights Breast Cancer Cell Functionality

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Mesenchymal Stem Cell Exosome Proteome under Ischemic Culture Conditions

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daily snapshot: December 20, 2016 at 07:09PM

Settling back into the apres ski routine at Glenburn Soda ... making an attempt on the nine festive sundaes before the end of December
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Deep Proteome Characterization Highlights Breast Cancer Cell Functionality

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daily snapshot: December 18, 2016 at 09:16PM

Evening walk with the these two
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Mesenchymal Stem Cell Exosome Proteome under Ischemic Culture Conditions

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Collaborative Transnational Biobanking for Rare Disease Research

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Food Authentication with Proteomic Analysis

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daily snapshot: December 10, 2016 at 08:27PM

Work in progress #acrylicpainting
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Client showcase: Shelly Deforte, biomathematician

As a full-service science communications agency staffed with editors, designers, writers and more, Talk Science to Me takes great pride in supporting all our clients by presenting their science in effective and engaging ways. Although most of our portfolio comprises larger organizations and institutions, we also work with individual authors and researchers to manage their writing and publishing needs.

One of our academic authors is biomathematician Shelly Deforte, who recently took up a post-doctoral position in bioinformatics at the University of Montreal. She describes her position as fully involved in supporting the research projects of a biochemistry lab by “writing custom code to do custom analysis” on the data.

Shelly’s work focuses on artificial intelligence, machine learning and in silico modelling, writing code that runs algorithms to analyze the libraries of data generated by experimental workflows. Her field of interest is intrinsically disordered proteins, looking for evidence of a lack of stable structure among proteome structure and sequence databases. Since structure heavily influences function, intrinsic disorder could signal a highly versatile protein; making predictive sense of how these molecules might behave or bind with other factors is important in drug discovery, for example.

Talk Science provided editing for two of Shelly’s primary research papers, a service she describes as extremely valuable. This included editing, copy-editing, proofreading and some fact-checking, ultimately delivering a final manuscript that was ready for journal submission.

So how does this kind of support help an academic biomathematician?

In the academic world, researchers are under constant pressure to publish their findings, submitting them to peer-reviewed journals, conferences and other venues. Publication enhances reputation for the academic institution as well as the scientist. Often the data come from collaborative research projects, meaning that writing a primary paper involves many authors in the draft and revision processes. Eventually, with all the changes and additions, it becomes difficult to spot grammatical errors, inconsistencies and typos.

“After all the revision and editing you and your authors do, it’s impossible not to become blind to the paper,” Shelly explained. “Also, when you’re familiar with a subject, it’s not always easy to see when something lacks clarity for the reader.”

Hiring an external editor can also help get a paper published. Since reviewers seem to prefer highly polished papers, submitting a manuscript that requires very little work prior to publishing increases the odds of acceptance. Furthermore, as journals economize, providing less editorial support and prepress oversight for submissions, errors can make it all the way into print. Shelly suggests that it is a good idea to avoid submitting them in the first place: working with a Talk Science editor to oversee final document revisions will prevent the risk of their immortalization!

Bioinformatics is rapidly becoming more important to scientific research as researchers struggle to make sense of complex data outputs. Biological systems under investigation are much more complicated than computers can deal with without specific programs to handle the multidimensional information downloads for analysis. Biomathematicians like Shelly are becoming increasingly involved in experimental design to ensure that data submission is in the correct format. When handled correctly, computational support in the form of algorithms, artificial intelligence and machine learning save time, sparing scientists from traditional manual analysis to speed up results.

In providing manuscript editing and submission services, Talk Science hopes to help share Shelly’s science effectively as well as free up valuable research time to pursue new directions in protein bioinformatics.

Learn more about our Talk Science clients in our client showcases.

Learn more about intrinsically disordered proteins in this useful review:
DeForte, S., & Uversky, V.N. (2016). “Order, disorder, and everything in between,” Molecules, 21(8), 1090, doi: 10.3390/molecules21081090.

The post Client showcase: Shelly Deforte, biomathematician appeared first on Talk Science to Me.

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daily snapshot: December 07, 2016 at 04:38PM

wordless wednesday: all change
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Stabilizing Tissues for Postmortem Peptide Preservation

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Protein Prep in Three Dimensions for Intact Protein Evaluation

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Stabilizing Tissues for Postmortem Peptide Preservation

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Cool science gifts for the cool science kids

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Protein Prep in Three Dimensions for Intact Protein Evaluation

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daily snapshot: December 01, 2016 at 12:53PM

Sometimes it good just to say, Sod it! ands go snowboarding :)
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Cool science gifts: 2016 edition

daily snapshot: November 29, 2016 at 09:31PM

Been adventuring again :)
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daily snapshot: November 27, 2016 at 01:28PM

Plugged in to The Archers; heading off for adventure. Slowly coming out of a hermit spell when I haven't felt like going out much. Weather, hormones, domesticity, midlife, whatever ... it all combined to squash me somewhat ... confidence, creativity, happiness. Now I have to get back on the horse, so to speak...
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In case you were wondering, part II

What’s the helium situation? …and other updates on stories we covered last year.

Helium

Although we’re still not comfortable with the frivolous use of helium gas in party balloons, a recent discovery certainly gives MRI fans, astronauts and the boffins at CERN, the European Organization for Nuclear Research, reason to celebrate.

At the end of June this year, scientists from the University of Oxford and Durham University announced success in a helium hunt collaboration with Norwegian exploration firm Helium One. By combining traditional prospecting with seismic imaging and helium geochemistry, the team located the gas bubbling out of the ground in the Tanzanian East African Rift Valley. They estimate that this reserve might be as large as 1.5 billion cubic metres, or enough to fill around 1.2 million medical MRI scanners.

It may not look much, but it helped find enough helium for 1.2 million medical MRI scanners: https://t.co/WVkIGS8n1f http://pic.twitter.com/RCRb0oOMLA

— Oxford University (@UniofOxford) June 28, 2016

Work done in the earth science department of each university predicted that volcanic activity could be important in releasing helium gas. The heat generated is enough to drive the gas out from rocks close to seismic activity and into gas fields just below the ground surface.

Although the research team and exploration firm still have to locate an extraction sweet spot, experts predict that the new reserve will ease the current helium shortage. They also note that the new approach can help find other helium reserves around the world.

In other gaseous news, it is encouraging to see the helium shortage taken seriously, especially by organizations outside the world of research. Last year, the British Medical Association called for a ban on the frivolous use of an invaluable and irreplaceable gas. Closer to home, the annual Vaisakhi Parade in Surrey went helium-free this year, and Victoria’s Backyard Weekender music festival might go the same way next year.  Although some of the opposition is from their potential as harmful marine pollution, others did mention the global shortage as a reason to avoid using helium balloons.

A bigger, better Higgs?

Somewhat related to the helium update, since CERN’s Large Hadron Collider (LHC) complex relies on the gas to supercool its magnets, was the suggestion that a new particle may have been detected. Although scientists wisely regarded the data as random glitches from a particle-smashing event, physicists also acknowledged that if proven, the results could open a whole new direction for physics, overturning the Standard Model proven four years ago by the Higgs boson discovery.

Infuriatingly, the collider shut down for winter maintenance, and then reopening got derailed by weasel activity in the electrics, preventing researchers in two groups from running further tests to see if the double bumps seen in their LHC data were real. No word on whether they were discovered by a Higgs Hunter…

Eventually, reopening was worth waiting for, but also disappointing for the two teams. Even though the 2016 operating season brought higher collision energies in the LHC, allowing researchers to investigate the Higgs boson in more detail and continue the search for new disruptive particles, it also saw the data bumps vanish. If you’d like to see what disappointment at CERN looks like and commiserate alongside the researchers, here’s a BBC documentary from August 10.

But wait—there’s more! Yet another particle might be waiting in the “wings.” In September, the High Energy Physics Group at the University of the Witwatersrand in Johannesburg, South Africa, announced the possibility of a Madala boson. According to a press release from the university, if found and confirmed, this new boson could help scientists understand more about dark matter. The previously found Higgs boson interacts with regular or known matter according to the Standard Model in physics; dark matter, which forms 27% of the known universe and cannot be explained according to the Standard Model, probably has its own counterpart—the proposed Madala boson.

Phew! While we’re waiting, why not make a particle pizza and munch along in solidarity?

The post In case you were wondering, part II appeared first on Talk Science to Me.

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Biobanking the Future: Male Fertility Preservation for Endangered Species Conservation

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Food Surveillance in China: History and Initiatives

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Food Surveillance in China: History and Initiatives

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Biobanking the Future: Male Fertility Preservation for Endangered Species Conservation

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daily snapshot: November 10, 2016 at 07:19AM

Last night's sketching #dog #pencildrawing #dogsofinstagram
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A Decade of Challenges and Solutions for Biobank Sample and Data Sharing

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Around town: All creatures, great and small

This weekend will see a gathering of the province’s veterinarians and staff in downtown Vancouver for the Canadian Veterinary Medical Association (CVMA) and the Society of British Columbia Veterinarians (SBCV) Chapter Fall Conference and Trade Show. The program seems predominantly small animal–oriented, but in reality, vets across BC handle all sizes of patient, quadruped and biped, skin, scales, fur and feather in their daily working lives.

Have you ever wondered just how oddly varied a day’s work must be for a veterinarian?

While your local GP will open the surgery door to see only one species waiting in line, anything goes in the veterinarian’s waiting room—mammal, reptile, avian…fish?

For an example of the oddness routinely encountered by veterinarians, the first time I met with a chinchilla on the consult list, something that looked like a gremlin popped out of the pet carrier onto the table—not quite the fluffy cat I was expecting. Luckily the practice library (pre-Internet days, oh my!) held an exotic pets manual.

“It’s like this in a dog; how would I treat a cat?” is a daily dialogue, made more difficult by having to remember that not all species handle drugs in the same way.

Penicillin? Okay in cats, but fatal in guinea pigs.

Local anaesthesia? Fine in sheep; be cautious in goats.

Ibuprofen? No, no, no in cats, but yes, yes, yes as an anti-inflammatory in rodents.

So that’s what going on the other side of the consulting table, but what about the benefits of veterinary science for us humans?

Apart from looking after the beneficial companion animal bond, veterinary science also covers public health in managing food chain safety and plays an important role in clinical research.

In this age of reductionist research and the ascension of disciplinary endeavors, veterinary research stands apart because of its breadth and interdisciplinary orientation. …. Veterinary research serves as the interface of basic science and animal and human health that is critical to the advancement of our understanding of and response to impending risks and to the exploitation of disciplinary advances in the pursuit of One Medicine.

— Critical Needs for Veterinary Research

Furthermore, many notable scientific discoveries for human health have been made first in animals. Cross-species versatility makes for an interesting and open-minded research life too. Veterinary research is a great example of a comparative approach to science since this is a big part of the vet school undergraduate years. Rous sarcoma virus, the first viral cause of cancer, was discovered in 1911…in chickens. Bill Jarrett’s work in 1964 on feline leukemia virus (FeLV) at the University of Glasgow veterinary school in Scotland laid the groundwork for the isolation of HIV almost two decades later. Disease in animals can also act as a sentinel for its emergence in humans: West Nile virus caused deaths in birds only weeks before hitting the human population.

Clinical and comparative superheroes indeed; the importance of veterinary research for human society should be well recognized and supported.

Mammals are mammals are mammals. There are more similarities than there are differences between the species. When these similarities [in illness] arise, they convey important information.

— Dr. Larry Norton in Wild science: Breakthroughs in animal health care may hold treatments for humans (Bill Briggs, NBC News, November 2, 2013)

So, next time you hear your veterinarian muttering under their breath, “white feet, don’t treat” as they scan for wonder drug ivermectin on the shelves, or you see them reach past the Carprofen for your cat, just imagine how many different species are running around inside their head during consultations.

The CVMA-SBCV Chapter Fall Conference & Trade Show
November 5–6, 2016, in Vancouver, BC

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Boo! Zombies are real!

With 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.

What?

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.”

How?

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.

Why?

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.

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

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Call for Applications: 3rd Annual TMT Research Award

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Transmembrane Electrophoresis Automates Sodium Dodecyl Sulfate Depletion

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Listeria – The Science of Adhesion and Food Safety

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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 :)
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Scanning Big Data for Rapid Response in Foodborne Disease Outbreaks

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Proteome Localization within the Arabidopsis Endosomal System

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Paving the way for Ada: Mary Fairfax Somerville

We’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.

However, 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.

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Does Bio-objectification Affect Clinical Care and Research Management?

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

Happy Thanksgiving from us to you xx
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daily snapshot: October 06, 2016 at 04:04PM

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