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Reviews of “Introducing Epigenetics: A Graphic Guide”

My book‘s been out for a few months now, so I thought I’d share a couple of my favourite reviews so far!

Here’s a video review from Amanda, aka @TangibleAnsible, from the “A Scientist Reads” YouTube channel:

The second review is from The Epigenetics Literacy Project, a website that connects journalists and the public to the latest epigenetics news:

Many do not realize or appreciate the awkward phase epigenetics is in and thus they are prone to misunderstanding or misstating findings in the field. But Ennis does an excellent job of explaining how epigenetics fits in as a subset of the fields of molecular biology and gene regulation. In fact, in the first ten pages, epigenetics and epigenetic changes are sparsely discussed, which should emphasize to the reader that this science has not trumped previous dogma on gene activity. Epigenetics is merely a piece of a larger puzzle.

The reality is that there is a broad spectrum of opinions about epigenetics, ranging from the purely pseudoscientific (e.g. your thoughts can stop or give you cancer) to believing the field to have little significance in the grand scheme of gene regulation to believing the theory of evolution needs to be rewritten because of epigenetics. Ennis does not shy away from some of these controversial ideas but does make sure to place the appropriate disclaimers.

You can read the full review here.

If you’ve read and enjoyed Introducing Epigenetics, please consider leaving your own review on Goodreads or your favourite book vendor’s site!

(Speaking of book vendors, a note to Canadian readers: there’s been some kind of glitch with the Canadian supply of the book, which the publisher is trying to resolve. Amazon.ca are still listing the book as “Temporarily out of stock” and my friendly local independent bookstore have also had problems trying to order it from their usual Canadian supplier, but you can order it online from Chapters or from a US site. It’s also available as an e-book, but to be honest I think the illustrations work better in the hard copy version).

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Quora contributions from August 2016 to March 2017

Quora is a question-and-answer site. You can view all my contributions here; selected highlights are listed below. I encourage you to check out the other answers submitted for each question, too!

Epigenetics

What molecular mechanisms regulate methylase activity?

Why is the epitranscriptome (epigenetic marks on mRNA) important when mRNA molecules last so transiently?

What is the difference between histones and nucleosomes?

What’s “Histone modification”?

What is the difference between acetylation and methylation?

Why does acetylation remove the positive charge on histones?

Why does trimethylation of histone H3 on lysine 27 (K27) result in chromatin repression?

Should histone modifications be labeled as an epigenetic modification? Or just a chromatin modification?

Are epigenetics a type of post-translational modification?

Could stem cells just be epigenetic?

I want to start learning about epigenetics. Where should I start?

What are the best books on epigenetics, for a layperson?

Cancer

Can cancer cells evolve resistance to treatment?

Why are familial tumors usually multiple compared to sporadic cases, even when the same mutation is responsible for both types?

Why can’t people with cancer donate their organs?

Viruses

Can we use mRNA silencing techniques to inhibit the HIV genome?

Other scientific topics

Once we insert a desired gene into the human genome, how is its expression limited to the specific target organs where the gene is needed?

Do our parents have the same DNA as us?

Do red blood cells have functional miRNAs?

My ex-husband and I both have blood type O (positive and negative). How is it possible that our son has type B+?

Miscellaneous

Do you think Goodreads should ask a few questions from a book before letting anyone rate it?

 

 

 

 

Are we ready for forensic epigenetics?

(Originally published on Occam’s Corner at Guardian Science, in February 2017)

Advances in epigenetics mean incredibly detailed profiles of criminal suspects might soon be reality. Is the legal system ready to use this information?

Picture the scene. A detective is addressing her team:

“The DNA test results are in. We’re looking for a white male suspect, 34–37 years old, born in the summer in a temperate climate. He’s used cocaine in the past. His mother smoked, but he doesn’t. He drinks heavily, like his Dad. We’re seeing high stress levels, and looking at the air pollution markers, let’s start looking downtown, probably near a major intersection”.

Science fiction? Yes, for now. But advances in epigenetics – the study of reversible chemical modifications to chromosomes that play a role in determining which genes are activated in which cells – might soon start making their way out of research labs and into criminal forensics facilities.

Take the idea of the epigenetic clock, one of the ways in which our cells and DNA can betray our age. Epigenetic patterns change throughout our lives, along broadly predictable paths, making it possible to infer age from DNA samples.

Steve Horvath at UCLA has developed a statistical model based on 350 potential epigenetic modification positions in the human genome that can estimate your age to within three and a half years. The rate of epigenetic aging seems to depend somewhat on race, and can be affected by some health conditions, but this kind of test is already at the stage when forensics labs are validating it for use in criminal investigations.

The things we get up to while our epigenetic clocks are ticking can also leave their mark on our DNA. Cigarette smoking correlates with characteristic and persistent epigenetic changes. The same goes for cocaine, opioids and other illicit substances. There’s also some evidence for epigenetic signatures of obesity, traumatic childhood experiences, exposure to tobacco in the womb, season of birth, exposure to environmental pollution, exercise, and possibly even the things our parents and grandparents did before we were born.

 
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Posted by on 2017/03/04 in epigenetics, genetics

 

“Cracking Cancer” on CBC’s The Nature of Things tonight

Tonight’s episode of CBC documentary series The Nature of Things with David Suzuki features an in-depth look at the BC Cancer Agency’s Personalized Onco-Genomics (POG) project, which is exploring the feasibility of sequencing DNA and RNA from cancer cells to help physicians select the best treatment for each individual patient.

Project co-lead Dr. Janessa Laskin also did a great interview about POG on CBC Radio’s The Current yesterday.

I got to see a staff preview of the Nature of Things episode on Tuesday, and I think the production team did an amazing job at presenting a balanced view of this specific project and of cancer genomics in general. If you’re in Canada, check it out on the CBC tonight at 8pm! It’ll be repeated on Saturday, and available online at the link above.

NB I’m not directly involved with this project, but pretty much everything we do in my department (Canada’s Michael Smith Genome Sciences Centre) touches on POG in some way. Many of my colleagues and friends are featured in the documentary – it’s always very cool to see people you know on TV! We’re all very proud of the work we do; I hope you enjoy seeing inside our world!

 
 

Sci-fi audio drama podcasts galore

Radio drama is making a big comeback in the form of podcasts, with plenty of high quality science fiction to choose from. Here are some of my favourites.

I’ve been a science fiction fan since I first read John Wyndham’s The Chrysalids as a kid. I quickly graduated to the Hitchhiker’s Guide to the Galaxy books (I’m proudly sporting a “Vote Zaphod Beeblebrox 2016” t-shirt as I write this), Red Dwarf, and countless other books, TV shows, and films – some of them great, some of them terrible, some of them (my favourites, if I’m honest) somehow managing to be both.

I’ve also been a podcast fan for many years. Ironically, however, given the origins of my beloved Hitchhiker series as a radio programme, I’d never combined the two interests until very recently; my phone’s playlist was full of documentary series. But then CBC Vancouver ran a story on a locally made paranormal mockumentary podcast, The Black Tapes (The X-Files meets Serial), and I suddenly found myself in a whole new world of audio drama – and discovered some phenomenal new science fiction.

The podcast format is ideal for old-time radio drama-style productions, which are making a big comeback. There seem to be new shows launching every week, and unfortunately many of them just don’t work – even when the story’s decent the characters’ voices sometimes all sound too similar, the actors haven’t rehearsed properly and are obviously reading from a script, or it’s not clear what’s going on in the big action sequences (apart from an awful lot of banging and shouting, usually). But when it’s done well, it’s a truly immersive experience and a wonderful way to enjoy some quality sci-fi while you commute, exercise, or plot galactic domination at the head of an army of evil robots.

My all-time favourite sci-fi podcast has to be Sayer (miraculously resurrected recently for a fourth season). The story of a colony established by a private company on an artificial moon is told almost entirely in one voice, that of the eponymous AI entity who runs the operation. The first few episodes focused largely on a single new member of the colony, and were fairly light in tone. However, the series got darker, more thoughtful (downright philosophical at times), and a lot more intricate as it went on to explore the origins and likely fate of the colony, and I was completely absorbed by the extremely clever use of sound and music (I almost missed my bus stop several times). They even managed to pull off an extremely satisfying ending to the original three-season arc, which is all too rare for a much beloved series. Very cleverly done, and highly recommended. I shall be listening to the whole thing all over again in anticipation of the new episodes.

Back on Earth, The Bright Sessions is also excellent. Imagine if Professor X ran a psychiatry practice instead of a school for gifted youngsters, and you’ve got the premise – Dr. Bright specializes in counselling young people with extraordinary powers, including time travel and telepathy. The early episodes each comprise a single session with seemingly unconnected patients, but as the story progresses the dots begin to connect into a larger conspiracy.

To The Manor Borne (By Robots) rounds out my top three. This utterly charming podcast consists of stand-alone stories, as told to placate a Beast, Destroyer of Worlds. The episodes are held together by an ongoing swashbuckling, time-travelling, body-swapping tale about the quest for the Beast’s origins and the means to its downfall. It’s enormously good fun, and I only wish the episodes came out more frequently.

I also enjoy ars PARADOXICA (time travel shenanigans), Limetown, (mockumentary about a mysterious town and its scientific shenanigans)and The Message (another mockumentary – the format works well on audio podcasts – about scientists figuring out a mysterious signal)Away from the strictly sci-fi genre, I highly recommend Greater Boston (if you like Wes Anderson movies, you will like this), Hello from the Magic Tavern (silly), The Lift (spooky), The Magnus Archive (creepy), and Uncanny County (quirky). If you’re still looking for more radio drama content, there’s a good list of paranormal and sci-fi podcasts on Reddit, and you can find additional shows on Twitter via the #audiodramasunday hashtag.

Whole new worlds are waiting for you on your phone!

originally posted on my personal blog

 

“Introducing Epigenetics: A Graphic Guide” now available in the UK!

I’m delighted to announce that my book was published today in the UK!

I received a few advance copies on Tuesday, and I’m really pleased with how it’s turned out.

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Pocket-sized!

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This is one of my favourite illustrations (although it’s hard to choose! Oliver Pugh did a fantastic job). I did my postdoctoral research on repetitive DNA, and I think RNA is one of the most interesting molecules of all time, so I might be a bit biased though.

I’ve also set up my author profile page on Goodreads.

The book is available for pre-order everywhere, and will be published on March 14th in the USA and March 20th in Canada and elsewhere. Links to all major vendors can be found here – or ask your friendly local independent bookstore!

 
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Posted by on 2017/02/02 in Books, epigenetics

 

Announcing “Introducing Epigenetics: A Graphic Guide” – coming in early 2017!

INTRODUCING-EPIGENETICS-14mm new1I’m very excited to officially announce that I have a new book coming out next year!

“Introducing Epigenetics” is part of the Graphic Guides series by Icon Books. I’ve written the text, and artist Oliver Pugh is currently working on the illustrations. He’s done great work on earlier books in the series, and I can’t wait to see his artwork for Introducing Epigenetics!

The book covers all aspects of the exciting field of epigenetics, from the basics of gene regulation and embryonic development to the role of epigenetic modifications in diseases and their treatment, evolution, and the controversial field of epigenetic inheritance. I had a ton of fun writing it, even though it didn’t leave me with much time to do anything else last year!

The book will be available on February 2nd in the UK and March 14th in Canada, Australia, and the US. Other countries TBD.

More details, including links to online vendors, available here.

 

 
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Posted by on 2016/08/13 in Books, epigenetics

 

Quora activity for January 2015 – August 2016

Quora is a question-and-answer site. You can view all my contributions here; selected highlights are listed below. I encourage you to check out the other answers submitted for each question, too!

Cancer

Would it be possible to avoid cancer by modifying our DNA?

Is whole genome sequencing of any use in cancer diagnostics?

If our body can detect cancerous cells, why do people still get cancer? Does it mean that we can improve our body’s defenses against cancer before even getting sick?

If 2/3 of cancers are caused by chance mutations, why should I work to help prevent cancer?

Is it possible that cancer is not actually a disease to be “cured”, but it is actually an inherent defect of genetics?

Is cancer an intrinsic feature of life?

Is worrying about cancer the biggest cause of cancer?

What are the chances (if any), that a blind person getting cancer in the eye would allow them to see again?

What cure would be most beneficial to discover: HIV/AIDS or cancer?

Can Ebola be treated with cancer drugs?

Epigenetics

If two people have identical DNA fingerprints, what other molecular evidence does forensics use to distinguish between biological samples?

Can a methylation pattern be sequenced?

What could potentially be the most exciting application of epigenetic research?

Why hasn’t Lamarck been acknowledged in the face of the burgeoning advances made in the science of epigenetics?

In what way does histone methylation prevent transcription?

Is the epigenetic system of a person heritable?

Is there a meaningful way to diagnostically test a patient for epigenetic changes caused by long term use of medications?

Other Scientific Subjects

Is it a possibility that parents of genotype AA have an offspring with AS?

What is the reason that viruses are inactive when not inside any organism? What is the mechanism?

Will the final solution to HIV be to just accept it as part of the human genome?

What can you tell about a gene based on its tissue expression patterns?

What are some interesting examples of people becoming infected with typically fatal diseases (e.g. Ebola, HIV/AIDS, rabies, anthrax) through unusual means or at long odds?

Could cellular environment (pH, temperature, molecular crowding, redox state) affect a cell’s interactome?

What causes mutation in viruses?

Which (multicellular) animal is most deadly to humans?

What would happen if all the DNA in my body suddenly disappeared?

What are the most useful lab hacks, tips and tricks for molecular biology/biochemistry?

Do viruses have nutritional value for any organism?

What will next-generation sequencing be called a generation from now?

When will we be able to sequence the genome of every living vertebrate on Earth?

What are the oddest organisms?

Biochemistry: Why does the yeast two-hybrid system system have low specificity?

About Scientific Research and Careers

What does a principal investigator at a molecular biology lab spend time doing during the day?

How common is it for scientists to hire people to write their grant proposals?

How do I improve my grant writing?

I want to apply for a grant for a project, but I have no idea how to write a proper grant proposal. How can I go about this?

What is your favorite annual scientific conference?

Does a biochemist/biologist have to know all the reactions of cellular respiration or other general topics by heart after graduating?

Miscellaneous

Is there racism in Canada? Why?

What’s the best story about “fighting fire with fire”?

What are some of the best moments while taking exams?

Why do people believe in the ancient aliens theory?

If cloning of people was legal, whom would you choose and why?

What are some great optical illusions?

Which is the best way to pass the PMP exam?

Why do some people choose to use Quora over writing a blog?

 

Quora activity for June – December 2014

Quora is a question-and-answer site. You can view all my contributions here; selected highlights are listed below. I encourage you to check out the other answers submitted for each question, too!

I haven’t been as active as usual over the last few months; I took a break over the summer, and then entered the busiest few months of my professional life (as well as doing my usual full-time job I also helped organise and run the 2014 Joint Annual Meeting of the International Human Epigenome Consortium and the Canadian Epigenetics, Environment, and Health Research Consortium, then studied intensively for my Project Management Professional exam, which I passed just before Christmas). I still managed to write a few answers though!

Cancer

Which cancer strains are contagious among humans and how can they be contracted?

Do you think the government knows the cure for many illnesses like cancer but hides the information to make more money off the unsuspecting general public?

What types of cancer are affected by epigenetics?

Epigenetics

How difficult is epigenome sequencing, as compared to genome sequencing?

What are all the elements of an epigenome?

What are some great resources to teach epigenetics to a class?

Does DNA methylation and histone acetylation add to the amino acids of the histone or nucleotide?

Other Scientific Subjects

Why isn’t there a cure for Ebola yet? Is it as mysterious as HIV?

What does it mean to have a genetic predisposition to a disease?

Why are longer DNA sequencing read lengths preferred over shorter read lengths?

What are the most amusing figures or images from academic journals and articles?

Do siblings who share the same set of parents each have the same distribution of parental DNA? Can one sibling have more of one parent’s DNA or would the parental DNA distribution be equal?

Does a chromosome contain a thousand genes, or is it gene pairs (i.e. 2000 genes in all)?

About Scientific Research and Careers

Why are biologists so secretive of their data?

What happens to old scientific grant applications?

What’s competitive research funding?

Miscellaneous

What has been the toughest decision of your life? Did it turn out to be the right one?

What is the wittiest thing a child has ever said to you?

Is the term “agnostic atheist” a double negative?

What are the best examples of people “gaming the system”?

What’s the worst logo failure you have ever seen?

 
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Posted by on 2015/01/03 in Quora

 

The epigenetics of The X-Files

(Originally published on Occam’s Corner at Guardian Science, in December 2014)

Epigenetics is helping us to solve DNA mysteries that cannot be explained by genetics alone. It might even help explain some of the spooky phenomena described in the 1990s science documentary series The X-Files

Epigenetics has the power to open up possibilities beyond those offered by genetics alone – including the occasional triple word score Photograph: Cath Ennis

Dana Scully was a scientist, always looking for a perfectly rational explanation for the strange phenomena encountered each week. Many of these explanations were based on genetics, especially in the “monster-of-the-week” episodes featuring assorted freaks and other abominations not part of the main alien conspiracy storyline. Memorable monsters included such delights as a sewer-dwelling fluke man, and a charming creature possessing the lethal combination of an ability to squeeze through any gap and a taste for human liver.

It was easy enough to explain some of these freaks as genetic mutants – the man with a tail and an unusual muscle structure allowing him to mimic facial features surely had some kind of mutation in a muscle fibre gene – but the scientific basis of many other cases remained unknown. This shouldn’t be surprising: science moves quickly, and we’ve learned a lot about genetics since the ‘90s. One of the major advances made since then is in the field of epigenetics – a field that I believe has the power to resolve some X-Files cold cases.

X chromosome inactivation can definitely be explained by epigenetics. X-Files? Less certain. Image from Reinius et al., BMC Genomics 2010, 11, 614.

Epigenetic modifications include the addition of a methyl molecule to the DNA itself (could this be the mysterious fifth letter that Scully found in a segment of alien DNA?), and changes to the histone proteins around which the double helix coils itself. This molecular highlighting affects how the DNA text is read in that region, helping to determine which genes are switched on or off in each cell.

Many unresolved X-Files cases that might be accounted for by a genetic mutation could just as easily be explained by an epigenetic modification of the same gene.

For example, in cancer (where the cell’s epigenetic patterns go just as awry as everything else), the same tumour suppressor genes that are often lost by mutation or deletion can also be eliminated by abnormal methylation patterns in that part of the DNA. If there’s also a “psychic abilities suppressor gene” lurking in our genome, then we can provide a perfectly rational explanation for multiple cold cases in one fell swoop.

But let’s move on to something a little more challenging.

An important feature of epigenetics is that the pattern of molecular highlighting isn’t fixed. The DNA sequence itself is essentially the same in every cell of the body and through all stages of life; in contrast, epigenetic modifications are different in different cells, change during processes such as metamorphosis (definitely in frogs, so probably also in shape-shifting extraterrestrial species), and can change in response to the environment.

Even identical twins (or, say, genetically engineered clones), who have identical DNA sequences, have different epigenetic patterns – and these differences increase as the twins get older. This helps to explain why identical twins aren’t actually identical, and also why some clones are evil and others are able to overcome their genetic programming to become productive members of society.

Experiences as diverse as chemical exposures, traumatic experiences, and exercise have been shown to cause epigenetic changes. I haven’t yet seen any published scientific papers documenting the epigenetic effects of exposure to alien abduction, alien virusesparasitic ice wormshallucinogenic fungal spores, or questionable tattoos, but I’m sure they would be spectacularly interesting and could account for the strange behaviour of some of the unfortunate people involved. They probably also explain Scully’s cancer; if carcinogens such as bisphenol A can operate at least partially via epigenetic mechanisms, I don’t see why alien experimentation techniques can’t do the same.

There’s even evidence that the epigenetic changes caused by some experiences, such as periods of starvation or drug use, can be passed on to future generations. Could epigenetic inheritance account for the supernatural abilities of Mulder and Scully’s son William? (Yes, William’s abilities were demonstrated in seasons eight and nine. Yes, I just said that I refuse to admit that these seasons ever happened. If Chris Carter doesn’t have to be internally consistent, then I don’t have to either). Some might even argue that epigenetic inheritance can also explain memories of past lives, but hey – that’s just silly.

In summary, the hypothesis that we can use epigenetics to finally close several X-Files cold cases seems to have some merit. (We can ascribe anything we can’t explain via epigenetics, such as invisibility and possibly the conception of baby William, to epic genie tricks instead). I hope the FBI are paying attention…

Add your own cold case explanations in the comments!

Cath Ennis is, like all the best X-Files episodes, based in Vancouver, Canada. She doesn’t really believe The X-Files was a documentary.

This article most definitely does not represent the official position of the International Human Epigenome Consortium. However, Cath and other consortium members did discuss some of the cold case explanations included in the article (on their own time and their own dime) during the 2014 Annual IHEC Meeting in Vancouver. Thank you Dena Procaccini and other participants for your contributions!

Cath is on Twitter as @enniscath, and on Words With Friends as Wonderbrit. The Truth is out there, and it’s worth at least eight points.