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Author: Brian Krueger, PhD | Views: 3351 | Comments: 0

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If you’re an avid follower of popular science in today’s news media, you might have noticed a recurring theme. Genomics is everywhere. On an almost weekly basis, the New York Times, the New Yorker, Forbes and a myriad of other outlets are publishing stories with overly optimistic ledes about doctors and gene sequencers being replaced by apps and iPhone accessories. You would be forgiven if you thought genomics was “solved” and we’re 5 years out from creating a Star Trek inspired “tricorder” that near instantly sequences your genome and tells you, without equivocation, what malady is afflicting you and how exactly to overcome said disorder. The fact of the matter is that we’re not there yet, not by a long shot.

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Author: Brian Krueger, PhD | Views: 757 | Comments: 1
Last by Ematiz Alom on Mar 08, 2015, 8:37am
The Advances in Genome Biotechnology conference starts tomorrow in Marco Island, FL. Twitter and the blogs have been a flurry of speculation about what the major vendors will present at this years’ meeting. In previous years we’ve seen the introduction of new, “disruptive” technologies such as the ion torrent platform, the Oxford Nanopore Minion and the PacBio RS. Like many, I have mixed emotions about this conference. It’s more CES than science. Given the history of the major announcements and where those products are now 3 and 5 years out it’s hard to get excited about a show stopper. While technically impressive, the MinIon is still mired in problems that were glossed over in the fanfare of the original announcement and PacBio is FINALLY starting to deliver on the promises it made eons ago. I should also mention my disappointment with Ion Torrent here. This is yet another company that made a major announcement at AGBT and failed spectacularly. Keith Robison thinks they still have a sho . . . More
Author: Brian Krueger, PhD | Views: 1276 | Comments: 0
Yesterday marked the kickoff of the JP Morgan Healthcare Conference in San Francisco. Following last years’ lead, Illumina once again used this platform as an opportunity to announce the release of a number of new products including 4 “New” sequencing systems ahead of the more scientifically focused Advances in Genome Biotechnology conference in February. At this same time in 2014, Illumina presented the HiSeq X ten sequencing system which is a system for population scale genomics composed of ten HiSeq X sequencers. Illumina touted this system’s reduced reagent price, increased speed, and expanded capacity. It has now taken much of the technology from this HiSeq X system and put it into two new lower tier models: the HiSeq 3000 and HiSeq 4000.

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Author: Brian Krueger, PhD | Views: 1951 | Comments: 0
Illumina, the world leader in short read DNA sequencing, made a series of very big announcements yesterday at the JPMorgan Healthcare Conference. These developments have many sequencing labs around the world excited and worried all at the same time. The excitement comes from the fact that it appears on the surface that Illumina has broken the $1000 genome* barrier – the worry comes from the realization that only a few of us can afford it.

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Author: Cynthia McKelvey | Views: 7956 | Comments: 0
For over two decades, Shark Week on Discovery Channel has been raising awareness of one of the ocean's most mysterious and powerful predators. Discovery originally started Shark Week with the purpose to dispel myths about the dangers of sharks, and to heighten the public's respect for the creatures. However, this year, many fans have felt outraged that Discovery may be straying further away from the original purpose of Shark Week. This year, Discovery unveiled the faux-documentary, Megalodon: The Monster Shark That Lives.

Megalodon, for the record, are definitely, absolutely extinct. They were super-sized sharks that once roamed the oceans some 2 million years ago.

Relative size of Megalodon (red and grey) vs. human. Source.
The Discovery special, on the other hand, suggested an alternative. Megalodon still roams the oceans, somewhere off the coast of South Africa. The documentary looked and seemed like any other documentary about real life events (however fantastic.) It convinced 70% of viewers that Megalod . . . More
Author: Cynthia McKelvey | Views: 4021 | Comments: 2
Last by Cynthia McKelvey on Apr 30, 2013, 1:10pm
Last summer, I became inspired to write an article about the potential benefits of the club drug, MDMA, otherwise known as Ecstasy or Molly. The blog post got turned into an article for my alma mater's science magazine, The Synapse, and was published a few months ago. With permission, I am cross-posting it here.


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Author: Brian Krueger, PhD | Views: 11714 | Comments: 9
Last by Michael Schatz on Feb 26, 2013, 12:13am
Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted. There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives. This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite the ridiculous parties and “showgirl” casino nights. The atmosphere here is unlike any other science conference I’ve attended. It’s like the bastard child of a Gordon Conference and a Las Vegas Porn Convention. I really hope that the deep pockets of Sequencing Centers are more influenced by the science than the free dinner parties and alcohol, but I have pretty low confidence in humanity. Regardless, I think everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology.

The PacBio talk came on the heels of what felt like a warm-up opening act from Jeremy Schmutz of the Hudson Alpha Institute. Schmutz has been working with a start-up that was recently acquired by illumina called . . . More
Author: Brian Krueger, PhD | Views: 3658 | Comments: 0
As the second day of AGBT kicked off, it became quite clear that this meeting would be dominated by medical genomics. There were a few talks sprinkled in about gut or sewer microbiomes but the vast majority of the talks the last two days have been on clinical genomic sequencing. This is fine by me since it’s exactly what we do in the Genomic Analysis Facility in Duke’s Center for Human Genome Variation. It’s really nice to see how other centers are approaching these problems. Unfortunately, this is one of the few opportunities we have to peek into each other’s operations.

Yesterday’s first talk was by Russ Altman of Stanford University. Russ has been a leader in the field of pharmacogenomics and he presented his work on developing the Pharmacogenomics Knowledgebase (PharmGKB, pharmGKB.org). He led by saying, “Don’t ever give a talk about a website,” and in his case it was true because WiFi in the conference room was down for the majority of his talk. He urged the crowd to follow along on the website, but only those of us with a cell connection could join him. Russ pointed out the major drawbacks of using GWAS and SNP chips for obtaining information about pharmacoenomic associations and joined pretty much everyone else in saying that the standard t . . . More
Author: Brian Krueger, PhD | Views: 3119 | Comments: 2
Last by Brian Krueger, PhD on Feb 21, 2013, 11:42pm
Today I dusted off my luggage and headed down to the annual Advances in Genome Biology and Technology meeting in Marco Island, FL.  Historically, this meeting has been the Detroit Auto Show of Genomics where companies and labs release their beautiful shiny new products and methodologies.  In past years, attendees were showered with fireworks displays and epic swag bags.  The tone this year is palpably more mutated.  One only has to point to the display banners located on the AGBT presenter stage for evidence of this: banners for Bronze and Silver Sponsors appear to hang waiting for accompaniment by Gold and Platinum brethren…there’s even space allocated for them.  

Despite the tightened biotech purse strings, the event appears from the outset to be extremely well organized.  There could be a few more power outlets for those of us carrying a small fortune in lithium powered devices, but I guess I’ll manage.  And of course there’s no live streaming or any form of web enabled anything…but I can gripe about that in a long winded and whiny post next week.

The evening opened with a brief introduction with a description of some new meeting changes.  This is the biggest AGBT yet with over 800 attendees.  A new abstract selection committee was created . . . More
Author: Jordan Gaines | Views: 4804 | Comments: 1
Last by Sneha Mokashi on May 08, 2013, 2:08pm
My friend texted me something today that she thought I'd find interesting.

She had a meeting for work in an office she'd never entered before. Immediately as she entered the room, conflicting feelings of happiness and awkwardness washed over her.

The smell. It wasn't necessarily good or bad—just distinctive. And it didn't smell like anything in particular. All she knew was that it had an odor exactly like her boyfriend's dorm room when she was a freshman in college—something she hasn't experienced in five years—bringing back the paired feelings of excitement and nervousness that come with new relationships. And those of, well, being in a boy's stinky dorm room.

We've all experienced this at one time or another: a familiar perfume, a family recipe in the oven, the scent of a bonfire—they all bring back a flood of memories, momentarily whisking us away to re-live our past. But why does this happen?

One of animals' most primal senses is that of smell. If you look at a rat brain, the olfactory bulbs (the two little notches at the top) take up a significant portion of the total surface area. In the human brain, the piriform cortex (our primary olfactory cortex) is composed of three primitive layer . . . More
Author: Jordan Gaines | Views: 4101 | Comments: 1
Last by jimbot on Jan 28, 2013, 7:14pm
The weekend before Christmas, I was sucked into a giant, enticing vortex of craving and desire, stuck for hours with the inability to leave—my only limitation being my wallet.

In other words, I went to Target.

And—again, in other words—I was like a bull in a China shop.

Back in 2009, Target introduced new gigantic, plastic, Playskool-esque shopping carts. Maneuvering the aisles is like passing a car on a one-lane country road in a Hummer.

Of course they're ridiculously cumbersome, but it's all a trick on the Target executives' part—the bigger your cart, the more you can fit in there. You'll look silly hauling around a couple packages of pens and a box of tissues to the checkout counter, after all. Better head to the appliance section and fill it with a microwave or plasma TV.

In this second installment, we'll explore how stores betray our sense of sight, tricking us to buy stuff we really don't want or need.

Retailers have—quite creepily, actually—studied our every move. In fact, they've found that we like to shop counter-clockwise, and stores with their main entrance to the right side sell more than their counterparts with doors on the left.

They also like to welcome us . . . More
Author: Jordan Gaines | Views: 3773 | Comments: 1
Last by Brian Krueger, PhD on Dec 10, 2012, 9:46am
On the first day of Christmas my true love gave to me...

...a bunch of crap I really didn't need.

With just sixteen shopping days until Christmas, it's easy to get roped into buying things we might not actually have on our gift list.

Most times, we're conscious of our impulse purchases—there's a great sale on this! I'll use that later!

But sometimes reasons for our frivolous purchases are not so obvious to us. Don't feel too bad—store chains actually hire researchers to study our shopping patterns and take advantage of our weaknesses.

Our brains are endlessly fascinatingly organs—but sometimes they betray us. The following is the first post in a five-part series on how stores trick our senses into shelling out more money than we may intend.

Taste

Did you ever take the Pepsi Challenge?

For those unfamiliar (or living under a rock), the Pepsi Challenge was a campaign started by Pepsi back in the 1970s where Coca-Cola was pitted against Pepsi in a blind taste test by consumers.

When it was revealed that most Americans chose Pepsi over Coca-Cola, sales skyrocketed.

How they tricks us: We consumers like brands, and we're loyal to them.

It make sen . . . More
Author: Jordan Gaines | Views: 1310 | Comments: 0
Sometimes our world can be pretty crappy.

There's violence and crazy people. Maybe your candidate didn't win the election. Perhaps you hate your job, and that—on top of life's other personal, familial, and financial burdens—is wearing you down. Maybe you got to your morning coffee after it went cold, and that set off a bad tone for the rest of your day.

If you're celebrating Thanksgiving this Thursday, don't forget the true meaning of the holiday between the stressful hubbub of cooking, shopping, planning, and appeasing Great Aunt Gertie: giving thanks.

As it turns out, expressing gratitude is more than just a nice idea—it's beneficial to your health and happiness.

Back in 2003, Robert A. Emmons (UC Davis) and Michael McCullough (Miami) were among the first to publish a study in examining the link between thankfulness and a person's well-being in the Journal of Personality and Social Psychology.

The researchers divided 192 undergraduate participants into three groups. All participants kept a weekly journal—the difference was what they wrote about.

Those in the first group (the "gratitude" group) were instructed to list five things for whi . . . More
Author: Jordan Gaines | Views: 2693 | Comments: 3
Last by Brian Krueger, PhD on Nov 06, 2012, 7:20am
A year ago today, I began this blog, "neuroBLOGical"!

Having my blog hosted on LabSpaces has allowed me to interact with so many interesting, insightful, thoughtful, and questioning readers, scientists and non-scientists alike—which is exactly how I envisioned my audience when I set out to write about the latest neuroscience research and hot topics.

And so, readers, I ask you for a small birthday gift. In the tradition of science writer Ed Yong and the SciAm Blog Network that just turned 1 in July, I want to know—who are you?

Whether you openly follow my blog or whether you lurk quietly, I'd love for you to tell me a bit about yourself and why you read this blog in the comments section below:

Who are you?

What is your relationship to science?

What drew you to this blog, and how often do you read it?

Do you follow LabSpaces on Twitter and Facebook?

How am I doing? What do you like, and how can I improve?

These questions are a guide, not a strict format—write as much or as little as you want. I truly appreciate the fe . . . More
Author: Jordan Gaines | Views: 1588 | Comments: 0
A couple weekends ago, I came down with coulrophobia. Unfortunately, I have yet to shake the disease.

Because we are Halloween masochists, my friends and I drove out to the Lancaster area for Field of Screams, which can be best described as a horror-movie-set-haunted-house on steroids. Sprinting from room to room offers a completely new, dizzying experience, with different themes and scary people to touch you or chase you down with chainsaws.

But this one room. This one room was unlike any other...

It zigzagged. The walls were tiled with 2x2" black and white checkers. There was a strobe light. I was holding my friend's hand and trying to keep my eyes shut through the flickering.

Out of nowhere, sitting in the corner, tiny and dejected, was this freaking clown. It looked so far away. Then suddenly, not one second later, it was IN MY FACE. The strobe light betrayed my perception of its speed and distance. I cried out. Please, just take me now, and do it quickly...

Hence my newfound coulrophobia, or fear of clowns.

But is coulrophobia a real fear? And, for that matter, what is fear?

Fear: a primer

A woman—known simply in the neuroscience world as S.M.—wa . . . More
Author: Jordan Gaines | Views: 3992 | Comments: 0
Think back to your childhood Halloween: 9pm, a school night, pillowcase full of candy.

Just as you plunge into your pile of peanut butter cups, fun size this-and-thats, and spider rings (weren't they so exciting?), Mom ruins the party. "You can eat three. Then go brush your teeth and get ready for bed."

Did you eat just three? Or did you sneak an extra Baby Ruth or two when she wasn't looking?

A study published earlier this month in Cognition suggests that willpower is not the only factor in play when it comes to foregoing that extra piece.

Instead, a child's belief about their superiors' reliability can change their willingness to wait for a better payoff later.

Psychologist Celeste Kidd and colleagues of the University of Rochester created a modified paradigm of the "marshmallow task." Originally developed by psychologist Walter Mischel in 1972, the task involves an experimenter telling a preschooler that they can eat a marshmallow, cookie, or pretzel. If the child abstains and waits 15 minutes, however, the experimenter tells them they can receive two treats.

Kids lasted an average of six minutes before grabbing the treat in front of them. When fo . . . More
Author: Jordan Gaines | Views: 2112 | Comments: 0
Every year around this time, science bloggers from all over unite as a single force (in a non-Twitter format, no less) at DonorsChoose.org. The science blogging networks engage in monetary battle, raising money to buy school supplies for needy classrooms across the country.

This challenge runs until November 5.



Check out the various projects put forth by science bloggers here and consider making a donation, no matter how small. If you cannot donate, spread the word by Facebook, Twitter, word of mouth, telepathy, etc.

Let's give kids what they need to get the education they deserve!

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Author: Jordan Gaines | Views: 2015 | Comments: 0
Do you have an ex?

Do you have a Facebook profile? Does your ex?

Do you stalk your ex on Facebook?

To the untrained eye, that photo of him eating dinner with...that girl...at Olive Garden is no big deal. But Olive Garden was our place, and—wait, is that the watch I got him? Oh, and it looks like he got into that grad school he wanted to go to. The one for which I edited his personal statement and quizzed him with GRE words...

Ugh.

I'm going to tell you something that you probably already know: you should stop doing this. And I'm armed with the psychology of why it's bad!

In a study published last month in Cyberpsychology, Behavior, and Social Networking, Tara C. Marshall of Brunel University in England examined how individuals who use Facebook have—or, uh, haven't—moved on after a breakup.



The participants comprised of 464 individuals—mostly college-age students (60%), and 84% of whom were female. They were recruited via an online survey which, if you ask me, should have established a criteria to create a 1:1 ratio of males to females. But they didn't ask me.

First, th . . . More
Author: Brian Krueger, PhD | Views: 3376 | Comments: 3
Last by Brian Krueger, PhD on Sep 28, 2012, 5:02pm
One of the big stories that blew up on the internet the other day was the publication of some results that reportedly show that females who have birthed males have male DNA in their brain. That’s pretty cool stuff! This isn’t uncommon, it’s called microchimerism, or the deposition of cells or DNA from the fetus to the mother or vice versa. It has been shown in both mice and humans that the blood of the mother contains snippets of fetal DNA and even whole cells. These have even been used to completely sequence a fetal genome using only the blood of the mother. The finding that these DNA fragments or cells can deposit themselves in the human brain is novel, and potentially cool from a brain regulation standpoint. Maybe baby boy brain cells change the mother’s brain?

However, a quick read of the abstract of the paper yesterday immediately raised a few red flags in my own brain (absolutely full of male cells, by the way). The “discovery” was made using quantitative real-time PCR and only quantitative real-time PCR on a highly repetitive male gene on the Y chromosome. Most people who aren’t scientists don’t . . . More
Author: Jordan Gaines | Views: 3283 | Comments: 0
Scientific literature is, to say the least, pretty dull.

It's rife with redundant phrases, confusing methodologies, and tiny graphs. Reading page after page of long words in small font is better than any over-the-counter sleep aid out there for getting the job done.

Occasionally, the rare gem will come along just when you least expect it, providing a readable (dare I say—enjoyable) account of the latest research.

So begins a paper published this past week in Neurology:

"It was a quiet Thursday afternoon when 'A.S.', a 68-year-old woman from a suburb of Chicago, awakened from a nap to the realization that something was terribly wrong.

What?! What's wrong! Must...keep...reading...

As the article continues, we learn how A.S. and another patient, J.D., adjust to their lives before and after their diagnoses of Bálint's syndrome.

A.S. couldn't find doors or cabinets in her house. She had difficulty naming familiar household objects, and she was unable to read a book or the numbers on her phone.

Armed with an ophthalmologist's' note declaring 20/20 vision with glasses, the next step was to visit a neurologist.

J.D.'s fir . . . More
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