Human Genomes, For Cheap

Wired Science has a good post about Complete Genomics, a new company that promises to sequence an entire human genome for a mere $5000. This is approximately 5% of the current price tag.

You may have heard of companies, such as 23andMe, offering genomic sequencing for only a few hundred dollars. But these companies focus on specific single nucleotide polymorphisms, or SNPs, that represent a small fraction of the human genome.  They will sequence about half a milion base pairs, but Complete Genomics is hoping to sequence all 3 billion.

Wired explains how these developments could revolutionize biomedical genetics research:

And even at $5,000, the consequences would be enormous: Human genetic research, which is now focused on just a few genomic regions, and ignores types of variation that can’t easily be measured, would finally be able to assume its full form…

The cost and difficulty of sequencing genomes has forced medical geneticists to take a painstaking and limited approach to their work, necessarily looking only at a few genes or mutations. Even whole genome association studies — the gold standard of modern genetics — are misleadingly named: Geneticists search for similarities and differences between people at a handful of genomic locations that are most likely to vary between people, but still ignore most of the genome. Truly-named whole genome associations don’t yet exist.

If non-SNP variations can be correlated with human diseases, then inexepensive whole-genome sequencing could finally help realize the dream of personalized medicine. For now, Complete Genomics hopes to attract business from biomedical researchers. But eventually, the same technology might help ordinary consumers download their entire genome onto their personal computer. In case you’re wondering, you’ll only need about 750 megabytes of disk space.

Elyn Saks: Patient cum Professor

I just finished reading The Center Cannot Hold, a new memior by Professor Elyn Saks of USC. Saks begins her first-person account of schizophrenia by chronicling her life as an undergraduate philosophy major, her time at Oxford as a Marshall Scholar, and her subsequent hospitalization at a British mental institution. Eventually Saks returned to the Unites States and began law school at Yale. There she had a second psychotic break that led to another hospitalization. Saks draws a stark contrast between the British hands-off approach to mental illness and the American system of restraints and punishment. This contrast inspired much of her scholarly work, which has focused on the legality of coercion in psychiatric treatment.

Saks’ success is remarkable in light of the fact that only about 10% of schizophrenic individuals have steady jobs. Saks has not only remained employed, but she has also become a leader in her field and a role model to many who suffer from mental illness. In fact, she credits her career as an enormous source of strength during the most turbulent periods of her life. Saks goes into more detail, and reads several excerpts from her book, in this video:

It’s over.

Is this what postpartum depression feels like? I just took the MCAT on Saturday, and now I don’t know what to do with myself. I thought most of it was manageable, but I definitely made a couple dumb mistakes along the way. My scores on the practice tests rarely correlated with my subjective impression of how I did, so I guess I’ll just have to wait a month in order to find out. Speaking of which, what part of grading a (mostly) multiple choice exam takes 30 days?

To those who plan on taking this test one day, here are my two cents:

• Start Early. I began studying about 3 months ago, though I only got serious about it 2 months ago. I also took last week off work, which was probably unnecessary. Anyway, the longer you have to study, the more comfortable you will be with the test’s format and timing.
• Expect the unexpected. While the scope of material on the exam is relatively limited, the questions are always applying these concepts in unfamiliar settings.
• It’s in the passage, dummy! It’s true that a good chunk of the questions can be answered without reference to the passage. But if you stumble across one that doesn’t make any sense, you probably skimmed over a subtle clue in the text. This is also true for VR, where the correct answers are usually paraphrased literally from the text.
• Practice, practice, practice. I used a combination of Kaplan Full Lengths and AAMC exams to prepare. The actual test was somewhere in between in terms of difficulty.

The Anti-Munchies

Marijuana is well-known for its ability to stimulate food intake, so it’s not entirely surprising that cannabinoid receptors are emerging as major targets for weight-contol drugs. European authorities approved sales of the CB1 receptor antagonist rimonabant (Sanofi-Aventis) back in 2006. Now Merck is announcing the development of another CB1 antagonist called taranabant, which reportedly decreases caloric intake. The research appears in the journal Cell Metabolism, but I can’t seem to access the article despite my fancy academic licenses.

Scientific American has a nice summary of the findings:

Heymsfield and his team found that obese people given low doses of taranabant consumed fewer calories, expended more energy and shed pounds. The scientists initially tested the drug on animals, which lost weight on doses that inhibited just 30 percent of their cannabinoid receptors. Armed with this knowledge, the researchers used positron emission tomography (PET) imaging to determine the amount (four to six milligrams) of taranabant that would achieve a similar goal in humans.

They found that obese patients lost significant weight during the 12-week trial at surprisingly low doses ranging from 0.5 to six milligrams; those who took a 12-milligram dose consumed 27 percent fewer calories than subjects given a placebo. The researchers reported that plump participants on the drug also expended more energy while at rest and appeared to burn more fat.

Blocking cannabinoid receptors does not come without a cost:

The medical team said higher doses had some potential negative side effects, most notably nausea, vomiting and moodiness. This was not entirely unexpected, Heymsfield said, given that it has the opposite effect of marijuana, which has been known to quell nausea associated with cancer treatments and, also, to calm rather than irritate people.

Perhaps subsequent pharmaceuticals will specifically target hunger and satiety systems without affecting other aspects of cognition. This is a challenging goal considering how little we know about the mechanism of action for drugs like rimonabant and taranabant. A 2005 Nature Neuroscience review argued that the body’s natural ligands for cannabinoid receptors (endocannabinoids such as anandamide and 2-AG) may operate at two levels. First, basal levels of endocannabinoids act on mesolimbic pathways to facilitate the motivation to eat and the subsequent rewards.  Second, the hypothalamus uses endocannabinoids to recruit other hunger hormones after periods of transient food deprivation.

The hypothesis of a dual action in mesolimbic and hypothalamic regions was substantiated by the finding that injection of endocannabinoids into these brain areas stimulates food intake in rats^{24, 25}. Furthermore, endocannabinoid levels vary in both the hypothalamus and the limbic forebrain (but not in the cerebellum, which is not involved in appetite regulation) during the four phases of feeding behavior in rats. These levels are highest during food deprivation and lowest during food consumption, as expected from endogenous orexigenic mediators²⁵. In the hypothalamus, these changes in endocannabinoid levels seemed to be inversely correlated with the changes that are known to occur in blood levels of the neurohormone leptin, which is pivotal in regulating the hypothalamic orexigenic and anoretic signals. Indeed, leptin decreases endocannabinoid levels in the hypothalamus, much as it does for other orexigenic mediators, and obese rodents with defective leptin signaling show significantly higher hypothalamic endocannabinoid concentrations²³. It has been suggested that an enhanced endocannabinoid tone is also linked to enhanced ghrelin levels in the bloodstream after food deprivation and may underlie some of the orexigenic effects of this peptide when injected into the rat hypothalamus—effects that are in fact blocked by antagonism at CB₁ receptors with rimonabant²⁶.

Despite the multitude of questions that remain to be answered, the development of new drugs like taranabant could help millions of people who struggle with obesity issues. Now that cannabinoid research has established clinical relevance (not to mention profit potential), you can expect to see a lot more of it.

The Hippocratic Oath, Revised: Do Less Harm?

The phenomenon of anesthetic awareness provides great fodder for Hollywood, but now it has also found its way onto the floor of the Supreme Court. Baze vs. Rees challenges the standard 3-drug lethal injection protocol on the basis that it may constitute cruel and unusual punishment, which is outlawed by the eighth amendment.

The current lethal injection protocol was developed in 1977 and consists of a fast-acting barbiturate (sodium thiopental) followed by a paralytic agent (pancuronium bromide) which prevents convulsions during the administration of a heart-stopping toxin (potassium chloride). Arguing on behalf of two Kentucky inmates, attorney Donald Verrilli made the argument that improper administration of the initial barbiturate could cause death row inmates to experience an “excruciating sensation of drowning or strangulation” before they pass away. Because of the paralytic agent, inmates would not be able to communicate their pain to executioners.

A glaring Catch-22 lurks behind this debate: the inmate will not experience pain if the anesthetic is administered effectively, but the American Medical Association (AMA) prohibits healthcare professionals from participating in executions. Interestingly, this hasn’t stopped many doctors from complying with government requests for supervision during executions. Atul Gawande wrote an excellent article profiling these individuals and the issues they face in the New England Journal of Medicine.

Particularly intriguing is the story of Dr. Carlo Musso, who participates in executions despite his personal belief that the death penalty is wrong:

He read about the ethics of participating. He knew about the AMA’s stance against it. Yet he also felt an obligation not to abandon inmates in their dying moments. “We, as doctors, are not the ones deciding the fate of this individual,” he said. “The way I saw it, this is an end-of-life issue, just as with any other terminal disease. It just happens that it involves a legal process instead of a medical process. When we have a patient who can no longer survive his illness, we as physicians must ensure he has comfort. [A death-penalty] patient is no different from a patient dying of cancer — except his cancer is a court order.” Dr. D said he has “the cure for this cancer” — abolition of the death penalty — but “if the people and the government won’t let you provide it, and a patient then dies, are you not going to comfort him?”

While the article is locked behind a subscription wall, NEJM has posted a free interview with Dr. Musso:

To be sure, these are murky ethical waters. While Dr. Musso makes a valid point about the inevitability of court-ordered executions, it seems like doctor participation sets a dangerous precedent. If doctors begin flouting the AMA’s code of conduct, then what will stop them from cooperating with torture in addition to executions? The U.S. government has already tried to make this happen.

For me, the obvious solution is to abolish the death penalty altogether, an idea that has already caught on in New Jersey. Indeed, Baze vs. Rees may be a veiled attempt to accomplish a similar goal at the national level. Writing for Slate, Dahlia Lithwick makes the point that this case is not really about pharmacology as much as it is about the constitutionality of the death penalty tout court. The Supreme Court’s decision to hear the case has imposed a de facto moratorium on executions across the country. I’m just crossing my fingers that this case doesn’t get closed anytime soon.

Method Of The Month: Osmotic Pumps

This post is the sixth in a series that aims to educate readers about the tools that are used in neuroscience research. Previously we discussed Radioactive Binding Assays, Novel Object Recognition, Calcium Imaging and EEG.

Currently I am running a study that examines the effects of chronic nicotine on sensory processing in mice. While I don’t mind coming into the lab on weekends, the prospect of visiting my animals 24/7 to inject nicotine wasn’t exactly practical. I could give daily or twice daily injections, but even that doesn’t really come close to approximating the behavior of human smokers.

That’s why we turned to a company called Alzet that manufactures miniature pumps for drug delivery in laboratory animals. These pumps can deliver small volumes of drug solution at a controlled rate over a period of up to six weeks. We opted for the 2002 model, with a reservoir volume of 0.2 mL and a flow rate of 0.5 µL/hr.

They are pretty easy to use: Just fill up the reservoir with concentrated drug solution and pop on the cap. Then, anesthetize the rodent and cut a small slit in its back using standard aseptic techniques. After opening a small cavity for the pump with a hemostat, insert the device and close the opening using medical staples.

After implanting these pumps subcutaneously, I couldn’t help but wonder if these things were actually going to work. How could a little piece of plastic control the flow of drug solution so precisely? If they worked because of osmotic pressure, then shouldn’t the flow rate depend on the concentration of the dissolved drug? I knew that osmotic pumps were popular, but I couldn’t shake the irrational fear that these $20 devices were just one big scam.

The only way I could settle my nerves was by figuring out how the devices worked. Luckily Alzet’s website is relatively transparent about the mechanism. Now I know that the osmotic pressure difference is actually between the animal’s body and the “salt sleeve” that surrounds the drug reservoir. From their website:

ALZET pumps operate because of an osmotic pressure difference between a compartment within the pump, called the salt sleeve, and the tissue environment in which the pump is implanted. The high osmolality of the salt sleeve causes water to flux into the pump through a semipermeable membrane which forms the outer surface of the pump. As the water enters the salt sleeve, it compresses the flexible reservoir, displacing the test solution from the pump at a controlled, predetermined rate. Because the compressed reservoir cannot be refilled, the pumps are designed for single-use only.

The rate of delivery by an ALZET pump is controlled by the water permeability of the pump’s outer membrane. Thus, the delivery profile of the pump is independent of the drug formulation dispensed.

Pretty nifty, huh? Even niftier is the accompanying animation:

Now I am much more confident that my mice are indeed receiving the expected dose of nicotine. In retrospect my fears were misplaced, but in science it never hurts to be skeptical/cautious.

Mouse Pain vs. Human Pain

Today I sacrificed a laboratory mouse. Unlike most of the mice in my current study, this one lost its implanted electrode, leaving him with exposed skull and brain tissue. This is not a healthy situation, so I had to euthanize him for his own well-being. Specifically, this involved CO2 administration followed by cervical dislocation (to remove any doubt). I did not enjoy this.

Incidentally, the topic mouse pain figures prominently in this month’s Harper’s, which features an article about the mouse’s ascent within the modern biomedical research industry. Although the article is locked behind a subscription wall, I recommend picking up a hard copy. In the meantime, here’s what I learned from it:

• The United States consumes 80 million rats and mice per year. Of the newborn male mice, 70% are euthanized because of their aggressive tendencies.
• Neither mice nor rats are covered by the Animal Welfare Act, a law enforced by the U.S. Department of Agriculture that is meant to protect research animals.
• The scientific community’s prime mouse vendor – Jackson Laboratories – was founded by Clarence Little, who developed his first mouse lines while still an undergraduate at Harvard. Some of them, such as the Dilute, Brown and non-Agouti (DBA) strain, are in continued use today.
• Jackson laboratories is currently developing ways to reduce the excessive consumption of mice by preserving sperm on ice and then producing strains on request.

The article advocates the inclusion of mice in future revisions of the Animal Welfare Act, which certainly seems like a good idea to me. Nonetheless, as one of many scientists that uses mice on a daily basis, I can assure you that we use the utmost restraint in mouse experimentation. We recognize their valuable role in curing disease and respect them as fellow animals.

Regardless, I think any researcher must subscribe at some level to the premise that human life is somehow worth more than mouse life. Call it speciesism, call it whatever you want, but I’d certainly rather 100 mice died than God forbid someone in my family. I view animal sacrifices as a necessary cost in the search for cures. Far from being merely hypothetical, life-saving cures discovered with mice are already here.

Encephalon 36

Welcome to Encephalon, the bi-weekly neuroscience blog carnival. In the 36th Edition, you will learn what STDs have to do with Alzheimer’s, how rats plan their decisions in a maze and why kids start speaking in nouns. Thanks for all the great submissions.

Brain Disease

Zachary Tong at Distributed Neuron reports on new evidence that neural progenitor cells migrate towards the site of strokes. Researchers injected progenitor cells into mouse brains and then induced artificial strokes in half the subjects. They tracked the progenitor cells and found direct migration of labeled cells in the animals with brain injury.

Zachary also investigates the diverse genetic causes for epilepsy. New research demonstrates that disparate mutations associated with the disease can cancel each others’ negative effects when co-expressed.

Evil Monkey at Neurotopia provides yet another reason to practice safe sex: avoiding Alzheimer’s Disease (AD). Herpes virus HSV-1 is a risk factor for AD and may accelerate the formation of amyloid plaques associated with cognitive decline.

Relatedly, Sandra Kiume at Channel N links to videos about memory loss from a conference at the University of British Columbia. The videos discuss tips for healthy aging in the context of cutting edge neuroscience research.

Computational Neuroscience

Jake Young at Pure Pedantry highlights a great paper in J. Neuroscience about how spatial information is encoded in the hippocampus. The authors made electrophysiogical recordings from rats as they chose between two alternative arms of a maze. These recordings revealed transient activation of neurons associated with each path, even before the rat embarked on either of them. This research proves that hippocampal maps are not solely for real-time encoding of spatial location but also for projections about future position.

In a related — albeit more theoretical — vein, Michael introduces his new blog Shared Symbolic Storage with a post about embodied cognition. Michael mentions a paper co-authored by Benoit Hardy-Vallée, an Encephalon contributor.

Imaging Studies

Ed Yong at Not Exactly Rocket Science reviews new research showing that the brains of children with attention deficit hyperactivity disorder (ADHD) exhibit delayed maturation of the prefrontal cortex and accelerated maturation of the primary motor cortex. The findings are encouraging because they suggest that the brains of patients with ADHD eventually catch with those of nonaffected individuals.

The Neurocritic has a great two part takedown of the New York Times’ latest foray into pseudoscience. He links to several rebuttals and contributes a healthy dose of common sense with this rhetorical question: “Did we really need fMRI to tell us that Mrs. Clinton should try to soften the negative responses of swing voters?”

Language

Michael at Shared Symbolic Storage offers a three part review of Baboon Metaphysics, a new book by Dorothy Cheny and Robert Seyfarth. The authors propose that social cognition preceded and made possible the emergence of language, instead of vice versa. Michael argues that this proposal neglects the mechanisms though which language can in turn influence our thought.

“Mama,” “Cookie,” “Nap.” Why do children learn nouns like these before other parts of speech? Dave Munger at Cognitive Daily reports on a creative study in which infants learning their first language were compared to older children learning a second language. This allowed researchers to figure out whether the early abundance of nouns is a function of age or an necessary feature of language acquisition.

That wraps it up for this issue of Encephalon. Bora at A Blog Around the Clock hosts Encephelon #37 on December 3rd. Email your posts to encephalon{dot}host{at}gmail{dot}com or submit using the online form.

The Beautiful Cerebellum

Okay, guilty as charged. It’s been a while since my last post, but in my defense, I’ve been dealing with a lot of midterms recently. Yeah, that’s right. I may have graduated college but I’m still finishing up pre-med coursework. My most recent exam was in Histology, which is turning out to be a pretty cool class.Histology is basically microscopic anatomy. By chemically fixing body parts, embedding them in wax, slicing into them into thin sections, and finally staining them with dyes like hematoxylin and eosin, it’s possible to observe the structure of organic tissue with a light microscope. My professor has introduced our class to an amazing online repository of histological preparations hosted by the University of Iowa.

One of my only complaints about the class is that we focus almost exclusively on structure, without much attention to function. This is an unfortunate consequence of time limitations, but sometimes I go out of my way to follow up on a specific topic. Usually learning the functional organization of a given tissue also makes it much easier to memorize the structural organization. Take, for instance, the structure of the cerebellum:

Memorizing these layers is not too challenging, but I found some functional diagrams that helped me make sense of this brain system. This one from the University of Illinois does a nice job of showing synaptic connections between the layers:

Here we can see that the Purkinje cells (the large, sparsely populated cells in the Purkinje Layer) are receiving synaptic inputs from a multitude of granule cells below them. Granule cells are present in great abundance, making up 70% of the body’s neurons. While a single Purkinje cell receives hundreds of thousand synaptic connections from granule cell parallel fibers, they receive input from only one climbing fiber. This second type of connection is quite potent, capable of inducing complex spike trains in postsynaptic Purkinje cells. In contrast the Granular Layer, the Molecular Layer is dominated by inhibitory interneurons with horizontal processes.

The structure of the cerebellum is actually quite elegant. Here is one more photo in which Purkinje cells are tagged with a fluorescent dye. It makes their intricate dendritic trees very apparent:

Link to an extensive Wikipedia article on the cerebellum.

Link to the Univerity of Iowa virtual slidebox.

Kevin Everett Benefits From Hypothermia Treatment

Kevin Everett, a tight end for the Buffalo Bills, was seriously injured a week ago. Immediately after hitting an opponent in a routine tackle, Everett fell to the ground motionless because of spinal cord damage. But while doctors were first pessimistic about his chances for recovery, he has since regained motion in some of his limbs and may be able to walk again. How did Everett escape complete paralysis?

Everett’s doctors employed a novel technique. On the way to the hospital, they started to cool his body by injecting him with two liters of ice-cold saline. After performing corrective surgery, doctors continued to cool his body by implanting a catheter into his femoral artery. This time, cold saline was recycled through intravenous balloons instead of entering his bloodstream. The technique cooled his body temperature from 98°F to 92°F.  The New York Times has a nice diagram along with their writeup.

At the very least, moderate hypothermia treatment does not hurt most patients with neurological injuries. At most, it may constitute a medical breakthrough. But how does it work?

The short answer is that nobody knows for sure. That said, there are plenty of hypotheses: cooling may reduce inflammation, slow down metabolism, regulate excitatory neurotransmitter signaling, stabilize the blood brain barrier and reduce dangerous free radical concentrations.

Everett’s treatment is part of a larger campaign to reduce football injuries by bringing state-of-the-art medicine to the field.  For instance, some teams are buying portable CT scanners to assess injuries immediately.