Drs. Miriam Goodman and Merritt Maduke receive tenure

With the road to tenure universally acknolwedged as being long and arduous, it gives me extreme pleasure to pass along the news that Dr. Miriam Goodman and Dr. Merritt Maduke recently received tenure promotions from Stanford University. If you are in the greater Silicon Valley area, pop by Stanford this Friday, 3/12, to help us celebrate the promotion of these two excellent neuroscientists. The party will be in room 100 of Beckman, starting at 12 pm.

For information about the research of tenured professors Goodman and Maduke, wander on over to their laboratory websites.

Goodman Lab, studying sensory transduction in C.elegans.

Maduke Lab, studying chloride-selective ion channels and transporters.

This week in Science: Octopi and Flies and Polar Bears, oh my!

A quick perusal of the ScienceNOW new released from Science yields a couple of interesting stories fun enough to be shared, but short enough not to warrant full fledged posts. Therefore, here they are, collected in one glorious package. Octopus mimics Flounder, confuses predators and biologists. Mentioned by the Lab Spaces blog (and tweeted and re-tweeted on Twitter last week) is a description of a particular species of octopus that has developed a unique camouflage. The Caribbean octopus mimics the peacock flounder while it swims, presumably to discourage octopus-loving predators with the appearance of an unappetizing flatfish. ScienceNOW provides video of said octopus, doing its best flounder impression.

Early polar bear discovered in Arctic tundra. The fossilized (and presumably frozen) remains of an ancient polar bear has been discovered by scientists in Norway's Svalbard archipelago. The male polar bear lived approximately 120,000 years ago, which for those of you who are counting, was at a time when wooly mammoths were still around. For more on why this discovery is so awesome, see the linked article. Perhaps with this discovery, scientists can finally begin contemplating a most important topic: who would win, polar bear or wooly mammoth? (In the swimming portion of the competition, my money's on the bear.)

Fruit flies contain intrinsic autopilot. Scientists have shown that fruit flies are able to adjust to changing wind currents and flight conditions on a time scale quicker than would be possible if the adjustment was a conscious effort: video at link. This research potentially explains the difficulty of fly swatting.

The award for most cheeky article name goes to: "Why are Dung Beetles so Horny", which is in fact about the unusually large horns of female dung beetles. Originally thought to be used exclusively during fights between males, researchers have identified a role for the horns sported by females, which are sizably larger than those seen on males. In short, it seems that females use their horns to conduct sumo-like wrestling matches. The winner gets the larger ball of dung, and is therefore able to produce more offspring.

Upcoming panel on fMRI, vegetative states, and consciousness

Following the recent publication of a fMRI study demonstrating signs of consciousness in patients previously diagnosed as in a vegetative state (written about by this blog, here), the Stanford Interdisciplinary Group on Neuroscience and Society are holding a panel discussion on fMRI brain imaging, vegetative states, and consciousness. The panel will include experts in law, ethics, medicine, and brain imaging research, and will discuss advances in diagnosing and communicating with patients in minimally conscious states. These experts include neurologist Dr. Christine Wijman, biomedical ethicist Dr. David Magnus, law professor Hank Greely, and an an unnamed neuroscientist.

The panel takes place on March 10 from 5-6 pm, in SLS Room 280B. Dinner will be served.

Dr. Wilder Penfield: Dramatic Subject

During Neuroanatomy class this afternoon, students were shown a truly amazing video dramatizing the work of Dr. Wilder Penfield, a surgeon who pioneered the use of cortical stimulation to localize the loci of epileptic seizures. Without further ado, for your amusement: Dr. Wilder Penfield.

The "Best" of Pubmed, Part 1

PubMed: the U.S. National Library of Medicine's great catalogue of biomedical journals. PubMed is the portal to published scientific research, listing over 19 million citations, the good and the bad of what biomedical journals deign to publish. And also the ugly.

Given how much time scientists (especially young scientists) spend worrying about publishing, it is sometimes cathartic to delve into the seedy underbelly of PubMed - to glance through those members of the 19 million citations whose subjects are humorous, awkward, or just plain weird.

Over the past couple of months, I have come across quite a few PubMed jewels: here are some of my favorites. Some of these I found, some were found by other members of the first-year Stanford Neuroscience Program. Some are not suitable for work, children, or those with weak stomachs and vivid imaginations - these I have marked: consider yourself warned.

In the category of Social Interactions:

Dogs catch human yawns. Joly-Mascheroni RM, Senju A, Shepherd AJ. Biol Lett. 2008 Oct 23: 4(5); 446-8.

Instrumental measurement of beer taste attributes using an electronic tongue. Rudnitskaya A et al. Anal Chim Acta. 2009 Jul 30; 646(1-2):111-8.

The inhibitory effects on adult male reproductive functions of crude garlic (Allium sativum) feeding. Hammami I et al. Asian J Androl. 2008 Jul; 10(4):593-601.

In the category of Oh, Ewww.

Nasal leech infestation: report of seven leeches and literature review. Chen WC, Chien CY, Yang CH, Li JH, Hwang CF. Eur Arch Otorhinolayngol. 2009 Dec 27.

In the category of Really BMJ? Really?

A precious case from Middle Earth. Bashir N et al. BMJ. 2004 Dec 18; 329(7480): 1435-6.

Effect of ale, garlic, and soured cream on the appetite of leeches. Baerheim A, Sandvik H. BMJ. 1994 Dec 24-31: 309(6970):1689.

Inexplicably, searching PubMed for the keyword "bouncing" yields this paper:

Qualities of the Ideal Protege. Melanson MA. US Army Med Dep J. 2009 Oct-Dec: 44-6

In the category of Not Suitable for Work/Children/Faint of Heart. (I'm going to leave the titles out in favor of non-rated R descriptions.)

Urologic problems caused by a household appliance during an activity that your mother told you would cause blindness.

Bats engaging in some non-vanilla bedroom practices (with video in the supplementary figures).

This list is far from complete: I expect to be posting more fantastical PubMed citations in the future. Until then, enjoy these, and remember: theres a journal for every kind of study out there.

Panda Genome Sequenced!

Last week in Nature, a large group of scientists announced that they had, for the first time, successfully sequenced the entire genome of the Giant Panda. Their paper describes the extraordinary amount of work required to sequence an entire genome. The researchers extracted the DNA of a 3 year old female living in the Chengdu breeding center. The task: to sequence all of the panda's 20 pairs of autosomes and 1 pair of sex chromosomes. And to do so without breaking the researchers collective banks. The method: create many, many short read sequences of DNA using parallel sequencing technology and piece them together to construct the full sequence. Using parallel sequencing (in particular the llumina Genome Analyser sequencing technology) allowed the researchers to avoid the "prohibitive costs associated with sequencing and assembling large eukaryotic genomes". To that end, the researchers constructed 37 paired-end sequencing libraries, containing a total of 176 gigabases of usable sequence, made up of sequences with an average read length of 52 base pairs. They fed this mass amount of data into a 32 core, 512 GB RAM supercomputer, piecing together a total genome 2.40 gigabases long.

Following the construction of their genome sequence, the researchers went on a meta-analysis spree, comparing the panda genome to both dogs and humans. The group reports that humans, dogs, and pandas all possess approximately 1.4 gigabases of non-repetitive sequence within their genome. Of that 1.4 gigabases, all three species have 846 megabases (~60.4%) in common. Dogs and pandas share ~83% of their non-repetitive sequence, with pandas and humans sharing ~72% and dogs and humans sharing ~64.5%.

The researchersand also searching for several genes of interest to panda aficionados, including the genes encoding for taste receptors. Interestingly, an analysis of the sequence for the T1R1 gene, which encodes the taste receptor for umami, shows a loss-of-function mutation. The authors speculate that this mutation may explain pandas' exclusively herbivorous diet, despite their taxonomic classification of carnivores.

For a gloriously detailed description of the sequencing process, and for more hints at the wonders waiting to be uncovered withinin the panda genome, the original article should be viewed in all its splendor. The Sequence and De Novo Assembly of the Giant Panda Genome. Li R, et al. Nature 463: 311-317 (2010).

A side note: the home of the 3 year old female Panda, the Chengdu breeding center, is a facility working alongside the Wolong Panda Breeding Center to conserve the Giant Panda through extensive breeding programs. The Chengdu center boasts a population of 83 pandas that have been bred from an original population of 6 wild pandas. Pictures of the Chendgu pandas, as well as video of the most recent group born at the Wolong Center are guaranteed to lighten any day with a hearty does of adorable.

Using Oxytocin to Treat Autism

From guest blogger Kelly Zalocusky: Oxytocin is a member of a neuropeptide family, the nonapeptides, that is conserved across vertebrates. Its close cousins include isotocin, particular to fish, and mesotocin, found in amphibians, reptiles, and birds. Members of this family are known for their role in prosocial behavior, particularly maternal and sexual behaviors. In humans, oxytocin has also been associated with trust and with the ability to process facial expressions.

Interestingly, children with autism are frequently found to have low circulating oxytocin and an abundance of oxytocin precursors in the blood, indicating a deficit in the synthesis of this important neuropeptide.

In this week's online early-release of the Proceedings of the National Academy of Sciences, Elissar Andari and colleagues explored the possibility of treating the social symptoms of high-functioning autism spectrum disorder patients with an oxytocin nasal spray. In a computer-simulated ball-tossing game, autism spectrum disorder patients showed no preference among "players" who reciprocated by regularly returning the ball, and those who never returned the ball. In those patients that received the nasal spray, however, trust and preference for the good/friendly player increased relative to the bad/unfriendly player, such that the autistic persons' reponses no longer differed significantly from those of healthy controls. Treated individuals also performed better in a face-scanning task, spending more time focused on socially-relevant face regions, such as the eyes.

For more information, see the full text of the article: http://www.pnas.org/content/early/2010/02/05/0910249107.full.pdf+html

Retractions: Failure of Facilitated Communication

Last December, doctors at Liege University hospital declared that a patient thought to be brain dead for 23 years following a car crash victim was actually conscious, and able to communicate. It turns out that apparent communication (enacted using a technique known as "facilitated communication") was merely artifact, and that the patient is, unfortunately, as comatose as was first believed.

Hopefully this public error should stand beside other extraordinary discoveries of higher activity in supposedly comatose patients.  As more techniques are used to examine putatively comatose patients, both scientists and the general public entertain extreme caution during the diagnosis and treatment of severe brain trauma, tempering an enthusiasm for newer, flashier techniques with the use of more classic diagnostic tools.

Note: This is not to say that comatose patients are ever misdiagnosed as being in a permanent vegetative state; there are, unfortunately, too many individual accounts of such an event, and happily, a rising number of patients whose consciousness has been discovered due to advances in modern medicine (see an earlier post from this blog regarding the use of MRI to diagnose brain states). Indeed, given the complexity of the human brain and our uncertain knowledge of how consciousness is generated, it behoves us (doctors, scientists, humans) to be cautious when it comes to the effects of traumatic brain injury, not allowing diagnostic decisions to be swayed by the popularity of any one test, no matter what findings (miraculous or not) it may propose.

No miracle as brain-damaged patient proved unable to communicate, by Denis Campbell. Guardian. (via @noahWG)

Nature's Editors on Paper Selection

For many researchers, perhaps especially for those in graduate school, the successful publishing of a paper in a journal such as Nature or Science is the pinacle of professional success. General wisdom, backed by hard numbers, shows how difficult it is to publish a paper in such high impact journals. But is that difficulty solely do to the immense competition for limited space? Or are researchers also battling a specific editorial agenda that seeks to pick papers for publication based upon a set of limited criteria. According to the editors of Nature, the answer to those questions is no.

Today in Nature, an editorial discusses the journal's paper selection process. The editorial seeks to address several "myths" about the selection process at Nature, including that "Nature's editors seek to inflate the journal's impact factor by sifting through submitted papers (some 16,000 last year) in search of those that promise a high citation rate", or that the editors "allow one negative referee to determine the rejection of a paper".

The editors seek to dispel these myths using specific examples and descriptions of their role during the paper submission/ peer review process. In the end, the editors claim, the choice to publish a paper in Nature is not based on the authors identities, the potential impact factor, or the opinion of any particular referee. Instead, they "make the final call on the basis of criteria such as the paper's depth of mechanistic insight, or its value as a data resource or in enabling applications of an innovative technique."

While their statements are interesting, I find it highly doubtful that any single editorial will dispel the pervasive and proliferative myths that will inevitably surround the process of entry into the upper echelon of published authorship. What is interesting to me are the potential motivations behind the publishing of the editorial. What stressor triggered Nature's editors to publicly refute these (rather specific) myths? The first paragraph of the editorial states that "as the current headlines make all too clear, controversies over scientific conclusions in fields such as climate change can have the effect — deliberate or otherwise — of undermining the public's faith in science." Are the editors of Nature reacting to events such as the high-profile retraction by Lancet of the Autism/MMR Wakefield study? Do they believe their reputation is at risk due to "number of false impressions that [they] have become aware of in and beyond the research community"? How specific are the reputations of scientific journals such as Nature outside the research community? Can we expect the general public to differentiate specific scientific journals, or is it more realistic to expect a more generalized view of the publication process?

What are your thoughts? For those researchers out there, thinking back to the days before you made your living doing research, do you remember paying attention/having a decided opinion about one scientific journal over another (or any scientific journal for that matter). Does anyone have friends/relatives/spouses/acquaintances who are both members of the general public and followers of the publications in Nature/Science/scientific journal X?

Nature's Choices. Editorial. Nature. 63, 850 (18 February 2010) | doi:10.1038/463850a

Renovating Stanford Hospital

For the past year, I've been hearing murmurs concerning a planned renovation of the Stanford Hospital. And as fond as I am of its odd exterior and asbestos ridden basements, Stanford Hospital is long overdue for a major renovation. This afternoon, I just happened to virtually stop by the Stanford Hospital website. While there, I found evidence that this much needed renovation will actually be occurring at some point, in the form of a dedicated website. This website presents the cunningly branded Project:Renewal, and claims that Stanford Hospital is slated to be rebuilt, with the Packard Children's Hospital getting an expansion. Also,  "outdated laboratories at the School of Medicine" will be "replaced". Judging from the project side map and pictures (see below), new Hospital Building will be built nestled amongst current buildings.

(A side note: is it just me, or does the intersection of Pasteur Drive and Quarry Road involve some creative reinterpretation of reality? Along the same vein, its possible the outdated laboratories previously mentioned are Edwards, Lane, and Alway.)

The Project:Renewal website features several artists renderings that are fully drool-worthy. Some of them are below.