Thursday and Friday of this week are the department's recruiting weekend. Having done these as a recruit, as well as the recruiter, I have a couple tips for recruiting:
1. Don't ask where else they are interviewing
This is my pet peeve. I can understand how this shows interest in a recruit, which one should do, but it comes off as incredibly insecure.
I see the recruiting process as an extended first date. The recruit and the department are trying to get a sense whether their interests are aligned, and whether they both feel they are of equivalent status. Both parties are trying to impress each other, while making it look effortless. And of course, as on many first dates, the recruit is visiting other departments and the department is interviewing other recruits.
So when someone asks, "Where else are you interviewing," I hear, "Are you seeing anyone else?" Which is a good way to avoid a second date. If you are interested in a recruit's science, and want to get to know more about them, you can ask, "What type of science are you interested in?" It doesn't matter what other departments they're visiting, because this one is the best.
2. Don't talk about science
I've been doing post-doc interviews lately, and most of the interviews are consumed with science, both mine and the lab I'm visiting. It can be fun to show off my research, and most people are excited to talk about their own research. After a few hours, though, it gets tiresome. At the end of the day, I've been overloaded by new concepts, and I'm getting tired of going over my boilerplate. Any conversational respite is appreciated.
I can only assume it's even worse for the recruits. Their interviews are two days long, and instead of interviewing with one lab, they see four. When they finally get around to talking to grad students at lunch or the after-party, they're usually exhausted. So when you talk to them, ask them about sports, movies, or short track speed skating. Anything but science.
Wednesday, February 17, 2010
Wednesday, February 10, 2010
Lab Fashion
Having been a scientist for going on six years now, I have little awareness of how outsiders view science, or scientists themselves. The best glimpses I get are from movies and television, where scientists are dressed in white lab coats, and work in colorful rooms. The truth, while not quite diametrically opposed, is much less sexy.
Almost no one in the lab actually wears lab coats. In fact, my high school biology teacher once joked that if you ever see a lab wherein everyone is wearing lab coats and goggles, you should run because they are working with very dangerous things. Typically, scientists dress like computer programmers, viz. jeans and a t-shirt. If you are more senior, you might wear what my friend calls the "scientist's uniform" of khaki slacks and a blue button down.
In fact, the dress code of the lab is so casual that I am instantly suspicious of anyone who dresses too well. When I see someone in a blazer, I wonder if they have a job interview. Or someone wearing a white lab coat, makes me wonder why they are trying to appear to be working (lab coats are of course essential for many lab procedures, like dissections. My rule of thumb is that you should never wear a lab coat without gloves). My lab recently bought lab coats for a few people, and they now wear them when they are doing any work in the lab, not just the dangerous or dirty stuff. It irks me. To be fair, one's attitude can be changed by the clothes one wears, and I would endorse any action that makes one work more effectively. I would need to see the data, though, that shows lab coats make them more effective.
Medical doctors are some of the worst offenders in terms of using the white coat as a status symbol. For doctors, the coats are certainly necessary when working with patients that may bleed or drip muccus. But the doctors often do not disrobe outside the office, and wear their coats in the cafeteria or on the way to their car. Part of being a doctor is certainly to make people as comfortable as possible, and wearing a lab coat may inspire confidence in patients. Like scientists, though, when they are worn too often, I become suspicious that they are compensating. It doesn't seem very hygenic, either, to be wearing your dirty safety clothes in public, but then again, I'm not a doctor.
Almost no one in the lab actually wears lab coats. In fact, my high school biology teacher once joked that if you ever see a lab wherein everyone is wearing lab coats and goggles, you should run because they are working with very dangerous things. Typically, scientists dress like computer programmers, viz. jeans and a t-shirt. If you are more senior, you might wear what my friend calls the "scientist's uniform" of khaki slacks and a blue button down.
In fact, the dress code of the lab is so casual that I am instantly suspicious of anyone who dresses too well. When I see someone in a blazer, I wonder if they have a job interview. Or someone wearing a white lab coat, makes me wonder why they are trying to appear to be working (lab coats are of course essential for many lab procedures, like dissections. My rule of thumb is that you should never wear a lab coat without gloves). My lab recently bought lab coats for a few people, and they now wear them when they are doing any work in the lab, not just the dangerous or dirty stuff. It irks me. To be fair, one's attitude can be changed by the clothes one wears, and I would endorse any action that makes one work more effectively. I would need to see the data, though, that shows lab coats make them more effective.
Medical doctors are some of the worst offenders in terms of using the white coat as a status symbol. For doctors, the coats are certainly necessary when working with patients that may bleed or drip muccus. But the doctors often do not disrobe outside the office, and wear their coats in the cafeteria or on the way to their car. Part of being a doctor is certainly to make people as comfortable as possible, and wearing a lab coat may inspire confidence in patients. Like scientists, though, when they are worn too often, I become suspicious that they are compensating. It doesn't seem very hygenic, either, to be wearing your dirty safety clothes in public, but then again, I'm not a doctor.
Tuesday, February 2, 2010
The Big Picture
This past month, I was taking the medical school module on Brain and Behavior. The course is intended to provide medical students an introduction to neurology and neuroanatomy, and the department thought it would be a good idea for the graduate students to take the class. I don't completely disagree with the idea, although there is a large scope for improvement such that Neurobiology students learn skills and information that are useful and relevant, as opposed to facts and trivia that we will forget soon. One thing missing from the course, and consistently missing from a lot of advanced medical/scientific courses is an appreciation for the beauty of the cell/tissue/organ, etc...
I was originally interested in Biology because to me, the human body was an elegant structure, a few trillion cells, acting in concert, were necessary to accomplish most things we would think of as mundane. To accomplish this feat we call life, there need to be feedback loops, feed-forward loops, intracllular signaling cascades, cell-cell communication locally and systemically each of which is regulated and the regulation is regulated. All these processes need to communicate with one another with temporal and spatial specificity. As we discover more about the processes that allow us to perform the functions we can, I believe it is important to continually appreciate the delicateness and the elegance involved in the sustenance of life amid very narrow thermodynamic limits.
I have found that the med school course focused on details, without much appreciation for the bigger picture. For instance, I understand that somatic sensory information is "perceived" by 1st order neurons in the dorsal root ganglion, before proceeding upwards in the spinal cord through the dorsal columns, terminating on dorsal column nuclei, decassating and continuing upward through the medial lemniscal pathway, terminating in the thalamus where neurons send information to the cortex. However, this does not help me appreciate the fact that this entire process takes a few milliseconds, during which information from multiple neurons have been combined to determine the identity of the stimulus and the appropriate response to it.
In contrast, there are classes which elaborate on biological elegance. For instance, in the concepts II lecture we had this morning, Rich Mooney spent quite some time elaborating on the fact that the auditory system has to use action potentials, which are about 1ms in duration, to code for stimuli that are microseconds long, i.e. they are coding stimuli that are 1000 times faster than their theoretical limit. Rich went on to elaborate on the mechanisms and details about how the process might occur, but held the process and the mechanism with a sense of wonder which reminded me why I care so much.
When conveying information about a certain topic, I believe it is just as important to inspire wonder as it is to elaborate on the components and interactions that characterize the system. I feel that is what distinguishes a good lecturer from a bad one. One need to have great oratorical skills or a vast vocabulary, but one must have the child-like wonder, and be able to inspire that in the audience.
I was originally interested in Biology because to me, the human body was an elegant structure, a few trillion cells, acting in concert, were necessary to accomplish most things we would think of as mundane. To accomplish this feat we call life, there need to be feedback loops, feed-forward loops, intracllular signaling cascades, cell-cell communication locally and systemically each of which is regulated and the regulation is regulated. All these processes need to communicate with one another with temporal and spatial specificity. As we discover more about the processes that allow us to perform the functions we can, I believe it is important to continually appreciate the delicateness and the elegance involved in the sustenance of life amid very narrow thermodynamic limits.
I have found that the med school course focused on details, without much appreciation for the bigger picture. For instance, I understand that somatic sensory information is "perceived" by 1st order neurons in the dorsal root ganglion, before proceeding upwards in the spinal cord through the dorsal columns, terminating on dorsal column nuclei, decassating and continuing upward through the medial lemniscal pathway, terminating in the thalamus where neurons send information to the cortex. However, this does not help me appreciate the fact that this entire process takes a few milliseconds, during which information from multiple neurons have been combined to determine the identity of the stimulus and the appropriate response to it.
In contrast, there are classes which elaborate on biological elegance. For instance, in the concepts II lecture we had this morning, Rich Mooney spent quite some time elaborating on the fact that the auditory system has to use action potentials, which are about 1ms in duration, to code for stimuli that are microseconds long, i.e. they are coding stimuli that are 1000 times faster than their theoretical limit. Rich went on to elaborate on the mechanisms and details about how the process might occur, but held the process and the mechanism with a sense of wonder which reminded me why I care so much.
When conveying information about a certain topic, I believe it is just as important to inspire wonder as it is to elaborate on the components and interactions that characterize the system. I feel that is what distinguishes a good lecturer from a bad one. One need to have great oratorical skills or a vast vocabulary, but one must have the child-like wonder, and be able to inspire that in the audience.
Saturday, January 30, 2010
Nobel Winner's Curse
Bert Sakmann visited Duke last Friday to give a seminar on his current work (streaming video here). By my count, he is the sixth Nobel prize winner I have seen speak. Three of them (Roger Tsien, Eric Kandel, and Torsten Wiesel) gave overviews of their important works, appropriate to the large audiences they were speaking before. The other three (Richard Axel, Bert Sakmann, and Susumu Tonegawa) spoke about the current research in their labs, and largely neglected what made them famous. From their perspective, like a famous rock band, they must decide between playing the audience's favourite songs, or playing the new songs, which while potentially not as good, are what they care about now.
Bert Sakmann is most famous for co-inventing the patch-clamp technique, which allows one to record the actual voltage of individual neurons in the brain. The basics of the technique is that you take a microscopically thin glass cylinder, called a pipette, and bring it so close to the cell membrane that the membrane adheres to the pipette. Ideally, this attachment is so strong that it creates a high electrical resistance, or gigaOhm seal. While you are attached to a cell like this, you can indirectly measure the voltages of the cell. However, to truly measure the cell voltage, you need direct access to the fluid inside the cell, which can be obtained by opening a hole in the membrane. This is traditionally achieved by literally sucking on a tube connected to the pipette. The idea that the fundamental technique of electrophysiology involves puncturing cells by sucking on a straw still tickles me.
Since inventing the whole cell patch technique, Sakmann, like many other famous scientists, has turned his direction "upwards" to more systems oriented questions. The specific system he is now studying is the barrel cortex. The barrel cortex is the part of a rodent's brain responsible for decoding what its whiskers are touching. Each whisker is has a small portion of the cortex dedicated to it called a "barrel."
People have traditionally thought of cortex as having an hierarchical structure, where information flows into one layer, then proceeds through the six layers of cortex until being output not another area of the brain. This theory has come from extensive work in the visual cortex of rats, cats, and other mammals. Sakmann's group recorded (using patch clamp!) from all of the layers of barrel cortex while stimulating the whiskers, and found that information reaches all layers of the cortex simultaneously, in contrast to visual cortex. Previously, people have postulated that perhaps cortical columns (small vertically organized units of cortex covering all six layers) were a general processing unit that had been repeated with variation in different parts of the cortex. By showing that barrel cortex works differently, systems neuroscientists must now be more careful in how the think about information flow. (I should also say at this point that I am not a systems neuroscientist, and do not have a firm knowledge of cortical processing or how information flows through the layers of different types of cortex. The novelty I present here is based on my interpretation of the seminar.)
In the other section of his talk, he showed recordings from layer five thick-tufted pyramidal cells in barrel cortex, and a part of the brainstem called POm. My understanding of this part was more hazy, but I believe he showed there is a cortico-thalamic-cortico feedback loop that acts as a threshold detector for input. His goal in identifying this feedback loop was to give insight into rat decision making, but to this graduate student studying barrel cortex in rats seems like an indirect way to study decision making.
Given he was a Nobel winner, I came into the talk with high expectations, which could not be met. Sakmann spoke to a packed house, as all Nobel winner's do. The faculty in attendance were extremely deferential, which was highly unusual. To these expectations Sakmann presented interesting, but not groundbreaking work, and if anyone else were presenting it, the crowd would have been 1/10th the size. His speaking style was assured, but uninspiring. As I mentioned at the start, Nobel winners have two choices: to present what they're famous for, or present what they care about now. And given the magnitude of what they're famous for, everything else pales in comparison. Maybe that is the Nobel winner's curse, to set such high standards that you cannot help but disappoint in the future.
Bert Sakmann is most famous for co-inventing the patch-clamp technique, which allows one to record the actual voltage of individual neurons in the brain. The basics of the technique is that you take a microscopically thin glass cylinder, called a pipette, and bring it so close to the cell membrane that the membrane adheres to the pipette. Ideally, this attachment is so strong that it creates a high electrical resistance, or gigaOhm seal. While you are attached to a cell like this, you can indirectly measure the voltages of the cell. However, to truly measure the cell voltage, you need direct access to the fluid inside the cell, which can be obtained by opening a hole in the membrane. This is traditionally achieved by literally sucking on a tube connected to the pipette. The idea that the fundamental technique of electrophysiology involves puncturing cells by sucking on a straw still tickles me.
Since inventing the whole cell patch technique, Sakmann, like many other famous scientists, has turned his direction "upwards" to more systems oriented questions. The specific system he is now studying is the barrel cortex. The barrel cortex is the part of a rodent's brain responsible for decoding what its whiskers are touching. Each whisker is has a small portion of the cortex dedicated to it called a "barrel."
People have traditionally thought of cortex as having an hierarchical structure, where information flows into one layer, then proceeds through the six layers of cortex until being output not another area of the brain. This theory has come from extensive work in the visual cortex of rats, cats, and other mammals. Sakmann's group recorded (using patch clamp!) from all of the layers of barrel cortex while stimulating the whiskers, and found that information reaches all layers of the cortex simultaneously, in contrast to visual cortex. Previously, people have postulated that perhaps cortical columns (small vertically organized units of cortex covering all six layers) were a general processing unit that had been repeated with variation in different parts of the cortex. By showing that barrel cortex works differently, systems neuroscientists must now be more careful in how the think about information flow. (I should also say at this point that I am not a systems neuroscientist, and do not have a firm knowledge of cortical processing or how information flows through the layers of different types of cortex. The novelty I present here is based on my interpretation of the seminar.)
In the other section of his talk, he showed recordings from layer five thick-tufted pyramidal cells in barrel cortex, and a part of the brainstem called POm. My understanding of this part was more hazy, but I believe he showed there is a cortico-thalamic-cortico feedback loop that acts as a threshold detector for input. His goal in identifying this feedback loop was to give insight into rat decision making, but to this graduate student studying barrel cortex in rats seems like an indirect way to study decision making.
Given he was a Nobel winner, I came into the talk with high expectations, which could not be met. Sakmann spoke to a packed house, as all Nobel winner's do. The faculty in attendance were extremely deferential, which was highly unusual. To these expectations Sakmann presented interesting, but not groundbreaking work, and if anyone else were presenting it, the crowd would have been 1/10th the size. His speaking style was assured, but uninspiring. As I mentioned at the start, Nobel winners have two choices: to present what they're famous for, or present what they care about now. And given the magnitude of what they're famous for, everything else pales in comparison. Maybe that is the Nobel winner's curse, to set such high standards that you cannot help but disappoint in the future.
Tuesday, January 26, 2010
Assembly and Stoichiometry of the AMPA Receptor and Transmembrane AMPA Receptor Regulatory Protein Complex (TARP):
Today in lab meeting I presented this recent paper from the Tomita lab regarding TARP binding to AMPA Receptors (AMPAR). Tomita, as a post-doc in the Bredt lab, was one of the first people to investigate TARP binding and function in depth. TARPs, as the name suggests, are auxiliary subunits of AMPAR, and are known to modulate AMPAR diffusion and conductances. They contain a PDZ-binding domain that can bind PSD-95, and thus indirectly link AMPAR to PSD-95. Single particle tracking studies have shown this binding can regulate AMPAR mobility in the synpase (Bats and Choquet, 2007). As for the conductances, recordings from AMPAR in oocytes show that AMPAR desensitization is slowed and reduced in the presence of TARPs (Priel et. al. 2005).
In this paper, the authors used fairly simply immunoblotting techniques to investigate how AMPAR form tetramers, how many TARPs can bind to AMPAR, and how TARP binding modulates AMPAR currents. Their basic method was to create AMPAR variants with different weights, so that when they formed tetramers from the different size monomers, the tetramers ran at different speeds. Around half of the amino acids in AMPAR are in the extracellular n-terminal domain (NTD), making the weight difference significant.
Their first interesting result used AMPAR lacking their NTD, but weighted differently using GFP. They found that when they mixed AMPARs lacking their NTD, they could form tetramers containing 1, 2, 3, or 4 of the GFP subunits, showing that the tetramers were not formed by dimer-of-dimers, but from monomers. In contrast, when they mixed full-length AMPAR with AMPAR lacking their NTD, their gel yielded only three bands, showing that the full length AMPAR formed dimers before being dimerized again into tetramers. From this they concluded that the NTD of AMPAR is important for the initial formation of dimers.
They next turned to finding how many TARPs can interact with one AMPAR. By transfecting differing amounts of TARP cRNA, running their gels, and staining for GluR1, they were able to find five different size bands, relating binding of 0-4 TARPs. When they used the minimal transfection situation, which allowed only one TARP to bind, they found that the binding of one TARP was enough to affect the channel conductance.
The above result, however, was in oocytes, and not actual neurons. To investigate the TARP binding in neurons, they used cerebellar granule cells in a stargazer mutant line, which lacks the TARP stargazin. By blotting for GluR2/3 in heterozygous mice, they found only two bands of protein, suggesting that AMPARs form associations with TARPs at a fixed stoichiometry. This fixed stoichiometry suggests that the TARP levels are either minimal or saturated. When they stained for stargazin, they found no unbound stargazin, and thus concluded that only one TARP binds to each AMPAR.
The most interesting aspect of this paper, to me, is how they were able to investigate what I consider a biophysical property - dimerization and stoichiometry - using simple biophysical techniques (and probably common ones in biophysics at that). The finding that the n-terminus is important for the initial dimerization does not seem new to me, as it has previously been shown that the n-terminus alone can form dimers (Leuschner and Hoch, 1999), and I have read reviews that the LIVBP portion of the NTD is the initial site of dimerization (Greger and Ziff, 2007). However, the finding that one TARP alone is enough to modulate AMPAR function is intriguing. I am not sure that I believe their finding that one and only one TARP binds to AMPAR in vivo, given how indirect the evidence is, and that they mention disagreement with another paper in their discussion.
Bats, C., Groc, L., & Choquet, D. (2007) The Interaction between Stargazin and PSD-95 Regulates AMPA Receptor Surface Trafficking. Neuron 53, 719-734.
Greger, I. H., Ziff, E. B., & Penn, A. C. (2007) Molecular determinants of AMPA receptor subunit assembly. Trends in Neurosciences 30, 407-416.
Leuschner, W. D. & Hoch, W. (1999) Subtype-specific assembly of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor subunits is mediated by their n-terminal domains. J Biol Chem 274, 16907-16916.
Priel, A., Kolleker, A., Ayalon, G., Gillor, M., Osten, P., & Stern-Bach, Y. (2005) Stargazin Reduces Desensitization and Slows Deactivation of the AMPA-Type Glutamate Receptors. J Neurosci 25, 2682-2686.
In this paper, the authors used fairly simply immunoblotting techniques to investigate how AMPAR form tetramers, how many TARPs can bind to AMPAR, and how TARP binding modulates AMPAR currents. Their basic method was to create AMPAR variants with different weights, so that when they formed tetramers from the different size monomers, the tetramers ran at different speeds. Around half of the amino acids in AMPAR are in the extracellular n-terminal domain (NTD), making the weight difference significant.
Their first interesting result used AMPAR lacking their NTD, but weighted differently using GFP. They found that when they mixed AMPARs lacking their NTD, they could form tetramers containing 1, 2, 3, or 4 of the GFP subunits, showing that the tetramers were not formed by dimer-of-dimers, but from monomers. In contrast, when they mixed full-length AMPAR with AMPAR lacking their NTD, their gel yielded only three bands, showing that the full length AMPAR formed dimers before being dimerized again into tetramers. From this they concluded that the NTD of AMPAR is important for the initial formation of dimers.
They next turned to finding how many TARPs can interact with one AMPAR. By transfecting differing amounts of TARP cRNA, running their gels, and staining for GluR1, they were able to find five different size bands, relating binding of 0-4 TARPs. When they used the minimal transfection situation, which allowed only one TARP to bind, they found that the binding of one TARP was enough to affect the channel conductance.
The above result, however, was in oocytes, and not actual neurons. To investigate the TARP binding in neurons, they used cerebellar granule cells in a stargazer mutant line, which lacks the TARP stargazin. By blotting for GluR2/3 in heterozygous mice, they found only two bands of protein, suggesting that AMPARs form associations with TARPs at a fixed stoichiometry. This fixed stoichiometry suggests that the TARP levels are either minimal or saturated. When they stained for stargazin, they found no unbound stargazin, and thus concluded that only one TARP binds to each AMPAR.
The most interesting aspect of this paper, to me, is how they were able to investigate what I consider a biophysical property - dimerization and stoichiometry - using simple biophysical techniques (and probably common ones in biophysics at that). The finding that the n-terminus is important for the initial dimerization does not seem new to me, as it has previously been shown that the n-terminus alone can form dimers (Leuschner and Hoch, 1999), and I have read reviews that the LIVBP portion of the NTD is the initial site of dimerization (Greger and Ziff, 2007). However, the finding that one TARP alone is enough to modulate AMPAR function is intriguing. I am not sure that I believe their finding that one and only one TARP binds to AMPAR in vivo, given how indirect the evidence is, and that they mention disagreement with another paper in their discussion.
Bats, C., Groc, L., & Choquet, D. (2007) The Interaction between Stargazin and PSD-95 Regulates AMPA Receptor Surface Trafficking. Neuron 53, 719-734.
Greger, I. H., Ziff, E. B., & Penn, A. C. (2007) Molecular determinants of AMPA receptor subunit assembly. Trends in Neurosciences 30, 407-416.
Leuschner, W. D. & Hoch, W. (1999) Subtype-specific assembly of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor subunits is mediated by their n-terminal domains. J Biol Chem 274, 16907-16916.
Priel, A., Kolleker, A., Ayalon, G., Gillor, M., Osten, P., & Stern-Bach, Y. (2005) Stargazin Reduces Desensitization and Slows Deactivation of the AMPA-Type Glutamate Receptors. J Neurosci 25, 2682-2686.
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