2016 Neuroscience Ph.D. Applicant Thread People Thing

[optogent]

3 hours ago, Yav Friendly said:

And you study optical genetics?

In order to test existing elegant theories and perhaps inspire new ones, the field needs powerful tools that can manipulate and readout the activity of large neuronal populations with genetic specificity. I think optogenetics is one of the more promising ways to get you theorists the data you crave.

[Neuro PolarBear]

5 hours ago, robot_control said:

@Micecroscopy Thanks for the comments. I think it would be more appropriate to ask the inverse question - how relevant, conventional, or advantageous would a neuroscience based degree be for motor control, vision etc. in the context or robotics. How the CNS program is viewed in the engineering and CS communities. 

Yeah, I think that's a better question. In my opinion, I don't really think the degree you end up getting will make that much of a difference or if one is more advantageous than the other, especially if you plan on doing the same type of research in each program. Obviously what you end up doing for your PhD will matter the most, but maybe some programs are better than others depending on where you want to go or end up after your PhD.

2 hours ago, optogent said:

In order to test existing elegant theories and perhaps inspire new ones, the field needs powerful tools that can manipulate and readout the activity of large neuronal populations with genetic specificity. I think optogenetics is one of the more promising ways to get you theorists the data you crave.

Optogenetics seems less likely to give you that data than calcium imaging, especially since it's so far off from the physiological ground truth by pumping neurons full of such high levels of exogenous opsins. In contrast, the most recent deconvolution, demixing, and spike inference statistical methods are getting better and better, as well as imaging methods like SLM microscopy and resonant scanning that enables the imaging of multiple planes and 3D volumes at once with fairly decent spatiotemporal resolution. Photoswitchable tethered ligands for optical pharmacology and voltaic imaging are also promising, but I don't think there has far along as calcium imaging.

Though I guess you were maybe referring to some of the more recent closed-loop optogenetics and two-photon imaging / all-optical electrophysiology methods?

[optogent]

1 hour ago, Micecroscopy said:

Yeah, I think that's a better question. In my opinion, I don't really think the degree you end up getting will make that much of a difference or if one is more advantageous than the other, especially if you plan on doing the same type of research in each program. Obviously what you end up doing for your PhD will matter the most, but maybe some programs are better than others depending on where you want to go or end up after your PhD.

Optogenetics seems less likely to give you that data than calcium imaging, especially since it's so far off from the physiological ground truth by pumping neurons full of such high levels of exogenous opsins. In contrast, the most recent deconvolution, demixing, and spike inference statistical methods are getting better and better, as well as imaging methods like SLM microscopy and resonant scanning that enables the imaging of multiple planes and 3D volumes at once with fairly decent spatiotemporal resolution. Photoswitchable tethered ligands for optical pharmacology and voltaic imaging are also promising, but I don't think there has far along as calcium imaging.

Though I guess you were maybe referring to some of the more recent closed-loop optogenetics and two-photon imaging / all-optical electrophysiology methods?

I don’t think you understand the term “optogenetics”. 

 

GCaMP protein imaging techniques are the most successful in vivo calcium imaging tools and are optogenetic tools. 

Chen, Tsai-Wen, et al. "Ultrasensitive fluorescent proteins for imaging neuronal activity." Nature 499.7458 (2013): 295-300.

 

Many tools within the optical pharmacology field are optogenetic tools.

Kramer, Richard H., Alexandre Mourot, and Hillel Adesnik. "Optogenetic pharmacology for control of native neuronal signaling proteins." Nature neuroscience 16.7 (2013): 816-823.

 

You can use SLM microscopy for optogenetic tools.

Packer, Adam M., et al. "Two-photon optogenetics of dendritic spines and neural circuits." Nature methods 9.12 (2012): 1202-1205.

[Neuro PolarBear]

2 hours ago, optogent said:

I don’t think you understand the term “optogenetics”. 

GCaMP protein imaging techniques are the most successful in vivo calcium imaging tools and are optogenetic tools. 

Chen, Tsai-Wen, et al. "Ultrasensitive fluorescent proteins for imaging neuronal activity." Nature 499.7458 (2013): 295-300.

Many tools within the optical pharmacology field are optogenetic tools.

Kramer, Richard H., Alexandre Mourot, and Hillel Adesnik. "Optogenetic pharmacology for control of native neuronal signaling proteins." Nature neuroscience 16.7 (2013): 816-823.

You can use SLM microscopy for optogenetic tools.

Packer, Adam M., et al. "Two-photon optogenetics of dendritic spines and neural circuits." Nature methods 9.12 (2012): 1202-1205.

I think this is largely a semantic argument. Just as I probably shouldn't have been so quick to take issue with your definition, I don't think you should have been so quick to dismiss mine or to imply that I don't understand the term. Moreover, I think my interpretation falls more in line with common usage.

I would definitely be quite hesitant about lumping GECIs, and optical sensors in the same category as optogenetic tools derived from microbial opsins. Given the extent and history of non genetically encoded calcium sensors, it seems easier to me to distinguish tools for monitoring and recording neural activity from those that manipulate and control it. I would also agree that the tools developed by Rich Kramer and Dirk Trauner could indeed by classified as optogenetic tools, but I think calling them as such is potentially misleading, and not as accurate as optical/optogenetic pharmacology or photopharmacology.

Moreover, I think many agree with these above sentiments. See for example, the responses to "How do you define optogenetics?" in Nat. Neuro's 10 year anniversary article: http://pyramidal.stanford.edu/publications/Adamantidis2015_NatureNeurosci.pdf

Häusser: There’s a broad definition and a narrow definition. The broad definition is rooted in etymology: any approach that combines optical interrogation with genetic targeting qualifies as ‘optogenetic’, and that includes the use of genetically encoded activity sensors. However, most people generally use the term optogenetics to mean the use of probes to manipulate activity, and (as is usual in English) usage normally wins.

Schnitzer:  Notably, our original intent was to cover both genetically targeted optical control and imaging under a single umbrella term. Nevertheless, I have subsequently always preferred a narrower interpretation of optogenetics that covers only the control approaches and the wonderful field that grew out of Karl’s seminal 2005 paper in Nature Neuroscience; the broader interpretation of optogenetics that includes imaging is so general that, in some respects, it can be vague. My impression is that a substantial majority of the usages of the term optogenetics in the neuroscience literature follows the narrower interpretation.

Of course, that's not to say that I wouldn't agree with, as Dick Tsien points out, that such a broad name could easily—and moreover probably should—refer to a larger set of tools, as you suggest. The fact that he still has to make this point, however, would seem to indicate that the broader interpretation is falling out of favor, even if he would prefer its usage.

And, yes, I am familiar with the papers that combine these various techniques, as I alluded to in my previous response. These are indeed quite elegant experiments! I do also think my original point still holds about inferring function and causality based on results from optogenetic manipulations. The opposite is also true, as noted by Bence Ölveczky in response to his recent paper: "Our paper cautioning against simplistic over-interpretations is being simplistically over-interpreted by many. Nuance is hard to convey."

[Yav Friendly]

18 hours ago, robot_control said:

@Micecroscopy Thanks for the comments. I think it would be more appropriate to ask the inverse question - how relevant, conventional, or advantageous would a neuroscience based degree be for motor control, vision etc. in the context or robotics. How the CNS program is viewed in the engineering and CS communities. 

What drew me to the CNS program was that it isn't a conventional neuroscience program - majority of its faculty and affiliates are not biologists. I felt that it combined neural networks based methods for vision and control which is an exciting area. As you said, I am really hyped up for the interview, and would like to make it click. I'm still waiting for a few other programs though, which might be better fits - particularly ETH, CMU (RI), and UWashington. Best wishes for your applications!  

The PhD salary in ETH is much much higher though.

[robot_control]

@Yav Friendly Are you applying for PhD this year, or are you continuing at ETH? If you are applying, where to, if you don't mind me asking.

[Yav Friendly]

1 minute ago, robot_control said:

@Yav Friendly Are you applying for PhD this year, or are you continuing at ETH? If you are applying, where to, if you don't mind me asking.

I am applying to the US. I just do not really enjoy the life here so much. I am a foreigner and find it hard to learn German. Plus I hate the food and can not cook every day.

I am not applying to anything really in control theory. My background is not enough for that. I am apply computational biology and aiming at POIs who do dynamic systems modeling of biological, cellular or physiological systems.

[Yav Friendly]

4 hours ago, robot_control said:

@Yav Friendly Are you applying for PhD this year, or are you continuing at ETH? If you are applying, where to, if you don't mind me asking.

I saw a ETH Control rejection on survey.

[nebulasector7]

I don't know if anyone else noticed it (it doesn't appear when you search neuroscience) but on the survey, someone reported that UCSD is sending out all invites by end of day tomorrow (1/12)!!!!

[airchina]

57 minutes ago, nebulasector7 said:

I don't know if anyone else noticed it (it doesn't appear when you search neuroscience) but on the survey, someone reported that UCSD is sending out all invites by end of day tomorrow (1/12)!!!!

Thanks for sharing! Can you specify a bit more about where you found this information? I don't see it on the survey with the search criteria, "UCSD neuroscience"

[proton]

6 minutes ago, airchina said:

Thanks for sharing! Can you specify a bit more about where you found this information? I don't see it on the survey with the search criteria, "UCSD neuroscience"

search "neurosciences" or "san diego"! another entry says they will send out tomorrow

[brainsbrainsbrainsbrains]

So do you guys think that MIT BCS is done sending out invites? I'm thinking that it may be better to accept rejection than hold on to false hope

[nebulasector7]

29 minutes ago, proton said:

search "neurosciences" or "san diego"! another entry says they will send out tomorrow

^^^^ yes, what she said!!!

 

[Yav Friendly]

5 minutes ago, brainsbrainsbrainsbrains said:

So do you guys think that MIT BCS is done sending out invites? I'm thinking that it may be better to accept rejection than hold on to false hope

Call'em. They sent last month. You have every reason to call dude!

[proton]

@brainsbrainsbrainsbrains similarly, I have no courage to actually ask WashU

[Asimio]

Oh Gosh, I'm guessing I'm not going to get in anywhere (no emails/calls).

Anyone get invites from Boston GPN or their brain and behavior program?

[Edotdl]

Any UCSF Neuro people that requested the 2/12-13 interview get confirmation yet? Ticket prices are going up...

[EveryDay]

19 hours ago, brainsbrainsbrainsbrains said:

So do you guys think that MIT BCS is done sending out invites? I'm thinking that it may be better to accept rejection than hold on to false hope

I personally think so, for sure. The fact that they sent stuff in mid-December and no one has heard back makes me think they are done.

But I'm still holding on to false hope.

 

EDIT: Nevermind, someone just said they got an interview email yesterday. I hate and love this new glimpse of hope.

Edited January 12, 2016 by EveryDay
info

[proton]

5 hours ago, Asimio said:

Oh Gosh, I'm guessing I'm not going to get in anywhere (no emails/calls).

Anyone get invites from Boston GPN or their brain and behavior program?

My friend heard from BU last year on January 29th!! So late but this might mean no one will hear until the very end of Jan---keep hopes up!

[Neuro PolarBear]

46 minutes ago, Edotdl said:

Any UCSF Neuro people that requested the 2/12-13 interview get confirmation yet? Ticket prices are going up...

I requested the other date and also haven't gotten an confirmation or response for that yet, so maybe they're still trying to sort it out?

[gs1992]

42 minutes ago, EveryDay said:

I personally think so, for sure. The fact that they sent stuff in mid-December and no one has heard back makes me think they are done.

 

But I'm still holding on to false hope.

Well someone just posted a BCS invite on the survey, keeping my hope alive for another month and a half...

[bdnf_13.1]

Nobody has heard from the Yale BBS Neuro Track right? I got a conflicting invite recently and don't want to leave these people hanging...

[Asimio]

2 hours ago, proton said:

My friend heard from BU last year on January 29th!! So late but this might mean no one will hear until the very end of Jan---keep hopes up!

Thank you. I had a terrible day at work after reading this thread and this consoled me, even though it might just be for a bit.

[kokobanana]

UCSD neuro just sent out invites! I hope to see some of you guys there!!

[wookiee_and_the_vet]

1 hour ago, kokobanana said:

UCSD neuro just sent out invites! I hope to see some of you guys there!!

Also just got one! Looks like dates are 2/16 or 2-17-2/19.