From connelly.bill from gmail.com Fri Oct 3 18:07:40 2008 From: connelly.bill from gmail.com (Bill) Date: Fri Oct 3 19:54:52 2008 Subject: [Neuroscience] Measuring transmembrane voltages - Sources of error and perforated patching Message-ID: <6d3baad6-dc65-4747-b0e0-1f0649d9c7cd@79g2000hsk.googlegroups.com> Hi, To get to the point I finally have got gramicidin perforated patching working regularly (~30mOhms in 15 minutes) however all my cells appear to be "resting" ~20mV more hypoerpolarized than they do when I do whole-cell recording using either a K-gluconate or KCl based pipette solution. Does this make sense to anyone? I presume this is something to do with the fact that during whole-cell recordings the cell interior eventually becomes the same as your pipette solution and hence there is no liquid junction potential (so the added voltage which was 'bucked' out of the system when the electrode was zeroed and the LJP was in force, and is added to your recorded membrane potential)? However in perforated patch mode, you have a difference situation, where different ions have different mobilities, not only based on their mobilities in solution, but their conductivity through the gramicidin pores? Or am I over analysing stuff here? From connelly.bill from gmail.com Sat Oct 4 16:00:28 2008 From: connelly.bill from gmail.com (Bill) Date: Sun Oct 5 15:59:45 2008 Subject: [Neuroscience] Gramicidin Perforated Patches and liquid function potentials Message-ID: Hi, I may have already posted this, but it isn't showing up on google groups, so I'm thinking there may have been a problem. To get to the point I finally have got gramicidin perforated patching working regularly (~30mOhms in 15 minutes) however all my cells appear to be "resting" ~20mV more hyperpolarized than they do when I do whole- cell recording using either a K-gluconate or KCl based pipette solution. Does this make sense to anyone? I presume this is something to do with the fact that during whole-cell recordings the cell interior eventually becomes the same as your pipette solution and hence there is no liquid junction potential (so the added voltage which was 'bucked' out of the system when the electrode was zeroed and the LJP was in force, and is added to your recorded membrane potential)? However in perforated patch mode, you have a difference situation, where different ions have different mobilities, not only based on their mobilities in solution, but their conductivity through the gramicidin pores? Or am I over analysing stuff here? From t.lewis from unsw.edu.au Mon Oct 6 20:34:42 2008 From: t.lewis from unsw.edu.au (Trevor Lewis) Date: Mon Oct 6 23:37:53 2008 Subject: [Neuroscience] Re: Neur-sci Digest, Vol 41, Issue 2 In-Reply-To: <200810061704.m96H4SV16388@net.bio.net> References: <200810061704.m96H4SV16388@net.bio.net> Message-ID: <200810070134.m971YhVW011811@smtp.unsw.edu.au> Hi Bill, Correcting for liquid junction potentials when doing perforated patches can be a rather tricky situation. First, you have the liquid junction potential between the patch pipette and the batch solution, which was 'zeroed' when the patch pipette was first placed in the bath. Second, there is the junction potential across the cell membrane permeabilized with gramacidin. This junction potential will be determined by the activities of the permeable ions on either side of the membrane and the permeability of the membrane with the gramacidin. Thus, you will need to find out the permeability of gramacidin - I guess that this information is in the literature, but I confess that I haven't looked. You will also need to make the assumption that the gramacidin conductance in the membrane is far greater than any other conductance that is present in the membrane under the pipette tip, and so dominates the junction potential; this is a fairly reasonable assumption. Depending on the composition of your pipette solution and the permeability of gramacidin, it may be necessary to also take account of the Donnan potential across the membrane under the pipette. For whole-cell recordings when the cell contents is dialysed with the pipette solution, the correction for the liquid junction potential is simply: Vm = Vp - LJP where the LJP is what was cancelled when the pipette offset was 'zeroed'. The LJP is best calculated using the Junction Potential Calculator in Clampex. Vm is the membrane potential and Vp is the command potential at the pipette. With the perforated patch, the correction is: Vm = (Vp + Vpf) - LJP where the Vpf is the potential you will need to calculate for the perforated patch potential due to gramacidin in the patch. If you look at the Junction Potential Calculator, there is some (small) online help with calculating perforated patch LJPs. If you want to discuss this further, happy to help out off-line. Regards, Trevor >Message: 1 >Date: Sat, 4 Oct 2008 14:00:28 -0700 (PDT) >From: Bill >Subject: [Neuroscience] Gramicidin Perforated Patches and liquid > function potentials >To: neur-sci@net.bio.net >Message-ID: > >Content-Type: text/plain; charset=ISO-8859-1 > >Hi, > >I may have already posted this, but it isn't showing up on google >groups, so I'm thinking there may have been a problem. > >To get to the point I finally have got gramicidin perforated patching >working regularly (~30mOhms in 15 minutes) however all my cells appear >to be "resting" ~20mV more hyperpolarized than they do when I do whole- >cell recording using either a K-gluconate or KCl based pipette >solution. Does this make sense to anyone? > >I presume this is something to do with the fact that during whole-cell >recordings the cell interior eventually becomes the same as your >pipette solution and hence there is no liquid junction potential (so >the added voltage which was 'bucked' out of the system when the >electrode was zeroed and the LJP was in force, and is added to your >recorded membrane potential)? However in perforated patch mode, you >have a difference situation, where different ions have different >mobilities, not only based on their mobilities in solution, but their >conductivity through the gramicidin pores? Or am I over analysing >stuff here? > > >------------------------------ > >_______________________________________________ >Neur-sci mailing list >Neur-sci@net.bio.net >http://www.bio.net/biomail/listinfo/neur-sci > >End of Neur-sci Digest, Vol 41, Issue 2 >*************************************** From jalegris from sympatico.ca Tue Oct 7 08:32:18 2008 From: jalegris from sympatico.ca (J.A.Legris) Date: Tue Oct 7 10:24:09 2008 Subject: [Neuroscience] Re: Izhikevich's Large Scale Mammalian Thalamocrotical model References: Message-ID: <9ab31593-8995-4589-807d-b3b3798f6f42@q5g2000hsa.googlegroups.com> On Sep 29, 10:57 am, "Fredo" wrote: > I'm trying to implement something like Eugene Izhikevich's model described > in "A Large-Scale Model of Mammalian Thalamocortical Systems", but I've run > into an issue I can't quite figure out. > > From the Supporting Information:http://vesicle.nsi.edu/users/izhikevich/publications/large-scale_mode... > > On page 8, he describes the current used in the equation on page 7 as: > I(t) = -Idendr - Isyn > > Then below, he provides the equation for calculating Idendr per compartment. > > He says in the text that the somatic and terminal dendritic compartments all > have a value of 0 of Idendr. > > So my question is, in I(t) = -Idendr - Isyn > > What is Idendr? Is it the sum of Idendr for the compartments attached to the > somatic compartment? The sum of all Idendr for all compartments? or > something else? > > Does anyone know? > > Thanks On page 8 at the end of section 2.1 he writes: "Each neuron has a somatic compartment and a set of dendritic compartments. The number of dendritic compartments of a neuron in each cortical layer is at least S*scale/M where S is the number of synapses the neuron receives in the layer (see Fig. 9), scale= 0.05 is the scale-down factor when we simulate fewer than 10^11 neurons, and the parameter M = 40 is the maximal number of synapses per compartment. The dendritic current at each compartment consists of the currents coming from the down ("mother") compartment (zero for somatic compartments) and up ("daughter") compartments (zero for terminal compartments) Idendr = Gdown (V - Vdown ) + From jalegris from sympatico.ca Tue Oct 7 09:10:56 2008 From: jalegris from sympatico.ca (J.A.Legris) Date: Tue Oct 7 10:24:15 2008 Subject: [Neuroscience] Re: Izhikevich's Large Scale Mammalian Thalamocrotical model References: Message-ID: <1e4dcad9-d9d5-408e-a438-3b5e1945c482@l76g2000hse.googlegroups.com> On Sep 29, 10:57?am, "Fredo" wrote: > I'm trying to implement something like Eugene Izhikevich's model described > in "A Large-Scale Model of Mammalian Thalamocortical Systems", but I've run > into an issue I can't quite figure out. > > From the Supporting Information:http://vesicle.nsi.edu/users/izhikevich/publications/large-scale_mode... > > On page 8, he describes the current used in the equation on page 7 as: > I(t) = -Idendr - Isyn > > Then below, he provides the equation for calculating Idendr per compartment. > > He says in the text that the somatic and terminal dendritic compartments all > have a value of 0 of Idendr. > > So my question is, in I(t) = -Idendr - Isyn > > What is Idendr? Is it the sum of Idendr for the compartments attached to the > somatic compartment? The sum of all Idendr for all compartments? or > something else? > > Does anyone know? > > Thanks Sorry, my first attempt at this reply was mangled. On page 8 at the end of section 2.1 he writes: "Each neuron has a somatic compartment and a set of dendritic compartments. The number of dendritic compartments of a neuron in each cortical layer is at least S*scale/M where S is the number of synapses the neuron receives in the layer (see Fig. 9), scale= 0.05 is the scale-down factor when we simulate fewer than 10^11 neurons, and the parameter M = 40 is the maximal number of synapses per compartment. The dendritic current at each compartment consists of the currents coming from the down ("mother") compartment (zero for somatic compartments) and up ("daughter") compartments (zero for terminal compartments) Idendr = Gdown (V - Vdown ) + SUM[up] Gup (V - Vup)" Observe that he does not say "the somatic and terminal dendritic compartments all have a value of 0 of Idendr". He says that the contribution to Idendr from the down ("mother") compartment is zero for somatic compartments and that the contribution to Idendr from the up ("daughter") compartments is zero for terminal compartments. In other words: Idendr[somatic] = SUM[up] Gup (V - Vup) Idendr[terminal] = Gdown (V - Vdown ) -- Joe From ganges.g from gmail.com Tue Oct 7 12:32:12 2008 From: ganges.g from gmail.com (ganges) Date: Tue Oct 7 13:11:50 2008 Subject: [Neuroscience] can some one suggest a good introductory book on Psychophysics? Message-ID: Dear all, Can some one suggest a good introductory book on Psychophysics? thanks in advance, Gangadhar. GARIPELLI -- Visit me @ www.idiap.ch/~ggaripe From lbrtchx from gmail.com Wed Oct 8 00:38:06 2008 From: lbrtchx from gmail.com (lbrtchx@gmail.com) Date: Wed Oct 8 11:41:04 2008 Subject: [Neuroscience] latest research on the what and how of our (and/or animal) brains' processing of concepts/numbers Message-ID: Hi, ~ I was reading "Thinking about Mathematics" by Stewart Shapiro, who talks about Donald O. Hebb's paper "The Organization of Behavior (1949)" and about his research on how our brains "process" numbers ~ Now, technology has advanced quite a bit since 1949, which made me wonder about the latest research on that area. I checked for books on this kind of topic and as usual you will find a lot of what I reader at amazon considered "pop neuroscience", which is exactly what I am avoiding ~ Could you point me to the latest research/seminal papers on the subject of synaptic plasticity and our brains "processing" of concepts/ numbers? I am primarily interested about papers/claims backed by actual physical investigations and it would be nice if they are oriented towards the epistemology and ontology of concepts/numbers. ~ Thank you lbrtchx From martinoneil95 from yahoo.no Mon Oct 13 13:11:54 2008 From: martinoneil95 from yahoo.no (Martin Oneil) Date: Mon Oct 13 19:23:38 2008 Subject: [Neuroscience] Mammalian cell lines for BiFC Message-ID: <36568.76895.qm@web28301.mail.ukl.yahoo.com> We have been asked to perform BiFC assays using a human protein that is most studied in nuerons. We would like to use a different mammalian cell line that is easier to work with. Does anyone have any suggestions of cell lines that are easy to transfect and image on a confocal microscope? Thank you in advance for your time _________________________________________________________ Alt i ett. F? Yahoo! Mail med adressekartotek, kalender og notisblokk. http://no.mail.yahoo.com From h.w.tse from live.co.uk Fri Oct 10 19:45:37 2008 From: h.w.tse from live.co.uk (HW) Date: Tue Oct 14 11:25:40 2008 Subject: [Neuroscience] VU0155041 a New mGlu4 selective positive allosteric modulator Message-ID: If you study group 3 metabotropic glutamate receptors, and having problems with PHCCC solubility and selectivity, check out VU0155041 which is more potent and selective than PHCCC, and it can easily dissolve in 1 eq. NaOH (aq). http://molpharm.aspetjournals.org/cgi/reprint/mol.108.049551v1 you can buy VU0155041 from Ascent Scientific http://www.ascentscientific.com/index2.php From ku.autismconf from gmail.com Tue Oct 14 16:23:07 2008 From: ku.autismconf from gmail.com (ku.autismconf@gmail.com) Date: Tue Oct 14 20:16:15 2008 Subject: [Neuroscience] Kean University (NJ) conference on the topic of Autism Message-ID: <7ee8a110-d076-4ace-8334-073da41da490@s9g2000prg.googlegroups.com> www.kean.edu/autismconference Autism: Putting the Pieces Together: An Interdisciplinary Conference for Teachers, Parents, and Professionals, on November 21, 2008. This regional conference will bring together families, teachers, school administrators, speech-language pathologists, occupational therapists, counselors, social workers, psychologists, community organizations and others affected by Autism Spectrum Disorders. Family members and professionals will have the opportunity to learn about the local, regional and national resources available to those whose lives ASD touches each day. Panelists also will discuss the latest discipline-specific research, as well as the various strategies used to cope with this disorder. The conference will feature top research and medical experts on autism from throughout the country. Keynote speakers include Jake Greenspan, one of the co-directors of DIR Support Services in Bethesda, Md. DIR Support Services is a child development center specializing in the use of the DIR/Floortime model. Jake and his DIR co-director Tim Bleeker, with the help of Dr. Stanley Greenspan, developed evaluation and intervention programs based on all aspects of the DIR model. Their goal has been to develop and implement these intervention programs for children with a variety of developmental and learning challenges. The conference lunchtime speaker is Jim Watkins, who co-anchors the Emmy Award-winning CW11 News at 10. Each weeknight, Watkins teams with co-anchor Kaity Tong, weatherman Irv "Mr. G" Gikofsky, and sportscaster Sal Marchiano. Jim and his wife Lauren Thierry, a CNN financial news reporter, are the parents of an autistic child who was born in 1997. Lauren made a much-praised documentary, Autism Every Day, which premiered to a sold-out audience at the Sundance Film Festival in Park City, Utah. From kiwasabi from gmail.com Tue Oct 21 00:16:19 2008 From: kiwasabi from gmail.com (kiwasabi) Date: Tue Oct 21 08:35:30 2008 Subject: [Neuroscience] The roles of dopamine? Message-ID: <9d72391e-64ec-410a-a97e-82651600e630@l77g2000hse.googlegroups.com> I've been very interested in the roles of dopamine for some time now ever since I read that it may be more related to motivation than to pleasure (as previously believed). It also seems to increase attention to a given task as the dopamine level increases. On top of all of this, it seems to be essential to goal-directed behavior. What are everybody's thoughts as to the functions of dopamine? By the way, if dopamine isn't specifically related to pleasure (but to the pursuit of pleasure), why is it so pleasant to be in a motivated, goal-directed state? I did a quick search in this group and one person a long time ago noted that he thought it was due to increased blood flow in the brain brought upon by in increases in dopamine. From jalegris from sympatico.ca Tue Oct 21 07:55:16 2008 From: jalegris from sympatico.ca (J.A.Legris) Date: Tue Oct 21 08:35:46 2008 Subject: [Neuroscience] Re: The roles of dopamine? References: <9d72391e-64ec-410a-a97e-82651600e630@l77g2000hse.googlegroups.com> Message-ID: On Oct 21, 1:16?am, kiwasabi wrote: > I've been very interested in the roles of dopamine for some time now > ever since I read that it may be more related to motivation than to > pleasure (as previously believed). It also seems to increase attention > to a given task as the dopamine level increases. On top of all of > this, it seems to be essential to goal-directed behavior. > > What are everybody's thoughts as to the functions of dopamine? > > By the way, if dopamine isn't specifically related to pleasure (but to > the pursuit of pleasure), why is it so pleasant to be in a motivated, > goal-directed state? I did a quick search in this group and one person > a long time ago noted that he thought it was due to increased blood > flow in the brain brought upon by in increases in dopamine. I wouldn't expect increased blood flow to be intrinsically pleasurable - for one thing it depends on whether you are the prey or the predator. To be in a goal-directed state, there must have been prior exposure to the conditions associated with that state, otherwise there would be no expectation of a reward. In effect, the conditions have themselves become conditioned rewards, the pleasurability of which depends on more than just dopamine. -- Joe From vishnuvyas from gmail.com Wed Oct 22 01:32:17 2008 From: vishnuvyas from gmail.com (vishnuvyas) Date: Wed Oct 22 09:03:15 2008 Subject: [Neuroscience] Datasets for brain activation and emotion Message-ID: <69a0b735-a03b-44b3-8363-ab05e94ff1a0@l76g2000hse.googlegroups.com> HI, I'm looking for datasets which contain emotion and the appropriate brain activation. Is there any publicly available dataset that I can use. - Jay. From kbrownk from gmail.com Thu Oct 30 23:19:25 2008 From: kbrownk from gmail.com (Kerry) Date: Fri Oct 31 13:17:02 2008 Subject: [Neuroscience] Rat (Long Evans) Cerebellar Cortex Size Message-ID: <7357694e-1405-4c68-b956-f16d61f58c0b@f37g2000pri.googlegroups.com> Does anyone know the approximate parasagittal length of the rat cerebellar (not cerebral) cortex or have a reference for where I could find it measured? I was given a slide with sagittally sliced sections that together make up 600 um of thickness and I want to know what proportion of the cerebellar cortex I have. The strain is Long-Evans though it shouldn't matter as I only need an approximation. Thanks, H From Matthew.Kirkcaldie from removeutas.removeedu.au Fri Oct 31 03:25:40 2008 From: Matthew.Kirkcaldie from removeutas.removeedu.au (Matthew Kirkcaldie) Date: Fri Oct 31 13:17:11 2008 Subject: [Neuroscience] Re: Rat (Long Evans) Cerebellar Cortex Size References: <7357694e-1405-4c68-b956-f16d61f58c0b@f37g2000pri.googlegroups.com> Message-ID: In article <7357694e-1405-4c68-b956-f16d61f58c0b@f37g2000pri.googlegroups.com>, Kerry wrote: > Does anyone know the approximate parasagittal length of the rat > cerebellar (not cerebral) cortex or have a reference for where I could > find it measured? > > I was given a slide with sagittally sliced sections that together make > up 600 um of thickness and I want to know what proportion of the > cerebellar cortex I have. Don't take this the wrong way, but that's kind of a meaningless question. The cerebellum is a tightly infolded three dimensional arrangement of a two-dimensional sheet; asking "what proportion of the cerebellar cortex" is represented by a parasagittal block 600 µm thick would require a pretty detailed analysis of the overall shape of the cortical sheet when unfolded, plus a projection of where the slice lay on the unfolded sheet. It would be easier to give a less nit-picking answer if you explained why you want to know - is it an estimate of volume, or asking if it's representative, or what? Cheers, MK. ** Posted from http://www.teranews.com ** From kbrownk from gmail.com Fri Oct 31 12:45:26 2008 From: kbrownk from gmail.com (Kerry) Date: Fri Oct 31 13:57:02 2008 Subject: [Neuroscience] Re: Rat (Long Evans) Cerebellar Cortex Size References: <7357694e-1405-4c68-b956-f16d61f58c0b@f37g2000pri.googlegroups.com> Message-ID: On Oct 31, 4:25?am, Matthew Kirkcaldie wrote: > In article > <7357694e-1405-4c68-b956-f16d61f58...@f37g2000pri.googlegroups.com>, > > ?Kerry wrote: > > Does anyone know the approximate parasagittal length of the rat > > cerebellar (not cerebral) cortex or have a reference for where I could > > find it measured? > > > I was given a slide with sagittally sliced sections that together make > > up 600 um of thickness and I want to know what proportion of the > > cerebellar cortex I have. > > Don't take this the wrong way, but that's kind of a meaningless > question. The cerebellum is a tightly infolded three dimensional > arrangement of a two-dimensional sheet; asking "what proportion of the > cerebellar cortex" is represented by a parasagittal block 600 ?m thick > would require a pretty detailed analysis of the overall shape of the > cortical sheet when unfolded, plus a projection of where the slice lay > on the unfolded sheet. > > It would be easier to give a less nit-picking answer if you explained > why you want to know - is it an estimate of volume, or asking if it's > representative, or what? > > ? ? ? Cheers, MK. > ** Posted fromhttp://www.teranews.com** Sorry, I should have been more explicit w/ the given purpose. I am not trying to use this information for any quantitative analysis. For now I am just trying to get an estimation of width (e.g. Euclidean distance from the most extreme sagittal points end to end). However, if I new the volume of the cerebellar cortex I could calculate the convex hull volume of the section I have to get a more exact proportion. I would guess the total volume is more readily available, but if I could find a picture w/ a scale bar of the cerebellum viewed from the rostral or caudal direction I could get an idea of how much section I have. The latter may be quantitatively meaningless but qualitatively, for those who have knowledge of the cerebellar cortical size and shape, one could infer what proportion of the cortex I am studying. A crude approximation is good enough as I am just trying to provide a cartoon that gives a rough idea (e.g. it is meaningful to say whether I have closer to 1% or 90% of the entire cerebellar cortex). Thanks, K