Neurobiology and Brain Physiology

Neurobiology and Brain Physiology

  • Chrystalleni Vassiliou asked a question:
    How can I choose between diphteria or different antibiotics to select monkey neurons in vivo?

    I am doing a project and I need a way to protect some cells and kill all the others in the temporal cortex of monkeys. We thought that we can use resistance to antibiotics or diphtheria toxin to do that and then inject the antibiotic/diphtheria on the area, but I am struggling to decide what is the best way to go. Could you please help me? or at least tell me what I need to consider when making my choice? Thank you

  • Sacha Bohler added an answer:
    What is the average lipid content of the human brain?

    Concentrations of lipophylic chemicals in the brain are often expressed as g/g lipid. But for my experiments I need concentrations in M. In consequence, I require the lipid content of the human brain, or, more specifically, of the substantia nigra pars compacta, if available. I have been going through the literature but so far to no avail.

    If anybody could provide this information, I would be very thankful.



    Sacha Bohler

    Dear Saak,

    Thanks for the reference. I already checked it, and it did not provide me with the answer I am looking for. It is nevertheless what I have currently used as a close approximation for my calaculations.

  • Marianne Levon Shahsuvaryan added an answer:
    Is there any advance in finding a validated target for sporadic Alzheimer's Disease (Not Familial or Prion related or other neurodegeneration)?

    It is a somber realization to those haven't as yet encountered and a grim fact to those who know the current and forecasted Alzheimer's Disease prevalance and impact.

    If the amyloid hypothesis is not causative but consequential, just as the cholinergic appears to be, and if no idea has been successfully translated into even a mediocre clinical benefit, how do we approach again the blank drawing board with a new hope?

    + 1 more attachment

    Marianne Levon Shahsuvaryan

    Recently due to its neuroprotective and antioxydative properties is used Minocycline - the second generation semisintethic antibiotic which penetrates blood-brain barrier

  • Luke Paul Crocker added an answer:
    Is crowd funding a viable alternative now that research grant awards are at an all-time low?
    Crowd funding has been successfully used to launch many new inventions, musical and artistic projects. Will scientists now turn to crowd funding or is this merely a passing fad?
    Luke Paul Crocker

    Another platform is Patreon, at least for those that work with more artistic fields. There are many options for how to run your funding through that. I use this platform for my artistic research and practice-led research in Japanese rope bondage (shibari and kinbaku) instruction and performances.

    Basically, how I have it set up is for those that pay $10 a month, get some of the raw data (usually photographs and snippits of current data); $25 per month gets video updates including the interviews with my partners, Q&A on the current reserch and practice, etc; $50 per month gets all of the above as well as weekly writeups of current progress in the research.

    Like any crowed funding, some make it big (one example is $24,000/2 weeks), and some flounder.This, I dont think will work for just any reserch work, but for the arts, it seems to run well.

  • Gila Behzadi added an answer:
    How to identify cortical layer boundaries in live brain slice?

    I am struggling to find cortical layer boundaries in mouse brain slice under differential interference contrast microscope. I typically use 400 um thick brain slice for my electrophysiology recording. Under 40x lens I kind of can see that the upper layers have smaller soma size and the soma is dense and in layer 5 the soma is bigger and sparse compared to upper layers.

    The best image I can find online is this one in somatosensory cortex (, in which mouse barrels in layer 4 can be easily identified.

    Could anyone give me some links of good examples for identifying cortical boundaries in live brain slice?

    Thank you in advance!

    Gila Behzadi

    According to Paxinos & Watson atlas:

    Barrel cortex: 2.3 mm posterior to Bregma,Lat 4 mm, V 1.5-1.8 from cortical surface (layer 4)

    Motor cortex: 1.7-2 mm rostral to Bregma, Lat 1.5-1.8 mm, V 1.7 from cortical surface (layer 5)

  • Boaz Barak added an answer:
    How many inject sites for rat striatum AAV-shRNA injection?

    I am going to inject AAV-shRNA into rat striatum, cause it is relative larger brain area, do I need to inject more than one site? Thanks.

    Boaz Barak

    The volume of injection depends on your virus titration. Based on the volume and the consequent infection area you should decide how many injection sites per hole. Then choose these sites locations based on the diameter: if each injection site covers for example 1/2 of the dorsoventral axis of the striatum (and it is not. It is just for the example) then you need two injection sites, one in 1/4 of the axis length, from dorsal point of the striatum (you can measure from the corpus callosum), and the second at 3/4 of the axis

  • Anirudh Kumar Satsangi added an answer:
    Are the benefits of meditation transitory or permanent? Do all types of meditation give same result?
    Yes, the benefits are permanent.
    No, the results are mostly different. There are, of course, some common results.
    Anirudh Kumar Satsangi

    Meditation results in the "conditioning" of nervous system particularly autonomic nervous syste.. 

  • Arne Brun added an answer:
    Which approach is better to make Alzheimer's Disease mice model?

    I will be doing an experiment to make an AD mice model and can't figure which is better, changing the doses of AB injected, or changing the time in between the injection until tested?

    I will be using Morris Water Maze to do the testing on the mices

    Arne Brun

    dear Emma,

    recent findings conccrning differences between man and rat has disclosed basic fundamental dissimilarities between the two, e g in terms of  astrocyte organisation and relations to neurons in humans but not in rat in addition to other differences that would seem to reduce the relevance of a rat model, sorry to say. Good luck anyway, Arne Brun

  • Benjamin Allitt added an answer:
    Is there any model that tries to explain the short-term synaptic plasticity using only the spike trains?

    Lots of works is done using the intracellular recordings, but I'm more interested in doing the same using only the spike trains.

    Benjamin Allitt

    So everyone is linking you to papers. Do vector strength and entrainment analyses. You'll find your answer there. Short term calcium binding may give you a physiological explanation outside of electrophysiological responses. 

  • Béatrice Marianne Ewalds-Kvist added an answer:
    Releasing agent vs. reuptake inhibitor?

    Selective norepinephrine and serotonin reuptake inhibitors (SNRI's) are commonly used in the treatment of cataplexy because cataplexy is the result of down dysregulated norepinephrine, itself the result of missing or greatly diminished orexinergic signaling.  

    However, cataplexy is also occasionally treated with Phentermine, which is a norepinephrine releasing agent.

    What happens when a person takes both a releasing agent and a reuptake inhibitor (not necessarily specific to this example, but generally)?  Is the result a greater concentration/availability of the protein you're after than you'd get with either individually?

    Béatrice Marianne Ewalds-Kvist

    All four are here on RG,

    R E Heikkila · H Orlansky · C Mytilineou · G Cohen,

    someone must answer you. I asked for their fulltext. 

  • Dilshan Harischandra added an answer:
    How to make MPTP-induced behavioral model?

    We have tried MPTP-inducing and already have done behavior test. But there is no difference among the control group, MPTP treated, and MPTP+drug treatment group.

    We injects 5 times / 5 consecutive days. 30mg/kg on Nature protocol, and tried open field test.

    If anyone has any thoughts on this case, please comment. Thanks.

    Dilshan Harischandra

    First of all I do not agree with Divaka's comment stating MPTP doesn't show behavioral phenotypes of PD. If you use publish well characterized protocol you can very well observe behavior deficits from MPTP. We routinely use Automated Open field test and rotarod to analyze behavior deficits. 

    To answer your question Myeung, what strain of mice you used? because I know that different strain of mice response to MPTP differently. C57BL6 black mice is the one that work best for MPTP treatment and work always! See some of the attached papers from our lab and Przedborski's lab for detailed protocol

    + 2 more attachments

  • Jordan Jahrling added an answer:
    Does anyone have a protocol for growing bEnd3 cells on Corning Transwell inserts?

    I am attempting to do some in vitro blood-brain barrier experiments using Corning Transwell pore inserts. Unfortunately, I have not had any luck getting my bEnd3 (mouse brain endothelial) cells to grow on the pore inserts. I have tried altering my seeding density but to no avail. The inserts are TC treated; nevertheless, I am planning to coat the inserts with collagen or lysine unless anyone is familiar with a working protocol. Any suggestions are appreciated. Thank you.

    Jordan Jahrling

    Hi Rashida

    I've never had to coat my plates, though I always use 10cm plates from Corning and have never used flasks. I can't imagine this would make much difference, but it's something. What density are you plating at? bEnd3 'prefer' to pack fairly tightly and do not grow well if they are plated too sparsely.

  • Manuel Gesto added an answer:
    5HIAA/5 HT turnover ratio in depression?
    Can anyone explain me the meaning/use of 5HIAA/5 HT turnover ratio in depression? Why is this ratio important from the utilization of serotonin in the brain? In simple terms.
    Manuel Gesto

    Hi Karolina,

    Maybe you can try this reference:

    Shannon, N.J., Gunnet, J.W., and More, K.E. 1986. A comparison of biochemical indices of 5-hydroxytryptaminergic activity following electrical stimulation of dorsal raphe nucleus. J. Neurochem. 47: 958–965.

    Best regards

  • Maria Rosa Peraita-Adrados added an answer:
    Do you know any article concerning myelinogenesis and sleep?

    The process of myelinogenesis starts at birth and last until 22 years of age.

    Sleep may play an important role in this process.

    In demyelinising diseases such MS sleep disturbances are the rule.

    Perhaps it will be interesting for this studies the myelin mutant taiep rat model

    by José R. Eguibar, Instituto de Fisiología, Universidad Autónoma de Puebla. Mexico)

    Maria Rosa Peraita-Adrados

    Hi Marco,

    Thanks for your reference that I did not know.



  • Vitthalrao Khyade added an answer:
    What is the physiological or anatomical difference between place cells and grid cells in the hippocampus?

    In the medial temporal lobe,there are specific types of neural cells such as place cells, head-direction cells, grid cells, and boundary vector cells which involved in cognitive map and spatial memory. Hippocampal “place cells” encode the rat’s location within an open environment independently of its orientation and fire in the specific position. The complementary encoding of the orientation, independently of location, is done by “head-direction cells” .I think all of them are pyramidal neurons. So Is there any physiological or anatomical difference between these kinds of cell?

    Vitthalrao Khyade

    Research Group, A.D.T. And Shardabai Pawar Mahila Mahavidyalaya, Shardanagar, Malegaon(Baramati) Dist. Pune – 413115.

    Objective: To Establish the Repository of Contributions of Eminent Scholars and  Information on Science and Culture  For The Society.                                                                   


         Fenton's reagent

    Fenton's reagent is a solution of hydrogen peroxide and an iron catalyst that is used to oxidize contaminants or waste waters. Fenton's reagent can be used to destroy organic compounds such as trichloroethylene (TCE) and polychloroethylene (PCE). It was developed in the 1890s by Henry John Horstman Fenton as an analytical reagent.[1]

    Iron(II) is oxidized by hydrogen peroxide to iron(III), forming a hydroxyl radical and a hydroxide ion in the process. Iron(III) is then reduced back to iron(II) by another molecule of hydrogen peroxide, forming a hydroperoxyl radical and a proton. The net effect is a disproportionation of hydrogen peroxide to create two different oxygen-radical species, with water (H+ + OH−) as a byproduct.

    (1) Fe2+ + H2O2 → Fe3+ + HO• + OH−

    (2) Fe3+ + H2O2 → Fe2+ + HOO• + H+

    The free radicals generated by this process then engage in secondary reactions. For example, the hydroxyl is a powerful, non-selective oxidant. Oxidation of an organic compound by Fenton's reagent is rapid and exothermic and results in the oxidation of contaminants to primarily carbon dioxide and water.[2]

    Reaction (1) was suggested by Haber and Weiss in the 1930s as part of what would become the Haber–Weiss reaction.[3] Iron(II) sulfate is typically used as the iron catalyst. The exact mechanisms of the redox cycle are uncertain, and non-OH• oxidizing mechanisms of organic compounds have also been suggested. Therefore, it may be appropriate to broadly discuss Fenton chemistry rather than a specific Fenton reaction.

    In the electro-Fenton process, hydrogen peroxide is produced in situ from the electrochemical reduction of oxygen.[4]

    Fenton's reagent is also used in organic synthesis for the hydroxylation of arenes in a radical substitution reaction such as the classical conversion of benzene into phenol.

    (3) C6H6 + FeSO4 + H2O2 → C6H5OH

    A recent hydroxylation example involves the oxidation of barbituric acid to alloxane.[5] Another application of the reagent in organic synthesis is in coupling reactions of alkanes. As an example tert-butanol is dimerized with Fenton's reagent and sulfuric acid to 2,5-dimethyl-2,5-hexanediol.[6]

    Biomedical applications
    The Fenton reaction has importance in biology because it involves the creation of free radicals by chemicals that are present in vivo. Transition-metal ions such as iron and copper donate or accept free electrons via intracellular reactions and help in creating free radicals. Most intracellular iron is in ferric (+3 ion) form and must be reduced to theferrous (+2) form to take part in Fenton reaction. Since superoxide ions and transition metals act in a synergistic manner in the creation of free radical damage, iron supplementation must not be done in patients with any active infections or in general any diseases.[7]

    Henry John Horstman Fenton (18 February 1854 – 13 January 1929) was a British chemist who, in the 1890s invented Fenton's reagent,[1] a solution of hydrogen peroxide and an iron catalyst that is used to oxidize contaminants or waste waters. Fenton's reagent can be used to destroy organic compounds such as trichloroethylene (TCE) andtetrachloroethylene (PCE). Born in London, Henry Fenton was educated at Magdalen College School, King's College London and Christ's College, Cambridge.[2] He became the university demonstrator in Chemistry at Cambridge in 1878, and was University Lecturer in Chemistry from 1904 to 1924.

    1.      Fenton H.J.H. (1894). "Oxidation of tartaric acid in presence of iron". J. Chem. Soc., Trans. 65 (65): 899–911. doi:10.1039/ct8946500899.


    3.      Haber, F. and Weiss, J. (1932). "Über die Katalyse des Hydroperoxydes". Naturwissenschaften 20 (51): 948–950. doi:10.1007/BF0150471.

    4.      Juan Casado,Jordi Fornaguera,Maria I. Galan (January 2005). "Mineralization of Aromatics in Water by Sunlight-Assisted Electro-Fenton Technology in a Pilot Reactor". Environ. Sci. Technol. 39 (6): 1843–47. doi:10.1021/es0498787. PMID 15819245.

    5.      Brömme HJ, Mörke W, Peschke E (November 2002). "Transformation of barbituric acid into alloxan by hydroxyl radicals: interaction with melatonin and with other hydroxyl radical scavengers". J. Pineal Res. 33 (4): 239–47. doi:10.1034/j.1600-079X.2002.02936.x. PMID 12390507.

    6.      E. L. Jenner (1973). "α,α,α',α'-Tetramethyltetramethylene glycol". Org. Synth.; Coll. Vol. 5, p. 1026.

    7.      Robbins and Cotran (2008). Pathologic Basis of Disease - 7th edition. Elsevier. p. 16. ISBN 9780808923022.

    ----------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    Acknowledgement: Girija Girish Tambe of  Vaishnavi  Xerox helped for Collection of images in the Science Spectrum of  5 September, 2015.   All the mistakes in the collection of information from website, it’s compilation and communication belongs exclusively to :                            

       Vitthalrao B. Khyade (And not to his pace making Shardanagar). Please do excuse for the mistakes.                                                                                                                                                                                                                                


    ------------------- Dr.APIS@World.Science.   -----------------------------------------------------------------------

                                     File: Dr.APIS.5.Sept@Fenton.Reaction                                                                                                      

    Compiled for: Science Association, Shardabai Pawar Mahila Mahavidyalaya, Shardanagar (Baramati) – 413115 India.

      With the Best Compliments From:  Shardanagar (The Agro – academic Heritage of Grandsire Padmashri Dr. D. G. Alias Appasaheb Pawar).

                                                                                    All the mistakes in the collection of information from website, it’s compilation and communication ( through email ) belongs exclusively to :  Vitthalrao B. Khyade (And not to his pace making Shardanagar).                                                                                                           

  • Luiz Ataíde added an answer:
    Do brain frequencies like "delta" and "theta" change independently while approaching sleep?

    I am researching about drowsiness and sleep detection. We know in general, frequencies from 1Hz to 16Hz (Delta, Theta ,Alpha, low Beta) increase while approaching sleep, while frequencies with 17Hz and higher (high Beta, Gamma) decrease. So do these signals change independently? For example, can we consider that the increase in Delta frequency is independent of the decrese in Gamma? Can we just see the Delta and say: "OK, you increased then the person is sleepy now" ?

    Luiz Ataíde

    I have an special interest on your research.

  • Serkan Cakir added an answer:
    How can I measure brain opioids and how can I store the chicken head samples?


    I will take blood samples during the slaughter of chicken, and also collect to head (as a result, brain ) samples.

    Even ıt is not exact procedure,

    I want to measure some opioids in blood and brain samples.

    Endorphine, encephaline, substantia P, noradrenaline, serotonine, cortisol etc ib blood and brain samples


    1-How must ı store the brain samples as soon as ı got after slaughter. May ı store the head samples (washed quickly) in -80 in 10 seconds for unchanged opioids level in brain.

    2- Which opioids are most important to define possible pain during nonstunning-slaughter?

    I hope one expert can help me?

    My best

    Serkan Cakir

     Dear Rossi,

    Many thanks for your detailed help.

  • Staffan Holmqvist added an answer:
    How many astrocyte cells are in in the rat brain?
    Do we know how many neurons are in the brain (human, rodent)?
    Staffan Holmqvist

    It seems that the more interesting feature of human vs rodent/primate astrocytes is not the relation in cell counts, but rather the shift in complexity of glia. It has been estimated a normal rodent astrocyte could support/modulate around 90,000 synapses within its domain. Human atrocytes with larger size, processes in combination with higher synaptic density is estimated to support 2 million synapses. 

    For further reading I recommend Oberheim, Goldman and Nedergaards review articles on the subject.

    2006 - doi:10.1016/j.tins.2006.08.004

    2012 - doi:10.1007/978-1-61779-452-0_3

  • Serguei N Skatchkov added an answer:
    Any suggestions on chromatin during brain development?

    Hi all,

    this is another of my mysterious questions. I am working with brain chromatin during development, in particular with P4 and P60 mouse brains, and I am always getting a weird result. whether I am preparing chromatin for ChIP or just isolating it after Mnase digestion, I always get a huge amount of DNA from P4 brains but very small amount from P30. Before you ask I treat every sample with almost 200ug of PK for 2 hours. My first thought was that DNA could get stuck to proteins and so I could lose it during my phenol chloroform extraction. I always start from same amount of nuclei so DNA amount should be same. Anybody can help me solve this?

    Serguei N Skatchkov

    Dear Gilda,

    The key players are polyamines (PAs), spermidine and spermine. Why? PAs work as casks to hold DNA. This stabilizes DNA structure and an extraction of DNA from brain is a process which should count (i) PA unbinding from DNA procedures and (ii) cell types you are isolating: (1) neurons versus (2) glial cells. Since in adult brain Glia outnumber neurons about 13 times in brainstem and ~3.5 time in cortex, so the nuclei of astrocytes, NG2 cells, oligodendrocytes, ependyma (all glial cells) contain most of DNA sampling from brain. Are you sure that the samples of collected nuclei are containing both cell types or you are loosing one of the types due to just isolation procedure?

    Another key is the age. While young brain is not much differentiated (glia versus neurons), after establishing adulthood (for rats and mice it is from 21 day to 60 days) the glial cella are maturated and glia outnumber neurons. Therefore, how do you collect nuclei and separate them, glial versus neuronal?

    Finally, In the cells ~80% of spermine and spermidine are bound on RNA and DNA. During development (and specifically during aging) PA amount is dropped down (the well known fact). As so, the amount of chromatin isolated will be also dropped down. For example your problem may be related to the concentration of PAs in your samples and therefore to amount of DNA isolated. Check your methods, how does it related to PAs cleavage from DNA, etc. Does my answer helps conceptually?

    Cordially, Serguei.

  • Yuan Li added an answer:
    Any suggestions on the roles of hexokinase II ?

    Hexokinase I is predominant form of hexokinase family in mammalian brain. But under hypoxic conditions, there is no obvious change in its expression. In contrast, hexokinase II, which is mainly expressed in insulin-sensitive tissues and malignant tumors, experiences a robust upregulation. I think it is a norm that only when a protein's function has been compromised,  then  its subsitute may undergo a change to adjust to this situation.So my question is why hypoxia exposure can induce a significant uptegulation of hexokinase II whereas it has no effect on hexokinase I in brain? Is it possible that it may play some other roles in hypoxic situations? Thanks ~~

    Yuan Li

    Thaanks  for your suggestion, Olivier Diaz. I have seen this paper before, but the source of lactate is not from neurons themselves. Howeve, under hypoxic conditions,  hexokinase II is  upregulated in neurons, even they can use lactate as fuel, they may also cause acidification  within cells since it is acid.

  • Alexandre Hiroaki Kihara added an answer:
    Do you think hanging drop 3D cell culture can be used for synapse study?

    This question is with regards to 3D culture. Do you think hanging drop 3D cell culture can be used for synapse study?

    Alexandre Hiroaki Kihara

    Yes, but I also recommend hidrogel based culturing.


  • Bert Bosche added an answer:
    Has anyone worked with Mannitol in a pig or other large animal model for blood brain barrier disruption?

    I'm trying to use Mannitol as a positive control for blood brain barrier disruption in a piglet model. I've seen a lot of work done in rat but that involved cervical artery catheterisation and large volumes of drug. I would prefer to do IV or subcut but am not sure on the dose required. 

    Any experiences working with mannitol would be greatly appreciated.

    Bert Bosche

    Hi Kate,

    I.V. Mannitol was and is still used to temporary "prevent" BBB disruption in large (or so called malignant) hemisphereic stroke or in other neurocritical diseases with BBB break-down and brain swelling (long-term outcome changes were disappointing). It works only temporary to decrease clinical makers like ICP most likely by its onkotic pressure (so in Neuro-ICUs it is sometimes life-saving). Therefore, I.V. injections may be critical for your purposes to disrupt the BBB. However, Paracelsus is calling: It all about the dose.

    I.P. can not work at all, because mannitol as a large molecule should not enter the circulation that good. It is rather made for not crossing endothelial barriers. 

    To disrupt BBB with mannitol you may need rapid changes of mannitol and thereby the onkotic pressure in the brain cirulation, then mannitol have a paradox effect leading to an "opening" of BBB. That means I.A. mannitol injection or as a compromise I.V. injection is the only way to bring it to the brain circulation in a rapid and higher dose.

    I hope these information will help a bit for planing your experiments.

    Best Bert

    Bert Bosche, MD/PhD
    Specialist in Neurology, Neurocritical Care,
    Neurosurgical Research Fellow - Post-doc Scientist
    in the Laboratory of Prof. Dr. R. Loch Macdonald
    Division of Neurosurgery
    St. Michael's Hospital and Li Ka Shing Knowledge Institute
    209 Victoria St., Room 517
    Toronto, Ontario, Canada M5C 1N8
    Phone: +1 416-864-6060 ext. 77641
    Mobil: +1 647-204-4757 or +49 173-7076734

  • Nicolai E. Savaskan added an answer:
    What is the difference between BV2 and N9 microglial cell lines?
    Nicolai E. Savaskan

    BV2 cells are more common although this says nothing about the suitability for assays. We can provide you with both such cell lines.

    Best Nic

  • Radim Brixi added an answer:
    How consciousness actually works
    As the basis for further discussion, I would like to suggest several of my articles proposing a new paradigm of the physics underlying cyclic cosmogenesis... With potential consciousness (awareness, will, qualia) being the fundamental subjective nature of unconditioned pre-cosmic absolute (0°K) space.
    The underlying "holonomic" (ref: Bohm, Pribram) "Astro-biological coenergetic" (ABC) fractal field theory offers logical proof why experiential or phenomenal consciousness cannot be an epiphenomena of the brain or its neural processes... And concludes that the working mind and long term memory are independent, radiant higher frequency phase order sub quantum harmonic hyperspace standing wave fields (that are resonantly interconnected with each other and the brain's overall EM field) — which carry the 3D information of conscious as wave interference patterned holograms on their 2D surfaces.
    This information is detected, reconstructed holographically, and perceived by zero-point consciousness (located at the ZPE center of the harmonic hyperspace fields) by means of projection and reflection of coherent radiation... e.g., visual consciousness is located at a zero-point in the pineal gland source of the brain's EM field (as well as its sleep and mood inducing hormones). All other sensory consciousness is non locally perceived at zero-points in the center of particular cells located throughout the body, and linked perceptively to the global center of individual physical self consciousness (located in the naval plexus) by BEC entanglement of ZP space. The focal points of higher states of consciousness are located at ZP centers of the six other chakra fields along the central axis of the body.
    The articles are published (with illustrations) at: (ABC theory) and at: (PDF) (web reprint of JCER article)
    Radim Brixi

    There are many states of consciousness. Some states seem not  to need brain or body.

  • Michael Hunter added an answer:
    Why does gray matter volume increase and decrease?

    Does anyone have an idea why sometimes gray/white matter increase over time due to skill learning, and sometimes they decrease?

    I've heard people say that maybe it decreases because the structures are becoming more efficient, but do we know what distinguishes or predicts increase versus decrease due to learning?

    Michael Hunter

    Cognitive and neuroscientific research over the past 60 years has shown that cognitive abilities, and their underlying neural architectures, change depending upon the experience of learning itself (Raisman, 1969; Cicchetti and Blender, 2007).

    Here is another paper/citation I hope you find useful:

    Driemeyer, J., Boyke, J., Gaser, C., Büchel, C., & May, A. (2008). Changes in Gray Matter Induced by Learning—Revisited. PLoS ONE, 3(7), e2669.

    Recently, activation-dependant structural brain plasticity in humans has been demonstrated in adults after three months of training a visio-motor skill. Learning three-ball cascade juggling was associated with a transient and highly selective increase in brain gray matter in the occipito-temporal cortex comprising the motion sensitive area hMT/V5 bilaterally. However, the exact time-scale of usage-dependant structural changes occur is still unknown. A better understanding of the temporal parameters may help to elucidate to what extent this type of cortical plasticity contributes to fast adapting cortical processes that may be relevant to learning.

    Principal Findings
    Using a 3 Tesla scanner and monitoring whole brain structure we repeated and extended our original study in 20 healthy adult volunteers, focussing on the temporal aspects of the structural changes and investigated whether these changes are performance or exercise dependant. The data confirmed our earlier observation using a mean effects analysis and in addition showed that learning to juggle can alter gray matter in the occipito-temporal cortex as early as after 7 days of training. Neither performance nor exercise alone could explain these changes.

    We suggest that the qualitative change (i.e. learning of a new task) is more critical for the brain to change its structure than continued training of an already-learned task.

  • Niccolò Bonacchi added an answer:
    How can I prevent backflow in intracranial mouse injection?

    We recently injected 3 microl of solution in mouse frontal cortex at coordinates AP 2.5-ML 2.0-DV 1.8 mm according to Paxinos. Injected speed was 0.5 microl/min leaving the needle at position for 4 mins after injection. Although speed was slow and quantity was not abnormally high, we still exepriencing quite some backflow of injected substance, even after injeting of only 0.5 microl.

    Doe anyone experienced (and solved) this issue ? 



    Niccolò Bonacchi

    Maybe I'm late to this discussion,

    I've been injecting in RAT, 0.4µl @ 0.1µl/min with a rest period of injection time * 2 with a hamilton pump, syringe and steel injector from chronic canulae implants (fom kopf I believe), these settings work fine.

    5µl seems like a lot especially for a mouse at mosts for a RAT I would go with 1.5µl! Also, the speed is important, the faster you go the more damage you create to the brain, and there is a limit to how much 'stuff' you can put in the brain without increasing too much intracranial pressure, there is a very limited amount of space in the skull and its mostly all taken by the brain, if you put too much stuff in it will have to come out by the path of least resistance which is the hole you just created to inject things in the first place. 

    Hope this helps.

  • Liz Unger added an answer:
    Does anyone have a good method to define Lambda in mouse surgery?

    Refering to Paxinos atlas for C57BL6 mouse sterotaxic surgery, average distance between Bregma (B) and Lambda (L) is 4.21 mm in mice of average bodyweight 26 gr.

    We experienced BL-distances far above this value (ranging 4.2-5.2) in same BL6 mice of different weight range (20 to 35 gr). Consequence of this is that corrected anterior-posterior coordinates are posterior to target (hippocampus).

    Either there is something wrong with definition of B, although this is not so difficult. More problematic may be defining L. 

    Does anyone has a good method to define L (or publication) or is it preferable to define L as the intersection of midline with lamboid sidelines?

    thanx in advance


    Liz Unger

    Hi Roland,

    Glad to hear at least one problem has been solved.

    3ul is considered a very large volume for a mouse. In the past I injected 1ul and that was considered the upper limit of what is acceptable (some even say that's too much). Typically people inject anywhere from 30-500nl. 

    Backflow is indeed a problem. My lab tried many things including backfilling the needle with viscous substances like mineral oil or collagen, and waiting up to 20 mins after injection to pull the needle out. Nothing really worked. The best results were achieved when we injected a smaller volume (<100nl). We ended up buying a nanoject for small volume injections, although I hear the picospritzer works well too. The nanoject uses pulled glass pipettes as the needles, so we had to borrow a pipette puller.

    I also inject at 10nl/s with a 5 min wait before bringing up the needle.

  • Sean Patterson added an answer:
    What is the best way to do a synaptosomes preparation from Postmortem Human Cortex?

    Dear all, I am trying to do a synaptosomes preparation from Postmortem Human Prefrontal Cortex (frontal). I read few articles, they used 1 to 5 gram at the beginning. I started with low amount of frozen brain, around 300 mg (PMI < 4 hours). From 300 mg weight of prefrontal cortex, I generally obtain ~25 micrograms of total protein from isolated synaptosomes. 

    Is anyone have any idea to increase the yield at the end (beside increasing the weight of the brain)? I do not have a high amount (weight) of human brain.

    Each minced prep is immediately homogenized by applying 20 slow stokes using a teflon-glas tissue grinder (grinding chamber clearance is 0.15 mm). Then I use layering of discontinuous sucrose gradient.

    I am thinking to use a glas-glas tissue grinder (grinding chamber clearance is 0.025 - 0.076 mm).

    I welcome any idea.



    Sean Patterson

    I've never heard of anyone preparing synaptosomes from chemically-fixed tissue and, frankly, I doubt it would work. Certainly, the material you are purifying would need characterization by electron microscopy to ascertain its composition. After formalin fixation, even the enrichment of synaptic markers by Western blot would be problematic. I really don't think that your problem here is the homogenization step.

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  • Khalid Eldahan added an answer:
    How can I label brain hemispheres for free-floating histology?

    I am running immunohistochemistry on rat brain tissue, and the sections will be stained while free-floating.  However, we need to reliably know the left from right hemisphere.  We cannot take a notch out of the cortex (which we have done previously), because we are taking a full survey of the brain.

    Could someone recommend a method to label the hemispheres?  Is there some sort of marker or pen that is visible to the eye but would not affect staining?

    - Thank you -

    Khalid Eldahan

    I would use a little dab of lipophilic dye, like DiI:

    Are you planning to use fluorescent IHC? If you do, just make sure that the dye doesn't overlap with the emission profile of the fluorophore you will use! 

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