Neurobiology and Brain Physiology

Neurobiology and Brain Physiology

  • Roya Kheyrkhah added an answer:
    Are there any EEG data from 7-12 years old children that are perfect and don't have any specific seizures and where can I find them?

    The most of data are related to disorders and disabilities, i want the perfect one of them. can any one help me? thanks.

    Roya Kheyrkhah · University of Tehran

    Thanks a lot  Mr Khatibi for your attention and guidance, I'm going to check it.

  • Christian Mühl added an answer:
    Emotion classification using EEG signals.
    I am worked on " Extraction of valence and arousal information for emotion classification ". I have 64 channel eeg data . how i can perform band pass filtration on this huge amount of data in Matlab for 2-40 Hz range.
    Christian Mühl · German Aerospace Center (DLR)
    Hi, as Swathi, I would suggest EEGlab or fieldtrip. Both offer functions for EEG processing that can be run with Matlab. EEGlab also offers a stand-alone version. The amount of data is actually not that big ;) Alternatively the FFT implementation pwelch or other filter functions of Matlab should be helpful as well. Good luck, Christian
  • What are the best criteria when choosing a concentric bipolar electrode for brain stimulation in in vivo electrophysiology?

    Good morning, I’m doing in vivo electrophysiology in anesthetized mice. I’m recording evoked filed excitatory post synaptic potentials (fEPSP) in the hippocampus CA1 stratum radiatum after the electrical stimulation of ipsilateral CA3 axons. I would like to test other concentric bipolar stimulation electrodes but I don’t have the knowledge necessary to wisely choose a configuration that might fit my needs. Thereby I would like to learn how to choose an electrode (even another that bipolar if it is the case) that might adapt the best for the brain region on which I'm currently experimenting on (which currently is the hippocampus) and perhaps others in a near future. Thank you.

    Dear Jose,

    The majority of the commercially available bipolar concentric electrodes are designed to provide the best performance in terms of spatial charge distribution. I usually work with electrodes from FHC (, and I can tell that they all work very well. I would specially recommend those with a beveled or pencil point shape and outer diameter ≤200 µm to reduce the tissue damage, specially when you target CA3 (~2500 µm depth in mice).


  • Laurie Galvan added an answer:
    What are the best markers I could to use to analyze by immunofluorescence synapses of midbrain neurons?

    Pre and post synaptic markers

  • Glenn Watson added an answer:
    Does anyone know the distance a certain optical light can diffuse in the brain issue?

    Hi, I am trying to use optogenetics to study the connection of two nucleus within rat brain. However, the distance between this two nucleus is only 1mm. Does anyone know the distance a certain optical light can diffuse in the brain issue? Thanks!

    Glenn Watson · Pennsylvania State University

    See the following article concerning light diffusion in different brain brain regions of mouse;

    See recent work by Ed Boyden's group as well addressing this issue;

  • Ravinder Jerath added an answer:
    What is the scientific explanation for the left part of brain controlling right part of body and vice-versa?
    I don't understand why if we stimulated children's right part of body, it can make left part of brain grow rapidly.
    Ravinder Jerath · Augusta Women's Center

    The reason the brain is wired on the contralateral side is explained in my recent article published in "consciousness and Cognition " journal. This article explains why in patients who have Contralateral neglect syndrome they can not locate objects on their contralateral side even though they have no visual impairment. Moreover these patients have inability to feel the left side of their bodies . The defect is commonly associated with stroke affecting right parietal cortex.

           The explanation answers the basic question as to how we see the world. The first figure in the article shows that what we see outside actually is seen internally by our brain in the same exact way, ie the left side of our vision is imaged on the left side of our head and body. The left side of our body unconsciously positions the left side of the scene we see outside. It may be hard to imagine however all we see actually is within self. The thalamus acts like a tiny brain . All the space around it formed by all the cells of the body and visual apparatus of the brain behaves like an empty  space that I have termed "3 D Default space " . It forms the internal world that we only perceive as darkness when we close our eyes. It truly is amazing how brain perceives consciousness in this space subconsciously. 

  • Priyaa Raj added an answer:
    What is the best way to enzymatically dissociate mouse brain tissue that gives a high yield for all cell types (neurons, astrocytes, microglia)?

    We currently use mechanical dissociation, but our astrocyte yield is low. We've tried papain (I'm not sure which concentration we used), but it did not give a good yield for neurons. We want to minimize cell death during dissociation as well as maximize preservation of cell surface markers (e.g. CD11b). Any suggestions? Thanks!

  • Rizk Sarhan added an answer:
    Do you think that a male without gonads is equal to a female without gonads?

    There are many differences between male and female body function, resulted from their endocrine specially gonadal hormones. can we imagine gonadectomized male and gonadectomized female to be the same like as a third null organism who have no any gonads. or otherwise male and female bodies would work in different ways independent to their gonads.

    Rizk Sarhan · Benha University

    female without gonads at any time is female but without some sex chracters like menstruation , normal breast development  but it differ for male according to the time and cause inutero  is female after delivery continue female but  if later he has feminine chracters , encchiodism  or other presentation  

  • Vigneswaran Veeramuthu added an answer:
    What are your thoughts on neurocognitive and neurophysiological changes in microgravity environment?

    The NASA is currently studying the spaceflight effects on neurocognitive performance while trying to establish empirically the extent , longevity and the neural basis to to past anecdotal  claims altered performance by astronaut returning from long term space exploration. The study includes structural MRI, functional imaging, diffusion weighted imaging  pre and post flight; and neurcognitve testing pre, intra and post flight. The details of the study could be found here

    What are your thoughts on this study?

    Vigneswaran Veeramuthu · University of Malaya

    Thanks John Jupe for your insights. Will go through some of your videos.

  • Jill R Glausier asked a question:
    Is anything known about the density of asymmetric synapses onto Chandelier Cells relative to Basket Cells?

    Do Basket Cells receive more excitatory synapses than Chandelier / Axo-axonic Cells? I'm specifically interested in parvalbumin-positive, but any information about asymmetric/excitatory inputs onto these cells types, relative to each other, is much appreciated. 

  • Jordan Jahrling added an answer:
    Is there a known drug or chemical that can be given to mice to induce blood-brain barrier leakage?

    I am looking at the effects of a compound on blood-brain barrier integrity. Preliminary results indicate that the compound improves tight junction expression in aged mice. I am looking for a way to induce BBB leakage in young mice to see if the compound can improve functional outcomes. I am aware that head trauma is widely used for this purpose but would like to avoid this route if possible

    Jordan Jahrling · University of Texas Health Science Center at San Antonio

    Thank you to everyone for the input. This is just a pilot so I think we are going to try LPS first and see what happens. All great suggestions and I appreciate the guidance

  • Abhiyan Viplav added an answer:
    How do you dinstinguish between dendrites and axons in neurons in culture?
    Eg by immunocytochemistry, is there a marker you can stain for? Or by e-phys?
    Abhiyan Viplav · Institute of Medical Physics and Biophysics , Münster

    Can anyone recommend a good antibody against non-phosphorylated Tau for axonal marker only ? Thanks a lot.

  • Susanne Burkhardt added an answer:
    Can anyone suggest a reliable reference gene for qRT-PCR normalization when comparing postmortem tissue between controls and Alzheimer's patients?


    I would like to know what housekeeping genes one can use to discern gene expression changes in prefrontal cortex of Alzheimer's patients by qRT-PCR.

    Many thanks.

    Susanne Burkhardt · Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen

    Hi Cemil,

    you could check hu Hprt1 or hu GAPDH, maybe also hu Pgk1!

    Cheers and good luck!!! 

  • Richard J Binney added an answer:
    In which topics can be summed up the importance of neuropathology in the practice of clinical neuropsychology?

    The neuropsychological knowledge can be applied in various ways in the treatment of those affected by a particular brain disorder that impacts on behavior.

    Some examples where knowledge related to pathology of the nervous system become useful:

    • Make inferences about the normal functioning of the central nervous system
    • Different disorders or disturbances can cause similar symptoms
    • Some neuropathological conditions may increase the likelihood of other disorders.
    • The presence of a certain neuropathological disorder does not mean that there can be another type of disorder

     I'd like to know your opinion, and if possible, some articles approaching this topic.

  • Pilar Martin-Lobo added an answer:
    Are there any tests suitable for testing visual working memory for children 6-12 years old?

    I wonder if there is any test of visual working memory good to test  children aged 6-12? Is there any good test for selective attention of children aged 6-12? I will be very appreciated if I can know the advantages of the recommended test over other tests and if I get a link to some references. Thank you so much!

    Pilar Martin-Lobo · Universidad Internacional de La Rioja

    In my opinion, is very interesting to applicate a test of eye movement to know the influence in visual attention. There is a test called K-D, about eye movements. Our study show that eye movement can influence in visual attention.  

  • Sheraz Khoja added an answer:
    What software can be used for unbiased counting of TH positive neurons in substantia nigra region?

    Hi. I am planning on doing unbiased counting of TH positive neurons in the substantia nigra region in our animal model. I would like to know if there are any good software out there to do unbiased counting. 

    Sheraz Khoja · University of Southern California

    Thank you Miguel! I will read your paper.

  • Gianluca Ragone added an answer:
    Is Drosophila melanogaster a good animal model for Alzheimer’s disease?

    Dorsophila melanogaster (fruit fly) has been used to study Alzheimer's disease as a model organism. I have read a review article on this issue:

    The article has discussed about several advantages and disadvantages of this animal model, but I am still wondering about what may be the major strengths and limitations when trying to translate the findings from fruit flies to humans, especially regarding studies on genetics or pharmacotherapy? 

    In addition, what are the behavioral tests that could be a good indicator for "cognitive function" or "memory" for fruit flies?

    Gianluca Ragone · University of Bologna

    for a complete literature overview of Alzheimer drosophila model: 468 papers.

  • Aaron T Wolman added an answer:
    Why would a male mouse be more likely to have a seizure then a female mouse?

    After inducing seizures in the two sexes of mice there is a much higher rate in which males have seizures. I cannot figure this out. Please help!

    Aaron T Wolman · Wilkes University

    Thanks everyone. I was really stumped on this one. 

  • Nurul Adhwa HAR added an answer:
    Why did studies prefer to co-culture bEnd.3 with C6 glial cells to establish an in vitro blood brain barrier (BBB) model using cell lines?

    I am interested to know why C6 is the famous cell line to be chosen to co-culture with bEnd.3 (endothelial cells). 

    Nurul Adhwa HAR · Universiti Brunei Darussalam

    Hi Robert. Thank you for sharing your experience on bEnd.3. It is good to know the worst case scenario that could happen to an experiment before actually initiating the experiment. I will keep your story in mind. Thanks!

  • Abel Torres Espín added an answer:
    I need to count the number of neurons of cortical rat brain slices. What is the best method to do it?
    I am interested in counting and comparing the number of neurons in different brain slices to confirm neuronal loss after injury. Thank you
    Abel Torres Espín · University of Alberta

    As it has said before, imageJ can help you to count the neurons. If the cells are far enough between them it is possible to count automatically using the analyze particles option in the analyze menu. If the cells are in touch the automation is a little bit difficult. You have some manuals about particle counting in the imageJ's website. If you use a nuclear marker to detect the neurons, like NeuN, you should not have problems to count automatically if the slice is thin or if you obtain the images by confocal.

    If you need more help, you can contact me at

  • Why does music evoke emotions or feelings?
    Music has many bodily effects. This is not trivial.
  • Jonathan T Ting added an answer:
    How can I improve the neuron survival rate in cortex?

    I want to do double or triple whole cell recording in L2/3 neurons in cortex. But the problem is that the superficial layers' neurons are always much worse than deep layers', and sometimes the surface of slices looks not so clear, and these make it difficult to choose good neurons to record. So are there any suggestions for improving the slice condition?

    Jonathan T Ting · Allen Institute for Brain Science

    It is not really true that you can get great slices at any age using sucrose cutting solution.  That was the whole basis for the brainslicemethods website since sucrose aCSF cutting is insufficient for many studies with animals at advanced ages.  However, it is true that you should be able to get good quality slices with minimal shriveling of cells at the surface at the P14-P21 mouse age. I would also suggest to check slicing angle and z axis vibration of the slicing instrument to ensure these are not causing problems.  Just the other day I did a demonstration where I cut slices by hand using a razor blade from a P14 mouse and was able to get beautiful cortical transcardial pefusion, no protective solutions...the slice prep is very robust at this juvenile age.

    As a side note, in some brain regions it is possible to get OK slices using sucrose cutting solution on young adult animals, e.g. see the work of Moyer and Brown on rat perirhinal cortex.  The brain regions with lower myelination will give the best result as far as preservation of the neurons for patch clamp studies.  I agree with Saak that motor cortex always looks worse than SS cortex or mPFC.  It seemed to me that mPFC was always clearer for visualizing deeper into the slices, either because of less swelling in this region, or due to lower myelination in this region relative to other regions.  In P21 mice I could generally see all the way through the mPFC to the other side of the damaged surface for 300 micron thick slices with proper IR-DIC optics (900nm bandpass filter).

  • Bruno Costa added an answer:
    Can anyone advise me in search of software for EEG sources?
    I'm doing source analysis. Does anyone know a software for source analysis like FD VARETA?
    Bruno Costa · Federal University of Rio de Janeiro

    Does any one know if it is possible to do the Anova estatistics on the software sLORETA? I think the software doesn`t have this option but some articles say that they did it as the file here.

  • Jason T Chisholm added an answer:
    Can Tetraiodthyronin (T3) be used for neuroprotection in stroke?
    As T3 has a positive influence on axonal growth, dendrite branching and development of myelin sheath I wonder if it could be used to increase the regeneration processes in post stroke patients.
    Jason T Chisholm · University of Kentucky

    One study of 737 acute stroke patients by Alevizaki et al, found low T3 levels, measured shortly after stroke onset, to be an independent predictor of poor outcome and increased mortality in acute stroke patients.  

  • Jonathan T Ting added an answer:
    Is anyone familiar with field recordings of hippocampal slices?

    We are trying to perform field recordings of hippocampal slices (CA1 neurons) from the rat brain.  Instead of seeing any biological response, we somehow get enormously large shocker effects.  I am new to the research area, and I was wondering if anyone had the same problem.  We use Axon pCLAMP 9.  and Digidata 1322A.

    Jonathan T Ting · Allen Institute for Brain Science

    If you are seeing mainly a 'presynaptic' fiber volley and no other response you may have one of these possible problems:

    1) incorrect preparation of the slice so that the fiber pathway is not maintained optimally.

    2) incorrect positioning of the stimulating or recording electrodes.  You should determine if your goal is to record fEPSPs or population spikes, as this will determine the optimal placement of electrodes.

    3) You may be experiencing strong presynaptic suppression, e.g. depression of the synaptic response due to high adenosine release or other metabolites.  This can be due to mechanical release, possibly from the harsh impaling of tissue with the stim electrode, or may occur if you do not allow sufficient time for slice recovery after sectioning.

  • Joseph M Fayad added an answer:
    Triple Transgenic and the modelling of Alzheimer's disease and the link with diabetes.
    Should we really be using information gathered from the triple transgenic mouse model of dementia to inform the development of novel therapeutics for Alzheimer's disease or to study the link between diabetes and dementia?
    Joseph M Fayad · U.S. Department of Veterans Affairs

    yes .alzhymer associated with metabolic syndrome seems to reverse in the early phases with gastric bypass surgery , making the group different from the typical prionic model that seems to loose weight rather than gain despite adequate intake . therefore any knowledge that can help understand the subgroup will also help to devise a much more targeted disease and the response to therapy .

  • Hossein Hassanpoor added an answer:
    What is the relationship between ATP and activation of a presynaptic neuron ?

    ATP has effect on astrocytes Ca oscillation and activation of interneuron in dentate gyrus of the hippocampus. However, I want know the source of ATP in extrasynaptic space. I think there is relationship between the action potential of pre-synaptic neuron and extrasynaptic ATP, but how? 

    Hossein Hassanpoor · Amirkabir University of Technology

    Dear Mirko
    Thanks for your answer. as you know in different papers, different point of view are considered. in some paper effect of ATP on astrocyte and interneuron has been considered. in some papers, astrocyte itself has been considered as a source of ATP.
    i'm really confused. How can i model the neuro astrocyte network by considering the ATP effect?

  • Paresh Chandra Ghosh added an answer:
    Is there any correlation between vascular pathology and psycological disease?
    Would a decrease blood supply, or an anatomical variant of the arteries predispose someone for psycological "fall out"? Any thoughts?

    Dear Madam

    Man is compose of physio and psycho. It has physical body as well as mind . both must be normal  to make  man healthy. Not only  vascular pathology, any pathology will effect man,s psychology causing psychological symptoms or disorders. pcg,Chennai

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