Neurobiology and Brain Physiology

Neurobiology and Brain Physiology

  • Guido Gainotti added an answer:
    Why is it useful for the neuropsychologist to possess a general framework of knowledge on brain pathology?

    The neuropsychological knowledge can be applied in various ways in the treatment of those affected by a particular brain disorder that impacts on behavior. I'd like to know your opinion or articles approaching this topic.

    Guido Gainotti · Catholic University of the Sacred Heart

    I also think that a good knowledge not only of brain pathology, but also of brain anatomy and, in general, of cognitive and affective neurosciences is necessary for a correct and in depth interpretation of neuropsychological data. A good knowledge of brain structure and functions is, indeed,  necessary to understand the patterns of cognitive impairment resulting from different kinds of brain lesions and to plan the corresponding rehabilitation

  • Nico Brand 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!

    Nico Brand · Universiteit Utrecht

    We have the Corsi Block Test in our Testmanager Minds package. For both children and adults. It adapts itself to the age of the test person. Block Span Forward, Backward and, and an ultra span test if desired. Instruction in English in addition to Dutch. Visit 

  • Lars - Winkler 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

    Lars - Winkler · Leibniz-Institut für Molekulare Pharmakologie

    Mannitol or other hyperosmotic solutions into the carotic artery works well, but just for a very short time. You can try systemic inflammation with LPS or TNFa but you will have side effects throughout the body! I guess there is no other way to proof your component by inducing a pathologic condition i.e. stroke (MCAO), TBI, SAB, brain tumor... You may open the BBB from the other side by injecting inflammatory or hyperosmolaric solutions or tumor cells directly through the skull into the parenchyma! This would affect only a small region were you can evaluate the leakage by MRI for example!

  • 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. 

  • 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 Type II astrocytes, or Type III astrocytes have not been chosen to co-culture with bEnd.3 (endothelial cells). 

    Nurul Adhwa Haji Abdul Rahman · 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.

  • jean pierre Brillard 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.

    jean pierre Brillard · Fertilavi

    Greetings, colleagues,

    There is definitely no way to assimilate a (posthatch) male without gonads to a female without gonads. As underlined by Christopher, the developmental biology and therefore the physiology between these two types of birds évoluâtes differently as soon as the phenotypic sex of the embryo is differentiated  (sex differentiation occurs about 7.5 days after the onset of incubation in chickens). Then, muscles, feathers, secondary sex characteristics will evolve differently up to and then after hatching. therefore, a castrated male will never develop similarly to a castrated hen...

  • 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

  • Yann Bernardinelli added an answer:
    Why are 2 organotypic hippocampal slices from the same animal so different in their baseline excitability and response to stimulation?


    organotypic hippocampus-cortex slices harvested at P4, washed in Hank's balanced salt solution, then maintained for 12 days in culture medium (50% minimum essential medium, 25% heat-inactivated horse serum, 25% hank's balanced salt solution, supplemented with (in mM) glucose 36, glutamine 2, HEPES 25, and 1% antibiotic/antimicotic, adjusted to pH=7.3, and filtered), at 37 deg C and 5% CO2; medium changed every 3 days.

    Dye loading: the mesh on which the tissue is cultured is cut out of the well, and transferred to a sylgard disk, where it is held in place by beads of crazy glue around the edge of the disk. The preparation is then lowered into 6 ml aCSF ( in mM: dextrose 30, CaCl2 1.2, KCl 3, NaCl 136, NaHPO4 1.25, MgCl2 1,NaHCO3 10) with 20 uL of 100 mM fluo 8 L-AM in a solution of 15% pluronic DMSO, aerated with a fine stream of bubbles of 95% O2, 5%CO2, for 40 min at 23 deg C.

    We then move the tissue to the recording chamber, through which the following aCSF flows: in mM: NaCl 125.4, NaHCO3 26, KCl 5, KH2PO4 1.24, MgSO4 1.3, CaCl2 1.5, dextrose 10. The solution is warmed to 27 deg C and flows at 4 ml/min. 

    We begin optical recording immediately after the prep is moved to the chamber. We expose the slices to 20 ms  of 450 nm wavelength light.

    In some preps there is spontaneous activity,  and stimuli produce robust firing in subsets of cells. In other preps there is no spontaneous or evoked activity, but when 20 mM KCl is applied a wave of neuronal activity can be recorded optically.

    So this is our problem: in slices harvested from the same animal, maintained in different wells but the same media under identical conditions, we get "normal" acitivity, or a complete lack of response, but the high K+ response shows that the tissue is viable.

    We are confident that this variability is due to small differences in loading/culturing/cutting conditions.

    Can anyone suggest what step in this process must be most tightly controlled to minimize this kind of variability?

    Alternatively, is this variability (1 "good" slice out of 3 slices) just the way it is with organotypic cortex-hippocampal slices?

    Yann Bernardinelli · University of Geneva

    Hi Nicholas,

    I won't discuss Ede's arguments against organotypics. He is true, this is probably not the best model for network behaviour but can be very useful to explore unknown molecular mechanism and cell physiology.

    Attila has very good point here. In top of that, there is a well known axon growing in organotypics. Wether this axon growing will create new connections and influence neuronal excitability is less clear. Considering your YES or NO responses I won't bet on those explanations.

    From my experience, some slice are not surviving well. Dying slices are thin and dark (transmitted light) and should be discarded. Here are my advice to improve your healthy slice ratio: 1) Speed up dissection even if the whole process will be more dirty (10min max from brain removal to slices in incubator). 2) Use high glucose content 3) Make sure slices are not covered by culture media and that the millipore membrane is intact. 4) Restrict the number of slices per membrane inserts to a max of 3. 5) Lower the incubator temperature during the first culturing days. 6) Organotypics work beatifully for rat slices, harder for mice (don't know why).

    Your Fluo-8-AM loading protocol looks very heavy! This is probably your main source of variability. Fluo-like molecules are pretty good calcium chelators. Too much dye loading will chelate the whole cellular calcium content and you won't be able to monitor physiological calcium change (could be ok for your high K+ control). I understand that your goal is to load neurons here. Indeed they are very hard to load with AM dyes as they preferentially load into glial cells and it's why you use so high dye concentration. My suggestions are the following: 1) use viral gene delivery of GCaMP6 with a neuronal promoter (AAV works well in organotypics) 2) Use Fura2 AM as it loads better in neurons than the Fluo family 3) Inject the dye (DeRoo et al 2008) instead of doing a bulk loading 4) Make sure that your loading chamber is well oxygenated. This is critical as you are loading dyes with a full slice immersion for 40min in static conditions (very nice hypoxic conditions)! 5) Make sure your AM bound is not hydrolized (use 50ug aliqots of dyes from a serious brand like Teflab) 6) I would wait at least 10min once the slice is in place under the scope and decrease ACSF flux.

    Hope this help


  • Ivan Chakalov added an answer:
    Can someone suggest a user-friendly vocoder program (software) for envelope extraction of speech?
    I want to extract a temporal envelope of a speech.
    Ivan Chakalov · University of Münster

    Thank you! All of you have been very helpful.

  • Fouad Lemtiri-Chlieh added an answer:
    Has any one had experience with automated whole-cell patch clamp in brain slice, such as ones from AutoMate Scientific?
    What are your thoughts on improving efficiency/performances using auto patch in slice?
    Fouad Lemtiri-Chlieh · King Abdullah University of Science and Technology

    As far as I know. I do not know of any such automated patch clamp for brain slices and Automate Scientific don't have anything like that. Could you please send a link to this system that you are describing?

    meanwhile, there are other automated sytems to patch clamp isolated cells (used for high throughput) amongst them is the patchxpress, you get gigaseals with this system because they use glass pipets (the one I saw had 16 amplifiers). There are also the IonWorks quattro and IonWorks Barracuda (you don't get Gigaseals with these, they use special chambers with holes in them...up to 96 I think or probably more with other cahmbers) but they are used to screen large amount of compounds (over hundred thousand chemicals) in ashort amount of time. you need to have a large pocket to buy these (>half a million USD - that was 4 years ago). And you need to have a huge library of these coumpounds to test, otherwise it's not useful. Bottom line, these systems are mostly by pharmaceutical companies or small companies that have the expertise and are hired by the big pharma to test like I said tens of thousands of coumpounds.

  • Fatiha Chigr added an answer:
    Which methods are most commonly used to measure (assess) neuroinflammation in the CNS?
    And neurodegeneration in mice.
    Fatiha Chigr · Université Sultan Moulay Slimane

    Using ELISA, W Blot or IHC, you can assess neuroinflammation by using anti-GFAP (for gliosis) and microglial markers. For better characterization, use anti-cytokines too.

  • Jennifer Keene added an answer:
    Does anyone know why Wako Anti-IBA1 (Cat # 019-19741) works in a perfusion fixed rat brain but not in post-fixed?

    We've previously had great imaging staining rat frozen rat brain slices with Wako Anti-IBA-1 when the rats were perfused with PFA. Due to some of the other stains on our new experiment we switched to a PBS perfusion and PFA post-fixing after slicing.  Most of our stains are having no problem but the IBA-1 isn't working.  Anyone else had a similar problem and figured out how to fix it?

    Jennifer Keene · Case Western Reserve University School of Medicine

    We've used antigen retrieval in the past but moved away from it when we were getting good images without antigen retrieval.  We can certainly try going back with the IBA-1 specifically,  as well as try reducing the fixation concentration 

  • Hossein Hassanpoor added an answer:
    What are the mechanisms for secretion of different gliotransmitters such as glutamate, GABA, and ATP by astrocytes?
    Receptors for all major neurotransmitters seem to be present on the astrocytic plasma membrane (Volterra and Meldolesi,2005), and activation of these receptors (because of neural activities) leads to an intracellular Ca2+ increase and subsequent release of gliotransmitters from glial cells (Perea et al., 2009).
    The problem is, how can the astrocyte understand which of the gliotransmitters should be released in different states, according different neural activities?
    Hossein Hassanpoor · Amirkabir University of Technology

    Dear professor Verkhratsky

    Many thanks for your valuable suggestions

  • Cainositas Cainosito added an answer:
    What is the meaning of "synaptic puncta"?
    Could you tell me what does the "Synaptic puncta" mean?

    Is it a synonym for synaptic surface?

  • Karla Kretschmannova added an answer:
    Does anybody have experience with zirconia ceramic blades for cutting brain slices?
    How many times can you reuse the blade? Can you use them with Leica Vibratome?
    Karla Kretschmannova · PsychoGenics Inc.

    Thank you very much for all answers. We are now using them for about a month (everyday cutting, 1-2 animals) and they really work very well! I can't believe we have not switched earlier....

  • Alfredo Pereira Junior added an answer:
    Do astroglial calcium waves support conscious computations - and what kind of computation?
    The existence of large-scale calcium waves has been proven and imaged 'in vivo' with two-photon fluorescence microscopy. Thrane et al (2012) showed that general anesthetics selectively eliminate these waves. In the attached powerpoint presentation I present a model that addresses the issue of astroglial contribution to conscious processing, and welcome your critical comments here in RG.
    Reference: Thrane AS, Rangroo Thrane V, Zeppenfeld D, Lou N, Xu Q, Nagelhus EA, Nedergaard M. (2012) General anesthesia selectively disrupts astrocyte calcium signaling in the awake mouse cortex. Proc Natl Acad Sci U S A.109(46):18974-9
    Alfredo Pereira Junior · São Paulo State University

    Terrence Sejnowski and colleagues are advancing our knowledge of the role of astrocytes in brain computational processes:

    Proc Natl Acad Sci U S A. 2014 Jul 28. pii: 201410893. [Epub ahead of print]
    Astrocytes contribute to gamma oscillations and recognition memory.
    Lee HS, Ghetti A, Pinto-Duarte A, Wang X, Dziewczapolski G, Galimi F, Huitron-Resendiz S, Piña-Crespo JC, Roberts AJ, Verma IM, Sejnowski TJ, Heinemann SF.
    Glial cells are an integral part of functional communication in the brain. Here we show that astrocytes contribute to the fast dynamics of neural circuits that underlie normal cognitive behaviors. In particular, we found that the selective expression of tetanus neurotoxin (TeNT) in astrocytes significantly reduced the duration of carbachol-induced gamma oscillations in hippocampal slices. These data prompted us to develop a novel transgenic mouse model, specifically with inducible tetanus toxin expression in astrocytes. In this in vivo model, we found evidence of a marked decrease in electroencephalographic (EEG) power in the gamma frequency range in awake-behaving mice, whereas neuronal synaptic activity remained intact. The reduction in cortical gamma oscillations was accompanied by impaired behavioral performance in the novel object recognition test, whereas other forms of memory, including working memory and fear conditioning, remained unchanged. These results support a key role for gamma oscillations in recognition memory. Both EEG alterations and behavioral deficits in novel object recognition were reversed by suppression of tetanus toxin expression. These data reveal an unexpected role for astrocytes as essential contributors to information processing and cognitive behavior.
    PMID: 25071179 [PubMed - as supplied by publisher]

  • Sunil Kumar added an answer:
    What is the neurobiological basis of subconscious brain?
    Theories of conscious and subconscious brain have been around for decades, but do we have any neurobiological understanding of the subconscious state of the brain? It’s been said or reported in encyclopedia that about 60 – 80% of the brain remains in subconscious state most of the time and carrying lots of thoughts, emotions and information from past and present, and these thoughts and information can drive and modulate mental content which can affect the behavior when retrieved and processed by the conscious brain. But do we have the molecular, cellular or neurological evidence of the subconscious brain and how the information from subconscious brain transfers to the conscious state?
    Sunil Kumar · Duke University

    Thanks to all for for very meaningful comments and sending the related links to understand some neurobiological aspect of subconscious brain. Although we need very intense research to really get close to complete understanding behind subconsciousness, but this really help to improve our understanding about conscious and subconscious state of brain. 

  • Hossein Hassanpoor 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?

    Hossein Hassanpoor · Amirkabir University of Technology

    Dr. Burgess said:

    "The differences between grid cells and place cells may well be due to their inputs, although some of the stellate cells in layer II of medial entorhinal cortex are probably grid cells, and they have some differences to pyramidal cells."

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