Questions related to Neuroanatomy
Hello, I would like to ask from everyone's perspective what is the biological relevance and impact if the neurons that are being affected by an exogenous stimulus is (1) peptidergic or non-peptidergic neuron, (2) and their respective class of nerve fibers?
Currently, I am still consolidating and distinguishing these concepts because I think these are important research questions in molecular and cellular neuroscience projects.
After decades of teaching Neuroanatomy for Behavioral Scientists and using many other sources, I have concluded that the functions of the central nervous system (CNS) can be reduced to thee types of processing: sensory, effector or motor, and memory. Agree or disagree? if disagree, please explain.
I am organizing online activities with M2 students to explore neuroanatomy using Allen Brain Atlas. I have already some ideas and prepared some activities around the expression of a protein implicated in Parkinson's disease but I would like to know if you have already used this Atlas for teaching and how.
I would like to scan calcium-indicator-dye-loaded neurons after fixation, just to know, which cells have been loaded. Fura and Carbodiimide fixation have been reported to retain fluorescence but I prefer paraformaldehyde fixation for several reasons. Is there a single calcium dye, which is not quenched after paraformaldehyde fixation?
I am trying to discern whether, in the brain (structure & function) of people with bipolar disorder/MDD/schizophrenia who experienced childhood trauma, there are:
1. already differences in children's brain structure & function that trauma further modifies and the person develops a mental illness OR (genetics first then trauma)
2. trauma changes the structure and function of the brain that the child's genetics further modifies and the person develops a mental illness (trauma first then genetics)
Has anyone researched this & if so, can you please share your findings or references you know of?
I am looking at cortical neurons in coronal sections from mice expressing Thy-YFP and a top secret genetic manipulation :)
I noticed these vacuoles in the apical dendrites of most of the neurons, and was wondering if anyone with an experienced eye can tell me if these look like some sort of artifact? The brains were perfused, fixed, sunk in sucrose, frozen, and sectioned on a microtome. Ice crystals? Freeze thaw damage?
I don't have a wildtype to compare it to right this second due to technical difficulties, but am impatient and thought I'd ask all of you first, ESPECIALLY because of what I found out when I googled apical dendrite vacuoles. Thanks!
Professional-school student with extensive ACE (child adverse events) history along with severe depression and anxiety diagnosed over previous year, presented with recent severe ADHD (I-Type) diagnosis at age 26.
Documentation confirmed maximum dose step therapy for various Amphetamine-based stimulants was completed but still not found to be fully affective.
Unexpectedly, they are currently prescribed daily 50mg Mydayis (Mixed salts of single-entity amphetamine product) along with 80mg Prozac, and consumming 300-400mg of caffeine.
Due to initial medication-only use producing very minimal stabilizing effects, but found to increase at re-introduction of SSRI and further increase with Caffeine reintroduction.
No adverse effects (cardiac, neuromuscular, neurocognitive) have been reported/measured in 4 months of aforementioned therapeutic combination.
NOTE: Adverse reaction to methylphenidate-based medications were identified early on.
Assessment of (remaining) presenting symptoms seems to overlap with tentatively defined SCT Criteria.
NOTE: Student has never been prescribed Strattera (only presently confirmed SCT-symptom relief medication)
Recent research has shown SCT + ADHD to correlate with much greater impairment in adults, do you think a combination of severe ADHD + SCT may result in required use of excess pharmacotherapy dosages that surpass established safe therapeutic/combination parameters?
In my research I have analysed structural volumes in MRI scans by manual tracing measures and correlated against automated measures, with particular interest in subcortical grey matter structures. As I am still a student it is interesting to gauge the overall need for the skill in the international community, either as a diagnostic tool or as an inter-rater reliability measure.
I am interested in scaling my coordinates for stereotaxic injections by measuring the distance from bregma to lamda in each of my mice and then scaling this to the "typical" value used in mouse brain atlases. This scaling factor should reduce some error that results from differences in mouse brain sizes. I would be most interested in knowing the bregma-lamda distance in the "average" or "typical" mouse used to map brain coordinates in the Paxinos Mouse Brain Atlas. Does anyone know this value? I see other people have used this method successfully in rats, where the Bregma-Lamda distance is 9mm.
I am performing stereotaxic injection in mice. In the Paxinos Mouse Brain Atlas it appears that the depth is relative to the brain surface at bregma (z=0). The hole I drill in the skull is tiny, so I cannot see the surface of the brain. I want to account for the distance between the skull surface and then add this value to my depth. This would include skull thickness, dura, and subarachnoid space, etc. Does anyone know what a typical value is? How much does it vary between mice and at different locations within mice? I'm injecting roughly 5mm rostral to bregma and 1mm lateral from the midline.
Now I'm planning about a clinical research about brainstem infarct. And I want an useful atlas of the brainstem.
I know of the two following atlas':
1. Stereotaxic atlas of the human brainstem and cerebellar nuclei : a variability study
F. Afshar , E. S. Watkins , J. C. Yap -- Raven Press, c1978.
2. Atlas of the human brainstem
George Paxinos, Xu-Feng Huang -- Academic Press, c1995.
I think textbook No.2 is better than No.1, but there is a small description about basis pontis.
I'd like to have a more detailed atlas. Does anybody have any information about a new brainstem atlas?
I'm stuck on some basic mouse anatomy for a project I'm doing looking at descending motor pathways that are involved in forelimb function. I'm trying to figure out if the medullary reticular formation in the mouse brain contains the lateral reticular nucleus. I'm also trying to tease apart which areas contain the gigantocellular, parvoceullar, and magnocellular areas.
as we know the specific frequency of sound stimulate the specific part of cochlea of ear that was named cilia(hair cells). subsequently ,the cilia convert the amplitude of the sound to corresponding frequency. nevertheless, is the brain sense the rhythm of the sound?
I need to find neutral cue words for my research on autobiographical memory and future thinking. I would really appreciate any information to have access to the word lists mentioned in the question. Thanks.
Neural circuitry underlying nocifensive response depends on the type of reflex. But, when we talk about withdrawal response, what are the neural elements involved?
I do stereotaxic injections into mPFC of mice brains. I've been trying to figure out a way to overlay a mouse brain atlas outline onto images of brain slices in order to determine the accuracy and precision of injections and if our expression pattern is within our target area.
I think there's a way to use ImageJ to do it, but I haven't had any luck as of yet.
I was wondering what programs and methods others have used and if they could provide either a brief walk through or provide a link to a paper or source that describes the process.
The image I've attached is a great example of what my end result should look like. I just don't know how to get there.
Thanks in advance.
I study adult neurogenesis in the dentate gyrus of the hippocampus and performed a double staining (4Month mouse brain, 40µm, free floating) for BrdU, and NeuN using flourescence ( Alexa Fluor 488, 555) conjugated secondaries.
I refer to one paper for quantification but problem is the total number is significantly different.(about 1/10)
In the paper, 10-12 sections (every 5th section of slides from each animal)
including the DG area were selected. The entire dentate gyri were scanned using a confocal microscope. Z series stacks of confocal images were obtained. The number of double stained cells were counted using the Image Pro Plus software.
I also used 10 sections and got Z stack images and counting a double positive cells using ImageJ.
Is there any things I miss?
I found another BrdU quantification method relative to the stereology. However, It is very complicated to me.
How to I easily count the cells that is representative of the entire DG. I've never done this type of quantification before.
Please let me know, if you have useful suggestions/links/protocols to learn quantification.
Thanks a lot!
I have some rat brain tissue already horizontally sectioned that contain the spinal trigeminal nucleus, facial nucleus, and paratrigeminal nucleus. I am hoping to use anatomical landmarks to quantify various cell types in these regions, but all of the papers I am finding that examine these regions use coronal sections.
Ideally, I would like to be able to differentiate subnuclei, but I would be fine with just having landmarks to differentiate the region borders.
I have tried using various brain atlases to determine landmarks, but my sections are much more thin (40 microns) then those typically included in atlases.
There are papers describing the population of cones and RGCs and their variation with eccentricity in the primate retina. I however cannot find a similar paper on bipolar cells. I would like to know the relationship (in terms of numbers or ratios) between cones and bipolar cells as well as bipolar cells and RGCs as a function of eccentricity. Thank you
Two papers are using the method.
One attached and the other cited here: "Single rodent mesohabenular axons release glutamate and GABA" Root et al 2014
I am pursuing a project that will require me to quantify excitatory synapses in rat spinal cord slices (fixed in PFA). I have a number of references and protocols which describe methods for quantification, but they all use tissue that is 5-15 uM thick.
I would like to use 20 uM thick slices (for a number of other standardized outcome measures), but am concerned that this could be too thick and create too much background/reduce resolution. If you have experience quantifying synapses in fixed tissue, do you believe that this would be an issue?
I'm using 35um horizontal brain cuts, spinning disc microscopy and Fiji to analyze stacks of 35 slices. I'm trying to meassure differences between two types of neuronal projections, in one condition they are very neat and parallel to each other, but in the other, they are very intrincated and more projections can be seen in the tissue. I have compared them using z projections, but I'm not sure what pluggins can I use. Not Sholl, because neuronal projections are not radial, and nuclei are not in the pictures. Any sugestions?
I'm currently using the Allan Brain Atlas's Mouse Brain Connectivity tool (http://connectivity.brain-map.org/) to look at the connectivity between certain sensory and association brain regions. However, most of the literature on neural tracer studies uses different nomenclature for brain regions, and more specifically almost the entire literature uses different nomenclature than the Allan Brain's Mouse Brain Reference Atlas.
For example in the literature, the primary auditory cortex is often referred to as A1, the Auditory Core areas (A1 + AAF), Brodmann area 41, or Te1. Yet, the Mouse Brain Reference Atlas uses the name 'Auditory Areas', which they subdivide in the 'Dorsal auditory area', 'Primary auditory area', 'Posterior auditory area', 'Ventral auditory area'. In this case, I figure, 'Primary auditory area' is the region that I'm looking for, as it probably corresponds to A1 (and maybe AAF too?).
If this is the case then I can of course estimate for each brain region described in the literature its relative position to the primary sensory areas and then sort of guess in what Reference Atlas region it most likely is.. However, this seems rather imprecise, and also it will take a very long time.
So my question here is:
1) How can I find out what the regions of the Mouse Reference Atlas comprise of?
2) Is there potentially a mouse brain anatomy database, which allows you to quickly look up all/most of the different names used for certain brain regions?
3) Is there a database to identify homologues for brain regions across species?
Also, other tips to tackle this problem would be most welcome.
Best wishes and many thanks!
I am now approaching to the neurophatological analysis. I have to detect differences in microglial morphology in brain slices stained in IHC. The aim is to distinguish microglial cells with different shapes and dimension with major objectivity. Is there a free software that can do that?
I am planning to quantify the expression level of a receptor in certain brain region. The technical challenges for me are:
1. IHC or in situ: is it valid to use the normalized fluorescence intensity of the receptor to DAPI for quantification?
2. Of course, the more accurate methods are Western blot or qRT-PCR. However, my interested brain region is difficult to isolate for RNA extraction due to anatomical location and small area size. Is any good way to extract RNA from certain neuron types from a brain region?
Any advise or comment is welcome. Thank you!
I am interested in the segmentation of the corpus callosum (CC) into its 5 regions: genu, body, isthmus and splenium. I was wondering, based on the Mouse Brain Atlas (Paxinos & Franklin), what coordinates would you use to separate these regions for coronal sections. I found one paper by Steelman et al. (2012) that gives the coordinates for each region (i.e. 1.34 to 1.44 from bregma for the genu etc.). However, most other papers I found either looked at the human brain, or just briefly mentioned they looked at the genu or splenium, without giving any other details.
Can Somebody help me on how I know how I can micro-direct the somatosensory representative area in Adult Rat Brain ?
I would like to find a relation between several cortical parameters I extracted from sMRI data (as gyrification, sulci depth, thickness of grey matter) and behavior. Does anyone know if there is an atlas or something similar (papers, references,...) that I can use?
Thank you very much!
There is a huge clinical literature on this mental disorder, but the problem stubbornly and tragically persists. I wonder if it is strongly grounded in amygdala pathology.
We are studying the neurobiological basis of ethnic variations in responses to similar life events.
I observed such an anomaly on a dried skull, and wonder if related to any neuro-anatomical subsequent/associated anomaly. Thanks+
I am doing cerebellar organotypic slice culture from mice p8 and would like to know if there is a way of making sure the slices are happy and alive?
I would also like to know if it is normal to see migration of cells (probably microglia??) outside the slice boundaries?
We want to observe by fluorescence microscopy or light microscopy the parallell fibers in rat cerebellum. Is it better to use sagital or coronal sections? Any suggestion for a marker?
I usually look at microglia isolated from mice brain using the standard percol gradient method without using Collagenase/DNAse steps i.e. just meshing the brain with 10 ml syringe plunger and then layering 30% brain cell suspension on 70% percol. This is the way I look for infiltrating lymphocytes (CD45 Hi) and microglia (CD45 Int CD11b+ cells) by Flow cytometry. The method works well for analyzing infiltrating lymphocytes but for microglia, I get the fluctuating data for the mice even within the same group. Is there any other clean and better way to isolate and characterize microglia from mice brain? Waiting for your suggestions.
I usually cut cryo sections of mouse sciatic nerve at servile postnatal stages, but detaching happens only with P1 slices. I guess it is because those sections are extremely small and have low adhesive force, but I really need to keep them on the slide since I have to run FISH on them.
Thank you for the help.
Hi guys, I am doing experiment of stereotactic intracranial surgery. I wander how to adjust the orientation of rat head in stereotactic to make sure I can injection drug precisely into the relative small area in rat brain as indicated in Paxinos rat atlas?
Thank you very much!
Is anyone aware of a paper where cuprizone is injected into the brain or spinal cord? I was just wondering if it was possible to induce local demyelination this way.
I was wondering if anyone know the specific or unique molecular markers for the following ANS fibers (I would like to do some immunohistology to distinguish between the non-ANS nerve fibers and the ANS nerve fibers, and between the ANS nerve fibers):
1) sympathetic fibers
2) parasympathetic fibers
3) enteric fibers
Thank you very much in advance.
What is the intracellular distribution of Matrix Metalloproteinase (MMP)-9 in fast motor neurons (if possible, which organelle)? Do they found in the axon terminal?
Additionally, do microglia express MMP-9 (it seems to me that I found some "localized" expression)?
I have a picture for your references (where green is the MMP-9 immunopositive reactions; red is IBA-1).
Hi, I am looking for data sources and/or references that describe brain mass increases in mammals with age. For context, I recently read a paper that shows captive mink brain mass peaks at approximately 3 months of age; i.e., the brain mass of the adult is less than that of a 3-month old. I want to know how common this brain mass growth pattern is, so I am searching for other references and sources for comparisons. Thank you all in advance.
I have tried making 10 um cryocut brain sections stained by H&E. I can measure the total cortical thickness, but it is really difficult to distinguish between the different cortical layers. The H&E staining procedure works great in the lab, so I wondered whether it the thickness of the slices that are the problem, or if I should choose another histochemical technique?
I´m working with 20 microns sections and whenever I mount them and leave them to dry, they shred. If I don´t let them dry, they´re fine, but they don´t stick to the slide, falling off in the staining process. I´m losing a lot of samples and I´m trying my best to find the perfect timing between mounting and staining, but nothing seems to work. Does anyone already worked with this and had the same problem?
I would like to perform RNA FISH and/or IHC on sections from mouse spinal cord and dorsal root ganglia...i was thinking about sectioning spinal cord within the vertebral column and a part of surrounding tissue where the dorsal root ganglia are present, but i have read the bone must be decalcified and that this procedure can affect histologic quality :( Does somebody have experience with this kind of tissue preparation? Thanks
I am confused with the score for body symmetry and Whisker response. By the way, I use intraluminal MACo as a model and do it on left MCA.
About the body symmetry
score 2- Moderate asymmetry: body lies on ipsi-lateral side, legs at the ischemic side are extended laterally, the tail is bent. My question is, do both ipsi-lateral side and ischemic side both mean left side or ischemic side mean right side? Since, left hemisphere controls the right part of the body.
And Whisker response
score 1- no response on the ipsi-lateral side , normal on the contra-lateral. Again, does ipsi-lateral means left side and contra-lateral means right side ?
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?
In fact, I am have a good struggling with coinjection of fluorogold &BDA in the same brain region. My protocol for this combination is quite similar to which L. Swanson reported in PNAS, 2010 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930585/), but with smaller injection current (+1-2 µA) and longer injection time (15-20 min). I can, however, get barely BDA labelled neurons or dendrites, but always very nice retrograde FG labelled cell bodies.
I almost always oberseve FG gets precipitated, especially up to first 5mm of glass pipette from its tip. I consider this might be a reason for a lack of BDA labeling in my case.
Any suggestions or comments? Thanks in advance!
I hope you all will be doing well. I have a question regarding cortical sample collection after MCAo surgery. I have operated 48hrs Permanent MCAo in rats. But after collecting the samples some of tissues did not clearly show apoptotic behavior when I applied different Ab. After surfing on PUBMED I have found the following from
“Overall, middle cerebral artery occlusion led to a remarkably consistent pattern of necrosis. The rostral limit was at the level of the intermediate olfactory tract; all animals displayed an infarction dorsal to the rhinal fissure which could attain the frontal and primary olfactory cortices. More caudally (+ 10. 05 mm) the pattern was the same; the nucleus accumbens was very rarely infarcted. At the level of the caudatoputamen (which was invariably damaged), the highest incidence of the infarction was seen at the ventral surface of the brain, corresponding to the primary olfactory cortex. The frontoparietal somatosensory cortex was affected to a greater or lesser degree. The infarction reached its maximum extent, in terms of necrotic surface area, at the level of the globus pallidus (+ 6. 28 mm). Again, the caudatoputamen was systematically infarcted though the degree of cortical involvement was variable. More caudally, the infarction size tended to decrease at the coronal section that corresponded to the level of the anterior hypothalamus. The tail of the caudatoputamen and the external capsule were frequently involved, whereas the involvement of the frontoparietal somatosensory cortex was more erratic. Thereafter, especially in the normotensive strains, the infarcted surface area decreased rapidly and was limited to the dorsal convexity of the cortex and the external capsule”. Journal of Cerebral Blood Flow and Metabolism 8:449-461 © 1988
From this I am confident that my sample collections region is mostly the upper layer of somatosensory cortex and according to this article it is the 2nd layer of primary olfactory cortex (piriform cortex). So I want to ask that which particular areas in cortex do I collect the sample/sampling and will be more grateful if somebody give me hints by mentioning some paper or some site.
I'll preface this post by indicating that I work primarily in bioinformatics, but I need to demonstrate some wet-lab skills in order to graduate with a degree in neuroscience.
I'm proposing a study that seeks to count various immunohistochemically-labeled cell counts and to quantitatively assess dendritic morphology/spine features from serial sections of the **same individuals**. I'm insistent on using the same individuals, because the opposite hemisphere is being fresh-frozen and used for RNAseq studies, so we want to correlate these changes with morphological/neuroanatomical features. The tissue in question will be saline perfused, immersion fixed in 4% PFA. I had planned to section the tissue at roughly 40-50 microns; hopefully just large enough to permit the study of a few intact dendritic arbors per slice (and also thin enough to permit antibody penetration for IHC).
Ideally, some variation of Golgi staining seems would have been great for dendritic arbors (e.g. Sholl analysis) and spine quantification. However, I've read that these approaches are generally poorly suited for pre-sectioned slices at my planned thickeness (e.g. they tend over-stain and become very rigid).
So I'm wondering if:
1) Anyone is aware of a modified Golgi protocol for thin sections (e.g. 40 microns; they can be free floating or mounted as needed to accomodate).
2) Anyone can suggest an alternative approach to Golgi-type staining that would facilitate the quantitative morphological study of the dendritic arbor and dendritic spine density/features.
I would like to apply a stain that will really make the diagonal band in the pigeon brain "pop-out". I can identify it in cresyl violet-stained sections, but sometimes it is quite difficult to make out boundaries. I'm thinking luxol fast blue (stain for myelin) may be a good. Suggestions, please?
I am recently planning to do some stereotaxic injections to some mice brain nuclei. Due to the various choices (in particular the G number) of Hamilton needles, I was wondering which one would be the best for my surgery.
If available, may I also have the "cat no" please? (I am thinking of purchasing one)
Thank you very much in advance once again!
I am injecting a virus (AAV9.Syn.GCaMP6s.WPRE.SV40) to express GCaMP6s in the mouse hippocampus. I am using young animals (around P20), and as most of the atlases I know base their stereotaxic coordinates in P56 animals, I cannot use them, so I'm injecting with no coordinates.
So, the first question would be: is there any atlas for young animals that I can use to inject more precisely? I haven't been able to find any so far.
Even though I am using no coordinates, I'm not having problems to hit the hippocampus. However, I almost exclusively see expression in the DG. Is this something common? Discussing this with colleagues, we came to the conclusion that even though the virus infects non-diving cells, it might be more effective infecting dividing cells, and in that case that would explain why the granule cells are more effectively expressing the protein. Does this make sense to you?
My last question (sorry this is getting so long) is regarding two-photon microscopy. I am trying different wavelengths for imaging the GCaMP (I know 920 nm is the optimal, but this is part of my experiment) and I think the shapes of the cells look different when I image them at different wavelengths. I don't really understand why this could happen. Does any one know anything about this?
Needless to say, I will be really grateful for any opinion or information regarding any of the points. Thank you for taking the time for reading the post. I hope to be able to help you in the future.
Are there any articles published about cerebral dominance in rodents (rats) and histological changes based on the cerebral dominance?
I am planning to do a stereotaxic injection to the medial forebrain bundle (MFB) of mice. I have tried AP:-1.2; ML:-1.1; DV:-5.0mm, but this does not seem to work.
I was wondering whether there is any preferences from anyone please?
Thank you very much in advance!
I have a question regarding the use of control as follows:
Although it is quite usual to setup 2 groups of animals (one for experiment, and the other for control), there is some paper/studies comparing between the 2 brain hemispheres (i.e. using one side of the brain as the experimental group while the contra-lateral side used as a control).
I was wondering what would be the advantages of using the other hemisphere as the control? Wouldn't the differences between 2 hemispheres (e.g. the functional differences between 2 brain hemispheres in human) make this control invalid?
If there is a choice between using individual or contra-lateral hemisphere as the control (while the study is not mainly comparing the differences between the cerebral hemispheres), then which way would be the preferred choice?
As M1 and M2 lie very close to each other, if I am going to do an implant to gather signals from only M1 neurons, is there any established way for me to locate accurately the M1 or M2?
The anatomical location of M1 and M2 can be referenced by the following:
Thank you very much in advance!
I'm looking for anatomical changes in parietal and occipital cortices in patients with MDD, but there isn't a lot of literature about it.
It is said that dendritic spines can naturally occur among primary mouse neurons and their density or morphology can be thoroughly assayed. So can anybody provide any information?
At the moment we want to evaluate effect of some chemicals at synaptic level, but we wonder how valid such effect on cultured spines is, given that synapses need extra modulation in vivo.
Thanks a lot if you could help!
I am performing patch-clamp recordings of cells from red nucleus in slice preparations. I tried both horizontal and coronal slices but I still encounter troubles with optical visualization. I can barely see cells since the huge amount of fibers passing through the red nucleus. The thickness of slices is 200-250 um. Do you have any suggestions to get a better visualization of cells?
How does brain sense teh temperature through scalp? Any ruote map?
From skin, we have fibres running from skin through spinal cord and to brain reaching somatosensory cortex. Is it same when first event occurs at scalp and not skin?
We are writing up on discussions for a paper. I was quite unsuccessful to find the actual sizes of these neurons (range). Can anyone with significant expertise suggest what the sizes are of these cell types on average. Even a ratio would be okay eg, cortical are x-times smaller than dopamine.... etc.,
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.
I just posted this in the CLARITY resource center forum, but posting it here too. We found this hydrogel perfused/embedded right hemisphere of a rat cortex to be nearly completely clear after sitting in clearing solution in 37 degree incubator for ~5 weeks completely unattended. Next to zero tissue damage and it looks by far better than any brain that we have run through our ETC chamber. Has anyone else seen this?
CHALLENGE to my Neuroscience, Neurophysiology, Neuroanatomy, Neuroengineering friends: I am looking for some papers that quantify the spinal subarachnoid space geometry in primates using MRI or other methods? Any suggestions? I can't find a single paper with information on this on google scholar or Pubmed after quite some time searching.