neuroscience - How does Golgi's neural histological stain work?

Some background information.

First of all one should notice, that Golgi staining belongs to so-called morphological types of stainings in neuroscience, where the actual anatomy of different neurons is revealed (compared to other techniques, like Ca-imaging or potential imaging).

Second, Golgi staining is a type of silver staining, there the sedimentation of silver or its salts (here: silver chromate) reveals the morphological traits of the cels.

And, third, Golgi staining is applied to fixed preparation. This means that the tissue (normally a brain slice) is pre-treated (here: with formol) to kill all cells and arrest every biological process.

What is known about the targets.

The common description of the target is quoted as "a limited number of cells at random in their entirety". This is the essence of Golgi staining:

1. Only single cells are stained, therefore there is no impediment from adjacent cell staining while deriving the morphological structure of the cells (very important for light microscopy where you have integrated input from different depths).




2. The cells are stained randomly, there is no known preference among neuronal cells for Golgi staining and I haven't seen any other types of cells in CNS stained with Golgi, therefore it is quite specific for neuronal cells (and leaving macro- and microglia, astrocytes etc. intact).




3. The cells are stained in their entirety, meaning that the complete cell is stained very nicely, showing detailed arborisation of dendritic tree, that was very important in studying of Purkinje cells in cerebellum.

Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?

Golgi staining is used mostly for brain slices (I have never seen or heard its application for other tissues). Traditionally one of the biggest cells here are pyramid neurons (NA, ACh-ergic) and one of the smallest are interneurons (often GABA-ergic) -- both are amenable to Golgi staining (reference) and there is no seemingly clusterization of stained cells by their size or transmitter type.

What is preventing us from using the advanced molecular biology techniques to understand the process?

I can name several reasons for this:

1. Since Golgi staining is applied to fixed preparation the tissue is already "damaged" (formol leads to dessication of cells and shrumping), therefore it is difficult to use some fine mollecular biology methods to investigate these tissues.




2. There is no way to tell which cells get stained beforehand. And as long as the microcrystallisation of silver chromate is started it can't be (easily) stopped and reversed. Therefore it is difficult to look at what caused the staining afterwards, then the whole cell is impregnated with silver.




3. I think there were no real attempts to crack the mistery of this staining: how intersting it might be, this seems to be an interdisciplinary question on the brink between biology and chemistry. So, maybe one day somebody will look into it and explain everything.

neuroscience - Carrying or packaging capacity of SAD B19 dG rabies virus

I'm wondering about the carrying capacity also referred to packaging capacity or loading capacity (how many base pairs can be packed efficiently into virions) of the pseudotyped rabies virus SAD-dG as described in the Wickersham, Callaway publications.

Wickersham, I. R., Finke, S., Conzelmann, K.-K., & Callaway, E. M.
(2006). Retrograde neuronal tracing with a deletion-mutant rabies
virus. Nature methods, 4(1), 47–49. doi:10.1038/nmeth999

Wickersham, I. R., Lyon, D. C., Barnard, R. J. O., Mori, T., Finke,
S., Conzelmann, K.-K., et al. (2007). Monosynaptic Restriction of
Transsynaptic Tracing from Single, Genetically Targeted Neurons.
Neuron, 53(5), 639–647. doi:10.1016/j.neuron.2007.01.033

pharmacology - Why is methylcellulose used in pharmaceuticals?

It is a filler/binding agent. Thus MC belongs in the context of a drug to the group of so called excipients. The study of the best suitable excipients (as a tradeoff of factors such as cost, and ease of approving the drug) is called
galenics.

Methyl cellulose is also present in your toothpaste and some of the foods your eat and in the construction industry. It can be considered to be metabolically inert for humans, but can serve as a matrix for enhancing bacterial adhesion and biofilm formation.

The gradual smudging and staining of your bathroom washbowl may be largely attributable to MC and bacteria.

MC is a polymer that is sold as dry powder of various mean chain lengths. It is hydrophilic and can retain large volumes of water.

biochemistry - Hydrophilicity and polarity

I think the answer is no.

The definition of polarity is basically that a molecule has a dipole, and as water has a very large dipole, if a molecule will mix with water readily, its usually pretty polar.

Water also can share its hydrogens in hydrogen bonding, which is an actual shared covalent bond where a hydrogen atom is shared between two acceptors. The hydrogen bond is fairly weak (~ 0.5 kcal/mol) but water does a lot of hydrogen bonding.

So hydrogen bonding and polarity are often a shared characteristic of an molecule, but are not the same thing.

Ions are quite hydrophilic but do not need to be hydrogen bond donors or acceptors. Chloride (Cl - ) is not a hydrogen bonding atom - its so acidic that it exists nearly entirely in the Cl- form in water solution. But its definitely electro negative and really soluable in water. Are Ions polar though? Chloride is symmetrical and so its not really polar.

Still is there a polar molecule which is neither a hydrogen bond donor or acceptor? Acetone and the cyanide ion (CN-) are a polar molecules which have no hydrogen bond donor, but can accept them.

I think sulfate is an example of a polar molecule which does not form hydrogen bonds.
Sulfate (SO4 -- ) has four S-O bonds arranged in a tetrahedron but each of them is highly polar - with 90% of the negative charge on the oxygen. But like the Chloride ion its so acidic that it much prefers its free ionic state. It would have very little hydrogen bonding character even when its in water. Sulfate can form hydrogen bonds, but I think they will only be stable when there are several of them at once. Sulfate binding protein has seven hydrogen bonds when it binds sulfate, using the chelation effect to make the binding strong enough to be stable.

genetics - What phenotypes can arise from gender-related aneuploidy?

Note that anyone with a Y chromosome is considered a genetic male. Also, aneuploidy is usually a result of nondisjunction (but can have other causes as well) and is usually not inherited.

1. 47,XXX is called Triple X syndrome and occurs in approximately 1 in 1,000 female births. These individuals usually appear normal, but may have tall stature, a small head, and delayed development. According to this case report, the tall stature is possibly due to SHOX gene triplication, in some cases. The short stature homeobox gene (SHOX) gene is a gene on the X and Y chromosome and is associated with short stature if a copy of the gene is missing or mutated. The case report states, "The enhancing effect of SHOX gene triplication on growth was ascribed to the concomitant absence of gonadal steroids in cases of gonadal dysgenesis, allowing a prolonged period of growth."




2. 47,XXY is called Klinefelter's syndrome. Here is an image/diagram of symptoms. These people may have gynecomastia (enlarged breasts), less muscle, less body hair, and hypogonadism (decreased testicular function, also resulting in smaller testicles and penis) due to lower testosterone production. These symptoms become more obvious after puberty, because individuals with Klinefelter's have less "masculinization" (for lack of a better word). Cognitive problems are usually present. It occurs in roughly 1 in 500 to 1 in 1,000 male births.




3. 47,XYY is XYY syndrome and has an incidence of 1 in 1,000 male births. They appear normal but may be slightly taller than average. This study looked at the cognitive and motor phenotypes of boys with Klinefelter's and XYY syndromes. It found that both groups have generalized cognitive impairment, but XYY has more profound language impairment and Klinefelter's has more significant motor impairment. Their hypothesis is that "the more severe language-based cognitive phenotype in XYY versus KS is likely to be genetically determined on the basis of abnormal dosage of specific Y chromosome genes, but not abnormal levels of testosterone because XYY is not associated with testicular failure."

There's also 45, X0 (Turner syndrome), in which girls have a webbed neck, broad chest, low-set ears, short stature, gonadal dysfunction, and often other conditions such as a bicuspid aortic valve, coarctation of the aorta, and vision problems. Image of symptoms. It occurs in 1 in 2,000 live births. Individuals usually have 1 X chromosome, but may also have 2 X chromosomes, with 1 of them being incomplete (source). The single copy of the SHOX gene (mentioned above) has been linked to the short stature in Turner syndrome.

Interestingly, people with 47,XYY and 47,XXX people often have normal fertility, but not in the other two cases. My uneducated guess is that the extra "normal" chromosome (for the person's sex) doesn't disrupt gonadal function.

human biology - Ammonia smell after physical exercise? What is the explanation?

There are two explanations which come to mind answering your question:

I asked if you eat a lot of protein, because the amount of protein which some body builders consume leads to renal failure. And one sign of renal failure is the smell of ammonia. It's a quite common problem. But I don't think this applies to you. Your protein intake shouldn't exceed 2g per kg of body weight per day, some body builder eat up 4g per kg.

Ammonia is normally linked to your protein metabolism, which is higher during and after sport. The smell of Ammonia can occur when your carbohydrate reservoir is depleted and the body is mainly using protein as fuel. This effect also occurs when fasting or in patients with diabetes.

Try to keep your blood sugar level raised during exercise by eating something, like a banana, powerbars (also known as high energy bar) or directly dextrose. Or eat more long-chain carbohydrates. And this always depending the form of sport you are practicing. Just like the pasta party prior to marathons.

evolution - How to get smallest subtree containing a set of nodes from BioPhylo?

I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and efficient in dendropy and ete2:

newick = '((raccoon, bear),((sea_lion,seal),((monkey,cat), weasel)),dog);'
taxa = ['raccoon', 'sea_lion']

import ete2
tree = ete2.Tree(newick)
pruned = tree.prune(taxa)

import dendropy
tree = dendropy.Tree.get_from_string(newick, 'newick')
pruned = tree.prune_taxa_with_labels(taxa)

I'm trying but failing to find equivalent functionality in the Bio.Phylo package. Trees do have a "prune" method, but it prunes a single node from the tree.