text:
Same target receptor different mechanism of action?
If different drugs have the same receptor as a target, does that imply that they have the same mechanism of action?

Not necessarily!
Biased agonism
It's reasonable to start with an expectation that agonists at the same receptor have the same effect, but that's not necessarily true due to biased agonism. Biased agonism occurs when binding of different agonists to the same receptor results in different downstream activation of second-messenger systems.
Psychedelics and serotonin receptors
A particular example I am familiar with (besides the Jarpe paper) involves the 5HT2a serotonin receptor. This receptor is a shared molecular target of several psychedelic drugs: LSD, psilocybin/psilocin, DMT and others. However, this receptor exhibits biased agonism (Berg et al 1998).
In fact, it seems like agonists at the 5HT2a receptor neatly segregate into those with psychedelic effects (eg: LSD/psilocybin) and without (eg: lisuride/ergotamine, also serotonin itself) based on the different downstream molecular signalling pathways that they trigger, despite binding to the same general site on the same receptor.
Other considerations
Drugs' mechanisms of action can also depend on concentration and on all the other possible targets for those drugs. Pharmaceuticals are often small molecule drugs and while they may have preference for certain receptors, they are rarely (probably never) purely specific.
For example, the NSAID class of anti-inflammatories all work through inhibition of cyclooxygenase enzymes, but they differ in their relative specificity for COX-1 and COX-2. If you are looking at two drugs that have the same effect on COX-2, but don't compare their effects at COX-1, you might be surprised to find they have different results.
For another class, SSRIs used as antidepressants also have effects on other monoamine transporters (dopamine and norepinephrine) but vary in how specific they are.

Berg, K. A., Maayani, S., Goldfarb, J., Scaramellini, C., Leff, P., & Clarke, W. P. (1998). Effector pathway-dependent relative efficacy at serotonin type 2A and 2C receptors: evidence for agonist-directed trafficking of receptor stimulus. Molecular pharmacology, 54(1), 94-104.
González-Maeso, J., Weisstaub, N. V., Zhou, M., Chan, P., Ivic, L., Ang, R., ... & Sealfon, S. C. (2007). Hallucinogens recruit specific cortical 5-HT2A receptor-mediated signaling pathways to affect behavior. Neuron, 53(3), 439-452.
Jarpe, M. B., Knall, C., Mitchell, F. M., Buhl, A. M., Duzic, E., & Johnson, G. L. (1998). [D-Arg1, D-Phe5, D-Trp7, 9, Leu11] Substance P acts as a biased agonist toward neuropeptide and chemokine receptors. Journal of Biological Chemistry, 273(5), 3097-3104.

Thanks for this enlightening answer.


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Why didn't the human Cerebrum evolve to have granule cells like the Cerebellum does?
The Cerebellum is much smaller compared to the Cerebrum yet it contains more than half of the total neurons contained in the brain.
That's mainly due to the granule cells in the Cerebellum which allows it become so densely packed with neurons.
But why is the Cerebrum not like that? Why isn't it as "compressed" as the Cerebellum? Doesn't it make sense for it to be more smaller and compact?

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

By "cerebrum" I assume you really mean the cerebral neocortex, since the cerebrum includes other subcortical structures that themselves are quite distinct (e.g., the basal ganglia).
Simply, the neocortex and cerebellum have completely different functions. The cerebellum performs a particular class of computations that are very different from the variety of computations performed by the cerebral cortex. They have completely different laminar structures, with neocortex being a ~6-layer structure, the cerebellum has just 2-3. There are a much higher diversity of connections and cell types in neocortex compared to cerebellum.
It seems like an optimal configuration for the cerebellum is a very high cell density. More cells doesn't necessarily mean "better", because the more cells you have the less space you have for connections. There is no unused or empty space in the neocortex: if you packed in some more cells you'd have to lose something else.

Doya, K. (1999). What are the computations of the cerebellum, the basal ganglia and the cerebral cortex?. Neural networks, 12(7-8), 961-974.

My bad, I didn't think about how important the individual connections were. Thanks for the answer!

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what happens to rna length if we have a termination site in additional to the original one
if we have an RNA transcription and we add an additonal temination site in  the middle , will i have two RNA molecules or just a short one ?

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

Assuming that by termination signal you mean transcription termination signal (and not a stop codon), you would have one shorter RNA molecule. You can have two shorter RNA molecules if there is another transcription start site after the termination signal, but there is no reason to assume this will be the case.
In some cases the RNA polymerase will skip a base and frameshift while transcribing a new RNA strand. This is known as transcriptional slippage, and it is taken advantage of by some viruses in order to make their genomes more compact by having several different mRNAs overlap each other.
In this rare case, having a termination signal does not necessarily mean transcription will terminate, it might be able to skip through parts of the termination signal and continue to the next termination site.

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How to approach identifying Melampsora species?
I'd like to figure out which species of Melampsora that is growing on this European aspen. What would be the right approach? Would a microscope or other tool help? Is there even more than a single species that attacks aspen?
These photos were taken of an aspen leaf in Stockholm.


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Exclusion and inclusion criteria for healthy controls in colorectal cancer study
I'm working on colorectal cancer, and I'm facing a problem in the sampling step, I can't figure out how to choose healthy subjects. In the literature, I've found many criteria that are different and sometimes not clear or the author don't mention how he chooses his control samples.
PS: I'll collect stool samples, not tissues.

Welcome to the world of poorly designed studies. Not saying yours is or will be, just  saying the confusion you feel isn't unwarranted. I wish I could offer you a solution.

https://medicalsciences.stackexchange.com

Providing more details (e.g. what you are going to study, how you are planning to do it, how others have done it) would invite good answers to this question. Also I agree with @anongoodnurse: selecting controls for a case-control study can be challenging. (There is a nice section on this in a textbook called  'Gordis Epidemiology', that might help. https://books.google.co.in/books?id=Xwl0DwAAQBAJ)


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What does Δcys mean after a gene name?
I am reading a paper and I have come across the following statement:

"Plasmids encoding full-length NCAM140 and NCAM140Δcys, intracellular
domain of NCAM140, and the NCAM140ID729–750 fragment were as
described".

I know that NCAM140 is an isoform of the NCAM protein with a molecular weight of 140kDa. However, I am not sure what Δcys means in NCAM140Δcys. Any insights are appreciated.

When describing mutations, $\Delta$ usually stands for deleted sequences. In this case it means the exchange of 4 cysteine residues in the NCAM protein by serines to disable palmitoylation and the association of the protein to lipid rafts. If you search for this specific mutation, you will find the paper from Niethammer et al., 2003, which describes the mutation. Figure 2a (below) shows a schematic view of the locus and is described as following in the caption:

Mutation of NCAM140 palmitoylation sites abolishes NCAM140 raft association.
(A) Schematic diagram of the structure of NCAM140 and
NCAM140Δ. The plasma membrane is indicated by the pair of vertical
lines. The semicircles represent the five Ig-like domains. The two
fibronectin type III–like domains are shown as black boxes. The
expanded segment shows the NH2-terminal sequence of the cytoplasmic
domain and the four cysteines that were mutated to serines in the
NCAM140Δ construct to remove all sites for palmitoylation.


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What does ΔC and ΔN mean with regards to a protein sequence?
I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement:

Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the
amino-terminal half of Frat (ΔC Frat) localized predominantly to the
cytoplasm of transfected MDCK cells (Fig. 1, A and B, i and iii).
Unexpectedly, the carboxyl-terminal half of Frat (ΔN Frat) accumulated
preferentially in the nuclei of transfected cells (Fig. 1B, iv).

I am not sure why the amino-terminal and carboxyl-terminal half of the Frat protein are referred to as ΔC Frat and ΔN Frat respectively. I know that the amino terminus of a protein is also referred to as the N-terminus, whilst the carboxyl terminus of a protein is referred to as the C-terminus. I am not sure why in this paper ΔC and ΔN are used to refer to the amino-terminal and carboxyl-terminal half of the Frat protein.
Any insights are appreciated.

This is just a simple technical abbreviation. Δ is used to mean deletion, so ΔC is used for the N-terminal fragment  as the C-terminal part has been deleted. One shouldn’t write answers in comments, but this doesn’t need any more.

The Frat/GBP (frequently rearranged in T-cell lymphomas/GSK-3-binding protein) protein is a proto-oncogene that regulates the Wnt signalling pathway. (van Amerongen et al., 2004)
The cited paper (Franca-Koh, 2002) noted a correlation between some forms of Frat and GSK3 cellular localization. Without Frat, GSK3 is cytoplasmic. In the presence of Frat, the heterodimer Frat-GSK3 translocates to the nucleus. As Frat is phosphorylated, it was unclear then what mechanism(s) was(were) involved. To investigate the role of Frat, the authors hypothesized that a region of Frat may be involved, not necessarily the whole protein.
They engineered deletion constructs and added an N-terminal FLAG tag for easy affinity purification. They used the symbol delta (Δ) for deletion. The N-terminal region of residues 1 – 129 encompassing Domain 1, i.e. deletion of the C-terminal region is called ΔC; likewise, the C-terminal region of residues 129-274 encompassing Domain 2, i.e. deletion of the N-terminus is called ΔN. They also engineered a green fluorescent protein (GFP) tag fusion protein variant. Here are their constructs as illustrated on Figure 1 of their paper:

Human ortholog
I aligned the residue sequence of the murine Frat with the human orthologs: it has 79% identity to human Frat1 and 68% identity to human Frat2. mFrat residues 1 – 129 (ΔC) and 129 – 274 (ΔN) correspond to hFrat1 residues 1 – 132 and 132 – 279, respectively.
Added Note
Here is a co-crystal structure of GSK3β (N-terminal lobe in orange and C-terminal lobe in cyan) complexed with Frat1 peptide 197-226 (forest green) and an inhibitor (N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide) (green) as deposited with RCSB as entry 5OY4.pdb . The presence of the inhibitor helps locate the active site in the image of the GSK3b protein kinase.

References
Franca-Koh, J., Yeo, M., Fraser, E., Young, N. and Dale, T.C. (2002) J. Biol. Chem. 277:43844-43848.
Van Amerongen, R., van der Gulfen, H., Bleeker, F., Jonkers, J. and Berns, A. (2004) J. Biol. Chem. 279:26967-26974.


text:
How can I list genes present on a given series of bands?
My question is related to this one. My interest relate to this deletion:

del(7)(q11q36)[12]

as defined by ISCN.
I would like to access a list of the genes found on the bands 11 to 36 of the 7th chromosome in humans. How can I do that?

There's a brief tutorial here on how to search by band. Here is a more extensive help document, and here is a human-specific help page, Basically:

Select the species and annotation release. We're Homo sapiens, by the way...
Select the chromosome you are interested in.
On the left side of the page, it says Region Shown: followed by two input boxes. You can search by band using standard cytogenetic nomenclature: 7q11 and 7q36. Enter these into the input fields and click Go. Here is 7q11:7q36.
There are various links to download data. Perhaps most relevant to you, there is a link on the left of the page which says Data As Table View. Here is said page, a list of genes at various levels of characterization.

Here is a table of different search queries you can use. There are a couple of ways to analyze the data:
Interactive Genome Browser:

Click on Genome Browser.
In the search field, enter the cytogenetic coordinates: 7q11;7q36. Press Go. Here is the resulting page.

Table Browser (for downloading data):

Click on Tools > Table Browser.
There are a lot of options. A tutorial can be found here. Most important for your search is region. Select the position radio button and enter your cytogenetic coordinates. I'll leave the rest of the options to you.

Nice answer! I like you offered directly the small tutorial and not only links to explainations. I also like you used the slogan for each data collection. Thanks

@Remi.b You're welcome, hope you find what you're after.

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text:
Why are nutrients from food absorbed more efficiently?
It seems to be common knowledge that micronutrients such as vitamins are more easily absorbed by your body when in your diet versus supplements such as pills.
I am wondering what the reasons for this are.

Does this answer your question? Is there evidence to suggest that nutrients in vitamin capsules are not as readily absorbed as the same nutrients in whole foods?

Welcome to Biology.SE! Note that "common knowledge" is often unreliable and this sort of claim should be referenced. We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For example, the "Related" links on your post include a very similar question on this site.  ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

magnesium in veg and bananas is in molecules like Chlorophyll, which is better to eat than: Magnesium chloride. ...
Magnesium sulfate.
Magnesium citrate.
Magnesium oxide. There are billions of micro-nutrients from many elements. When the source is already, previously metabolized by another organism, the nutrients probably exist in a less concentrated matrix and in less strongly bonded organic forms than synthetic lab-nutrients. Laboratory and rock-sourced nutrients are often more concentrated and have not previously been metabolized, in molecules like globin and chlorophyll.


text:
Assembly of polypeptides expressed from different chromosomes to make a fully functional protein
In case of human beings, the whole genome is divided in 23 pairs of chromosomes in somatic cells. It has been observed that in case of many proteins (e.g. immunoglobulins, hemoglobin) different polypeptides are assembled together which are expressed from different chromosomes. My question is- what guides them to assemble them for the making of a fully functional protein??

They have complimentary interfaces on their surfaces and it is energetically favourable for them to stay together once they have found each other by Brownian motion. Often they are highly unstable alone. So it is simply thermodynamics and a decrease in Gibbs free energy.
This happens across life. Enzyme complexes in bacteria are on the same operon, especially in thermophiles, because they come together at a faster speed. In Eukaryotes it makes no difference as the mRNA needs to be processed etc.


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Which sample type is more proper for whole genome sequencing in AML patients? Peripheral blood or bone marrow?
I intend to perform whole genome sequencing in AML patients in order to find genomic abnormalities, particularly translocation and gene fusions. However, I am not sure whether it is better to obtain peripheral blood or bone marrow or if there is no significant preference between them.
Please, provide me with scientific resources to refer to.
Thank you in advance.

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). You also need to specify why you are doing this and what you mean by "proper". I would also guess that this is going to depend on many factors including what is already known about the patients and the resources available. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

In particular, note that bone marrow biopsies are painful and carry a non-trivial risk of infection (and other negative outcomes) for the patient. Consequently, I double any responsible institution is going to let you get that kind of sample unless you can come up with a compelling reason for doing so (from the perspective of the patients).

Thank you immensely for taking your time and guidance. Regards


text:
Where do the Ca ions that causes neurotransmitter release from synaptic bouton, come from?
I hope the information you share will help clarify the following doubts and gaps in my knowledge:

Where do the Calcium ions in the influx (which then triggers the neurotransmitter vesicles) come from?
Are they traveling all the way from the ER of the neuron in the soma?
Are they stored locally within the neuron somewhere around the synaptic bouton?
Are they coming from outside the neuron cell?

And if you have some extra knowledge to dish out then:

Is it channels or pumps that cause this influx of calcium ions?
If these are channels then are they ligand-gated, voltage-gated or made more permeable via some other mechanism?

Thank you for reading :)

Short answer
Neurotransmitter release is triggered by an influx of calcium ions from the extracellular space into the cytosol through voltage-gated calcium channels in the plasma membrane.
Long answer
Typical synaptic vesicle release is triggered by calcium influx through T-type calcium channels. These are voltage-sensitive channels in the plasma membrane; calcium flows through these channels from the extracellular space and is bound by synaptotagmin, a type/family of proteins associated with the vesicle fusion machinery (the SNAP/SNARE complex) to trigger (or, more precisely, to increase probability of) vesicle release.
Like just about every important class of proteins, these channels can be regulated by various mechanisms: gene expression, trafficking/colocalization, subunit composition, phosphorylation, etc. See the Iftinca & Zamponi review.
Calcium from internal stores, released by various mechanisms (calcium-induced, IP3-induced, can also be important to neuron plasticity and homeostasis but does not need to travel from the soma (ER extends throughout the cell). In some special cases, these internal calcium stores can be involved in release (see for example Babai et al 2010), but this example is from in photoreceptors in the retina which use a different release mechanism than typical neurons (they don't fire spikes, they have graded potentials and graded release probability, etc). Internal stores can also influence spontaneous release probability and may modulate release probability (see for example the review by Collin et al) but are not the primary "trigger" for release.
For more on the basic synaptic machinery, I'd recommend any edition (though of course recent is always best) of the textbook "Neuroscience" by Purves and coauthors.

Babai, N., Morgans, C. W., & Thoreson, W. B. (2010). Calcium-induced calcium release contributes to synaptic release from mouse rod photoreceptors. Neuroscience, 165(4), 1447-1456.
Collin, T., Marty, A., & Llano, I. (2005). Presynaptic calcium stores and synaptic transmission. Current opinion in neurobiology, 15(3), 275-281.
Iftinca, M. C., & Zamponi, G. W. (2009). Regulation of neuronal T-type calcium channels. Trends in pharmacological sciences, 30(1), 32-40.
Dale Purves, George J. Augustine, David Fitzpatrick, William C. Hall, Anthony-Samuel LaMantia, Richard D. Mooney, Michael L. Platt, Leonard E. White. (eds) (2018). Neuroscience. New York: Oxford University Press.

I can't thank you enough ... thank you! I had been using the molecular biology of the cell 6th edition by alberts and coauthors but I'll look into investing in "Neuroscience" by Purves as well.

@pulkitsinghal Principles of Neural Science (Kandel) is another good textbook (the content will overlap a lot with Purves, so I'd recommend either/or rather than both).


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Why does the peak magnitude of the cardiac pacemaker action potential not increase to levels closer to the Ca++ equilibrium potential?
it does for K+ and Na+ but not calcium? why?

The equilibrium potential at any point in time is determined by the relative permeability of ions and the reversal potentials for those ions, according to the Goldman equation/GHK equation. The voltage of the cell moves towards that equilibrium potential at a rate that depends on the membrane time constant (determined by the capacitance and resistance/conductance of the membrane).
In a typical neuron, during the rising phase of an action potential, the conductance of sodium compared to other ions is very large, large enough that you can almost ignore the other ions, so the peak of the action potential gets fairly close to the sodium reversal potential. Often there is also permeability to calcium, which pushes it even closer to sodium reversal.
However, in cardiac pacemaker cells (and in cardiac myocytes), although there is a big increase in calcium permeability, the relative permeability to other ions isn't quite as big, so the "weighted average" of ion conductances and their reversal potentials gives an equilibrium potential somewhere in the middle.


text:
What is the consensus in the scientific community over COVID-19's mode of transmission?
I've read from many news and scientific sources that COVID spreads primarily through respiratory droplets, but I've also read multiple sources that have said we don't entirely know yet. Is it fomites, droplets, or aerosols? Is it some combination? Do we have a complete understanding of it?
With how infectious the B117 variant appears to be, it seems like it would spread through aerosols, since most other infectious diseases that are very contagious tend to spread through aerosols, like measles, tuberculosis and varicella. If that's the case, why do so many sources keep claiming that it's through droplets? I've also read an article on the Johns Hopkins website that suggested the scientific community was initially wrong about the mode of transmission for tuberculosis, so is that possible for COVID?
Thank you!

"I've read from many news and scientific sources that COVID spreads primarily through respiratory droplets, but I've also read multiple sources that have said we don't entirely know yet". Please can you try edit your question to include links to where you found those statements (ideally primary sources). It'll improve the question and any potential answers. Thanks.

The terminology really depends on the scientific field. You also have to be aware that sometimes terminology is simplified for the purposes of presenting information to the general public.
A droplet can really mean anything from a few micrometers up to several millimeters and it does not necessarily have to be spherical. The key point is that the virus may spread through droplets.
Aerosols typically refer to small solid particles or liquid droplets, maybe less than 20 micrometer in size, but again, it depends on the field.
In quiescent air, any heavy (more dense than air) particulates (solid or liquid) which are about 1 micrometer  or less will remain suspended in the air for several hours due to Brownian motion and also the fact that their gravitational settling velocity is small.


text:
Poisonous Snakes consuming poison (chemical)
While travelling with my Son to a religious shrine, we saw a dead snake lying on the road.
My Son asked a curious question to me "Dad, if Poisonous snakes consume poison (Chemical), Will they die"?
I feel the answer is depends upon the type of poisonous snake viz Cobra, Python etc and how much the reptile has consumed the poison. i.e. quantity.
What is the correct answer?

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

Does this answer your question? If a venomous snake somehow gets it's own venom in its body, will it be affected by it?

If any living thing consumes enough of a poison it will die. But I feel that is not what you want to ask.
Perhaps you meant to ask if a snake will die if it drinks its own venom? That would make more sense as a question.
In English, venom  and poison mean different things when talking about a toxic chemical produced by an animal.
Poison is a toxic chemical produced by an animal that is meant to be ingested/eat/drink.
Venom is a toxic chemical produced by an animal that is meant to be injected into the bloodstream.
So a snake bite has venom, but a colourful tree frog has poison on its skin.
Venom is typically not nearly as harmful if ingested, even if by a different animal, because it is meant to act directly in the bloodstream


text:
What can we expect when we culture a mould in a liquid?
I am currently running a short project in my school, where I am trying to look into the biodegradation of dyes from textile effluents using Fursarium sp. Most of the articles that I have read uses a spore suspension as the seed, because it is easy to quantify, and also perhaps reproducible. Well, I was thinking about how vegetative cells, may have different metabolic traits, so what can I expect are the results if I use the vegetative cells as the seed? Also, if I were to use the vegetative cells as the seed, is it considered semi-quantitative if the seed (vegetative cell) is retrieved on an agar plug of equal diameter?

I expect the vegetative cells (mycelia) to grow much faster


text:
Howthe body differentiate between foreign and native protein? How does it know when to create an immune response?
How the body differentiate between a foreign and a native protein?
Suppose there is a bacteria, it has lot's protein on its membrane, with specific structures. How does our body know it's the foreign protein? How does it know, the particular configuration is native or foreign?

Welcome to SE Biology. Please finish reading  the [tour] to find out about this site, and the Help on Asking Questions. You will see that you are expected to do some research before posting, and such research would make it clear that there are whole books written on this topic, and it certainly is not possible to explain it in less than a book chapter. Unfortunately that does not make your question suitable for this list. Any brief answer here is unlikely to be as useful as professionally written and illustrated resources.

Can you please suggest me any book? I am new to biology.


text:
Does gene isoform have different genetic location?
I would like to understand how a gene is assigned to a specific coordinate (e.g. NOC2L Chr1 879583(Start)   894679(End)). Next, let's say NOC2L gene has a few different isoforms, do those isoforms have different start and end site? What is the definition of start and end site of a gene?

You are asking several questions here, and on this site we can prefer to deal with one at a time for indexing purposes. One of your questions is the definition of the start and end of a gene. This question is easily answered in terms of the transcript, but more difficult if one considers enhancer sequences. I suggest you read about this. Your other question is about isoforms, which arise in two ways, either by gene duplication and divergence or differential splicing. Again these topics are well covered in the literature. As for assigning co-ordinates, that is just mapping.

The genes are defined by a reference genome - one that is considered the standard for comparison to. This reference is defined by which build of the genome you are comparing to, so there are different builds based off different assemblies of information. These are updated as new, more complete sequencing of the genomes (e.g. low complexity areas etc) are completed. At the moment for humans we are up to GRCh38 (Genome Reference Consortium, human build 38).
In general most gene positions won't change significantly between builds as these are fairly well defined - we can recognize promoter sequences, and the start condon (ATG) and stop codons (TAG, TGA or TAA) too. The sequence of the genes is largely conserved, so by comparing several sequences of the same area, we can see which bits are conserved within that sequence and thereby identify if it is a gene. We can also compare to sequenced cDNA (from mRNA) which is the transcribed form of the DNA and identify the sequence from that.
With respect to isoforms; it depends on the isoform, sometimes this form has a shorter or longer sequence, but often it is an altered (but same length) sequence that a proportion of the population carries. However, generally most of the sequence will be the same or very similar to the reference gene.

With all due respect for your attempt I must point out the weaknesses in this answer as someone upvoted it. I don't see that reference genomes have anything to do with this. People were looking at genes for different isoforms long before reference genomes. Also start and stop codons for translation are not relevant to the ends of the gene. And some isoforms result from gene duplication and divergence and others from differential splicing.

@david - The OP asked how the start and  end positions were defined on the chromosome, I simply gave the most parsimonious answer based on the likelihood that the OP has a bit of a limited understanding of the topic. AFAIK this is how it is done these days; no longer assigned relative to banding in a karyotyping exercise.

This answer does not mention the word "co-ordinate". Nor does it explain how the co-ordinates were defined in the chromosome, given that the ends are not sequenced. The title of the question suggests that the main concern of the poster is isoforms and asks about starts and ends. This answer does not address this.

Thanks a lot for all of these responses, I apologize for responding so late, and yes it's true that I have very limited understanding about this. I raise this question because, I have a data from NCBI that tells the position of each gene (like the example I've given in the post). However, I heard from my colleague that gene isoform can actually have different start and end position. Thus, I am wondering why NCBI just give us 1 fix position instead of giving us all the known isoform start and end position (if it's really different).


text:
Are there any organisms, extant or extinct, that have only one neuron?
Nervous systems are useful in one way because they allow for integration of complex information. They are also useful because they transmit information very rapidly, over a large distance.
However, that last function can be done without an actual nervous system; presumably, all you need is one cell. Some individual sensory neurons can transmit an impulse at 120 m/s, which in and of itself would be useful in many circumstances.
So, are there any species that have only one neuron? There may have been many one-neuron creatures in the early days of animal evolution, but it's also possible that nerve nets appeared together, as a unit. I also suppose there are some small multicellular organisms that have a single excitable cell, but it's up for debate whether we should call those "neurons" or not.

In evolution things don't just pop into existence. So, it's unlikely that a single neuron originated by itself. The question is, what would that neuron do? It would communicate to at least one other cell, right? Otherwise the transmitted signal would be lost and useless. And where is the signal coming from? Neurons generate signals either by receiving signals from other neurons or, for specialized sensory receptors, through some changes in the environment. The receiving cell could be a muscle cell, so your minimal network would consist of a sensory neuron and a muscle cell. Upon a detected change in the environment, the neuron would signal the muscle to contract.
In evolutionary basic organisms we can find action potential like excitability and synapse-like cell-cell contacts in non-neuronal cell types. This hints towards a step-wise development of these functions before actual neurons arose (wiki, paper). Even one-cell-organisms have neuron-like features (sensory input dependent polarization, intracellular signal propagation, coordinated movement). If cell-cell communication or excitability are not limited to neurons, what makes a neuron a neuron? This is also a matter of definition, as discussed in the paper mentioned above.
What makes neurons unique is their property to propagate signals in a network. That's why the neuronal nets of jellyfish are usually seen as the first appearance of neurons in the evolutionary tree. While organisms without a nervous system are able to respond to their environment by signal transmission between non-neuronal cells, I am not aware of any organism that possess only a single cell which we would now call a neuron. At the stage where neurons arose, animals were already a more complex arrangement of specialized cells for different functions. You would therefore assume, that also the neuronal predecessors were a group of cells within the organism.

Expanding on @Frieke's answer, evolution often adapts old functions for new processes. So, just as how membrane polarization is useful in unicellular organisms (Irazoqui and Lew, 2004) but can be exploited for neuronal depolarization, vesicular release also has unicellular prototypes (Oliveira et al., 2010) that preface eukaryotic neurotransmitter release. And, as (Bucher and Anderson, 2015) in Frieke's answer states, this vesicular release largely uses the same proteins and machinery in prokaryotes and neurons.
Another way that single celled organisms can be thought of like neurons is that, just as how a brain is formed of a network of neurons releasing neurotransmitters onto each other, prokaryotes too can ostensibly form neural networks with individual cells communicating with one another Wiki; (Cohen et al., 1999). Think of a soup of bacteria that receives and integrates information en masse.
But no, I think it would be misguided to say that a single celled organism could be called a neuron but that's not to say it can't have homologous functions and roles.


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Can light function as a neurotransmitter?
Any animal with an eye has photoreceptors, which are essentially light-sensitive neurons. Green algae have channelrhodopsin, which are ion channels that open and close in response to light. Clearly, the nervous system and its molecular components have evolved to use light effectively.
I'm wondering if light can act as a neurotransmitter in the classical sense; that is, the presynaptic cell releases a photon, which travels across the synaptic cleft and interacts with a receptor, depolarizing the postsynaptic cell. Light can be generated in vivo through chemiluminescence, and as with channelrhodopsin, different proteins can activate in response to different wavelengths or intensities. I suspect this would be much faster than traditional chemical signaling.

I'd be hesitant about using the term 'neurotransmitter' as it specifically refers to a chemical synthesised by the presynaptic neuron. But I see no reason why a neuron couldn't transfer electromagnetic radiation that is then picked up by another neuron (possibly via rhodopsin). Imo you could probably have a functioning signalling network with bioluminescent/light-sensitive cells but whether that actually occurs in nature, I'm not sure.

Hmmm i feel like a paper was just published about this. Let me go digging around to see if i can find it

I don't think there is a theoretical reason why this wouldn't be possible.  However, I think there might be some practical problems with a system that relied upon light signaling.
1) It would be susceptible to interference.  Many bio-luminescent organisms are transparent, so other sources of light could depolarize a post-synaptic cell.  Light also penetrates tissue in organisms that are not transparent.  Blue light can penetrate 2 mm of human tissue and higher wavelengths like red can more than double that.  I could see light acting to replace signal molecules in quorum sensing though.
2) Neurotransmitters aren't really much of a limiting factor in nervous system speed. A monosynaptic reflex travelling a short distance might take 30 milliseconds, but neurotransmitter transmission is only 1 of those milliseconds.  In more complicated neural pathways, the speed of neurotransmitters might only account for 1/100th of the time.  So, if we're just imagining time-saving nervous system improvement, fiber optic neurons are the way to go.

An emitted photon could go any direction, also go "inwards'. Indeed an optics would be needed.

Adding to the list of why it might be practically infeasible: it might be less energetically favourable for cells to create light than for them to keep using chemical transmitters. Also, it would require the ability of the organism to evolve a specialised way mechanism of bioluminescence, which might not confer any advantage to the organism.

There are four main criteria for identifying neurotransmitters, these are very strict for the definition of something as a neurotransmitter or not.

The chemical (in your case light) must be synthesized in the neuron or otherwise be present in it.
When the neuron is active, the chemical must be released and produce a response in some target.
The same response must be obtained when the chemical is experimentally placed on the target.
A mechanism must exist for removing the chemical from its site of activation after its work is done.

I'm currently not aware of light fulfilling these criteria so it cannot be cataloged as a neurotransmitter. This is the definition I found in wikipedia, but you'll also find it in any neuroscience textbook like Kandel or Purves

The markup you used is reserved for program code. I deleted it and replaced it with bullets. Can you add references?


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What is the physical reason that a weak muscle means that its antagonistic muscle will tighten?
I've read online (probably from these two sources Athlean-X and Mike) that when one has a tight muscle that the antagonistic muscle tightens up as a defense mechanism. What I am trying to understand is why the body does this. From my intuition it seems that tightening up just makes the tight muscle vulnerable to wanting to stretch it and snap it, so I can't imagine how tightening is a good idea biologically. Furthermore, even if I choose not to stretch it (which is the instinct) it doesn't inform me what the real issue is nor does it seem as a way to defend anything. Thus, how is tightening up defending anything? How does this (perhaps from an evolutionary perspective) make sense? Why does this happen?


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Blocking buffer for actin and fetuin-b in western blot
I have been working on western blots for about a month now using actin and fetuin-b primary antibodies to no avail. My background is always high and I only had one good result. I want to know if there is a certain blocking buffer I should use instead of 5% milk with my membranes to get a better result.

There are commercial ones available (usually pretty expensive, but work ok), you could also use BSA for blocking instead.

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I have only used milk for blocking a couple of times but it was always beaten by bovine serum albumin (BSA), casein, or BSA/casein.
My standard blocking buffer is 1 - 5% BSA in tris-buffered saline with 0.1% tween20. I have also used the Western Breeze kits from Invitrogen and in my hands their blocks and alkaline phosphatase detection reagents were very reliable. The preservatives that they include in the stock reagents also allow the block to be reused for up to a week if handled and stored appropriately; keep everything clean, use up to 4 times, and store @ 4 degrees when not in use.
Some antibodies will require specific blocking buffers to perform well.
Background can come from many sources so if you have background with both primary antibodies you should check for other issues as well. Background is a very general term and can be caused by many things, a few I can think of are;

Overheating during transfer
Primary/secondary antibodies binding to the membrane.
Primary/secondary antibodies binding non-specifically to the proteins.
The interaction of detection reagents with buffer components (phosphate and alkaline phosphatase, tween)

When I was working with actin antibodies I used 2% horse serum in PBST to block and to incubate with antibodies. Or just washed membrane really good from 5% milk in TBST(like 5 times 5 minutes in TBST) because goat antibodies doesn't like milk. But I incubate with milk for 45 min-1h. You can also wash 3 times 5 minutes with TBST after secondary antibodies and then 2 times 5 minutes with TBS. It really helps.

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What is meant by the term synaptic targeting?
I am studying whether a protein interacts with the mitochondria in the synapses of neurons and I have come across the term "synaptic targeting". I am reading this paper and I have come across the following:

During synaptic development, proteins aggregate at specialized pre-
and postsynaptic structures. Mechanisms that mediate protein
clustering at these sites remain unknown. To investigate this process,
we analyzed synaptic targeting of a postsynaptic density protein,
PSD-95, by expressing green fluorescent protein– (GFP-) tagged PSD-95
in cultured hippocampal neurons.

I am not sure what exactly is meant by the term "synaptic targeting". I have tried Googling the definition but all I get are links to journal papers. I think that synaptic targeting refers to where in the synapse (e.g. presynaptic or postsynaptic ending) a protein is located, but I am not certain. Any insights are appreciated.

PSD-95 is a protein located in the post-synaptic region inside a cell. In fact it's named for this, "post synaptic density-95" referring to the dense appearance of the post synaptic area on an EM microscope and this protein's presence there.
"Synaptic targeting" in this context refers to how that protein gets to where it belongs (the synapse) in the cell, rather than just floating around in the cytoplasm by simple diffusion.


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What are the advantages of heterologous expression systems?
I am doing research in a lab and I am relatively new to wet lab work. Many experiments that people are doing in my lab include overexpressing a protein of interest from another species (e.g. mouse) into CHO cells via transfection. I have learnt that these are examples of heterologous expression systems.
I was wondering in general, what are the advantages of heterologous expression systems? I have read that you can use them to study the function of a protein in a well-defined, controllable environment. However, I was wondering what other benefits/uses are there to these kinds of experiments?
Any insights are appreciated.

To add on @ user47696’s answer, heterologous expression systems also enable large-scale production of recombinant proteins, particularly in the E. coli and the yeast systems. Foreign hosts may also provide a system that is simpler than the natural sources for the studies on proteins' functions.


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Is it necessary to calculate lane normalisation factor when doing western blot data analysis?
I have recently done my first western blot and I am doing data analysis to quantify my blot. I have labelled my membrane against inactive GSK3 and active GSK3 which are phosphoproteins so I am using total GSK3 as an internal loading control. I have read some guides and handbooks  about western blot data analysis and I have seen that some of them calculate a lane normalisation factor to account for variations in signal intensities of the loading control. For all loading control bands in each lane, they divide by the loading control band with highest intensity to get the lane normalisation factor. Then for each band of the target protein of interest they divide by the lane normalisation factor to get the normalised intensity.
I was wondering in general with western blots is it good practice to calculate the lane normalisation factor when doing the data analysis? Any insights are appreciated.

Generally speaking, the proper way to quantify a western blot is to normalize to a loading control such as Actin or GAPDH. In this case it would be (pGSK3/Actin)/(GSK3/Actin) as total GSK3 is not a loading control. A loading control is to protein that is accepted as unvarying in concentration across multiple samples if the same protein amoun is used, and to my knowledge GSK3 would show more biological variability than accepted loading controls. This would be considered the best practice to compare protein concentrations across samples.
That being said, if all you care about is the ratio of active to total, pGSK3/Total GSK3 is probably sufficient to assess if your manipulation changed active/inactive:total ratios. For example, in autophagy assays you can measure autophagic flux by measuring LC3-I to LC3-II, and I've never seen them normalized to a loading control since its a ratiometric readout contained within a single sample.


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In enhanced chemiluminescence in western blots, will the horseradish peroxidase eventually get used up?
I am learning about enhanced chemiluminescence in Western blots. I have read online that in enhanced chemiluminescence that horseradish peroxidase (HRP) catalyses the oxidation of luminol to 3-aminophthalate, with this reaction resulting in the emission of light. I am using HRP-conjugated secondary antibodies on my Western blots, and applying the ECL reagent to the membrane to detect the signal.
I was wondering, in this chemical reaction, if the ECL reagent is left on the membrane long enough, will eventually all the HRP get used up (especially if you reapply the ECL reagent to the membrane)?

I’m voting to close this because it is unclear what you mean by "used up": Consumed as a reactant? OR Are you asking about the stability of HRP over time? In either case this seems like something you can easily look up so in addition to being unclear it is under researched. Finally, from the way this is currently phrased it appears you mean the first of these possibilities, which seems like "homework" — i.e. "trivial to biology professionals".

The HRP is an enzyme so it isn't a component of the reaction. By definition, enzymes only catalyze reactions but aren't an actual component of the reaction. As such they don't get used up during the reaction and are able to continually catalyze molecules until they run out of luminol in this case. The only thing to be concerned about is the membrane drying out and denaturing the HRP.
An anecdotal story, but I remember an intern dropped an extremely diluted microliter (~1/200k) of HRP conjugate into a liter bottle of TMB (A liquid that turns blue after exposure to HRP) and the entire liter bottle turned deep blue overnight. So a tiny amount of enzyme definitely didn't get used up despite a massive molar excess.


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Can CRISPR also remove DNA viruses?
If I'm not mistaken only RNA viruses insert themselves into the host genome. As an example of DNA viruses, herpes viruses for example do not insert themselves in the host genome.
Can CRISPR cut DNA that isn't in a chromossome, like a DNA virus?

If my question makes some weird assumption, I'm sorry. I'm here to learn and the fact that I'm asking a question is precisely because I don't know all the facts.. Thanks for your answer already!

It can cut the DNA anywhere. Why do you think it should be a part of the genome? Read a bit about CRISPR; it was originally discovered as anti-viral defense system in bacteria.

By some definition of "remove". The answer below highlights papers that edited the (DNA) virus to make it less infective.

In eukaryotes only RNA viruses, in some prokaryotes DNA viruses can do it as well, they don't have the same barriers eukaryotes have. .

Yes, this should in principle work, and a number of groups have shows that it works in cultured cells:

We found that CRISPR/Cas9 introduced InDel mutations into exon 2 of the ICP0 gene profoundly reduced HSV-1 infectivity in permissive human cell culture models and protected permissive cells against HSV-1 infection.... Combined treatment of cells with CRISPR targeting ICP0 plus the immediate early viral proteins, ICP4 or ICP27, completely abrogated HSV-1 infection. We conclude that RNA-guided CRISPR/Cas9 can be used to develop a novel, specific and efficacious therapeutic and prophylactic platform for targeted viral genomic ablation to treat HSV-1 diseases.

--Inhibition of HSV-1 Replication by Gene Editing Strategy
There's also been at least one trial in an animal model:

Using a hydrodynamics-HBV persistence mouse model, we further demonstrated that this system could cleave the intrahepatic HBV genome-containing plasmid and facilitate its clearance in vivo, resulting in reduction of serum surface antigen levels. These data suggest that the CRISPR/Cas9 system could disrupt the HBV-expressing templates both in vitro and in vivo, indicating its potential in eradicating persistent HBV infection.

--The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo


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where to buy DNA sample kit? why isn't it easy to find online?
I guess you can say that it's a hobby of mine to research my ancestry and gather as much information from my family's history as I can. Being a student I can't afford to pay for mtDNA or Y DNA test of my relatives. For the first time I'll be doing it for myself fortunately :)
Now I came up with the idea of storing saliva samples of my oldest relatives just in case they pass away. I'm afraid that can happen at any time since they are getting very old. I guess it's a good plan for now. It still depends on how much a DNA sample kit costs. I'm not going to say any brand names here, but it'd be very nice if someone pointed me out where I can buy self-collecting saliva sample kits on the internet. I've found producers, but no online store.... I also wonder why this is the case.

yurihbss, you might get more of a genealogy perspective if you asked this on Genealogy & Family History SE

Most people using these tools for research and diagnosis have long-established connections and providers of industry standard tools. Most companies that provide these tools need a steady, reliable source of income, and historically demand for those tools comes from facilities such as hospitals and labs, not DIY biotechnologists (who typically can not afford the tools), so they focus on getting their products to the population demanding them most. There is budding interest in providing research and development tools to the general public such as this startup's stated goal:
http://www.the-odin.com/about-us/
But generally you have to go to a company's website, select the product you desire, and request a quote based on how many kits you'd like to order. The process isn't as easy or accessible for DIYers simply because the demand has not been great enough until recent technological advances such as CRISPR and DNA sequencing technologies made it cheap enough to run these tests on home equipment. It's similar to how not every computer geek could afford a CPU of a certain speed 20 years ago, but now CPU's of that speed are wide spread.
Salimetrics has some swab kits available for under 100 USD here
http://store.salimetrics.com/saliva-collection-methods/
Oragene offers saliva collection kits and this link details some storage options.
http://blog.dnagenotek.com/blogdnagenotekcom/bid/40944/Best-Practices-for-Long-term-Storage-of-Oragene-DNA-Samples
A list containing price per sample of oragene sample kits can be found here:
http://genomics.pitt.edu/pricing/price/HSCRF%20Genomics%20Research%20Core%20Price%20List.pdf
Some issues with collecting a saliva sample for DNA testing are neutralizing the enzymes and materials present that will degrade the DNA, and then isolating, storing, and testing the DNA. These techniques are usually used by trained professionals, once again highlighting the reason companies do not focus on selling to individuals, but to professional organizations.
An overview of the process of saliva collection and links to a few providers of the tools required to acquire your sample can be found here:
http://www.the-scientist.com/?articles.view/articleNo/43347/title/Tools-for-Drools/
This is a handbook detailing some tips on techniques used for collection and storage:
https://www.salimetrics.com/assets/documents/Saliva_Collection_Handbook.pdf
I am not affiliated with any of the companies mentioned above but if linking them is a no-no here on Stack Exchange the links will be removed and I will mention the companies only as examples. Hope this helps!


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Evolutionary advantages of wet nose of cats and dogs?
Everyone knows that some animals, at least cats and dogs, keep their noses wet and cool. But why did they evolve it? What evolutionary advantages does it provide? Smell-sensing cells need cooling for precision, may be? Or the liquid dissolves smellful gases into itself, simplifying analysis this way? Or may be it just simplifies cleaning the nose from the previous sniffing act?

there's a lot of information to be found with a quick google search - you're risking having the question closed due to poor research effort.

The OP is asking for an accurate answer, although his research seems little but he just put some intuitions. I don't think this would be down voted.

Why did it evolve ?

Mammals with rhinaria tend to have more acute olfaction, and the loss of the rhinarium in the haplorrhine primates is related to their decreased reliance on olfaction, being associated with other derived characteristics such as a reduced number of turbinates.
The rhinarium is very useful to animals with good sense of smell because it acts as a wind direction detector. The cold receptors in the skin respond to the place where evaporation is the highest. Thus the detection of a particular smell is associated with the direction it came from.
  The rhinarium is adapted for different purposes in different mammals according to ecological niche.
In aquatic mammals, development of lobes next to the nostrils allow them to be closed for diving. In mammals that root, the rhinarium often develops into a hard pad, with the nostrils off to the side. In the elephants it has become a tactile organ. In the walrus, it is covered with stiff bristles to protect it during foraging for shellfish. In many animals the form and purpose of the rhinarium remains to be elucidated.

Essentially it is the case of having a better sense of smell provided by the extended surface area, which has evolved to fit whatever the organism in question needs. I'll update this when I find this in a few more papers.
I took this from the wiki:
http://en.wikipedia.org/wiki/Rhinarium
How does it work ?

A model of the canine nasal airway, developed from a 3-D
  reconstruction of high-resolution magnetic resonance imaging (MRI)
  scans, was used to study the aerodynamics of canine olfaction.
  Simulation results reveal that a unique olfactory airflow pattern
  exists within the canine nasal cavity during sniffing that is critical
  for efficient olfaction.
Calculations show that this novel olfactory airflow pattern provides a
  crucial residence time for odorant absorption in the sensory region
  and promotes spatiotemporal fractionation of odorant mixtures along
  the olfactory epithelium.
The canine nose functions similar to a chromatograph that imposes
  odorant-specific deposition patterns upon the thin mucus layer
  covering the nasal cavity....The results show that deposition patterns
  are primarily influenced by the intricate olfactory flowfield and the
  odorant solubility in the mucus layer.
Highly-soluble odorants are quickly absorbed near the entrance to the
  olfactory region, and thus do not reach the periphery with significant
  concentrations. In contrast, insoluble odorants are deposited more
  evenly and may even exit the olfactory region without being completely
  absorbed. Predicted odorant deposition patterns correspond with the
  anatomical organization of olfactory receptors known to occur in
  keen-scented (macrosmatic) mammals, providing a mechanism that helps
  explain the excellent olfactory acuity of the dog.

In short the mucus on a dog's nose 'pre-sorts' smells by trapping the passage of some odour particles more than others along the nose, with different types of molecules being picked up at different "depths" in the nasal cavity.
You can read about it here:
Craven, Brent, Gary Settles, and Eric Paterson. "The Aerodynamics and Transport Phenomena of Canine Olfaction." APS Division of Fluid Dynamics Meeting Abstracts. Vol. 1. 2008.
Lawson, Michael, et al. "Odorant Transport and Deposition in the Canine Nasal Airways." APS Division of Fluid Dynamics Meeting Abstracts. Vol. 1. 2009.
Craven, Brent A. A fundamental study of the anatomy, aerodynamics, and transport phenomena of canine olfaction. ProQuest, 2008.

A downvote because it is a wiki copy-paste. You are perhaps rightfully making a lmgtfy point here, but you could at least add a personal concluding sentence that directly addresses the question. Please ping me as I am happy to retract downvote and/or upvote once edited

@AliceD sorted.

Great! Thanks. Now I could simply skip the wiki stuff and read your answer :)


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What is this worm like creature?
Recently while cleaning my garden, I saw this worm like creature which resembles a leech but is humongous in size if I compare that with commonly found leeches in my area, Kolkata, West Bengal, India. I did not see something like this before so, I captured a snap of this creature and posting it here to know more about it if someone can give me a hint.

Possible duplicate of Identifying a thin, black, worm-like creature with a hammer-shaped head

This question already has an answer here


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Evolution and Phenotypes.
This may be better suited for the English language SE, but When discussing evolutionary changes in species is it proper to refer to their phenotypes?
In this context:

"Imagine if a cow did not have to cart around however many gallons of
  culture nor expend personal time and effort into chewing its cud. It
  could lose all that anatomy and energy expenditure from its phenotype."

it could just be me, but it sounds strange using it in that context.

Yes, absolutely. That's what a phenotype is (definition from the biology online dictionary):

noun, plural: phenotypes
(1) The physical appearance or biochemical characteristic of an
  organism as a result of the interaction of its genotype and the
  environment.
(2) The expression of a particular trait, for example, skin color,
  height, behavior, etc., according to the individual’s genetic makeup
  and environment.

I don't see anything strange in the sentence you quoted. It is phenotypes that are selected for. Genotype differences that don't affect phenotype will have no selective advantage (or disadvantage) and cannot be acted upon by evolutionary forces. What else would you use when discussing evolutionary changes? That's what the word phenotype is for.


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Has anyone who has ever isolated synaptosomes using subcellular fractionation before know what the 'crude/heavy membrane fraction P2' is?
I am reading a journal paper where they analyse the proteome of synaptosomes. In this paper, they isolate synaptosomes from the hippocampi of mice. I know that synaptosomes contain the complete presynaptic terminal along with the postsynaptic membrane and post-synaptic density.
I am trying to understand the subcellular fractionation protocol they used for isolating the synaptosomes in the materials and methods section.
I know that synaptosomes are isolated from the subcellular fractionation of homogenised tissue. What I don't understand is what is meant by the 'crude membrane fraction P2'. I am wondering what exactly this crude membrane fraction P2 is because it is from this fraction that synaptosomes are isolated (via sucrose density gradient centrifugation).
I have read other papers where they also isolated synaptosomes. However in these papers they also mention that they homogenise brain tissue, and isolate the synaptosomes from the crude membrane fraction P2.
Any advice is appreciated.

The first google result I get for the search term "crude membrane fraction P2" is a paper from 2014 with the title Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient. It includes a step-by-step protocol; I'll post the most relevant steps here:

Low Speed Centrifugation to Remove the Nuclear Fraction (Yields Supernatant S1)

Centrifuge the homogenate in a fixed angle rotor at 900 x g for 10 min at 4 °C. Transfer the supernatant (S1) to a new, labeled 13 ml tube and resuspend the nuclear fraction pellet (P1) in 500 μl of 0.32 M HEPES-buffered sucrose. NOTE: The (P1) fraction can be stored at -80 °C and used for western blot analysis of the nuclear fraction.

Enrichment of the Crude Synaptosomal Fraction (Yields Pellet P2)

Centrifuge the supernatant (S1) at 10,000 x g for 15 min at 4 °C. Remove the supernatant (S2) and reserve 500 μl in a microcentrifuge tube to store at -80 °C for subsequent protein quantification and western blot analysis of the cytosolic/light membrane fraction. Resuspend the remaining crude synaptosomal fraction pellet (P2) in 1 ml of 0.32 M HEPES-buffered sucrose solution and then add another 3 ml of 0.32 M HEPES-buffered sucrose solution.
Centrifuge at 10,000 x g for 15 min at 4 °C. Remove the supernatant (S2’) and reserve 500 μl in a microcentrifuge tube to store at -80 °C for subsequent protein quantification and western blot analysis of the cytosolic/light membrane fraction. Save the washed crude synaptosomal pellet (P2’) in the polypropylene tube.

So S and P refer to the supernatant and pellet after centrifuging, respectively. P1 and S1 are from the first round of centrifugation; the pellet P1 contains the cell nucleus and the supernatant S1 goes on to the next steps. The second round of centrifuging gives P2 and S2. P2 contains the synaptosomes, but also other membranous material which will need to be removed as S3 in later steps.


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Why do neurons turn black in Golgi staining?
I am learning about the Golgi staining of neurons. I know that to this day it is unknown why some but not all neurons in a tissue get stained. I have read online that to harden the neural tissue, Golgi submersed samples for up to 45 days in a 2.5% potassium dichromate solution. He then soaked the samples in a 0.5-1% silver nitrate solution for different amounts of time to dye some of the cells black.
I have read a number of online sources about Golgi staining but none of them explain why neurons turn black. Is it a chemical reaction between potassium dichromate and silver nitrate that turns the neurons black?
Any insights are appreciated.

First result on google for these reactants: when a colorless solution of silver nitrate is mixed with a yellow-orange solution of potassium dichromate, a reddish precipitate of silver dichromate is produced. AgNO3(aq)+K2Cr2O7(aq)→Ag2Cr2O7(s)+KNO3(aq) The black is result of contrast between brightfield backlight and opaque precipitate.

The black/brown color is because silver chromate is in the cells.
As you say, the precise mechanism is unknown but this is more about why exactly silver preferentially precipitates within neurons by this procedure, and not other cell types, and also importantly why it does so so sparingly - the key to the Golgi method is that only a minority of all neurons actually get labeled, and get labeled very strongly. If all neurons and processes would be labeled, you would not be able to see any of the details in a single cell.
Pasternak, J. F., & Woolsey, T. A. (1975). On the “selectivity” of the Golgi‐Cox method. Journal of Comparative Neurology, 160(3), 307-312.
Scheibel, M. E., & Scheibel, A. B. (1978). The methods of Golgi. Neuroanatomical research techniques, 89-114.
Špaček, J. (1992). Dynamics of Golgi impregnation in neurons. Microscopy research and technique, 23(4), 264-274.

Out of curiosity, I spent a while trying to find a counterexample of this stain being used in non-nervous tissue. I cannot find anything. It seems to be so widely used for neurons/glia and for nothing else. Curious whether and why the chemistry has been restricted in utility to nervous tissue only...

Yes, according to Spacek (1992)

the Golgi deposit has been identified as silver chromate by Fregerslev et al. (1971) and Chan-Palay (1973).

I don't know why it's black when in neurons and not dark brown though...
Actually Spacek (p. 265) describes the crystals as dark brown.

It's more of a dark brown, it's not that easy to tell the difference in a microscope, especially looking against a brightfield - any dark color is going to throw a substantial shadow.


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Are there any online resources for visualising on which band of a chromosome a particular gene is located?
I am studying some genes that are expressed in the brain. I use the online database UniProt to get information about the proteins encoded by the genes of interest. However, I would like to know on which chromosome and which band of the chromosome the genes are located.
I was wondering whether there are any online tools that I can use where I can type the name of a gene of interest and I can get a visualisation of which chromosome the gene is located as well as the band? Any insights are appreciated.

Well, given the protein, you can use http://www.ncbi.nlm.nih.gov/protein/ then just above the sequence it mentions the chromosome and band e.g 4q31. But no visualisation here. I did see a visualisation tool for human proteins 8 years ago but I forget where.

The UCSC genome browser is good for genome visualization. Searching for HBB, for example, gives the follow data by default:

You can also search by band and get a list of genes.


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Why is it often assumed that biological samples from mice follow the normal distribution?
I am analysing Western blot data. In the experiment, I am looking at the expression level of a certain protein of interest in the brains of wild-type and knockout mice. I have seen online that many biological measurements, especially from animals such as mice, are assumed to follow a normal distribution (and thus hypothesis tests such as t-tests and ANOVA can be applied). I have used a t-test to analyse my data, however, I was wondering why is it that measurements from mice are assumed to follow a normal distribution? Any insights are appreciated.

Does this answer your question? Do biological phenomena follow Gaussian statistics?

Many biologists (and reviewers) seem to lack a fundamental understanding of statistical testing. For me, it usually comes down to normality testing, and sample size. If I'm working with particularly small sample sizes, I'll often stick with non-parametric testing regardless of normality (and I don't think it's uncommon to see non-parametric tests in such reports). Second, I always test for normality prior to reporting a parametric test with normality assumptions. Along with any data transformations, normality testing should be reported in a paper's methods, but may not always be.

The normal distribution is often used as a "default" distribution because it is in fact quite common in measurements overall. And indeed, whenever there are a bunch of small additive errors in a measurement, the central limit theorem leads us to expect that the distribution will approximate a normal distribution. This is not a safe assumption to make, however, because there are also many cases where the error is not dominated by small additive factors.
Indeed, gene expression is one of the phenomena that are definitely not normally distributed at the single-cell level! Instead, strong genetic expression should be expected to show a log-normal distribution, due to the multiplicative factors in the chemical rates involved. Low levels of expression tend to have a Gamma distribution instead.  If there is feedback regulating the expression levels, of course, all bets are off, and even more so if you are considering a population-level measure rather than measures at the single cell level.
What typically will still have a normal distribution, however, is the error induced by an instrument as part of the measurement process (not the biological part of the assay, just the physical, e.g., measuring the intensity of a light shined through a sample). So if you assume a normal distribution, you are essentially placing a bet that the variation in your measurement process is higher than the biological variation. From my experiences with animal studies, I would say that this is rarely a safe bet to place.


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DNA extraction kit for microbial mats, rocks, and soil in a remote area
I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For the sequencing, I plan to use either the Field Sequencing Kit or the Rapid PCR Barcoding Kit from Oxford MinION. However, I am unsure how to extract DNA before using the Oxford Minion kits (and in a manner, of course, that complements it).
Are there DNA extraction kits that can followed up Oxford MinION kits and can be performed without heavy equipment for the following sample types?
a) microbial mat
b) soil
c) lava rock
Thank you for sharing your advice!

Those are some pretty tough samples to get high-quality DNA from, even in a lab. Your best option is probably to place samples in a nucleic acid preservation buffer and carry them out for extraction later.
That said, there are some potential solutions. Akonni has some kits that don't use any centrifugation and they claim they'll work on soil and stool, so they might be good enough for your applications. They kind of seem like they're based on the same principle as this kit-free protocol (this protocol is for Plasmid DNA, but I'm sure it could be adapted for Genomic DNA with a little R&D on your part). In either case you'd probably want to look into a portable bead-beater to disrupt/lyse your samples. This will shorten your DNA fragments through shearing, but it's probably necessary to get good extractions from any of these materials.
A few companies also make portable centrifuges that run on 12V car plug adapters, assuming you'll have a vehicle somewhere within walking distance. That could open your options up to using a Powersoil kit or even something like a phenol-chloroform extraction, which you might not need a bead-beater for. (Note: you absolutely would need a properly fit-tested, full-face respirator with the appropriate chemical filters to do phenol-chloroform work without a proper fume hood, plus a way to haul out your waste).
If it were me, I'd still probably use a preservation buffer and do the extractions and analysis back at the lab.


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What is the probability that a gamete will only contain father's chromosomes
As it is depicted in most textbooks, cross-over does not occur between the two "outer" sister chromatids. By independent assortment during Meiosis I, there is 1/2^23 chance that all father's chromosomes, with one pure father's chromatid, will end up in the same daughter cell. Does this mean that roughly one in eight million people does not have any genetic material from one of his grandparents or is there some more independent assortment during Meiosis II, which makes this outcome extremely unlikely? (more like 1/2^46)
More generally I would be interested in the probability that a gamete will contain more than 60% ,70%, 80% ... of only one of your parent's genes.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, it would be helpful if you could be clearer about what you are asking — for example, it seems that you sometimes use parent when you really mean grandparent. Thanks!

In organisms like humans it is VERY rare for sister chromatids not to undergo at least once crossover. You may want to look into the term obligate crossover. It's not entirely clear from your question, but your reference  to 'two "outer" sister chromatids" makes me wonder if you are confusing a convenience in drawing an illustration with a biological fact.

So if I understand it correctly, it is very unlikely that any of the four chromatids in the tetrad will remain unchanged after the crossover occurs, right?


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What are these near microscopic white bugs from my comb?
I saw a whole bunch of white bugs crawling on my comb in the medicine cabinet, they didn't photograph well but I did manage to get a bunch of them in mineral oil and eventually take some micrographs.
The good news is that a dermatologist says I'm not infested with anything and, after nuking the bathroom with poisons and cleaning products, they haven't come back.
Here's 3 different specimens at 40X and 100X.  The live ones seemed to be in the 0.2 to 0.8 millimeter range.
(Click for larger images)

What are these things?

excellent photos!  Thanks!

@JohnC (reacting to your comment below): your specimens do not appear to be the bird/rodent mites I'm familiar with. See Bug Identification: Tiny Bugs and Tiny white very hard cell bug! Please help to identify!. Your specimens seem morphologically different and smaller.

I agree with the answer given below that these are mites (8 legs helps to confirm this), but I'm not convinced that they're dust mites. I think you could also rule out Sarcoptes scabiei. Also doesn't look like any species of Cheyletiella I can find.

Do you have any pets or have you been around any animals lately? Do you have any animals living inside or outside the home? (even pests?). Do you have any bite marks or irritation? (if so, can you describe it?)

@theforestecologist, no animals inside home, no evidence of recent pests, no obvious bite marks, although itching has always been a thing with me.  I do work at an animal shelter, where are the animals have strong flea/mite/tick controls/medicines.

What country are you in? It seems USA "household" wood mites grow to about 0.5mm which is probably why could see them https://www.h2ouse.org/how-to-get-rid-of-wood-mites/

Those look like they could be dust mites and are certainly some sort of mite. Dust mites are found everywhere in homes and are around 0.2 mm in length.
Dust mites image by Gilles San Martin:

Dermatophagoide pteronyssinus (European house dust mite):

Dermatophagoides farinae (American house dust mite):

You can learn more about dust mites from the BBC and the US NIH.

The leg configuration does not match and most of my beasties are 2 to 3 times bigger than a dust mite. (Can you even see those with the naked eye?)

I've added a couple of images that appear to have been prepared more like to you did and which clarify that the leg positioning is very similar. Dust mites are visible (reported to be up to 0.3 mm) — if you are you sure yours reach 0.8 mm in size then they probably are a different species of mite.

I'm told elsewhere that my bugs are probably bird, or maybe rodent, mites.  I want to wait a couple days for more answers, then I'll accept one here.

Makes sense — there are also likely to be better sites for getting an answer than here. If you are in North America (USA or Canada) BugGuide seems like a good resource.


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Passing out from drowning
How long does it take to pass out from oxygen deprivation? The person is panicked and screaming so they accidentally breathe water into the lungs. So how long would it take for them to pass out? After they pass out they are administered Mouth-to-mouth resuscitation immediately and are only out of it for a couple of half a minute. Then they are taken to the hospital. Would there be any long term affects to the body?

A couple of half a minute? Anything under 5 minutes is a 90% chance of being safe if resuscitated. Drowning people don't make much noise because they are too distracted by the water. They only fill their lungs significantly after becoming unconscious.
simple description:
https://www.dedhamhealthfoundation.org/water/victim-recognition/stages-of-drowning/
complex description:
https://en.wikipedia.org/wiki/Drowning#Pathophysiology
The damages that occur are: lung injury, cardiac arrest, brain injury from oxygen deprivation.
The breathing pattern and physiology vary depending on hyperventilation, panic, physical exertion, fullness of the lungs at the time of submersion, so there is no simple answer to your query.
When they breathe significant amounts of water, it is because they have just lost consciousness and their body relaxes.
While they are is still conscious, they hold their breath for as long as they can, voluntarily / because they have breathed a sip of water and their epiglottis shuts and seals closed, by reflex.
There is a spasm called laryngospasm which occurs when the person is at the end of their breath and their body is trying to breath but their epiglottis is closed, that occurs at very low oxygen levels and a high oxygen debt because of the panic, so unconsciousness is only a few seconds away when the throat is convulsing, and it continues to convulse when they are unconscious and 90% of the time they breathe water and their heart continues beating.
I can't find how long it takes to have cardiac arrest after asphyxia or wet drowning. Probably it is not very well studied becuase it is so dangerous.
There is also the mammalian dive reflex, which occurs mostly in children who are suddenly immersed in freezing water. It can cause their metabolism and heart rate to go into slow motion, and stops circulation to their extremities, causing them to survive for more than 15-30 minutes.

This is a kayak trip heart rate with immersion in cold water.
From avalanche asphyxia, the heart can continue 15-20 minutes:
https://www.scancrit.com/2013/08/27/heart-rate-monitor-watches-avalanches/
There's a dutch man who lost his wife and then started diving in freezing water, and he can stay in freezing water for 30 minutes using conscious mammalian dive reflex.


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Meaning of Phred score - probability of base calling error
I learned that Phred quality scores are logarithmically linked to error probabilities. For example, if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly are 1 in 10.
How is it possible to have 10 possiblities when you can only have 4 bases (ACGT) ?
When assigning a base, there are only three ways to be wrong to me.

Phred score is a measure of the probability that a base call is wrong/right.
Your understanding of this probability as "if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly are 1 in 10", is not entirely accurate.
Quality scores calculation and base calling are specific to the machine. The way an Illumina HiSeq calls a base is different from how PacBio does it.
For example, Illumina uses high precision cameras to record the colors generated during sequencing (each color represents a base). Moreover, it does not sequence a single molecule of DNA but a cluster. Now, the machine's base calling software will calculate the reliability of the light signal being interpreted as a base (let's say A). Several parameters are considered in this calculation.

For each base call, a number of quality predictor values are computed.
  Quality predictor values are observable properties of clusters from
  which base calls are extracted. These include properties, such as
  intensity profiles and signal-to-noise ratios, measure various aspects
  of base call reliability. They have been empirically determined to
  correlate with the quality of the base call.

 Illumina Technical notes: Understanding Illumina Quality Scores

Likewise, different machines have different techniques for reading a base signal and computational models to calculate the accuracy of the signal.

How is it possible to have 10 possiblities when you can only have 4
  bases (ACGT) ?

Why not? You are just calculating what is the probability that a base is not adenine. The minimum probability should be more than 1/4, at or below which the base call wouldn't probably even assign the base as adenine.
Imagine it like this: if adenine is represented by blue light and you see that in the spot there is not a pure blue signal but some interference of other colors (noise) which represent 10% of the signal. There can be other parameters too that make the calculated blue signal to deviate from the "ideal signal". The percentage of non-overlap with the perfect signal would be the error.

if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly are 1 in 10

This does not mean that there are 10 different possibilities for a base.
This means that you have 10% chance that the base is different from the one that was called.
If the base called is an A with a score of 10, it has 90% chance of really being an A, and 10% chance of being either C, G or T. If we assume that the probabilities of each of the 3 other bases are equal, this would be:
             |   A   |   C   |   G   |   T   |
-------------+-------+-------+-------+-------+
P(real_base) |  0.9  | 0.033 | 0.033 | 0.033 |

However, I'm not sure that the probabilities of C, G and T are really equal: it could well be that, due to the specifics of the sequencing technology, some (read base, real base) pairs are more common than others.


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How can a joint extend or flex?
The idea of a joint flexing or extending doesn't make sense to me, I can see how a leg or an arm might extend or flex but how does a joint extend or flex ?
"The hip joint is most stable when it is extended and the ligaments are taut."
Does that mean in the state that is most right in this picture ?

It is really unclear what you are asking, the picture you show is that of the hip joint extending and flexing.

Which is why I specify the “figure/state which is most right”

That doesn't help, lets start with whether you mean right as opposed to left or right as in correct?

 Short Answer
The words extension and flexion actually mean to increase or decrease the angle of a joint, respectively. In other words, the terms are directly related to the joints themselves. Bones can only move relative to each other at joints, so when the angle between two bones increases or decreases, that action is occurring at the joint. In other words, the joint acts as a vertex of the angle of movement.

 Long answer
In general, one should think of extension as "increasing the angle of a joint" and flexion as "decreasing the angle of a joint" (see here, here, here, here, here, here or here for reference). From Saladin's 2015 Anatomy textbook$^1$:

Flexion = a joint movement that , in most cases, decreases the angle between two bones.

Put differently,

Flexion refers to a movement that decreases the angle between two body parts.

I think where you are confused is that you do not understand what a joint is. A joint is anywhere where two bones articulate (or touch). Although various types of joints exist, those that readily move well enough to receive movement terms such as flexion/extension are called synovial joints.
At any given synovial joint, two bones are able to move relative to each other due to a cavity that provides space for movement -- the synovial cavity. Put differently, bones (which are solid, unbending objects) move relative to each other during our body movements, and this relative movement occurs at joints.
Using your example of arms and legs:
When your arm flexes/extends, what's happening is that the head of your humerus is moving inside the glenoid cavity of the scapula. This movement at the "glenohumeral joint" results in the entire arm (humerus and all distal components) either swinging forward or backward  due to the angle of the glenohumeral joint increasing or decreasing (though, actually, other movements are possible as well). The same applies to the hip.
Another example is the "elbow" joint -- which actually consists of 2 joints: the humeroradial and humeroulnar joints. Consider when you "flex your arm" as in showing off your bicep. Yes, your lower arm (forearm) moves, but the movement all occurs at the point of the elbow at these two joints. In other words, the elbow joints form the vertex of the angle between your upper and lower arm bones. When you "flex" your arm, the angle of these joints decreases. When you return your elbow to being straight (i.e., "extend" your elbow), your are increasing the angle of the humeroradial and humeroulnar joints.

$^1$ Saladin, K. S. 2015. Anatomy & Physiology: The Unity of Form and Function. Seventh ed., McGraw-Hill, New York, NY. 1248pp.


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In DNA replication, are there phosphodiester bonds in the primer ? between the RNA nucleotides before being replaced
When hydrogen bonds happen between the RNA nucleotide bases and the DNA bases , do phosphodiester bonds form between the RNA nucleotides in the primer ?
No source I read is clear about this, are their bonds between the RNA nucleotides ?

@Dirigible — I suspect that the poster is talking about Okazaki fragments, and wishes to know whether they are covalently linked to the growing DNA. If so, I seem to recall a similar question previously. However the question is unclear. Poster, please clarify your question and preferably present a diagram, or link to one, so we can see what aspect seems unclear to you. The accompanying text would help — it could be that rather than the texts being unclear, there is something in the explanation you are misunderstanding.

I have posted an answer. However, this seems like a basic question and is easily answered by consulting sources such as Wikipedia. As such I'm flagging this question as "homework" since it "addresses a basic biology concept that may seem trivial to biology professionals". ——— Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

A primer is by definition a short single strand of nucleic acid (i.e. a series of nucleotides linked together by phosphodiester bonds). See also this wikipedia article.


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What happens if a circulating naive B cell is met with a polysaccharide/lipid antigen?
These antigens should provoke a T-independent response, so will they differentiate then and there to form short-lived plasma cells?
Or do they have to go to lymphoid tissue, enter a B follicle, and then differentiate?
and can they differentiate into short-lived memory cells and short-lived plasma cells? Or only the latter?

Depending on the class of the antigen, B cells can be activated via different mechanisms. T-independent (TI) immune response can be induced by two types of antigens, namely TI-1 and TI-2 antigen (1).
TI-1 antigens are mostly lipopolysaccharides (1). They activate naive B cells by directly binding to the Toll like receptors expressed on the surface of B cells. Binding induce proliferation and differentiation into effector B cells, which secrete antibodies against particular antigen (2). Eventually, most of these effector B cells will mature to become large plasma cells. Most plasma cells will die within a few days, but some can survive in the bone marrow for months or years and continue to secrete antibodies into the blood (2).
TI-2 antigens include polysaccharides, glycolipids, and nucleic acids (1). They have no intrinsic B-cell-stimulating activity and activate B cells via repetitive cross-linking of membrane immunoglobulin receptors. Such activation has only been found in mature B cells, meaning that they won't activate a naive B cell (3).
Resource
(1) Cruse J, Lewis R, Wang H. Immunology Guidebook. 1st edition. Academic Press; 2004. ANTIGENS, IMMUNOGENS, VACCINES, AND IMMUNIZATION. Available from: https://www.sciencedirect.com/sdfe/pdf/download/eid/3-s2.0-B9780121983826500261/first-page-pdf
(2) Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. B Cells and Antibodies. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26884/
(3) Janeway CA Jr, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. B-cell activation by armed helper T cells. Available from: https://www.ncbi.nlm.nih.gov/books/NBK27142/


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Do factors other than concentration gradient and membrane permeability affect the diffusion potential?
If, hypothetically, the concentration gradients and the permeability of 2 different ions (Na+ and K+ for example) in 2 separate solutions are the same, will the diffusion potentials be different?
I'm trying to gain an intuition for the concept of diffusion potential and equilibrium potential.
It read this topic from 2 physiology textbooks but haven't really found an answer anywhere. I understand that the diffusion potential is the potential difference generated when an ion moves through a membrane down its concentration gradient. I also know that it is determined by both the concentration gradient and the permeability, but, does the type of ion itself matter if the charge on the ions is the same?

You can determine the diffusion potential mathematically with the Nernst equation. If it's not in the Nernst equation, it's not necessary.
The charge of the ion matters (including valance), the temperature matters. Some universal constants are in the equation but these don't vary.
Other factors that potentially matter are found in the other parameters, like the permability.


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Is casein hydrolysate the same thing as casamino acids?
Probably a dumb question, but these seem identical. If a protocol calls for one, can I use the other instead?

Roughly, yes they are similar, but there are processing differences- the real difference is filtering. A product containing simply casein hydrosylate will only be roughly filtered with lots of peptides (like body builder products). Whereas casamino acids should be primarily clean/free amino acids (like nutrients for bacteria).
The actual manufacturing methods will be proprietary for the manufacturer... but you can trust that they are basically doing whatever works best to obtain the individual amino acids and/or whatever is cheapest for obtaining a useable product.
I have used bodybuiling and several other grades of casein products for growing bacteria. I have found that although various products may get the job done there are some serious drawbacks to casein products not intended for growing bacteria.
Differences include clarity of media, cleaning of glassware/fermenter/bioreactor, sudzing of aerated media, and the microorganism. Some microorganisms won't grow very well, and generally, those that can may still not grow quite as well or as fast... so that extra 10% or 20% cfus may be important (or maybe not since the price for quality may be 10 times higher).
The quality-features vs price must be weighed by the grower. Personally, I sometimes autoclave a cheap casein product in one (easy to clean) vessel then rag-filter it into another (then autoclave it again) for growing bacteria... but that's because I have about a thousand pounds of rough casein hydrosylate, and only a kg or so of casamino acids (for particular studies). This method does not eliminate all of the problems but it does reduce some of them.


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Which of the response is faster? voice or hand action?
After taking certain stimuli and making the the decision to do certain action, which one response (output) (out of 2 possible output-ways, voice and hand-movement) would act faster?
For example lets say I'm playing a car video game that can be controlled by voice.
If i say "left" it will turn left and so on.
If I'm controlling that car by hand then I could just steer to the left.
So, if i'm not considering energy required for hand to move and all.
Which will get the signal to my brain faster, my mouth or my hand?

The title and concluding sentence don't seem to match: is your question which output is faster (title) or which stimulus is registered quicker by the brain (last sentence)?

Which output is faster, using voice or hand?

You could also ask a related question in Psychology & Neuroscience

Assuming that we are talking about a situation at the physical limit of the brain:
Speaking a word will always be slower than pushing a button.
A whole word requires a contraction of the diaphragm to push out air so this air can be modulated by another sequence of contractions and relaxations of the vocal chords.
So contracting finger muscles is very similar to speech initiation however for a computer to respond (in the example you were playing a video game) the computer needs to recognize the full word and then map it to an output before actually implementing the left turn.
So adding the extra processing time of the computer and the actual extra production time of the vocalization you're better off pushing buttons.
As a matter of curiosity if the physical limit situation is relaxed; whenever there is a mismatch in both sensory receptors as well as outputs, the brain does its best to compensate. Think of something dropping on your foot, the visual information is actually delayed so that the sensory stream (that has to go up all of your leg and spine) catches up.


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Help to recognize spider
It is unusual to see such size spiders in Lithuania, so I was wondering what kind of spider it is and if it is strong enough to bite through humans skin.
I've googled for biggest known spiders in Lithuania, but mentioned few species don't look alike - mine has way thinner legs, but I'm not an expert.
I've placed 1 euro cent coin for size - it's diameter is 16.25mm

The long hairy legs make me think that this might be a spider belonging to the Tegenaria genus, or something related.

I agree it's a Tegenaria spider, probably Tegenaria parietina.

So Tegenaria helped me search further and it looks like it is Tegenaria atrica - turns out it is not so rare in Northern Europe, male leg span can be up to 75mm, mine was shorter, but still amazing to watch how fluently those long legs move.

Yes it looks like Tegenaria. We have plenty of these trying to get in the houses in autumn in Switzerland (not as North as Lituania but cold winter time)


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Production of $CO_2$ basal metabolism test

Can the production of $CO_2$ be used as a type of basal metabolism test? Explain.

The answer to this is obviously yes, but I don't know how to explain it. Would the following be a good explanation?

The faster your metabolism the more cellular respiration your cells do, and you produce more $CO_2$, so $CO_2$ output can be used as a type of basal metabolism test.

Yep, you got it.