Why do mice have a higher metabolic rate than humans? Mice and other small animals have higher metabolic rate than humans.

How does that happen on cellular level, if we look on one cell in the mouse body?

What is it in this cell that will be different?

How is that regulated inside mouse cell?

In endothermic and ectothermic animals, ie. warm and cold blooded animals, metabolic rates are inversely proportional to size of the organism.

  Quoting from https://www.biog1445.org/demo/04/metabolicrate.html

  This is because smaller animals have a higher surface-to-volume ratio,
  thus a larger relative heat loss to the environment per unit time. To
  maintain a constant body temperature despite rapid heat loss across a
  body surface, a small animal must oxidize food at a high rate. Because
  the relative amount of food consumed and the pace of digestion,
  respiration, and so on must rise with decreasing body size, there is a
  lower limit on the size of endotherms. The smallest mammals are
  shrews, which weigh only about 4 grams. They must eat nearly their own
  body weight of food every day, and starve to death is just a few hours
  if deprived of food.

This is shows that smaller animals, like mice have a much faster metabolic rate than that of larger animals like humans or elephants.

When talking of within the cell, the mitochondrial content of a muscle cell of a mouse would be increased to produce more energy from one feeding than that of a human. This is because cells themselves increase the number of mitochondria based on the requirement of the body, thus a muscle cell of a human has more mitochondria than a neuron, since muscle cells have to utilize much more ATP to function. This phenomenon, known as mitochondrial biogenesis would be observed in mice vs human cells.
In mice, having more mitochondria would be an evolutionary advantage, as only those producing the optimal amount of energy would be able to survive the loss of energy to the surroundings and the process of natural selection would leave mice with relatively larger numbers of mitochondria in their cells.

(For more info)
https://en.wikipedia.org/wiki/Metabolic_theory_of_ecology
http://www.sciencedirect.com/science/article/pii/S0378111900005825


Genome Assembly Using Reads I'm taking an online bioinformatics class and I am stuck on a problem. The resources I have found don't help that much. Here is the problem:

"Assemble the error-free reads from a circular genome on the dataset below. You do not need to consider the reverse complement of the reads.

Dataset: CGTTCT CTAG GACGT TAGAC

As the reads do not have the same length, convert the reads to 4-mers using the approach proposed by Idury and Waterman."

I believe this means I need to convert this into sets of 4 characters each. Do I simply break them up by taking the first 4 characters and last 4 characters like this?

CGTTCT: CGTT --> TTCT
CTAG: CTAG --> CTAG
GACGT: GACG --> ACGT
TAGAC: TAGA --> AGAC

And end up with a new dataset of: "CGTT TTCT CTAG GACG ACGT TAGA AGAC"?

Or is there more to it than that? Thanks for any help.

Actually the new data set will be,

for k = 4 (k-mer value)

CGTTCT -> CGTT GTTC TTCT

or

Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/


On what basis is each chromosome given a number? On what basis is each chromosome given a number? There appears to me to be no visible ordering between each pair. Is there any reason other than differentiation?

Chromosomes are generally ordered by size in terms of number of nucleotides. The first chromosome is the biggest. Note that when there are sexual chromosomes (as it is the case in mammals or birds for example), the pair of sexual chromosomes are typically considered last irrespective of their sizes.

Note that in some species the ordering has been decided and further studies have shown that the actual size order does not perfectly match the ordering. This is for example the case in humans, where chromosome 11 is actually bigger than chromosome 10 (thanks @canadianer).

Numbering is mainly just a simple naming system. It is just handy to be able to refer to a chromosome as chromosome 3 rather than having to somehow describe this chromosome for other to understand what we are talking about.


How to determine sensitivity in a dose-response curve? In a dose-response curve the % inhibition can be plotted against concentration antagonist. In our case, the effect of the antagonist is tested in different genetic variants of a microbe.

When trying to determine the potency of a drug on the different variants, I compared the IC50 values. The lower the concentration required for 50% inhibition, the more potent the drug.

When comparing drug efficacy, I compare the concentrations required to reach Emax or the maximum inhibition that each drug can exert - which turns out to be 100% inhibition.

To compare sensitivity, how does one proceed?

I think you are after the slope of the dose-response curve:

Dose-response curve. Souce: Merck

The slope indicates the change in response per unit dose, which translates to sensitivity.


What will happen when humans are injected with plant growth hormones Will plant growth hormones (PGHs), (let us consider auxins for example) poison our body or not?
I do realise that when you eat a shoot, auxins get digested and are less likely to be poisonous but when taken as an intravenous injection can auxins cause some changes to the body?
I mean even if they do not poison a body, some osmotic changes are bound to happen.
According to this link, if the water was injected in not so little amounts it is bound to cause cells to burst.

EDIT: Now according to this link, plant hormones are actually beneficial to human body.

How is it possible if they don't have any receptors in humans or any other vertebrates?

I will only give an outline based only on auxins otherwise the question may be deemed too long.I hope this helps a bit.

The first auxin was isolated from the urine of pellagra patients.

Most natural auxins are indole derivatives which are the intermediates or final products of tryptophan metabolism.Both vitamin B3 and auxins are consequences of tryptophan metabolism. [source]

POSSIBLITY 1-

Thus, auxin injected may be eliminated through urine.

We already understand that substances that are excreted via urine are either toxic to the body or above threshold.Perhaps this idea was harnessed by researchers to construct researches which proved that auxins have anti-cancer properties.

  given that the chemical structure of plant and human auxin is identical and that cytokinin IPA is found in human cells bound to tRNA assisting protein expression, presumably supplied by the consumption of vegetables in the diet, and that we observe a positive effect of plant hormones on pluripotency and key anticancer gene expression levels in mammalian cells [1],[2]

POSSIBILITY 2-

In proper dosage may be utilised for its anticancer properties.

Cytochrome and a series of enzyme system in liver cells are known to detoxify indole

Protein putrefaction in the large intestine results in formation of indole.This indole is carried by the portal system to the liver where it is detoxified to indican  with the help of the cytochrome P450 isoenzyme system and consequently eliminated via urine.

POSSIBILITY 3-

Thus auxins (being indole derivatives and moderately hydrophilic) may be detoxified in the liver and then excreted.
REFERENCE:[1],[2],[3]


Is there any difference between strain and mutation/mutant? Experts are closely monitoring the strain, which has rapidly spread
through the country's south.

Source
Most of the media/newspapers are calling VOC-202012/01 a COVID strain, instead of a COVID mutation/mutant.
Is there any difference between strain and mutation?

You can think of "strain" roughly analogous to how you would think of "breed" in the context of dogs or horses.
There might be some key mutation that identifies members of a strain over non-members, but you would expect to find other genetic differences as well. "Strain" for a virus is not referring to a particular mutation but to the viruses on one side of some fork in their evolutionary history.


Why do plants not have fat cells, and store their reserves in vacuoles instead? Why don't plants have fat cells, but instead store reserves in vacuoles. And vice versa, why do humans feature fat cells instead of depositing storage molecules in vacuoles?

Short answer
Parallel evolution can generate similar traits in unrelated organisms based on unrelated structures.

Background
First off, the question is based on a few misconceptions:

First, you are making an apple-and-pear comparison; Fat cells are cells - vacuoles are organelles. Fat cells store fats in liquid droplets, called adiposomes, which are lipid-rich cellular organelles that regulate the storage and hydrolysis of neutral lipids and are found largely in the adipose tissue. Vacuoles have a variety of functions, namely 1) contribute to the rigidity of the plant through hydrostatic pressure; 2) store nutrient and non-nutrient chemicals and 3) break down complex molecules. The latter two functions are quite reminiscent of the function of lipid droplets in animalia.
Plants do not store energy reserves in fats like animalia do. Instead, plants store starch, which is not a hydrophobic lipid, but a hydrophilic glucoside polymer.

Apart from these specifics, the question can be tackled more generally - unrelated organisms can solve the same 'problems' (like storage of energy rich compounds) through parallel evolution (wings in bats and birds for example). Why does a bat wing contain fingers and a bird's wing doesn't? Because they developed the ability of flight through different, parallel adaptations.


Why do I see so many handicapped dorbeetles? Living in southern Germany, I often visit nearby forests and pastures.
From early spring to autumn, I frequently see lots of dorbeetles on my wanderings. An estimated amount of 50% of those bugs seem to be somewhat handicapped or crippled. All of them share the same symptoms:

They stretch their legs away from their body, moving them in a
swimming-like manner, which causes them to be unable to get over the
smallest rocks or plants. It looks very clumsy, almost drunk. Often they draw back one of their rear-end legs, getting caught in parts of plants.
Many of them are lying on their backs, struggling to get back on
their feet. When I turn them around, they will start walking in the
fashion I described above, falling over again almost instantly

Like already pointed out, not all of the dorbeetles behave like this. I see lots of bugs that seem to be perfectly fine, too.

What can possibly cause this?

I do not know for certain but one possibility is an internal parasite.

A number of parasites have been documented to alter the behavior of the hosts to suit the life cycle needs of the parasite.  For example, Toxoplasma is a parasite use rats and cats as hosts. Toxoplasma alters the behavior of the rats so that they no longer respond to the smell of a cat. That makes the rats much more likely to be captured by the cats, which transfers the parasite to the cat from the rat (Berdoy et al. 2000).

This YouTube video shows how a fungal parasite of ants alters the ant behavior to help the fungus reproduce.

My favorite example, which I use in my introductory biology course, is Euhaplorchis californiensis, a parasitic fluke. The parasite lives in marshy habitats, such as Carpinteria Marsh in California, USA. This parasite uses wading birds (herons and egrets), a snail and a fish as it's host.  The adult lives in the gut of the wading birds. Eggs from the adults pass out with the bird feces. Horn snails consume the fecal material and the eggs.  The eggs hatch inside the snail. The larvae actually castrate the snails so that the snails cannot reproduce. Instead, the snails only feed, which provides nutrients for the parasite larvae. The larvae then leave the snail and swim into the marsh, where they are consumed by the California killifish (Fundulus parvipinnis). The parasite works its way from the gut of the fish to the brain, where it releases chemicals that alter the behavior of the killifish. Normally, if a killifish sees a wading bird, it would dive deep. Instead, the parasitized fishes no longer dive. They remain near the surface and swim eratically. This behavior makes it much easier for the wading bird to see and catch the killifish. The parasite is transfered back to the wading bird, and its life cycle begins again. Details of this fascinating life cycle can be found in (Shaw et al. 2010).

Therefore, it is possible that the behavior of the dorbeetles is being influenced by an internal parasite. These dung beetles may consume a parasite when they ingest dung from a certain species. The parasite could alter the behavior of the beetle making them more vulnerable to a particular predator, thereby continuing the next step of the parasite's life cycle.

Your description of the beetle behavior would fit this hypothesis but I stress that I do not know this. I raise the idea as one possibility among many.

A good not technical book on parasites is Parasite Rex by Carl Zimmer. It covers the biology of parasites, the many ways that parasites can affect their hosts, and the creative scientific minds that uncover the complex life histories of many parasites. (I have no connection to the author or the book.)  The book covers the above examples and more in some detail.


How exactly does marijuana damage brain cells? I've heard that THC can cause permanent damage to brain cells. I've also heard this reffered to anti drug propaganda. Another theory i've read is that temporary effects reduce intelligence but long term results are not affected. If Marijuana does cause permanent brain damage how does it do so? How exactly does it kill the cell?

There is no damage of brain cells, as in the context of lesions in neurodegenerative disorders. There are, however, two mechanisms attributed to the memory loss associated with cannabis/marijuana and these are purely physiological responses.

Astrocyte mediated: CB1R (cannabinoid receptor) in astrocyte gets activated and promotes glutamate release. This glutamate induces Long Term Depression in post synaptic neuron.
Synaptic currents can cause both LTP and LTD. The properties of the synaptic current wave dictates the outcome. Please refer to review articles on LTP and LTD for more information.
GABAergic interneuron mediated: CB1R activation in GABAergic interneurons (inhibitory neurons) causes activation of mTOR pathway and promotes protein synthesis. CB1R activates mTOR through PI3K/Akt.


What is the meaning of "Rb is in the active state"? I am reading about cyclins, cdks and Rb (Retinoblastoma) and some of the terminology is not clear to me.
I understand that when CDK phosphorylates Rb, it disconnects from E2F, and E2F can act as a transcription factor. My question is about the terminology.
My questions are:

When people say "Rb is active", do they mean "active = phosphorylated state" (where E2F is free from Rb) or do they mean "active = not phosphorylated state"?

Does "active cyclin" means cyclin is going to join CDK and cell cycle proceeds? or is "active cyclin = cyclin is not activating CDK and cell cycle paused"?

Active CDK means CDK is activated by cyclin and cell cycle can proceed?

In general, Maybe one can say that binding (Rb with E2F or Cyclin with CKD) means activation and disconnecting means inactivation?

Thanks!

(Image source: Kolch, Walter, et al. "The role of Raf kinases in malignant transformation." Expert reviews in molecular medicine 4.8 (2002): 1-18.)

The terminology of "Rb is active/inactive" refers to the activity of inhibiting E2F.
So active Rb inhibits E2F, while inactive Rb doesn't inhibit E2F.
With regard to Rb and phosphorylation - the story seems to be more complex ([1] describes Rb as an enigma).
According to [2] (this quote is from the summary of the paper by eLife):

  Narasimha, Kaulich, Shapiro et al. now present biochemical analyses of
  Rb proteins that show— completely unexpectedly—that the cyclin D
  complex adds just one phosphate group to Rb during the G1 phase,
  although this group can be added to one of fourteen different sites.
  The resulting 'mono-phosphorylated' Rb varieties can each sequester
  different transcription factors and stop them working.At the
  restriction point, many more phosphate groups are then rapidly added,
  and the Rb protein is inactivated by a different cyclin. This
  cyclin—called Cyclin E—then drives cells into the next phase of the
  cell cycle. Establishing how cyclin E is activated is a priority for
  future research.

+ 3. Wikipedia's Cyclin-dependent kinase (CDK) page says:

  By definition, a CDK binds a regulatory protein called a cyclin. Without cyclin, CDK has little kinase activity; only the cyclin-CDK complex is an active kinase.

Wikipedia's Protein kinase page says:

  A protein kinase is a kinase enzyme that modifies other molecules, mostly proteins, by chemically adding phosphate groups to them (phosphorylation).

And here is a nice visual explanation from Life: The Science of Biology (10th edition):

So both "active CDK" and "active cyclin-CDK complex" (and according to the other answer, also "active cyclin") refer to the case in which a cyclin is bound to a CDK to form a cyclin-CDK complex, such that the CDK might phosphorylate some substrate.
(I didn't mention the cell cycle here on purpose, as I am not an expert, and so I am wary of claiming that an active CDK always pushes the cell cycle forward. If I understand correctly, we still don't know exactly how each cyclin-CDK complex affects the cell cycle.)

As for your last question:

  In general, Maybe one can say that binding (Rb with E2F or Cyclin with
  CKD) means activation and disconnecting means inactivation?

As mentioned above, you could say that about a cyclin and its CDK.
Unfortunately, you can't say that in general. E2F here is a counter example (it is inhibited when Rb binds to it and activated when Rb disconnects from it).
However, you could say that in general, when something binds to a protein, the protein might change its shape, which might lead to activating or inhibiting some function.

[1] Dyson, Nicholas J. "RB1: a prototype tumor suppressor and an enigma." Genes & development 30.13 (2016): 1492-1502.

[2] Narasimha, Anil M., et al. "Cyclin D activates the Rb tumor suppressor by mono-phosphorylation." Elife 3 (2014): e02872.


How is a substance classified as a vitamin? From wikipedia

  A vitamin is an organic compound and an essential nutrient that an organism requires in limited amounts.

There are many essential nutrients to an organism. Glucose for example. However, not all of them are classified as vitamins. Is there a clear, non-arbitrary definition of vitamin? If not, who decide what ought to be called a vitamin?

1) Vitamin D is a bit of an umbrella term that actually refers to a whole group of related molecules. One of these, vitamin D$_3$ (cholecalciferol) is formed spontaneously from ergosterol in the presence of UV radiation, which happens in the skin when exposed to sunlight. Cholecalciferol is then converted to calcitriol, the active form, in the liver. Here is some information on the metabolic pathway.

2) Actually, if you consider the definition carefully, only a few molecules are essential for human growth and nutrition, in the sense that they cannot be replaced with something else, and are required in small amounts. For example, the majority of amino acids can be synthesized by the body from other amino acids, and are therefore nonessential. The remaining amino acids are essential nutrients because there is no synthesis pathway -- but they are required in large amounts and not considered vitamins. This distinction between "large" and "small" might sound strange, but it is important since it tells you if the nutrient is consumed for energy/growth (like amino acids) or has some "supporting" role, such as antioxidants, cofactors for enzymes, or hormones (like the vitamins).

That said, it is sometimes a bit fuzzy if a nutrient is essential or not. Vitamin D is a borderline case: it should perhaps not be called a vitamin, since it can in fact be synthesized by most adults in adequate amounts. However, vitamin D deficiency can occur if one does not get enough exposure to sunlight, and this can cause the disease rickets. Some researchers have suggested that this is one factor behind evolution of lighter skin in northern human populations, since dark skin pigment reduces UV radiation needed for vitamin D synthesis.


What is the size (diameter) of the SARS-CoV-2 virus? You can easily find a lot of pictures of the SARS-CoV-2 virus. But although it should be trivial for an electron microscope to measure the size, I am not able to find accurate size information.

What is the size (diameter) of the SARS-CoV-2 virus?
(Why does some virus particles seem to have a different size?)

Electron micrographs of negative-stained 2019-nCoV particles were generally spherical with some pleomorphism (Figure 3). Diameter varied from about 60 to 140 nm. Virus particles had quite distinctive spikes, about 9 to 12 nm, and gave virions the appearance of a solar corona.

--A Novel Coronavirus from Patients with Pneumonia in China, 2019

Figure 3 from that article:


What problems do invasive species cause ? Why do we value species?  What is so bad about invasive species?  Why value biodiversity?

Here is an attempt at a partial answer.

  What is so bad about invasive species ?

Invasive species have been introduced to a new habitat by humans (or by natural means).

They usually do not have a predator in a new area nor are the pathogens in the area very adept at infecting them. So, they may proliferate rapidly and compete with the native species. They may also be ferocious predators as their preys do not have defenses against them.


What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure? I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb and allowing for the change in a particular amino acid, to ultimately visualize the change in tertiary structure caused by that substitution.

Are any programs capable of performing an amino acid substitution on a molecule loaded by .pdb and showing the change in tertiary structure?

One application that I am aware of that will do this, as well as much else besides, is Swiss-PDB Viewer aka DeepView. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.


What is recemose inflorescence? In recemose inflorescence

Main axis continues to grow,
The flowers develop in acropetal succession ,
Opening of flower is centripetal

But according to definition

Acropetal succession : flowers opening in succession from base to apex
Centripetal : the younger flowers are towards the centre and the older towards the outside...

I can't understand that if lower flowers or flowers towards centre open first then they should be older but according to above statement flowers at base are younger. Is there other concept that I don't know?

Inflorescence is a flowering shoot that bears more than one flower. There are two types of inflorescence Cymose and Racemose. Of the two types of inflorescence Cymose inflorescence is more primitive and Racemose is derived. (Parkin 1914)

Racemose

In this type of inflorescence the main axis does not end in a flower, but it grows continuously and develops flowers on its lateral sides in acropetal succession (acropetal (adj.) - of leaves or flowers; developing or opening in succession from base to apex ).

Acropetal sucession is observed in raceme, the simplest racemose
inflorescence.

Now Capitulum or Head, it is another type of racemose inflorescence in which

  the main axis or receptacle becomes suppressed, and almost flat, and the flowers (also known as florets) are sessile (without stalk) so that they become crowded together on the flat surface of the receptacle. The florets are arranged in a centripetal manner on the receptacle, i.e., the outer flowers are older and open earlier than the inner ones.

In the following L.S. of sunflower you can see the disc florets developing/opening in centripetal manner.

P.S. I'm not a botanist but a candidate of B.Sc Zoology. I had Botany as my additional subject so I answered it from my knowledge.


Database of Multicellular and Unicellular organisms? I'm trying to annotate a list of organisms taken from NCBI for cellularity (unicellular or multicellular). Does any of you ever found a database with association between an organisms' name or taxa and whether it is unicellular or multicellular? Desirably, I would like to get information both on species level and on higher taxonomic level (phyla, classes, etc.), but any information on this is welcomed.

In case it matters, I'm using Perl to do this annotation.

Thanks in advance

More like a comment:

It doesn't seem that such a database exists, but I think it's relatively easy to create a list of multicellular taxa and the rest should be considered unicellular. Since you use ncbi taxonomy, you can easily get higher-level parent for any species, so there is no need to define cellularity for individual species.

The challenging groups would be different algal and fungal taxa, but there are some good reference books. You also have to decide, whether to introduce a separate category for colonial/coenobial/filamentous organisms.


How do you biologists draw a protein when you write a paper? The following is one example of protein structure diagram that I want to put in my research paper. I took this from

Koniev, O. & Wagner, A. “Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation.” Chem. Soc. Rev. 44, 5495–5551 Jan. 2015, DOI: 10.1039/C5CS00048C

As a Chemist, the only drawing tool I have used so far is ChemDraw and it does not provide such protein structure; The only protein diagram it provides is a Y-shaped IgG. How do you biologists draw such convoluted proteins when writing a paper? Do you use a specialized software for this?

As mentioned in the comments, diagrams like these are generated by software. The one I use is Chimera, it is free. The structure of the protein is recorded as a list of atoms and their 3D coordinates, as well as bonds, helices, sheets, etc. When a structure file is loaded, the software generates a 3D model based on the data. The user can rotate the model, move it, zoom in, change the color, an many other options, then export a 2D image when they are satisfied. If you want to use structure data files other researchers have generated, the Protein Data Bank is probably the best resource. Research articles that involve new structural data will list the PDB numbers of their structures near the end. In the article you link, the authors include pdb accession numbers for the structures they used for their figures. For the image you use as an example, here is the caption:

  Fig. 56 PEGylation of four solvent-accessible Tyr residues of chymotrypsinogen (pdb: 1EX3) reported by Francis et al.


Do stem cells have no epigenome? Till now I thought that embryonic stem cells have no epigenome as they are pluripotent. (I thought that since epigenome is what gives a cell its identity, no cellular identity means no epigenome) I saw something similar to this on this Wikipedia page. After fertilization, the paternal and maternal genomes are demethylated in order to erase their epigenetic signatures and acquire totipotency..
Other sources mention 'reset' in place of 'erase'.
This paper rather suggests that stem cells do have an epigenome. Specifically, genes associated with self-renewal are silenced, while cell-type-specific genes undergo transcriptional activation during differentiation..
I am not very literate in biology, please excuse me if I made a mistake.

So there are a couple of things to bear in mind.

pluripotent does not mean that all genes are active. It means that the stem cells have the ability to form different cell types. However, it still needs to keep the cellular programme of a neuron for example silent. So the epigenome is still present to keep other cell type programmes silent until there is a transition.

DNA methylation is not the only source of epigenetics. Active and inactive genes also correspond to particular post translational modifications on tails of histone proteins. In the cell, DNA is wrapped around histones to form what is known as chromatin.

Hope that is a starting point to answer your question


How to compare diversity between different ecosystems? I've used the Shannon Wiener Diversity Index for a single ecosystem (species as categorical variables). Do you know any alternative indices, especially ones that compare diversity between different samples/ecosystems ?

Have a look at the Wikipedia page on Diversity Index

Here are the indices that the wikipedia page describes

"True Diversity" Index
Species Richness
Shannon Index
Rényi entropy
Simpson index
Inverse Simpson index
Gini–Simpson index
Berger–Parker index

The article also links to related concepts such as

$\alpha$ Diversity
$\beta$ Diversity
$\gamma$ Diversity
Isolation Diversity
Relative Species Abundance

The literature is important on the question of measuring species diversity, ecosystemic function diversity and genetic diversity. What you want to use very much depends on your interest. Just to cite one other example: In the conservation literature, total sum of branch length over a phylogeny is sometimes used as measure of diversity and is sometimes used for prioritize populations (see for example Curnick et al. 2015). This method implicitely assume that more distantely related branches have different ecosystemic functions and keeping many of these functions is good for conservation purpose.


CRISPR guide RNA design and primer synthesis I am trying to knockout huntingtin gene from HeLa cells (human epithelial cells). I used CRISPR explorer and benchling.com to determine the best guide RNA sequence that would bind to the target DNA sequence and cas9 could then make the cut. The gRNA I have is as follows:

GGAGGCCTCGGGCCGACTCG
Strand (-)

The next step for me is to design the primers with the following sticky ends

Forward primer: 5'-TTGTTGN(19)-3'
Backward primer: 3'-ACN(19)AAA-5'

The problem I'm having is writing the oligonucleotide sequence of the primers. Since the gRNA strand is negative, I'm assuming it's a 3'-5' sequence, hence the reverse of it will be the 5'-3' sequence, which I can then just use as the forward primer. Sequentially, I can take the reverse and complement of this forward primer sequence to then determine the backward primer. Is that correct? I appreciate all your help.

Thank you,
Abdullah Chaudhary

A quick check with BLAST returned the following result:

Homo sapiens huntingtin (HTT), mRNA
Sequence ID: NM_002111.7Length: 13669Number of Matches: 1
Related Information
Gene-associated gene details
GEO Profiles-microarray expression data
PubChem BioAssay-bioactivity screening
Range 1: 267 to 286GenBankGraphicsNext MatchPrevious Match
Alignment statistics for match #1

Score           Expect  Identities  Gaps        Strand
40.1 bits(20)   0.017   20/20(100%) 0/20(0%)    Plus/Minus
Query  1    GGAGGCCTCGGGCCGACTCG  20
            ||||||||||||||||||||
Sbjct  286  GGAGGCCTCGGGCCGACTCG  267

The sequence you have is 5'-3' and it matches the Minus strand on the Human genome. You don't need to reverse the sequence!


What is genomic imprinting? What is a  genomic imprint? How does genomic imprinting take place?

If I say that "this" allele is maternally imprinted does it mean that the allele of the gene is passed only by the mother? If a pedigree is given, how can we identify whether the trait is paternally imprinted or maternally imprinted?

Please try to explain all this in as simple words as possible.

**** "What is a genomic imprint? How does genomic imprinting take place?"**

Genomic imprinting is an epigenetic mechanism  of inheritance which allows genes to be expressed differently depending on which parent they come from. This means it is modification of the genome, or changes what the genome produces, without changing the nucleotide (DNA) sequence. The result of imprinting in diploid organisms is that one of the two alleles is silenced.  This page provides a good overview of imprinting.

Two major mechanisms are proposed called DNA methylation and histone modification though others may yet be discovered. DNA methylation silences a gene by adding methyl groups to nucleotides (it modifies the nucleotide but not the sequence) which affects how they are expressed, whilst the exact mechanism is unknown (at least I can't find one on scholar) it does appear to be a key factor in some cancer growths. Genes can also be silenced by histone modification, binding a gene to histones reduces its activity, ie it produces less product.

Genomic imprinting was first described in Mealy Bugs (or at least this is one of the first described) which silence half of their genome in males. Whilst females are fully diploid, the male is also diploid but one half of the genome is silenced, making them effectively haploid. This is done by turning one half of the genome heterochromatic.

  ****"If I say that "this" allele is maternally imprinted does it mean that
  the allele of the gene is passed only by the mother? If a pedigree is
  given, how can we identify whether the trait is paternally imprinted
  or maternally imprinted?"**

Specific control of a gene, rather than entire chromosomes described above, is only known in plants and some mammals. In this case, when a gene is imprinted, the gene is silenced. An example is Igf2 in mice described in the below diagram which is maternal imprinting (ie the mothers allele is silenced). When the mother has a mutant allele and the father a normal allele and normal offspring is produced. When the male passes on the Igf2 mutant the offspring is mutant because the mother's normal copy was imprinted.

  The Igf2 gene can be seen in the above diagram. This is the one of the
  first evidences of genomic imprinting discovered. In the first part of
  the diagram a mutant gene trying to make the mouse offspring dwarf is
  passed from the mother. It can be seen that the mouse is not dwarf
  because the allele for size in this mouse is an imprinted. The
  maternal allele is not expressed, so the dwarf trait is not expressed
  in the offspring, only the normal size trait from the father is. In
  the second part of the diagram the father passes on the mutant gene
  and therefore all the offspring will be dwarf because the size trait
  is completely dependent on the paternal allele, which in this case is
  dwarf. - Creating Variation

The page this diagram and quote comes from also has a good section on genomic imprinting.


Mysterious spherical mass of feathers (Reddit) Original posting from Reddit

I am posting this here in the hopes that an ornithologist might be able to shed some light on this unusual finding.  Locality is Boise, Idaho.

This appears to be a roughly spherical mass approximately 6 cm diameter, most of which comprises tightly packed feathers with a central core of dermal tissue.  The mass has been parasitized by maggots.

I speculate that this is some kind of tumor, which detached from the afflicted organism, and the decaying tissue attracted flies after detachment.  But that's just a guess.  If anyone has seen such a phenomenon before, please feel free to enlighten me!

Note, I am not the individual who found this object.  I am merely relaying the question to this forum.

This is a flap of feathered skin from a Mallard, birds do not shed their skin. The bird in question is likely dead or at the very least, severely injured.

The skin and curved feathers has curled up around itself into a "ball". As it's flattened/separated you can see there is reddish skin with some tissue on it the maggots have gathered on. The feathers here are relatively small and curved and the pattern is SPOT ON for the breast/belly feathers of a Mallard.

While it's not really obvious in the photo of the Mallard below, it is very common for them to have that little bit of pale edging on the dark reddish-brown feathers, as seen in the first photo.

Photo by Jo Garbutt (Flickr: https://flic.kr/p/jVbHwP )


What are the trade-offs between polymerase chain reaction (PCR) vs Loop-mediated isothermal amplification (LAMP)? I've heard that LAMP could be a good alternative to PCR for DNA strand amplification and detection because the equipment required is cheaper, more portable, and the amplification is faster since all happens at a single temperature.

Since this system has clear advantages, I'm curious what are the downsides that prevent it from completely overtaking PCR/qPCR?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862059/ mentions some disadvantages:

  However, this technique has some limitations. Complexity of multiple primers’ designs for multiplication of new gene regions and selecting the suitable regions in the gene sequence for efficient design of primers, complicated product having cauliflower-like structures with different sizes, lack of commercial kits based on LAMP technique and complexity of this method mechanism are some of its drawbacks limiting its popularity among the researchers; and it not as common as PCR-based method.

but they just don't seem that important compared to the large benefits for diagnostic usage.

For example, from this video https://www.youtube.com/watch?v=L5zi2P4lggw I understand that more primers are needed, but is it that hard to "just create a few more primers"? Aren't those just deterministically determined from the target DNA of interest in this  case?

I can see why the cauliflower structures matter for certain applications, e.g. I guess those messy strands are not going to go through an Oxford Nanopore pore for sequencing, but do they matter when we just want to know if the DNA of interest is present or not?

Related articles:

https://www.researchgate.net/post/What_is_the_difference_between_a_PCR-RT_and_loop-mediated_isothermal_amplification_LAMP
https://www.ncbi.nlm.nih.gov/pubmed/22051073

I later learnt that there are other isothermal amplification amplification schemes out there as well, maybe  I knew about those I would have asked a more generic isothermal question:

RPA
which is apparently used in Abbot ID NOW system according to this and is being used for Covid-19 diagnostics.
HDA
NASBA
NEAR
Strand Displacement Amplification

Having to use more primers is definitely one of the big reasons. Primer design is difficult and time-consuming, and even more so if you're dealing with similar targets. For instance, if you're trying to differentiate closely related bacterial strains, having to design primers for 6 or 8 regions instead of just two is going to lower your ability to differentiate the strains. It's even worse if you're working with viruses - these mutate quickly and therefore your LAMP primers will fail to amplify the virus sooner than normal PCR primers.

LAMP is good because it's cheap and portable, but there are portable PCR thermocyclers starting to be produced (eg. miniPCR, Biomeme) and so diagnostically speaking, it's a lot easier to just use existing PCR primers that have been validated and are widely used, instead of creating new primers that you'll have to validate all over again.

The primers again are important if you're trying to amplify multiple targets - it's a lot easier to create degenerate or consensus primers for a standard PCR than it is for LAMP, and also easier to distinguish multiple target bands on a gel, which isn't possible for LAMP.

It can vary, but in my personal experience, I have always found Taqman-based PCR to be more sensitive than LAMP. You can't use Taqman probes with LAMP. You also can't use LAMP for cloning, and melt-curve analysis isn't possible with LAMP, which is useful for detecting primer dimers and diagnostically for distinguishing between targets.

So, LAMP is good because it's cheap, requires less equipment, can be done in the field with minimal reagents, and tends to be more robust than PCR as it is less prone to be affected by inhibitors. This means it is great for in-field diagnostics in developing regions. But there is a range of things PCR can do that LAMP can't, and the complex primer design alone will prevent it from overtaking PCR.


What does probe number and segmentation mean in copy number variation (CNV) data In TCGA Copy number variation (CNV) data there is a column with title Num_Probes. What is the meaning of probe number with respect to the sample data below?

Chromosome  Start   End Num_Probes  Segment_Mean
1   61735   62152   4   1.1973
1   62920   12777697    6514    2.2882

According to wikipedia, probes are usually 100-1000 bases long. Then does it mean in the first row above that, it took 4 probes to identify the region(61735 - 62152). In that case what would be the meaning of Segment_Mean?

The data you posted looks like it was produced by GISTIC, a program commonly used by TCGA to detect copy number changes. Assuming the data really is GISTIC-produced, my understanding is that "Segment_Mean" refers to the average Log2 Ratio of the probes in that particular segment. Looks like the copy-number of your 4-probe segment in your example is slightly less than half the copy-number of the longer segment.

You can also try using the GISTIC Google-Group to learn more.


What are tail currents? This is a voltage clamp on an ion channel. When the voltage is stopped there is a still a current at the end (the tail current). I understand that the gates aren't completely closed because of which there is still some current flowing.

What I don't understand is that why does the current suddenly jump to a small value? Shouldn't it gradually go down?

OK, I know this is old, but here goes. The tail current is the current at -55mV after the voltage step, here:

The current shrinks as the voltage changes, this causes a massive shift in the driving force for the ions either side of the cell membrane. Going from -125 to -55 mV for the largest step. As commented, the dense vertical bands either side of the step are due to fast capacitance readings, basically ignore unless you want to go down a whole other avenue.

The reason for the tail currents is some channels remain open and close gradually after the step ends "tailing" off. We can't really say what channels these are as we know nothing about the recording conditions/cells involved. However these currents are large, so most likely to be sodium/potassium.


Are 2A cleavage sites functional in bacteria? In mammalian cell lines, 2A self-cleaving peptides are frequently used to for expression of multiple genes from a single transcript. They've got some issues, e.g., leaving some proteins as fusions, but so do all of the other options, so 2As are a pretty good choice for many situations.
I have found 2As being used in many other organisms as well, including yeast and plants, but they seem to generally not be used for bacteria.  I've found a couple of articles (e.g. [1], [2]) that do claim to have successfully used 2A sequences in bacteria. If this actually worked well, however, I would expect to see it much more widely used.
Are 2A sites in fact functional in bacteria and, if so, are there any issues that inhibit their use there?

2A self cleaving peptides do apparently work in bacteria (as the papers in your question suggest), but it seems that they are not commonly used in these chassis simply because they are not needed.
For context, in prokaryotes, translation is initiated by the ribosome binding to a shine-dalgarno (SD) sequence on the mRNA. These SDs can be placed anywhere along the mRNA strand, and so multiple SDs can be present. This means that translation can begin at multiple points along the mRNA, and hence proteins can be co-expressed by one promoter by including multiple RBSs and stop codons within the expression unit (i.e. promoter-RBS-CDS1-stop-RBS-CDS2-stop-terminator).
However, in many eukaryotes, translation begins at the 5' end of the mRNA where the ribosome is assembled, and scans along the mRNA until it finds the start codon. Once the protein has been synthesised and the stop codon reached, the ribosome falls off of the mRNA. This means that if there was another CDS encoded after the first stop codon, it won't be translated.
It should be noted that it is possible for eukaryotes to generate mRNA encoding multiple proteins, but as it was assumed for a long time that this was unique to prokaryotes, there is less research for this in eukaryotes. This paper has some useful information: https://academic.oup.com/femsyr/article/2/2/215/536601.
Because of these differences, for most applications, if co-expression in bacteria is required it is much simpler to add in multiple RBSs and stop codons than to rely on something like 2A peptides which, as you mentioned, do not always work and can result in fused proteins. However in eukaryotes, techniques such as 2A peptides are important considerations for co-expression as poly-cistronic mRNA (mRNA encoding multiple proteins) seem to be much less common.
This doesn't mean that there aren't applications for 2A peptides in bacteria, but they are much more specific and hence their use doesn't turn up so much in the literature.
These wikipedia pages have some good reading and references:

https://en.wikipedia.org/wiki/Internal_ribosome_entry_site
https://en.wikipedia.org/wiki/Eukaryotic_translation

Disclaimer: I don't work with eukaryotes so most of the information about gene co-expression and how common it is has been gathered from reading for this question.


Statistical method for characterizing the relationship between body mass and metabolic rate There is a dataset that contains body mass ($x$) and metabolic rate ($y$) from many different organisms. It is common to fit the data to the model of the form $y=ax^b$ and estimate the parameters $a$ and $b$ (see Kleiber's law and The Metabolic theory of ecology). In doing so, it is also common to log transform $y$ and $x$ and create the linear relationship log($y$)=log($a$)+$b$log($x$) and perform linear regression analysis based on the log transformed data. Is this approach better than directly estimating $a$ and $b$ based on nonlinear regression for $y=ax^b$ (because results are different)?

Short answer: The results of the two approaches (linear versus non-linear model) do not match because the relationship between body mass and basal metabolic rate does not strictly follow a power law.

It is indeed the case that if the relationship between two variables follows a power law the two approaches should provide comparable results, but important differences could arise due to Jensen's inequality. In order to test whether the reported differences between the two approaches are due to Jensen's inequality or to some biological factor I obtained data from Kolokotrones et al. (2010) who have in turn taken them from McNab (2008). Kolokotrones et al. (2010) investigated the issue of whether a power law is appropriate by performing linear regression on log-transformed data but they did not attempt to fit the data with non-linear regression.

I've fitted a non-linear model of the form:
$$ B = \alpha M^b$$ , where $M$ the body mass (in grams) and $B$ the basal metabolic rate (in Watts),
which gave coefficients $\alpha = 0.005$ and $b = 0.87$.
I also fitted a linear model of the form:
$$ log_{10}(B) = blog_{10}(M) + log_{10}(\alpha) $$
which gave coefficients $ \alpha = -1.7 $ and $ b = 0.72 $.

It appears that the results of the two approaches are indeed different. Below I plot the results of the two fits. On the variables' original scale we see that the linear model fails to predict observations from species with large mass and that the non-linear model does much better in this respect (upper left). However, when we look at the two models after log-transform, it is clear that the non-linear model fails to predict many observations from species with low mass (upper right). Looking at the residuals of the non-linear model we see that the errors are multiplicative as the variance of the residuals is increasing with (log-transformed) fitted values (bottom left). This indicates that fitting with a linear model on log-transformed data is warranted. However, the plot of linear model's residuals over log-transformed fitted values (bottom right) confirms that the linearity assumption is violated. Thus, neither method is appropriate for this dataset and the quadratic term the authors of the cited paper added in the linear model fitted on the log-transformed variables appears to be warranted in order to account for the observed convexity.

We can conclude that for this dataset the results of the linear model approach do not match those of the non-linear model approach because the data do not strictly follow a power law. Rather, the megafauna appears to follow a different trend compared to smaller animals. Kolokotrones et al. (2010) found that adjusting for temperature improved the linear fit, in addition to the inclusion of the quadratic term. The resulting model was:

$$ log_{10}B = \beta_0 + \beta_1log_{10}M + \beta_2(log_{10}M)^2 + \frac{\beta_T}{T} + \epsilon $$

The R code used to generate the results for this answer along with the data used can be found in the following git repository in GitLab:
https://gitlab.com/vkehayas-public/metabolic_scaling

 References
Kolokotrones, T., Van Savage, Deeds, E. J., & Fontana, W. (2010).
Curvature in metabolic scaling. Nature, 464:7289, 753–756. https://doi.org/10.1038/nature08920
McNab, B.K. (2008). An analysis of the factors that influence the level and scaling of mammalian BMR. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 151:1, 5-28. https://doi.org/10.1016/j.cbpa.2008.05.008.


Cardiac cycle and atrial contraction During atrial contraction ("a" in the figure), why does the ventricular pressure match the atrial pressure? The ventricular pressure generally stays the same throughout passive filling until it reaches the point where atrial contraction occurs. Why is there a sudden change in the ventricle pressure during atrial contraction? I can understand the atrial pressure would increase when the atria contract, but the ventricles have not contracted yet so the ventricle pressure shouldn't increase. The ventricle pressure can increase greatly when the volume exceeds a certain value and the elastic tissue of the heart cannot stretch anymore. However, the volume here is only about 110ml, so it has not reached that point. I can only think of one explanation:

The pressure is equilibrated between two sides of an open valve.

However, this doesn't explain why the atrial pressure is slightly greater than ventricle pressure during filling; it also doesn't explain why the aortic pressure is slightly greater than the ventricle pressure near the end of ejection.

While blood is flowing into the ventricle, it can never be at a higher pressure than where blood is flowing from: if it was, the flow would be going in the other direction. Flow is always from higher to lower pressure, if there is no pressure difference there is no flow.

Before atrial contraction, the ventricle can have no more pressure than the uncontracted atrium, which in turn can have no more pressure than the veins (vena cava or pulmonary depending on which side of the heart we are talking about). When the atrium contracts, it increases the pressure in the atrium, which causes a flow of blood into the ventricle. Whenever a fluid flows, there is a pressure drop that depends on the resistance (very much like voltage in an electrical circuit). However, the AV valve is fairly big and open, so there is little pressure drop from the atrium to ventricle.

  The pressure is equilibrated between two sides of an open valve.

...is mostly true if the valve is large enough. There is still some pressure drop, though: if there wasn't, there wouldn't be flow.

There is no need for the ventricle to be at maximum capacity for pressure to increase. Imagine if you squeeze one side of a balloon: the pressure in the balloon increases, which you can tell because the balloon stretches and expands in the areas you are not squeezing; it need not be at the maximum capacity of the balloon for this to happen. Same for the heart.

As far as the higher pressure in the aorta, I this diagram is slightly exaggerating where the pressure difference starts, but as the ventricle relaxes there is a brief time where you get a small backward flow because the relaxing ventricle ends up having less pressure than the proximal aorta. This pressure drop is what closes the aortic valve (or the pulmonary valve, same process).


Why do nerve gas victims have chronic neurological issues? The article on Wikipedia says the following:

  The effects of nerve agents are long lasting and increase with continued exposure. Survivors of nerve agent poisoning almost invariably suffer chronic neurological damage and related psychiatric effects.

Unfortunately, the original paper seems to be paywalled. Why does this happen? Is it because it takes a long time to replenish the acetylcholinesterase inhibited by the nerve agent?

Here is the link to the original paper.

Most of the nerve agents (and quite a number of commercially used pesticides) fall into the class of organophosphates (OP). Their mechanism of action is the inhibition of the acetylcholin esterase which leads to the build-up of acetylcholine in the body and thus a permanent activation of mucarinic and nicotinic acetylcholine receptors.
Irreversible inhibitors of AChE may lead to muscular paralysis, convulsions, bronchial constriction, and death by asphyxiation - and organophosphates can act as these. See here for some more information.

According to reference 1, four different toxic effects can be differentiated:  The cholinergic syndrome, the intermediate syndrome, organophosphate-induced delayed polyneuropathy (OPIDP) and chronic organophosphate-induced neuropsychiatric disorder (COPIND).

The cholinergic syndrome is happening in the acute phase of the OP poisoning and can be explained by the inhibition of the acetylcholin esterase.

All quotes are from reference 1:

  In cases of human poisoning, general acute symptoms of peripheral
  nicotinic and muscarinic intoxication are clearly apparent.
  These symptoms include miosis
  (unreactive to light); sweating, rhinorrhea, lacrimation, and
  salivation; abdominal cramps and other gastrointestinal symptoms;
  respiratory difficulties and cough; dyspnea, constriction sensation in
  the chest, wheezing; twitching of facial muscles and tongue, tremors,
  and fasciculations; bradycardia and ECG changes, pallor, and cyanosis;
  anorexia, nausea, vomiting, diarrhea, and involuntary urination and
  defecation. These signs and symptoms are accompanied by central
  effects such as dizziness, tremulousness, and confusion; ataxia;
  headache, fatigability, and paresthesia. Finally, seizures,
  convulsions, twitching, coma, and respiratory failure may also occur.
  If the subject survives the first day of poisoning, personality
  changes, mood swings, aggressive events and psychotic episodes
  including schizoid reactions, paranoid delusions, and exacerbations of
  preexisting psychiatric problems may also ensue.

The intermediate syndrome happens after the acute phase, around 7,7% of the patients develop it.

  The term Intermediate Syndrome (IMS) was first described by Senanayake
  and Karalliedde (1987) because it appeared in the interval between the
  end of the cholinergic crisis and the onset of OPIDP. Following
  exposure to various OP pesticides, clinical manifestations of IMS
  typically occur within 24–96 h, and affect patients without
  fasciculation or other cholinergic signs. The reported incidence of
  IMS ranges from 7.7% to as high as 84% (Shailesh et al., 1994).
  Although IMS is well recognized as a disorder of neuromuscular
  junctions, its exact etiology, incidence, and risk factors are not
  clearly understood. IMS generally occurs among patients with prolonged
  and severe inhibition of AChE, although not every patient with severe
  AChE inhibition develops IMS. Other risk factors of IMS include
  delayed metabolism of OP pesticides due to toxicokinetic factors or
  impaired organ function, severity of poisoning, elevated muscle
  enzymes, plus adequate or late oxime therapy. IMS has been linked with
  exposure to specific OP pesticides displaying the dimethyl phosphate
  moiety (e.g. fenthion, dimethoate, monocrotophos, dichlorvos,
  methylparathion) but has also developed after exposure to parathion
  (ethyl phosphate) and methamidophos (phosphoramidate; De Bleecker et
  al., 1993; Yang and Deng, 2007).

The organophosphate-induced delayed polyneuropathy (OPIDP) cones later and has been connected to the phosphorylation and subsequent ageing of the neuropathy target esterase by the OP (see reference 1 and 3).

  OPIDP is relatively rare neurodegenerative disorder in humans that is
  characterized by loss of function and ataxia of distal parts of
  sensory and motor axons in peripheral nerves and ascending and
  descending tracts of spinal cord. The early neurological symptoms
  usually are sharp, cramp-like pains in the calves, tingling in the
  feet and hands followed by distal numbness and paresthesia. Pain and
  weakness in muscles spread rapidly and patients become unsteady and
  unable to keep their balance. Progressive leg weakness occurs,
  together with depression of tendon reflexes. Symptoms may also appear
  in the arms and forearms. Sensory loss may be mild. Muscle tonus of
  the limbs gradually increase and spasticity appears in the lower
  limbs. Physical examination reveals distal symmetrical and mainly
  motor polyneuropathy, with wasting and flaccid weakness of distal limb
  muscles, especially in the lower limbs. In severe OPIDP quadriplegia
  with foot and wrist drop were observed as well as mild pyramidal signs
  (Lotti, 1992). There may be some functional recovery in less severe
  cases with more distal involvement and sparing of spinal cord axons,
  but pyramidal and other signs of central neurological involvement may
  become more evident with time. The recovery affects only sensory
  nerves, while motor neurons may permanently lose function as indicated
  by Morgan (1982) who described the lack of improvement over 47 years
  in 11 patients poisoned with TOCP.

The chronic organophosphate-induced neuropsychiatric disorder (COPIND) happens to persons with a chronic exposure to OP and is most likely caused by permanent damages to the central nervous system (CNS), but the real cause is not known yet.

  The most common symptoms of COPIND include cognitive deficit
  (impairment in memory, concentration and learning, problems with
  attention, information processing, eye-hand coordination and reaction
  time), mood change (anxiety, depression, psychotic symptoms, emotional
  lability), chronic fatigue, autonomic dysfunction, peripheral
  neuropathy and extrapyramidal symptoms such as dystonia, resting
  tremor, bradikynesia, postural instability and rigidity of face
  muscles

References

Neurotoxic effects in patients poisoned with organophosphorus
pesticides
Long-term health effects of nerve agents and mustard
Neuropathy target esterase (NTE) and organophosphorus-induced
delayed polyneuropathy (OPIDP): recent advances


Below which temperature human muscles don't work? When one exposes theirs body parts to cold environment (especially foot and hands), they may be numb, with temporarily blocked both muscles.

What is typical body temperature below which human muscles don't work properly?

Moreover, what is the mechanism behind it?

EDIT:

Interested in case when muscles almost cease to work (e.g one is not able to grasp a cup), not just in small perturbations to strength.

If you dissect striated muscle out of most-any organism, the actual contractile apparatus works over a wide range of temperatures. So that's at the single-muscle-fiber scale. The muscle itself continues to work at all (thawed) temperatures below body temperature -- the problem comes with its regulation.

The shivering response -- a centrally controlled  involuntary contractile pattern -- overwhelms voluntary muscle control. So the mechanism behind loss of muscle coordination in hypothermia is the same as the shivering mechanism. When the core temperature drops, the midbrain starts over-riding voluntary control of the muscles. When the core temperature drops far enough; around 32C, the shivering often slows down or stops. Voluntary movement becomes compromised probably because the brain simply isn't working; neuron firing rates are so slow that sensation, processing, and motor responses are all critically impaired.

The feeling of numbness does not actually directly accompany a loss of muscle contractility. You can walk pretty much indefinitely on frozen feet if you can keep your balance (and you keep your core temperature up.) Lots of people survive severe frostbite of their feet (their feet do not often survive, however.) The reason why it seems your hands don't work when they get cold is that you can't feel what you're doing (note; your hands can be much colder than your core body temperature.) But the muscles themselves work right up until they freeze solid.

UPDATE:
 Here's a paper that directly addresses the scenario posed by OP -- the decrease in grip strength with temperature.   Figure 1 of that paper illustrates their experimental setup; they measure the contractile strength of the index finger while manipulating the temperature of the rest of the hand. They show that contractile function is impaired with temperature and look at temperatures as low as 12C.

They measure as much as a 50% impairment on twitch tension upon cooling to 12C. It's interesting that they review results suggesting that some of this effect is intrinsic to the muscle fiber (not neurological), showing that I should refine what is meant by "continuing to work" in my opening paragraph. (I meant having an ability to generate contractile force when equilibrated in solution containing sufficient ATP and Ca$^{2+}$, not the ability to contract optimally.) For fun, I linearly extrapolated the final arm of Figure 5 and found that the 'voluntary tension' approached 25% at 5C. This suggests that total failure of the voluntary contraction happens somewhere below the freezing point of water (muscle would freeze at a temperature lower than 0C because of colligative effects.)


Why do our epiphyseal plates close up in our late teens or early twenties? What causes our epiphyseal plates close up in our late teens or early twenties?

I realize that one's genetics plays the main role in this. I assume there is a gene that controls the epiphyseal plates in our long bones. I guess there would be genes dedicated to every single epiphyseal plate found in our body too. So to rephrase the question:

Why does the gene for our epiphyseal plates turn off in our lates teens or early twenties?

During Endochondral ossification  chondrocytes in the plate are rapidly dividing, newer daughter cells stack facing the epiphysis while the older cells are pushed towards the diaphysis. As the older chondrocytes degenerate, osteoblasts ossify the remains to form new bone.

In puberty increasing levels of estrogen, in both females and males, leads to increased apoptosis of chondrocytes in the epiphyseal plate. Depletion of chondrocytes due to apoptosis leads to less ossification and growth slows down and later stops when the entire cartilage have become replaced by bone, leaving only a thin epiphyseal scar which later disappears. Once the adult stage is reached, maximum height is reached.

Your question addresses the genetics of this process however it is more so regulated by the endocrine system. There has not been a single gene assigned to growth plates, or its regulation, and I find it unlikely that there ever will be.

Rather, endochondrial ossification takes place because of hundreds of genes interacting with each other. If you start to look at genes involved in apoptosis and the estrogen receptor pathway, you will begin to appreciate more the complexity behind the physiology.

I have a hunch you were looking for a gene, that with age just shuts off, or turns on. Recent evidence has show this does in fact happen as methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002629


What is this worm or larva I found in my walls We were recently doing some major remodeling in our 1920s era home and found what looks like a nest of small meal worms. I am wondering if anybody can identify them! Here are some photos:

Our home is in Denver CO. I didn't see any living examples so it is possible they have been there for nearly 100 years.

You are correct!, those are definitely mealworms. If you're not already aware, mealworms prefer to live in dark places (so under/in woodwork is expected) and typically eat decaying material, but are also partial to consuming new plant growth.

During the larval stage of a mealworm (of which will eventually grow into a Darkling Beetle), a mealworm will undergo 10-15 molts before pupating. That being said, the collection of carapaces that are shown in your picture is probably the work of just a few beetles.

I cannot attest as to how long it takes for a mealworm carapace to deteriorate, but sure, those remains could very well have been there for decades. If the location in which you found these remains has a dirt floor, you could possibly try identifying trails that were left by the developed beetles. Their trails looks like this:


Why Do Ruminants Require A Multi-Compartment Stomach To Digest Food? Cows, camels, sheep, goats, etc being ruminants must chew their food repeatedly by regurgitating their food from their first stomach compartment and chewing their 'cud'. This then finer chewed material makes its way to the various stomach compartments to be digested.

These animals are eating plant material, the same plant material animals such as elephants, horses and hippos eat as well. However, these animals only have one stomach compartment.

Why does one need a multi-compartment stomach and one does not if they are all eating the same/similar food?

There is more difference than just the parts of plants that are eaten.

Two of their stomachs - rumen and reticulum are not used for digesting food at all. Multiple rounds of chewing and mixing with saliva, wich result in very small particles of undigested food help the bacteria in those stomachs reach, digest and use that cellulose-rich plant material. Cows "eat" the bacteria from their stomachs and the grass is just food for these bacteria. You could say that cows are not herbivores but secondary consumers.

Look at this picture (from Wikipedia article on ruminants, a good place to check all this in more detail but still simpler than most professional books):

See that the ruminants have the same second and third part of their digestive system (though the bacteria use up most of carbohydrates, so some difference in absorbed material), but have an additional part in the front - where the microbes digest and ferment the food, that the ruminant has provived them. The reticulorumen needs to be large in order to provide space for all that plant material and bacteria.


Is there any reason for the variation in mitochondrial DNA size? As my textbook An Introduction to Genetic Analysis points out, yeast mitochondrial DNA has approximately 78 kb of genetic data, while the human mitochondrial DNA contains 17 kb. Is there any evolution reason for this drastic change in size? Also, are there any particularities about mitochondrial function that have been compromised with this reduction in size?

References

Griffiths, Anthony J. F. An Introduction to Genetic Analysis. New York: W.H. Freeman, 2000.

One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed homing endonucleases genes (HEGs).  These genes are typically found in introns that encode site-specific DNA endonucleases.  These endnoclueases cleave the HEG- alleles during yeast mating leading to DNA recombination using the HEG+ allele as template.  I suspect over time as organisms became more complex and HEGs become unable to mobilize they would become fixed in the organisms genome.  Upon being fixed there is no selection pressure to maintain the open reading frame of the HEG or the intron its encoded within (ref).  This causes the eventual loss of the HEG and intron since they provide no real benefit to the organisms genome.

I don't know how much of the yeast mitochondrial genome is taken up by these introns.  I believe that there are 4 of them in yeast some of the introns also require reverse transcriptase for splicing and mobility.  Other fungal species can have many more introns and sometimes weird things like introns embedded within introns.


What spider is this in Idaho? I have killed maybe 5 of these little bastards as I have a 3 year old and dont want her bit.  Should be able to zoom in quite a bit. Just hold CTRL and hit the plus symbol.

Whitish top
brown legs
stripped maybe yellow or white on the butt with black
Seen them all times of the day.

Kinda reminds me of the ant-mimic spider but I am unsure, need assistance.

And a close up:

I'm just about 100% certain that this is a Hobo Spider, which belongs to the species Eratigena agrestis. As stated in my comment, the blemish on the vacuum cleaner's plastic makes it difficult to observe the full pattern on the spider's abdomen, which would have otherwise made for a much quicker identification.

Once realized though, the distinguishing feature for me was in fact the pattern on the abdomen. If you look at the picture I provide and consider at the abdomen, it looks like a face with two eyes, a mouth, some hair, and a beard; i.e., a hobo. Now look at the picture in the OP -- the exact same "face" can be seen, excluding the right "eye" of the hobo (our left), due to the blemish on the vacuum's plastic. The "hair" at the pedicel, the down-turned "mouth", and the "beard", are all visible in both images, and are near perfect matches. The legs, overall body coloration, size & proportionalities, and slight discoloration on the cephalothorax, also match.

I had to maximize the OPs image to 200% zoom to get a detailed enough view of the spider to then make these conclusions.

This species spider is most commonly found in your region, that being north west USA, however, they've also been seen in Asia and Europe. And as for if this is a venomous spider (since you're concerned about your daughter): according to Wiki, this kind of spider doesn't bite unless forced to defend itself, and, the CDC does not consider it to be dangerously venomous.


How much time do the different mechanisms of gene regulation need to take effect? I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference.

If non-active regulator genes using each of the different mechanisms were activated, what would be delay (on average) between each of those genes' activation and their downstream regulatory effect?

People often imprecisely say that type of regulation takes place on the order of many minutes to hours, and that may be as precise as you can get given the variable kinetics of any given pathway.

Also, all genes in eukaryotes require general transcription factors, but basically all of them also require activators to act first to recruit the GTFs and histone modifying components (which allow GTFs and their friend RNA polymerase to access genes). So, they are generally downstream of activators and their recruitment is part of what contributes to the kinetics in euakryotes.

For RNAi, the kinetics of knockdown in RNAi could largely depend on the rate of degradation of the protein (which is HIGHLY variable). Even if you take away the mRNA, the protein is still there until it's degraded. If it's normally degraded fast, the kinetics of mRNA degradation will be limiting. If it's slow, then you have to wait for the protein to be degraded by its natural mechanisms (https://en.wikipedia.org/wiki/Proteasome).

Sigma is saying RNAi effects can be seen in around 24 hours

http://www.sigmaaldrich.com/life-science/functional-genomics-and-rnai/sirna/learning-center/mission-sup-reg0/experimental-design0.html#s3

Thermo is implying something similar by saying RNAi effects can be seen for 5-7 days post-transfection (i.e. they imply that it can be seen after a day).

https://www.thermofisher.com/ca/en/home/references/ambion-tech-support/rnai-sirna/tech-notes/duration-of-sirna-induced-silencing.html


Why does colchicine not affect the source plant itself? Colchicine, being a mitotic poison that blocks spindle fibre formation, should affect its source plant. It should also stop its cells from dividing. So how do they grow?

I think that there might be some cells that synthesise it seperated (by many layers of cells) from other cells. So the rest cells are not affected.

Colchicine is an alkaloid and a secondary metabolite of the plant- a crocus, primarily functioning to protect the plant (like, from consumption by herbivores).

WHY COLCHICINE DOES NOT AFFECT THE PLANT:

It is transported far away from its site of production to the tissue storing it so does not come in contact with normal metabolically active plant cell machinery.
In the storage tissues colchicine is compatmentalised in vacuoles specific for colchicine storage.

The vacuoles are bounded by tonoplast which contains special proteins that facilitate active uptake of colchicine from the cytoplasm into the vacuole protoplast but do not conduct the movement of colchicine from the vacuole to the cytoplasm.

The scientific studies are detailed here.


Protocol for checking pipette calibrations using absorbance readings of a dye in solution? I've been looking around the net looking for a nice protocol to validate micropipette calibrations using absorbance readings of a dye in solution. Does anyone have one they can share? I'd highly appreciate it!

I see what you are getting at however this would be a very WRONG way of calibrating such an instrument. If dyes varied among trials it would throw off your calibration. Also, you would need to generate some sort of standard curve to equate absorbance to weight, since true calibration of these instruments is done by weighing the volumes they dispense (1g = 1ml water). The weight of water and the weight of your dye solution will not increase the same in terms of moles/g. Also a scale is far easier to calibrate that the detector in any spectrophotometer. Calibrate pipettes by weighing the volume of water they dispense. It should be done in a chamber that inhibits evaporation and you need a precision scale.

Here's a reliable guide for pipette calibration

enter link description here


Are there people cured of HIV by means of HAART? I wonder if there people who were cured of HIV only by means of highly active anti retro-viral therapy (HAART) or other drugs rather than by bone marrow transplant?

I know that HAART can suppress HIV below detectable level but are there people who stopped HAART and did not experience the HIV levels rising?

This very recent (and freely available) review pretty much sums the problem up in the introduction:

http://dx.doi.org/10.1038/clpt.2012.202 (Barton et al., 2013: Prospects for Treatment of Latent HIV)

And here's an update more specifically on the problems with actually curing an individual of HIV infection, if you have access: http://dx.doi.org/10.1016/S0140-6736(13)60104-X (Katlama et al., 2013: Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs)

Essentially, current antiretroviral therapy (ART) is able to nearly fully suppress active HIV, practically restoring the individual to a healthy status, including the prevention of transmission from them. However, the therapy needs full adherence (missing a dose can already cause viral loads to rise) and is lifelong. The reason for this is because HIV integrates into the genome of host CD4+ T cells, of which there are latent populations in places difficult to reach with therapeutics such as peripheral lymph nodes.

Apparently, some rare individuals actually achieve a "functional cure", i.e. the body is able to suppress viral replication for a given period of time (5 years) without ART. But these patients "are characterised by a favourable HLA profile and potent HIV-specific CD8 T-cell responses that are associated with a low viral DNA reservoir" (Katlama et al). They also mention another group of five patients who did not seem to have a favourable genetic profile and were still able to control HIV following cessation of ART for several years (http://dx.doi.org/10.1097/QAD.0b013e32833b61ba Hocqueloux, 2010: Long-term immunovirologic control following antiretroviral therapy interruption in patients treated at the time of primary HIV-1 infection). So it seems there are plenty reports of people who are able to remain free of detectable viral loads and maintain CD4+ T cell counts for a long time after treatment, but it doesn't seem like any of them stay permanently virus-free.


If the brain has no pain receptors, how come you can get a headache? I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.

Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.

So it lead me to the question: How come people can get headaches if the brain has no nerves?

Brain, indeed, cannot feel pain, as it lacks pain receptors (nociceptors). However, what you feel when you have a headache is not your brain hurting -- there are plenty of other areas in your head and neck that do have nociceptors which can perceive pain, and they literally cause the headaches.

In especially, many types of headaches are generally thought to have a neurovascular background, and the responsible pain receptors are associated with blood vessels. However, the pathophysiology of migraines and headaches is still poorly understood.


What terms or concepts are used to describe the morning metabolic phenomenon involving glucocorticoids, glucose, and blood pressure? A recent conference report described using a vaccine-based strategy to blunt a surge of high blood pressure that occurs between 5 and 8 a.m.  Apparently most heart attacks and strokes occur during this period, which makes this of special importance.  Presumably this ties in with preceding work showing that ordinary blood pressure medication is more effective when taken in the evening.
When I read about the "dawn phenomenon" (reduced glucose tolerance in type II diabetics) it is often treated in isolation.  Because glucocorticoids are a factor in the dawn phenomenon, it makes sense they could be involved in raising blood pressure during the same period.
This makes me wonder how much more I have missed.  There seems to be something special about the morning period in metabolism, something deserving of some name as fundamental as "sleep".  Yet I don't have one to use, and I don't know why it evolved, how its timing is determined, what its advantage is, whether it correlates with worker productivity, whether early risers and late risers and night shift workers have this period at the same time and so on.  Medical labs typically open at 7:30 a.m. - do they reference the time in relation to any of these phenomena?
Thus the question: what terms or concepts would you suggest to help someone research and pull together existing knowledge about the metabolic changes that occur in the morning?

Morning surge, Prewaking surge, Sleep-trough surge, Rising surge.
Example of article using the terms:
"Morning Surge in Blood Pressure and Cardiovascular Risk"
https://www.ahajournals.org/doi/full/10.1161/HYPERTENSIONAHA.110.157149
This one is interesting in that it lists other articles and the term they used for the period you are looking for.


Food allergen-related skin reactions and intestinal inflammation? Are there any connections between food allergen-related skin reactions causing intestinal (or more broadly, gastrointestinal) generalized inflammation?

If such a link exists, is it related to any of the inflammatory bowel diseases (Crohn's, colitis, irritable bowel syndrome)?

Afaik the most probable trigger of IBDs (Crohn's, colitis ulcerosa) are changes in the gut microbiota due to western lifestyle (high intake of some nutrients e.g. milk fat). These changes cause an inflammation in the susceptible (genetic factors) people. So the cause of IBDs is very likely not an allergic reaction.

According to wikipedia IBS is not an IBD (inflammatory bowel disease). It is a functional disorder of the bowel, so not so serious as the IBDs. Its possible causes are low grade inflammation of the bowels and neuroendocrine disregulation. It has genetic factors as well. The pathomechanism is not fully understood yet.

There are many bowel diseases which can be caused by specific foods, e.g. celiac disease, lactose intolerance, and so on, the list is long, many of them can be caused by food protein intolerance. It is my understanding of protein sensitivity that skin conditions are caused by B-cell (IgE) mediated immune response, while bowel conditions are caused by T-cell mediated immune response. Ofc. there is connection between them, so it is possible that a certain type of protein induces skin symptoms and intestinal symptoms as well. Based on the current studies I think food sensitivity is not related to IBDs, and probably not related to IBS as well.

  CD is associated with dramatic changes in the gut microbiota and this
  was particularly evident for individuals with ileal CD.

2008 - Molecular analysis of the gut microbiota of identical twins with Crohn's disease

  Molecular profiling of faecal bacteria revealed abnormalities of
  intestinal microbiota in UC and IBS patients, while different patterns
  of Bacteroides species loss in particular, were associated with UC and
  IBS.

2010 - Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota

  Breakdown of the normal microbial community increases the risk of
  pathogen infection, the overgrowth of harmful pathobionts and
  inflammatory disease. Understanding the interaction of the microbiota
  with pathogens and the host might provide new insights into the
  pathogenesis of disease, as well as novel avenues for preventing and
  treating intestinal and systemic disorders.

2013 - Role of the gut microbiota in immunity and inflammatory disease
2014 - Role of the gut microbiota in inflammatory bowel disease
pathogenesis: What have we learnt in the past 10 years?

  Crohn's disease and ulcerative colitis are idiopathic, chronic,
  relapsing, inflammatory conditions that are immunologically mediated.
  Although their exact etiologies remain uncertain, results from
  research in animal models, human genetics, basic science and clinical
  trials have provided important new insights into the pathogenesis of
  chronic, immune-mediated, intestinal inflammation. These studies
  indicate that Crohn's disease and ulcerative colitis are heterogeneous
  diseases characterized by various genetic abnormalities that lead to
  overly aggressive T-cell responses to a subset of commensal enteric
  bacteria. The onset and reactivation of disease are triggered by
  environmental factors that transiently break the mucosal barrier,
  stimulate immune responses or alter the balance between beneficial and
  pathogenic enteric bacteria. Different genetic abnormalities can lead
  to similar disease phenotypes; these genetic changes can be broadly
  characterized as causing defects in mucosal barrier function,
  immunoregulation or bacterial clearance. These new insights will help
  develop better diagnostic approaches that identify clinically
  important subsets of patients for whom the natural history of disease
  and response to treatment are predictable.

2006 - Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis.
2011 - Proinflammatory Cytokines in the Pathogenesis of Inflammatory Bowel Diseases
2014 - Role of Regulatory B Cells in Chronic Intestinal Inflammation: Association with Pathogenesis of Crohn's Disease
2013 - Effects of Enteral Nutrition on Crohn’s Disease: Clues to the Impact of Diet on Disease Pathogenesis

  The composite human microbiome of Western populations has probably
  changed over the past century, brought on by new environmental
  triggers that often have a negative impact on human health1. Here we
  show that consumption of a diet high in saturated (milk-derived) fat,
  but not polyunsaturated (safflower oil) fat, changes the conditions
  for microbial assemblage and promotes the expansion of a
  low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia2.
  This was associated with a pro-inflammatory T helper type 1 (TH1)
  immune response and increased incidence of colitis in genetically
  susceptible Il10−/−, but not wild-type mice. These effects are
  mediated by milk-derived-fat-promoted taurine conjugation of hepatic
  bile acids, which increases the availability of organic sulphur used
  by sulphite-reducing microorganisms like B. wadsworthia. When mice
  were fed a low-fat diet supplemented with taurocholic acid, but not
  with glycocholic acid, for example, a bloom of B. wadsworthia and
  development of colitis were observed in Il10−/− mice. Together these
  data show that dietary fats, by promoting changes in host bile acid
  composition, can markedly alter conditions for gut microbial
  assemblage, resulting in dysbiosis that can perturb immune
  homeostasis. The data provide a plausible mechanistic basis by which
  Western-type diets high in certain saturated fats might increase the
  prevalence of complex immune-mediated diseases like inflammatory bowel
  disease in genetically susceptible hosts.

2012 - Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice

  The pathogenesis of IBS seems to be multifactorial, with the following
  factors playing a central role in the pathogenesis of IBS:
  heritability and genetics, dietary/intestinal microbiota, low-grade
  inflammation, and disturbances in the neuroendocrine system (NES) of
  the gut

2012 - Irritable bowel syndrome: Diagnosis and pathogenesis
2014 - Melatonin Regulation as a Possible Mechanism for Probiotic (VSL#3) in Irritable Bowel Syndrome: A Randomized Double-Blinded Placebo Study
2012 - Irritable Bowel Syndrome: Methods, Mechanisms, and Pathophysiology. The confluence of increased permeability, inflammation, and pain in irritable bowel syndrome


Why doesn't submersion in water kill fungi? I have read that fungi cannot live without air. Does a couple of minutes in a swimming pool full of chlorinated water kill them as it would a mammal? I've never heard this suggested. Will they survive by enjoying trapped air? Or by "holding their breath" for a long time?

There is a lot of anecdotal evidence that frequent visits to the pool help with fungal infections. Surely, someone from the scientific community must have noticed too, right? So why don't we frequently hear people suggesting to go swimming to treat these infections?
Because scientific results suggest the opposite!
Incidence of occult athlete's foot in swimmers

In our results, 22 swimmers had positive cultures (15%), 8 of these cases had no lesions (36%). They included 7 infections with Trichophyton mentagrophytes (87.5%) and one with T. rubrum (12.5%). We observed one case with a dual infection. Only one sample from the inanimate environment was positive. This study showed a significant incidence of occult athlete's foot in swimmers. To control this endemic problem, adequate preventive measures must be taken.

Foot Infections in Swimming Baths

A 10% random sample of all bathers at a public swimming bath were examined for tinea pedis and verruca.
The overall incidence of tinea pedis was 8·5% and of verruca 4·8%. The incidence of tinea pedis in 205 male adults was 21·5%, in 288 boys 6·3%, in 60 adult females 3·3%, and in 220 girls 0·9%. The incidence of verruca in juveniles ranged from 4·2% in boys to 10·5% in girls.
It was clear that both infections spread within the baths, and since a relatively small proportion of users admitted to taking precautions to avoid contracting or developing infections it seems advisable that more publicity about recommendations on foot care should be provided.

Onychomycosis in Icelandic Swimmers

The prevalence of
culture-positive onychomycosis was 15% in women and 26% in
men. Our results suggest that onychomycosis of the toenails is
at least 3 times more prevalent in swimmers than in the rest of
the population.

Does this mean that not only is going to the swimming pool not a cure of fungal infections, but it is actually the cause? Well, maybe not. While the articles show that there is a larger incidence of fungal infections among swimmers, they only show correlation, not causality. People who partake in sports activities have a bigger chance of having these infections than the general public. These are also the people who are more likely to go swimming.
To settle the matter for good, we need an article named "Prevalence of fungal infections among occasionally swimming couch potatoes" :-)


What happens to tube nucleus of the pollen tube after fertilisation? Background:
Pollen tube contains a vegetative cell and a generative cell. The vegetative cell contains the tube nucleus, and the generative cell contains two male gametes. The two male gametes fuse with the egg to form the embryo and with the polar nuclei to form the triploid endosperm in angiosperms.

Question:
What happens to the tube nucleus of the pollen tube after/during fertilization?

Research:

This site says that the tube nucleus disintegrates.
This article does not mention about disintegrating nor discuss anything about the fate of tube nucleus.

Short Answer: It disintegrates.

Background: Although I was unable to find any primary reference, there were many secondary references stating that the pollen tube does disintegrate. In very short, after the pollen tube reaches the female gametophyte, the pollen tube nucleus disintegrates. For the 'why', it disintegrates to let the two sperm cells pass through, and also since its function of controlling the growth of pollen tube has finished.

For citation, you can have a look at:

Fertilization - Wikipedia
Advanced Biology -
A new mainstream text for the new specifications
Advanced Science; Michael Kent, 2000
Sexual Reproduction in Angiosperms; Kimball's Biology Pages
BIOPL 2410 Introductory Botany; KNiklas, TSilva; Cornell University
The Structure and Functions of Flowers - LeavingBio.net (image source)


How can binaural beats change mental state? Can anyone tell me how binaural beats of 10 Hz can cause a person to calm down and one of 40 Hz to cause someone to heighten their attention. All I know is that they work on the principal of Brainwave Entrainment. I am confused as to how can a 10-Hz difference in 2 sounds cause the brain to change its state of mind! A detailed but simple explanation would be great.

It is thought that binaural beats entrain the brain in the frequency of the binaural beat. These beat frequencies show up in the EEG.

The EEG in turn represents synchronous activity in the cerebral cortex (Fig. 1).

Fig. 1. EEG frequency bands and their associate mental states. source: Conor Russomanno

Now if you look at where 10 Hz EEG waves show up it is in the alpha frequency band associated with a relaxed mental state. The 40 Hz band on the other hand is associated with beta activity associated with an alert state.

Indeed, presentation of beta-frequency binaural beats have shown to improve the performance on psychophysical tasks and performances were better than when binaural beats were presented in the theta-delta range (Lane et al., 1998).

Reference
- Lane et al., Physiol Behav (1998); 63(2): 249–52


ATP production via aerobic respiration Just started learning about aerobic respiration today, specifically Glycolysis.

We were told that aerobic respiration produces 38 ATP, while anaerobic respiration produces only 2.

However, we're also told that:

Glycolysis produces 2 ATP
Link reaction produces 6 ATP
Krebs cycle produces 24 ATP (18 from NADH, 4 from FADH, and an extra 2)

This only adds up to 32 ATP, so where is this other 6 coming from? Or is this information incorrect.

In short, the difference stems from different values regarding the number of ATP attributed to the electron carriers in the electron transport chain (ETC).

My guess is that your class didn't go too far in depth on the subject, and also that your class or text is using mixed sources of information.

I have overviewed (general) glucose metabolism here, but feel free to skip this section if you don't need it.

Glucose metabolism is generally composed of 4* processes:

Glycolysis: a 6-C glucose molecule is broken down to 2 pyruvate molecules producing a net gain of 2 ATP and 2 NADH (electron carrier) molecules. Note that this is a net gain.
Pyruvate Dehydrogenase Complex (PDC): Here Pyruvate is made into Acetyl CoA, which enters the Krebs Cycle (step 3). This is the Link reaction step that you mentioned. This step produces a 1 NADH molecule per pyruvate.
Krebs Cycle (TCA): The Krebs cycle is central to cell metabolism and produces a lot of electron carriers, netting 1 GTP (ATP energy "equivalent"), 3 NADH, and 1 "FADH2" (electron carrier) PER Acetyl CoA entering the TCA.
Oxidative Phosphorylation (ETC): This step converts your electron carriers into ATP. It does this by using the energy released by electron transfers (e- are transferred from your electron carriers NADH, FADH2 to intermediate compounds to oxygen. This provides the energy to actively transport protons) to pump protons (H+ atoms) across a semi-permeable membrane to create a electro-chemical gradient. These H+ atoms will flow down this gradient through the channel of the ATP synthase, creating ATP. Currently, it is pretty widely accepted that an NADH molcule provides enough energy to net 2.5 ATP, and a FADH2 molecule provides enough energy to net 1.5 ATP.

As a result, we get the following:

+2ATP, +2NADH
+1NADH x2
(+1GTP, +1FADH2, +3NADH) x2
-10 NADH, +2.5ATP x10; -2FADH2, + 1.5ATP x2

This yields 2+2+25+3=32 ATP, which is what you obtained in your calculation.

However, a previously accepted value states that the 4th step nets 3 ATP/NADH molecule and 2 ATP/FADH2 molecule. Running the same calculation, we obtain 2+2+30+4, netting 38 ATP, causing the discrepancy you notice. I wouldn't say either set of values is universally accepted, but I would say that 32 ATP is generally recognized as the "right" answer.

  In other words, 32 ATP is the result of the more recently accepted equivalences of 2.5ATP/NADH and 1.5ATP/FADH2 in oxidative phosphorylation, whereas 38 ATP is the result of the older pair accepted equivalences of 3ATP/NADH and 2ATP/FADH2.

Some notes and caveats:

Please note that in (most) Eukaryotes, the NADH produced in the cytosol (Glycolysis) is "reduced to FADH2" via the mitochondrial shuttle as the high energy electrions enter the ETC. This means that each NADH produced by glycolysis only nets 1.5 ATP, resulting in 30 ATP/glucose in majority of eukaryotes.

It is also important to note that the numbers that I have provided are mostly used in classroom calculations for general systems. Real organisms will often deviate for a multitude of reasons. Further, some organisms may not follow this rule at all.

*A few sources might classify the PDC as part of glycolysis or as part of the TCA.


Why does beta-2-Thienylalanine inhibit bacterial growth? I'm trying to obtain a better understanding of the Guthrie Test, which checks whether people have a disease called PKU.
The Guthrie test uses bacteria to check for Phenylalanine (the amino acid) in blood samples. If both Phe and B-2-thienylalanine are available on the medium, the bacteria will grow. However, if only B-2-thienylalanine is available the bacteria will not grow.

In all of the articles I can find, I have seen no explanation, just a link to a paper that I can't find on the internet.:
" A standard culture of Bacillus subtilis was incubated on agar in the presence of an antagonist of phenylalanine (B-2-thienylalanine), which prevents the bacteria from growing.3 " Link
The reference they mention here is:
"The inhibition assay: Its use in screening urinary specimens for metabolic differences associated with mental retardation" by R. Guthrie from 1960.

Do we know what mechanism this protein is inhibiting?

Any help would be greatly appreciated.

β-2-thienylalanine is an analogue of phenylalanine. It is incorporated into proteins in place of phenylalanine, and the resulting proteins are inactive because of the substitution. Consequently growth medium supplemented with β-2-thienylalanine will not support bacterial growth.

Addition of phenylalanine to a medium containing β-2-thienylalanine will result in a competition between the two compounds - if there is an excess of phenylalanine then this will out-compete the analogue and incorporation of the analogue will be minimised, allowing growth. Blood from a patient with PKU contains phenylalanine, so the addition of this to the growth medium will relieve inhibition of growth.

Here is a link to a patent application in which a screen for E. coli strains overproducing phenylalanine was based upon the same principle.