Are tendons and ligaments classified under the muscular or bone system? Are tendons and ligaments classified under the muscular system or the bone system?

Basically they are not bones or muscles and that's why I have doubt.

Tendons are intrinsically part of muscles. Ligaments are not. So for your question, we need to create a classification system which is a bit artificial, based on the tissue structure of the various components of the musculoskeletal system.

  The musculoskeletal system is made up of hard and soft tissues. The hard tissue includes bones and cartilages (articular cartilages), while the soft tissues are the muscles, tendons, synovial membranes, joints capsule and ligaments. (emphasis mine)

Here is an illustration of the biceps brachii muscle (arm) from Kenhub:

It looks a little different in real life, but this clearly illustrates how tendons (the white things at the ends of the muscle) are part of the muscle. So, to answer your question, tendons are part of the muscular system (a term that I have never used as a physician. I would just say "muscles".)

Ligaments are supporting structures of fibrous tissue of nearly the same composition as tendons, but do not arise from muscle per se. (For a reason I cannot comprehend, little research is devoted to the embryonic development of ligaments.)

These are the ligaments of the elbow (and more fibrous connective tissue):

Clearly they are not bone, and they are not muscle.

If you need to artificially divide muscle vs. skeletal systems, then:

Muscle: muscle and tendons
Skeletal: bone and cartilage
"Other": ligaments, bursae, synovial fluid and membranes, etc.

The easiest thing to define is what is bone and what is not bone. Then bone may well stand alone, even without cartilage. But no one would say cartilage is part of the "muscular system".

So I hope you see that this way of separately classifying tissues which are meant to work together is artificial and perhaps misleading.


How can TMS induce enough depolarization to cause an action potential? Creating an action potential needs at least tens of mV potential difference across the membrane to occur.
But the membrane is really thin, surely less then 0.01µm (some reference give 25A).

Then the potential gradient, that is to say the electric field E, must be very strong :
The order of magnitude of the needed electric field is much greater than 10mV/0.01µm = $10^{6}$ V/m

But TMS produces E of the order of 200 V/m on the scalp, which is even less inside the brain. Then how can TMS induces neurons depolarization ?

I think my mistake was to believe that the electric field has to be somewhat perpendicular to the membrane, so that it can directly apply a voltage difference across the membrane, and that the resistance inside and outside the axon was the same, so that a tangential field was useless.

In fact these are false : depolarization and action potential creation happen where the axon is parallel to the electric field and where the gradient of the tangent field is the bigger.

Here you have a complete explanation but I think we can make a simplified one :
http://stbb.nichd.nih.gov/pdf/Nerve_Fiber_Stimulation_Model.pdf

Let's look at a membrane model (Hodgkin-Huxley) :

As we said if we try to apply an electric field $\vec{E}$ along $\vec{y}$ , it should be incredibly strong to produce a trans-membrane potential $V$ strong enough to create an action potential.

In between the inside an the outside of the membrane you have all the channels and the capacitance of the membrane. but I think the crux of the matter here are the resistances inside and outside : the small surface of a section of axon limits the conductivity, whereas the outside is supposed to be bigger so that its resistance is negligible.

As a result if you apply a gradient $\frac{dE_{x}}{dx}$ you can create trans-membrane current and potential:
because of the gradient, the fields $E_{1} = E(x)$ and $E_{2} = E(x+\Delta x)$ are different : $E_{2} = E_{1} + \frac{dE_{x}}{dx}\Delta x$.
Then using electricity laws :
$$i_{m} = I_{1} - I_{2}$$
$$i_{1} = -\frac{ E_{1} \Delta x}{R}$$
$$i_{2} = -\frac{ E_{2} \Delta x}{R}$$

then :

$$i_{m} = \frac{\Delta x}{R} (E_{2}-E_{1}) = \frac{\Delta^{2} x}{R} \frac{dE_{x}}{dx}$$

This trans-membrane current will produce a potential across the membrane which will be proportional to $\frac{dE_{x}}{dx}$, electromagnetic stimulations shows that TMS can easily produce gradients strong enough to create actions potential.


Why do humans transport glucose but not sucrose like plants? The reason why plants transport sucrose rather than glucose is due to the fact that it is more efficient and that nearby cells would not take up all the glucose too quickly.

Hence the plant convert glucose to sucrose before transporting them throughout the plant.

However, why is that humans and other animals all transport glucose in their bloodstreams? Why is it that they do not convert glucose to sucrose before transporting them since, as mentioned above, it would be more efficient?

Short answer digestion and absorption.

Animals have to digest sucrose into it's component sugars before it can be absorbed. Turning it back into sucrose afterwards would take energy and have no real benefit so it has had no reason to evolve.

The real question is why do plants make sucrose, and the answer is by living at a much slower pace,As you mentioned it is has slower uptake on the cellular level which is fine for plants but a detriment for more energy demanding animals. Stability is the other concern, sucrose is a lot more stable than glucose, animals are burning through glucose as fast as they can release it from storage so it doesn't matter how stable it is, whereas plants keep it around for longer and move it slower so it has a chance to breaks down on the way which would be a problem. Sucrose is more chemically stable than glucose and slightly more favorable osmotically (takes less water to dissolve the same energy value of sucrose than glucose) Both of these reasons make it more beneficial for plants to convert the sugars to sucrose, (if starch was water soluble they would likely only convert it to that.) They do this right at the end of photosynthesis then break it down just as it is being used in respiration so the energy investiture is minimal, while for animals they would be spending energy to break it down (digestion), then energy to put it back together, then energy to break it down again for respiration, its two extra steps for no benefit.

Just as a extra you can see why animals would evolve to break it down for absorption since as has been mentioned glucose is easier to absorb, whereas plants don't have to worry about extracting it from anything.


Can a portion of human skin cells be modified in some way to generate light? I have come across some species of living organisms who are able to emit light at whim. Can that ability be incorporated into a portion of human skin (a specialized tissue)?

Genetic modification of any cell to overexpress a fluorescent protein will not 'generate' light, per-say: fluorophores absorb particular wavelengths and re-emit in less energetic wavelengths, dispersing some energy as heat. (Perhaps there is some semantic choice here, but there is no transduction to light from another form of energy.)

Bio-luminescence, on the other hand, can be considered generation of light. There are proteins commonly found in marine animals (which skin cells could be engineered to express) which convert chemical energy to emit light.

With regards to generation of electricity, I think this gets a bit interesting...

The electron transport chain (ETC) in the inner membranes of our mitochondria carry out a series of redox reactions which serve to oxidise food metabolites (thus freeing electrons). In order to maintain the free energy gradient that favours this directional cascade of reactions, electrons and protons are finally accepted by a continual supply of oxygen atoms, producing water. (You may be aware that aerobic respiration consumes oxygen and produces water.) In nature (in aerobes), oxygen acts as the final electron acceptor, or an electron sink.

Bacteria also have electron transport chains for their respiration (mitochondria were once bacteria, after all), and people have wondered whether these redox reactions could be used to produce a current instead of reducing oxygen to water as the final step. We normally use current in the form of electrons moving along a metal wire.

This is the idea of a "microbial fuel cell". Just like a battery produces a current from a chemical redox reaction, the ETC might be recruited in to producing a current from its chemical redox reactions.

I think this is a very difficult piece of bioengineering, since the ETC is integrated in to respiration and needs to be de- & re-coupled to some kind of inorganic mediator and ultimately a circuit; and also because the ETC produces very low voltages, I think.

There is a nice wikipedia page on microbial fuel cells that you might find interesting, if you think this is relevant to your question.


E. coli, risk of infection? There has been a warning about E. coli contaminated water in South Florida. Now I'm wondering are there empirical data or historic cases which show a correlation between E.coli levels in tap water and risk of infection in the population drinking this water. Which pathogens, that could be transmitted through tap water, are common in this area?

The maximum temperature for E. coli to survive is dependent on the strain. E. coli from warm areas can easily survive 45 °C and more. The minimum number of E. coli to ingest in order to become ill is also dependent on the strain. Whether you become ill at all is also dependent on the strain. You harbor many billions of E. coli in your digestive tract without becoming ill, so without further information on the released strain, it's really hard to tell.

One of the suggestions from the WHO Guidelines for drinking water quality is to boil the water in order to desinfect it.


What proportion of proteins require chaperone-assisted folding? I am new to the field of biochemistry (I am a chemist, actually).

I have long known the process of folding as the process that leads to the minimum energy conformation of a protein.

Now, I am introduced to the chaperones, that I didn't know before.

What I am wondering is: my previous view of folding, as a proces of "self-assembly" (the protein folds without external assistance as it is assembled by the ribosome) is real, or any folding process is assisted by chaperones?

If both processes exist, how frequent is the "assisted" folding, compared to the spontaneous process?

I'm reminded of a lovely review in Trends in Biochemical Sciences that discusses chaperone independent, partially dependent, and fully dependent proteins in prokaryotes.  The conclusion was that smaller polypeptides are less likely to require chaperone assistance. This is their figure:

That principle still holds to a certain extent (in prokaryotes), but folding assistance is now more broadly understood to include much more than just specific proteins identified as molecular chaperones. The Anfinsen postulate (that the final tertiary structure of a protein depends only on its primary structure) may still hold for small globular proteins, but folding in vivo is almost certainly always assisted. Since you're coming from the perspective of a chemist, don't think of it as a reaction between two molecules in solution. It's a reaction in a gel packed with complex sugars, lipids, proteins, and nucleic acids.

If you're skeptical of the perspective of a crowded cytoplasm, read the review I linked. It's an important but often under-appreciated aspect of in vivo biochemistry. There is much more to read about it. You might try looking up Allen Minton (AP Minton) and macromolecular crowding in your favorite database.


What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat? 5'... ATGCC|CCGTA ...3'

3'... TACGG|GGCAT ...5'

or say

5'... AAGT|TGAA ...3'

3'... TTCA|ACTT ...5'

or in generalised way; on each strand;

ABCDEF|FEDCBA

Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat?  Does they really exist in nature?
(I could not yet found any helpful answer in web, including wikipedia.)

UPDATE

I asked this question because the term "palindromic sequence" is not like the situation in OP but "palindromic sequence"  is like this:

5'... ATGCTTTC|GAAAGCAT ...3'

3'... TACGAAAG|CTTTCGTA ...5'

or  in general;

5'... A B C D E F | M N P Q R S ...3'

3'... S R Q P N M | F E D C B A ...5'

Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3').

BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each single strand when read (3'---> 5') or (5' ---> 3').

like

5'... A B C D E F | F E D C B A ...3'

3'... S R Q P N M | M N P Q R S ...5'

From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.

This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like

I EAT CAKE

EKAC TAE I

So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.

  One other Q/A site mentions about a term "mirror repeat", with exact same  situation as OP,  but gave no reference and further biological importance.

    http://www.answers.com/Q/Mirror_repeats_in_DNA

  Latest revision of Wikipedia also mentions a term mirror repeat and everted repeat, but no further explanation and hyperlink is given.

  Another result from google search.

    URL: https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg

I think the situation you showed should be called mirror-everted repeats: to my knowledge they occur very rarely, and I only found references in this and this articles, even though no graphic explanation is provided.


Does human brain produce nicotine? I had a discussion with a high school student about the effect and production of nicotine. He mentioned that nicotine is naturally produced in our brain so when the person takes to smoking, the brain stops producing its own nicotine and starts craving it from an external source. According to him, this is how nicotine addiction develops. How true is this?

The students also claimed that nicotine in cigarettes is harmless. I have already seen the answer about how toxic it is to humans, but I would love to know:

What's the lethal dose for nicotine via ingestion (not inhaling)?
How does nicotine compare to other toxic substances - for example, cyanide or any other known poison? Is it more toxic or less toxic?

THANK YOU

No, the human brain does not produce nicotine. The brain has nicotinic acetylcholine receptors, but the endogenous agonist for these receptors is acetylcholine, not nicotine; they aren't named "nicotinic" because they are for nicotine but just because nicotine happens to act on them. Many other human receptors are named similarly, based on discovering the molecular basis for sensitivity to exogenous compounds.

The human LD50 for nicotine is reported between 0.5-13 mg/kg depending on age and other factors, but LD50 is only appropriate for evaluating acute toxins; many substances, including nicotine, are most often encountered in small chronic amounts, but concentrated availability of nicotine in insecticides or vape juice can be a plausible source for sufficient doses for acute toxicity. Studies of nicotine toxicity in relationship to smoking are going to be based on much smaller doses over many more administrations.


How does transition of osmoregulation occur in fishes when they migrate from sea to rivers and vice-versa From my high school level knowledge I can recollect that there are two types of migration in fishes-

From marine to fresh water
(like in Hilsa which grows in the marine water but migrates to the fresh water only for reproduction and then the young return back to the marine water)
From fresh water to marine
(like in eels that live in the fresh water but migrate to the marine water to reproduce)

The only mechanism I had read about osmoregulation in aquatic organisms was via the ionocyte cells in the gills of the fish.

So my question is:

How do they change their osmoregulatory mechanism during this migration?

Just a follow-up:

Are there any other mechanisms by which they osmoregulate

I found a publication related to the osmoregulation in salmon that might be interesting to you. I'm copying the abstract because it basically answer your question.

  Smoltification, also called parr-smolt transformation, is a complex developmental process that consists of a number of independent, but coordinated changes, in the biochemistry, physiology, morphology and behavior of juvenile salmon in their transition from freshwater to seawater life. A key component of smoltification is represented by the physiological adaptations that enable smolts to thrive in hyperosmotic environments. Instrumental to this process is the ability of smolt gills to gradually become capable of actively secreting salt through specialized cells known as mitochondria-rich (MR) cells, ionocytes or chloride cells. NaCl secretion by teleost gills is therefore accomplished via the secondary active transport of Cl - and the passive transport of Na + . The driving force for active transport is provided by Na + /K + ATPase, which maintains low intracellular Na + and high intracellular K + concentrations. However, this NaCl secretion mechanism needs at least two different ion channels: A CFTR type chloride channel for the passive exit of Cl - and a potassium channel to recycle extracellular K + , which is a thermodynamic prerequisite to work under conditions imposed by high extracellular salinity in seawater. The characteristics of K + channels required for NaCl secretion from MR cells into seawater are still unknown for Salmo salar and only recently have begun to be studied in other teleosts.

You can find the complete paper here.


PCR efficiency or DNA yield with single primer How to calculate number of DNA molecules synthesized after 'n' no. cycles with single primer (either only forward primer or reverse primer)? Is there any formula to calculate the DNA yield after such PCR?

Supposing, I am setting a PCR reaction for 100 template DNA molecules for 30 cycles, with only one primer - forward primer for target gene. How many DNA molecules will be generated at the end of 30 cycles. All other conditions remain the same.

Thanks.

Technically, if you use only 1 primer, it will not be PCR anymore.

But that's what gonna happen if you have 100 template DNA molecules (made of strand A and complimentary strand B) and abundance of primer (say, 10x, or 1000 molecules):

At first cycle primers will bind to template DNA, but only to one strand (for example, A)
DNA polymerase will extend those primers, creating complimentary strands B'. Some strands B' will be shorter than template because DNA pol is not perfect
DNA-primer complex will melt at the beginning of cycle 2
At the beginning of cycle 2 primer molecules will again bind to template, again to strands A, and process continues

Since there is no step where strand A is being copied, this process will be linear, not a "chain reaction". At each cycle you will get the same amount of strands B'.

It is hard to say how much B' molecules you will get at each cycle, but at the end of 30 cycles, it will be at best 30x of the first cycle. Remember, though, that DNA polymerase degrades, and cycle 30 will be less efficient than cycle 1.

Assuming perfect polymerase, and that extension time is long enough, you will get 100 strands B' on cycle 1, 100 strands B' on cycle 2 and so on. At the end of 30 cycles you will have 30x100 strands B', and 100 strands A and 100 strands B.


Can someone identify this plant? Can someone identify this plant? It was growing under my 2 year old's climbing wall / play house thing. I live in West Virginia, USA and it's currently June 3rd (if that helps from a climate standpoint).

I know there are some potentially dangerous invasive plants like the giant hogweed. I hope someone here can help me identify this and give me any tips on what to do about it if it is in fact hogweed.

As @dd3 stated, it's a spiny (or prickly) sow thistle. It's an annual common in most of the US.

The leaf itself does not have a stem, and if you break the central stalk, it should be hollow and there should be a milky exudate. The plant spreads by fluffy seeds produced from a small dandelion-like flower.

If you pick it while young, it won't hurt (as much); if you prevent it from flowering, it should not spread, although unsprouted seeds can sprout still for a few years (it can come in on the wind as well.)

Prickly Sowthistle


Reproduction number of a SIR model with mortality We know that reproduction number $\mathcal{R}_0$ is $\frac{\alpha}{\beta}$ for the following system, such that if $\mathcal{R}_0>1$, there is an epidemic in the population.

Now, assume the system below with mortality rate of $\delta$:

I'm wondering which one of options below represents ${R}_0$?

${R}_0 = \frac{\alpha}{\beta + \delta}$
${R}_0 = \frac{\alpha}{\beta \delta}$
${R}_0 = \frac{\alpha}{\beta}+\frac{\alpha}{\delta}$

Could you mark the right option with its justification?

Thanks

The only answer that makes numerical sense is 1. The product of two rates beta and delta (recovery * death) doesn't mean anything in SIR. And in answer three you're doubling the rate of infection (alpha). Looking at the other way, for R_0 it doesn't matter how people leave the Infected class, once you're either dead or recovered you no longer are transmitting the disease. Therefore you can say that some value Zeta is the exit from Infected class and Zeta would be the sum of all rates which remove a person from being Infectious


Can PCR tubes be made of different materials than plastic? Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?

The key property would seem to be, at first glance, thermal conductivity. According to this table copper wins. But then, what about chemical reactivity? Maybe gold is a better choice. And that brings us to cost and disposability. These factors make the choice of a metal problematic. That leaves plastic and glass. Glass has better thermal conductivity, but clearly it has other drawbacks.


Which of the following is NOT a type of tropism? Which of the following plant movements is NOT a tropism?

Plant stem growing toward light
Plant structure growing away from light
Plant roots growing in response to gravity
Vines coiling around tree trunks
Leaflets folding after losing turgor pressure

Please help, I am stuck!  Thank u :)

The answer is #5, Leaflets folding after losing turgor pressure. This refers to a phenomenon called plasmolysis.

1 - positive phototropism, incorrect

2 - negative phototropism, incorrect

3 - gravitropism, incorrect

4 - thigmotropism, incorrect


Can people with AIDS get tattoos? When I do a Google search, most of the results are about whether or not people can get HIV / AIDS from getting a tattoo through dirt needles. I am, however, curious whether or not it is possible to get a tattoo if you have AIDS.

Quoting wikipedia's entry on tattoos:

  Tattooing involves the placement of pigment into the skin's dermis,
  the layer of dermal tissue underlying the epidermis. After initial
  injection, pigment is dispersed throughout a homogenized damaged layer
  down through the epidermis and upper dermis, in both of which the
  presence of foreign material activates the immune system's phagocytes
  to engulf the pigment particles.

If your immune system is not working properly, I can imagine that the phagocytes might never respond to the tattoo ink and that the pigment might not ever enter the fibroblasts?

Posted due to certain inaccuracies in comments and answers provided to this question regarding the Human Immunodeficiency Virus.

It should be noted that while it may not affect the ability for macrophages in the dermis to phagocytose the heavy metals found in the inks used in tattooing, and thus not interfere with the fixing of a tattoo in an HIV+ person, the Human Immunodeficiency Virus, the virus responsible for Acquired Immune Deficiency Syndrome (AIDS) does in fact have the ability to infect any cell type that expresses the cell surface glycoproteins CD4 and CCR5.

Cells that express CD4 and CCR5, barring mutations seen in the bone marrow received by the Berlin Patient (Timothy Ray Brown), among them CD4 "Helper" T-Cells, Macrophages, and certain Dendritic Cells, are all capable of being infected by the HIV virus.

Glycoprotein 120, found on the surface of the HIV envelop, binds with high affinity to CD4. The coreceptor CCR5 then binds to the gp120 CD4 complex and allows the HIV envelop to fuse with the plasma membrane of the host cell. The fusion then delivers the viral nucleocapsid and associated proteins into the cytoplasm of the cell and the infection takes place.

If I had to venture guess, I would say that as Macrophages tend to be present within the dermis of the person for extend periods of time, there is likely enough of a population present in the skin to have the macrophages necessary to fix the inks used in tattooing.


Mouse meta-globin mRNA problem This is an mRNA strand of mouse meta-globin:

  5'-ccccagauacggaauucgaau-3'

  A) Which small RNA (below) is most likely to regulate expression of
  meta-globin?

  5'-auucgaauuuucuaucugggg-3'
  5'-ggggucuaucuuuuaagcuua-3'
  5'-ccccagauacggaauucgaau-3'
  5'-uaagcuuaaggcauagacccc-3'

  B) This RNA most likely?

  acts as an siRNA
  inhibit meta-globin translation
  increase meta-globin translation
  help transport meta-globin mRNA back into the nucleus

My attempt:

I think A is 2 because the strand is complementary and will bind nicely to the mRNA strand.  For B, I'm between 2 and 3, but cant decide.

There are always exceptions but you can consider some general rules.

A is 1 i.e the sequence that is perfectly complementary (2 is complementary but direction is parallel — cannot base-pair), then B would be 1 (siRNA). Reasons (some are just based on general rules of siRNA design):

siRNAs have to be perfectly complementary
The size is also perfect for a siRNA (21nt)
U/A (2-3 residues) at the 5' of the siRNA
U at 10th position
GC content 43% (ideal 30-50%)

See here for guidelines for siRNA design.


Training Data for Secondary Protein Structure prediction using neural network I am trying to find some training dataset for prediction of Secondary Structure of Protein. I am having problems finding them online.

The standard benchmark dataset is the one from Lindahl, which consists of 976 × 975 target-template protein pairs.

  Lindahl, E. & Elofsson, A. Identification of related proteins on family, superfamily and fold level. Journal of molecular biology 295, 613–625 (2000).

It is for example used in the following articles:

Improving Protein Fold Recognition by Deep Learning Networks
Improving protein fold recognition by random forest

Another resource is SCOP: Structural Classification of Proteins.

  Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.


Questions about RNA Polymerase I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph.

  RNA polymerase reads a DNA template in the 3’ to 5’ direction to
  synthesize RNA in the 5’ to 3’ direction. Transcription can occur in
  either direction, but not in either direction from a single promoter.
  RNA polymerase can only transcribe in one direction (5’ to 3’) with
  respect to reading one strand of the template DNA in the opposite
  direction (3’ to 5’). In general, each promoter recruits RNA
  polymerase to a particular site and indicates in which the direction
  RNA polymerase will move along the DNA. As RNA polymerase is moving,
  there will be only a single strand that can be used as a template to
  allow 5' to 3' synthesis of a transcript.

Sentence 1:

What's the difference between reading and synthesizing RNA?

Sentence 2:

What's the difference between synthesizing and transcribing?

Sentence 3:

Didn't this just contradict sentence 2?

Sentence 4:

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Sentence 5:

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

Question:

I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

What's the difference between reading and synthesizing RNA?

What's the difference between reading and writing a book? Synthesizing RNA means producing an RNA based on a sequence in DNA. Reading it means processing RNA that is already produced. Reading also implies that protein will be produced based on the sequence in RNA.

  What's the difference between synthesizing and transcribing?

"Synthesize" means to produce any chemical molecule. "Transcribe" is specifically the synthesis of RNA form DNA via a polymerase (as opposed to for instance inorganic synthesis of RNA de novo, as might be done in a chemistry lab).

  Didn't this just contradict sentence 2?

It's just saying that genes can be oriented forward or in reverse. Reverse genes are on the opposite strand, so they are still 5' to 3' (the 5' ends of the two strands are on opposite ends of the DNA). But every gene must still have a promoter on its 5' side.

And actually, that bit is not quite true: There are bidirectional promoters that will cause transcription in both directions.

  If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Usually, it will transcribe (so it will also synthesize, or "read"). But technically, RNA pols belong to a family of proteins which are "molecular motors", meaning that their fundamental activity is to move along DNA step by step like a little monkey climbing a ladder. With RNA pols, RNA synthesis is coupled to this movement, so each step on DNA also causes a letter to be added to the RNA they are making.

Also, technically the RNA pol is not only moving and making DNA, but also unwinding the two strands of DNA and separating them. But this may be outside the scope of your material.

  My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

RNA comes out matching the sequence of the gene (except for T->U), and it is assembled through basepairing to DNA. If it paired with the strand the gene is on, the RNA would come out as the reverse complement of the gene. Instead it is assembled on the opposite strand, which is already the RC of the gene. RC of RC of a sequence is the same sequence. Thus we say RNA is transcribed from the "non-coding" strand, but keep in mind that these coding/non-coding assignments are arbitrary and only used by us humans, the cell does not have a special marking for it (beyond the 5'/3').

  I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

It's very simple: DNA is a directed (because of 5'/3') string of ACTG. It is coupled to another, complementary string that runs opposite to it. The sequence on either strand may be meaningless, or parts of it may encode genes. Genes consist of a promoter, some sequence, and terminator. RNA pols can slide along either strand, but only in 5' to 3' direction, so they will slide in opposite directions on opposite strands, like cars on a two way street. When RNA pol encounters a promoter, it starts synthesizing an RNA: It separates the two strands, and lets single RNTPs basepair with the opposite-direction strand, when they do so it glues their phosphate backbones together. It keeps sliding and making RNA like this until it reaches another sequence, the terminator, at which point it stops assembling RNA and releases it. The RNA snaps off DNA and goes off on its merry way, the two strands of the DNA that were separated by RNA pol come together again.

Thus for every promoter-terminator pair, whatever sequence is in between them will be transcribed into an RNA. These are basically genes. These genes may be on either strand of DNA, and they must always be oriented along the 5' to 3' of the strand they are on. Thus genes on opposite strands will appear "reversed" with respect to each other.


Why is weight gain a symptom of Cushing's Syndrome? Cushing's syndrome results from increased levels of cortisol in the body.

Cortisol as I understand it however, promotes the breakdown of glycogen and amino-acids in the process of gluconeogenesis, to increase blood sugar - opposing the action of insulin.

Why then does Cushing's syndrome lead to weight gain rather than weight loss?

Cortisol is released when body goes through stress situations like while working out in gym, physiological activities outdoor etc. As you have already mentioned about what Cortisol does, it accumulates in the body after the stress situation and then with the intake of food and other nutrients it replaces the consumed carbohydrate and fat in the body i.e. a kind refueling. So this is how Cortisol maintains the body weight normally if our body gets enough exercise or has proper metabolism.

Whereas in Cushing' syndrome which comes usually by taking glucocorticoid drugs, or diseases that result in excess cortisol, adrenocorticotropic hormone (ACTH), or CRH levels. In this case Cortisol content will be more than the normal level which in turn requires more carbohydrate. So cortisol metabolizes the food and reefuels the body even when there is no requirement within the body. So because of excessive cortisol content body simply gets excessive fat accumulated in various parts which mainly results in obesity.

One more explanation from High level of Cortisol effects:

Chronically high levels of cortisol plays a big role in the development of obesity.

  Cortisol helps the body handle stress; so, when stress goes up,
  cortisol also goes up. Cortisol stimulates fat and carbohydrate
  metabolism during stressful situations. This leads to increased blood
  sugar levels required for fast energy. In turn, this stimulates
  insulin release which can lead to an increase in appetite.

  Adrenaline increases alertness and metabolism by helping fat cells release
  energy. When the immediate stress is over, the adrenaline levels
  return to normal. But, cortisol lingers to help bring the body back
  into balance after stress. One of the ways it gets things back to
  balance is by increasing appetite to replace the carbohydrate and fat
  used for the flight or fight response.

  The problem is that in today's society, stress-causing situations do
  not really require the body to use up a lot of energy. So, cortisol
  ends up causing the body to refuel after stress even when it doesn't
  really need to refuel. This excess fuel or glucose is converted into
  fat resulting in increased storage of fat.


Connectivity Relation between axon terminal synapses and dendrites With regards to the synapses between axon terminals and dendrites, what is the relation between a given neuron's axon terminals and its neighbouring neurons' dendrites?

Does each axon synapse on only a single dendritic spine from another neuron, whereby all other connections that axon makes are with distinct neurons, or
Can multiple axon terminals from a given neuron end up connecting to a single neuron via multiple dendritic spines?

Synapses are pretty much one-to-one
Here's some EM pictures of synapses, from Wikimedia commons:

You should gather from these images that these are super organized structures. There's a dense, dense gathering of cellular machinery at the synapse that creates a dark electron-dense region shown by the arrows. There's no room for more than one cell to be directly involved in this area, it's one membrane closely coupled with another membrane. It's as if you put the palms of your two hands together.
Some neuromodulators (and sometimes traditional neurotransmitters) are not released synaptically, though, and are just dumped into the extracellular space from where they diffuse in to the cleft or bind outside the synaptic region.
There can be multiple connections between two given cells
Though a synapse is a one-to-one connection, axons make multiple synaptic contacts as do dendrites. Though this can mean that cells receive and send input to 1000s of different cells, it's also very common for there to be multiple individual synapses between two specific cells.
For some examples, Tamas et al 1997 looked at synapses made from inhibitory interneurons to excitatory cells in visual cortex:

All presynaptic cells established multiple synaptic junctions on their postsynaptic
target cells. A basket cell innervated a pyramidal cell via fifteen release sites; the numbers of synapses formed by three dendrite-targeting cells on pyramidal cells were seventeen and eight respectively, and three on a spiny stellate cell; the interaction between a double bouquet cell and a postsynaptic pyramidal cell was mediated by ten synaptic junctions.

Note in this paragraph they are literally talking about 5 specific pairs of cells, where they trace both cells in EM. This is an exhausting process. The presynaptic cells were one basket cell, three dendrite-targeting cells, and one double bouquet cell. The post-synaptic cells were all pyramidal cells except one was a spiny stellate cell. In the five pairs they found 15, 17, 8, 3, and 10 connections. Of course they could have missed some, too.

Tamas, G., Buhl, E. H., & Somogyi, P. (1997). Fast IPSPs elicited via multiple synaptic release sites by different types of GABAergic neurone in the cat visual cortex. The Journal of physiology, 500(3), 715-738.


Strange Cordeyceps-looking Mushroom in Australia In the past few weeks, after the rain started up I noticed these mushrooms around my local area. I'd never seen them previously out of the 20 years I've lived here (a town in Queensland, Australia).

Sometimes they have a net-like section, and they sometimes have 10+ flies around a mushroom cluster.

What are these mushrooms? Are they common in Australia?

You found a member of the stinkhorn family, The Phallales (in the family Phallacea), probably a Veiled Lady (Phallus indusiatus) or a Phallus multicolor (they have other names as well.) They are common in Asia, Africa, the Americas, and Australia. Don't eat them; they're attractive to dogs (lovely aroma!) and there have been dog deaths.

These fungi produce a spore slime which has an intense smell of rotting meat or sewage, which is why flies are attracted to them.

They are commonly found in rotted woody material.


Hydrophobic proteins in the body? I know that we can get hydrophobic amino acids, but are there any proteins in the body whose surface is hydrophobic? If so what is their typical function and where can they typically be found and if not why not?

Are there any proteins in the body whose surface is hydrophobic?

Sure. Although you are right in thinking that most proteins have hydrophilic surfaces, some are very hydrophobic. My favorite example is Elastin, it is the main component of the skin which grants it elasticity. In fact, the hydrophobic nature of elastin is what confers it its function. The idea, briefly said, is that a insoluble/hydrophobic structure will tend to minimize it's surface area with water, so if you stretch such a substance (i.e. increase the surface area), it will pull back to the minimum surface area state.

Reference: Li, Daggett. Molecular basis for the extensibility of elastin. Journal of Muscle Research & Cell Motility (2002).


What is a coupled reaction and why do cells couple reactions? I was wondering what exactly a coupled reaction is and why cells couple them.  I read the wikipedia article as well as several others, such as life.illinois.edu but I still don't get it.  Could someone explain it to me?

A reaction where the the free energy of a thermodynamically favorable transformation, such as the hydrolysis of ATP, and a thermodynamically unfavorable one, are mechanistically joined  into a new reaction (or may be envisaged to be so joined) is known as a coupled reaction.

To put it another way, two or more reactions may be combined mechanistically such that a spontaneous reaction may be made 'drive' a non-spontaneous one,   and we may speak of the combined reaction as being 'coupled' (see, for example, Silby & Alberty (2001), quoted below). The combined reaction may be catalyzed by an enzyme, in which case the 'thermodynamic push' is provided by the coupling agent (such as ATP) and the 'kinetic push' is provided by the enzyme.

We need to take into account a very important point. As pointed out by Atkinson (1977),  the coupled reaction is a different reaction to the reaction we are trying to 'drive', with different overall stoichiometry and hence a different overall equilibrium constant (Atkinson, 1977, p52).

A coupled reaction does not "push a reaction past its equilibrium" (see Atkinson, 1977, p52). No enzyme, for example, can push any reaction past its position of equilibrium. This is forbidden by the second law. (If your favourite kinetic mechanism does not obey the second law there is, as Eddington put it, "no hope"). An enzyme (or enzymes) can however, cause a reaction to proceed further than it normally would by catalyzing a different reaction (or series of reactions).

Perhaps (in lysine biosynthesis from aspartate), nature requires the the (NADH-linked) reduction of a carboxylic acid to an aldehyde, a reaction normally considered  irreversible. And lets spell this one out: the equilibrium constant for a reaction such as the following:

        NADH + carboxylic acid = NAD+ + aldehyde        (1)

greatly favors aldehyde dehydrogenation so much so that the left-to-right transformation has never (to the best of my knowledge) been demonstrated (more on this below).

Lets first phosphorylate the carboxylic acid using ATP as coupling agent to give aspartyl-phosphate (aspartate kinase):

         aspartate + ATP = aspartate-4-phosphate + ADP        (2)

Now let's reduce the 'activated' acid (aspartate-4-phosphate) using NADPH as electron donor, where the equilibrium constant of the following reaction is  very much to the right  (aspartate semialdehyde dehydrogenase):

  aspartate-4-phosphate + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+

So we have got our product (the aldehyde) from our 'starting material' (the carboxylic acid), but at the 'expense' (as we would see it) of  ATP hydrolysis.

We may think of the above reactions as being 'mechanistially coupled' by the formation of aspartyl-phosphate such that the overall equilibrium constant for the following reaction is much more favourable than that of Eqn (1)

  aspartate + ATP + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+

Or, perhaps in more abstract terms, the coupled reaction may be represented as folows:

  carboxylic acid + ATP + NADPH + H+ ⇌  aldeyde + Pi + NADP+

The reduction of a carboxylic acid to an aldehyde has been given a thermodynamic 'push' by the coupling agent  (and a kinetic 'push' by the enzymes).

Before we move on to some specific examples let's consider three further points.

(i) What makes ATP a good coupling agent? To again quote Atkinson (1977, p48), a good coupling agent has two requirements: firstly, it must be thermodynamically unstable. That is, it must be "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48). The hydrolysis of ATP nicely fills this criterion. Secondly, a good coupling agent must be kinetically stable. Again ATP 'fits the bill': solutions of ATP in water are stable (Atkinson, 1977, p48).

ATP (-39.7 kJ/mol), of course, is not the only useful coupling agent, or even the 'best' one. phosphoenol-pyruvate (-61.9 kJ/mol) , creatine-phosphate (-43.5 kJ/mol)  and acetyl-phosphate (-43.1 kJ/mol) are others. The figures in brackets refer to free energy of hydrolysis and are taken from Silby and Alberty (2001, p 282).

(ii) The coupled reaction need not involve direct hydrolysis of coupling agent. Any reaction in which ATP is converted to ADP has received a 'thermodynamic push equivalent to the free energy of hydrolysis of ATP' (Atkinson, 1977, p49). In essence, the concept of a coupled reaction is an abstraction, created by us for our convenience.

(iii) To state the obvious, a coupled reaction is exactly that: coupled.  The coupling may be 'chemical', as in many of the examples below, or may be conformational (as in ATP synthase), but there must be in some sense a mechanistic joining into a new (real) reaction. Two reactions occurring in isolation, even if one is ATP hydrolysis, are not coupled.

Specific Examples

An example of a coupled reaction is the  glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12; GAPDH) reaction [see here] .

 Glyceraldehyde-3-phosphate + NAD+ + Pi → 1,3-diPhosphoGlycerate + NADH + H+

We can think of this reaction in terms of two separate reactions which are coupled mechanistically by the enzyme. (i) The NAD+ linked oxidation of an aldehyde to a carboxylic acid (the aldehyde dehydrogenase reaction) and (ii) the phosphorylation of a carboxylic acid. (Like ATP, a phosphorylated carboxylic acid may be considered a 'high energy' compound, that is one where the equilibrium for hydrolysis lies very much to the left in reaction 2 below).

Reaction 1

 RCHO + NAD+ + H2O → RCOOH + NADH + H+

Reaction 2 (Pi is inorganic phosphate).

 RCOOH + Pi → RC(=O)(O-Pi) + H2O

As stated above, the NAD+-linked oxidation of an aldehyde (reaction 1) is practically irreversible. That is, at equilibrium it has proceeded almost totally to the right. As stated above, the position of equilibrium of reaction 2 lies very much to the left.

How can one 'drive' the formation of a phosphorylated carboxylic acid by coupling it to the (spontaneous) NAD+-linked oxidation of an aldehyde?

A simplified version of the GAPDH reaction is as follows (a more complete mechanism, supported by a lot of experimental evidence, may be found in Fersht (1999), which I quote below).

Step 1.  Formation on an enzyme-linked thiohemiacetal.

 E-SH + RCHO → E-S-C(R)(H)(OH)

A sulphydryl on the enzyme (part of a Cys residue) reacts with the aldehyde group on the substrate to give a thiohemiacetal.  (In the representation above, groups in brackets are all connected to a single (tetrahedral) carbon atom).

Step 2. The thiohemiacetal is oxidized by enzyme-bound NAD+ to a thiol-ester (the key step).

 E-S-C(R)(H)(OH) + NAD+ → E-S-C(=O)(R) + NADH + H+

This (enzyme-bound) thiol-ester is a 'high energy' intermediate wherein, it may be envisaged, the free energy of aldehyde oxidation has been 'trapped'.

The final step of the GAPDH reaction is now spontaneous (proceeds to the right).

Step 3. Attack on the thiol-ester by inorganic phosphate (Pi is inorganic phosphate)

E-S-C(=O)(R) + Pi → E-SH + R-C(=O)(O-Pi)

Thus, the free energy of NAD+-linked aldehyde oxidation has been 'sequestered' and used to 'drive' the thermodynamically unfavourable phosphorylation of a carboxylic acid, by coupling the two reactions via a ('high energy') thiol-ester: the coupled reaction is a different reaction.

The 'thermodynamic price' is that the GAPDH reaction (unlike NAD+-linked aldehyde oxidation) is freely reversible: the coupled reaction has a different overall equilibrium constant.

As stated above, this is a simplified version of the GAPDH reaction.  The (tetrameric) enzyme contains a tightly bound NAD+ for a start, and this needs to be taken account of.  A fuller account may be found in the following reference:

Fersht, Alan. (1999) Structure and Mechanism in Protein Science, pp 469 - 471, W.H. Freeman & Co.

For a fuller treatment of coupled biochemical reactions, see

Silbey, R.J. & Alberty, R.A. (2001) Physical Chemistry (3rd Edn) pp 281 - 283.
Atkinson, D. E. (1977) Cellular Energy Metabolism and Its Regulation.
Academic Press, New York

Pyruvate kinase (EC 2.7.1.40) [see here] is another great example of a coupled biochemical reaction.  In this case the reaction is almost irreversible in the direction of ATP synthesis!

The standard transformed free energy (ΔGo') for the hydrolysis of phosphoenol-pyruvate (PEP) to pyruvate and phosphate is ~ - 62 kJ/mol.  This represents an equilibrium constant of about 1010 in favour of hydrolysis! (see Walsh, quoted below, pp 229-230).

For comparison,  ΔGo' for ATP + H2O → ADP + Pi is about - 40 kJ/mol.

Thus the pyruvate kinase reaction may be viewed as a coupled biochemical reaction where the free energy of PEP hydrolysis is coupled to (almost irreversible) ATP synthesis.

Why does PEP have such a large negative ΔGo'? The enol form of pyruvate does not exist in appreciable quantites in aqueous solution at pH 7 (Pocker et al., 1969; Damitio et al., 1992).  PEP may be considered a 'trapped' form of a thermodynamically unstable enol which is released upon hydrolysis, thus 'pulling' the equilibrium to the right. (see Walsh, quoted below, p 230, for a more thorough explanation).

Personally, I have always considered the reaction catalyzed by PK to be pretty amazing.

Edit

In response to this question on the standard free energy of hydrolysis of phosphoenolpyruvate (PEP), I'll add the following.

The thermodynamically stable form of PEP in solution at 'physiological' pH is the enol form.  That is, the enol from predominates.

PEP hydrolysis may be formally divided  into two parts:
(i) the hydrolysis of the phosphate ester to give the enol form of pyruvate,
followed by (ii) tautomerization to the (thermodynamically stable)  keto form of pyruvate (Chiang et al., 1992).
Thus it is the enol form of PEP that predominates in aqueous solution at pH 7, but pyruvate exists predominately in the keto form under similar conditions.

In their in-depth study, Chiang and co-workers attribute 47% of
the free energy liberated by  the hydrolysis PEP to the ketonization of the enol form of pyruvate, and
conclude that "nearly half of the high energy content of this molecule resides in its masked  enol function" (And of course, they mean 'high energy' in the Lipmann ('squiggle') sense, that is PEP has a high standard free energy of hydrolysis).

We need to be careful with the following and acknowledge that the language is somewhat loose: we may
think of PEP as a molecule where the thermodynamically unstable form of pyruvate (the enol form)
is 'trapped' in a (thermodynamically stable) phosphate-ester linkage, which will be 'released' on hydrolysis. And to emphasize, the thermodynamically stable form of PEP is the enol form.

IMO, Chiang et al. (1992) is a very nice paper that rigorously backs up conclusions with strong experimental evidence, but it is surprising that they did not quote Walsh
 who (again, IMO) is the first to give the correct explanation?

References

Chiang,Y., Kresge, A. J. & Pruszynski, P. (1992) Keto-Enol Equilibria in the Pyruvic Acid System: Determination of the
Keto-Enol Equilibrium Constants of Pyruvic Acid and Pyruvate and the
Acidity Constant of Pyruvate Enol in Aqueous Solution  J. Am. Chem. Soc. 114, 3103-3107
Damitio, J.,  Smith , G.,  Meany , J. E.,  Pocker, Y. (1992).  A comparative study of the enolization of pyruvate and the reversible dehydration of pyruvate hydrate
J. Am. Chem. Soc.,  114, 3081–3087
Lipmann, F. (1941). Metabolic generation and utilization of phosphate bond energy.  Adv. Enzymol. 1, 99 - 162.
Pocker, Y., Meany, J. E., Nist, B. J., &  Zadorojny, C.  (1969) The Reversible Hydration of Pyruvic Acid. I. Equilibrium Studies.  J. Phys. Chem.
76, 2879 – 2882.
Walsh, C. (1979) Enzymatic Reaction Mechanisms.  W.H. Freeman & Co.

Oxidative Phosphorylation

Perhaps the most important coupled reaction is that which occurs in oxidative phosphorylation where the oxidation of  fuels via the respiratory redox chain is coupled to  the  'synthesis' of ATP.

I have 'steered clear' up to this point, as it is a very complex area and difficult to do justice to in a few lines.

In the chemiosmotic theory of oxidative phosphorylation (due primarily to Peter Mitchell)  electron transport via the respiratory chain to molecular oxygen creates a proton  gradient across the inner mitochondrial membrane by pumping protons outwards. This proton gradient, or protonmotive force, is used to 'drive' the following  reaction to the right:

ADP + Pi ⇌  ATP + H2O

This is commonly referred to as 'ATP synthesis' but, more correctly perhaps, it  maintains our coupling agent  "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48), that is far from equilibrium in the hydrolysis of ATP.

Although all of oxidative phosphorylation may be considered a coupled reaction, all that will be (very briefly) looked at here is the reaction catalyzed by ATP synthase, which may be considered to catalyze the following coupled reaction.

 ADP + Pi + H+(Out) ⇌ ATP + H2O + H+(In)

This is an example of vectorial catalysis, but it is much more. The ATP synthetase has been described as a "splendid molecular machine" (Boyer, 1997b).

It is an example of sequential, cooperative catalysis between 3 active sites where the the release of products (ATP) at one site is dependent on binding of substrates (ADP and Pi ) at another.
It is an example of indirect conformational coupling where the proton gradient effects the release of of tightly bound ATP by eliciting sequential conformational changes in all active sites .
It is an example of a binding-change mechanism, where the proton gradient is responsible release of ATP from the enzyme, but plays no role in its synthesis.
Perhaps most dramatically,  it is an example of rotational catalysis, where the indirect rotation of a protein subunit brings about the sequential conformational  changes in the active sites.

Much of the mechanism of ATP synthetase is due to Boyer: this includes the prediction of rotational catalysis and the formulation (and defense) of the binding-change mechanism (see Boyer, 1997a,b). For some nice dynamic diagrams on the mechanism of action, see this SO answer.

Perhaps the most important considerations from the standpoint of the present discussion is the subtlety  of the coupling effect or 'mechanistic joining': it is brought about by a conformational change due to rotation of a protein subunit, and it is mediated though the dissociation of ATP from a subunit and not through its 'synthesis' from ADP and Pi at an active site.

[Aside] In a most famous experiment, rotary catalysis was 'physically' demonstrated by Kinoshita and  co-workers by attaching an actin filament to the rotating subunit of the enzyme and viewing under a fluorescent microscope (see here), which showed that rotation is anti-clockwise (viewing the enzyme from the 'membrane' side) when the enzyme is hydrolyzing ATP. A nice YouTube video, which seems to be base on the original Noji experiment, may be found here .

References

Abeles, R.H., Frey, P.A. & Jencks, W.P. (1992) Biochemistry.  Jones & Barlett, Publishers.
Boyer, P. D. (1997a) [Nobel Lecture] Energy, Life, and ATP (pdf available here)
Boyer, P. D. (1997b) The ATP Synthase. A splendid molecular machine Annu. Rev. Biochem.  66, 717–749
Mitchell, P. (1978) [Nobel Lecture] David Keilin's Respiratory Chain Concept and Its Chemiosmotic Consequences (pdf available here)
Walker, J. E. (1997) [Nobel Lecture] ATP Synthesis by Rotary Catalysis (pdf available  here)


Monitoring fish growth I am new to experimental design and would like to perform the following experiment but I am not sure if my setup is correct or not so far. My idea is below.

Let's say you want to optimise the growth conditions for the small fish. You have been using a standard type of food that has worked reasonably well. But now, three new brands of fish food have become available and you want to conduct an experiment to test which food works best and whether it is worth changing to one of the new food types.
Based on previous experiments, you reckon that you will need 10 replicates to have a good chance
of finding meaningful differences. There are aquaria and tanks of different sizes available so you are not constrained by the equipment.

For this experiment, I assume there will three treatments (the three new brands of fish food). I will call them A, B and C. Since we are testing three different brands of fish food, I will replicate the brands of fish food three times so there will be nine tanks used in this experiment in total. I will label them from 1 to 9. Each tank will randomly receive different food brands of food every day.

But now, how will I find meaningful differences in the growth of the fish if I apply different treatments randomly on the tanks? Also, how many fish do you recommend I use for this experiment and how often should I monitor the growth of the fish? Or do you have another suggestion of how I could set up this experiment, help. Your help will be much appreciated. Thanks in advance.

This is a good experiment!

3 types of food: ok
9 tanks: ok
Apply different treatment randomly - no!  You are right - no way to tell with random.  It is like comparing McDonalds to vegan diet - you have to stick with your diet to be able to tell a difference in the end.  So Tank 1,2 and 3 get food A.  Tank 4,5,6 get food B.  Tank 7,8,9 get food C.  Each tank gets only that food type.
You need to add the same weight of food to each tank.  More food = more weight.  I am not sure how much is a reasonable amount; it depends on your fish.  Get out what looks like a reasonable amount and weigh it.  That is how much food each tank gets each day.  You could weigh a bunch of quantities and set them aside - maybe in an old egg carton?  That will make it easier to feed the fish each day.
Have the same number of fish in each tank. 3?   Ideally fish are same species and all about the same size to start because different size fish might not all gain weight at the same rate.  I am picturing 11-cent goldfish.  3 per tank makes 9 / food type and 27 in all which is good.
You can gauge growth by fish weight.  When it is time to weigh the fish, fill a bowl with aquarium water, put it on the balance and zero the balance.  Now you will get the weight of whatever you add to the cup because balance is ignoring weight of cup and water.  Sweep a fish out of the tank into the bowl and weigh it.  Then dump it back in and repeat with next fish.

If you can tell the fish apart each one can be weighed separately and I think should also be named with a name that starts with the letter of its tank because that is fun.  For example TankB4 will contain Burr, Black Beauty and Buzz.  Tank C7 will have Clyde, Caesar and Coco.

Keep track in your lab notebook of each fish and its weight
Take a photo of each one when you start and one when you are done.  This will make a great poster.

You can weigh fish every day or maybe every 3 days if you think handling them is too stressful.
You can track weight for each fish, average weight for each tank, and average weight for all 9 fish (3 fish / tank x 3 tanks / food type) over time.  You will graph each of these.  You can use Excel or do by hand.

If a fish or 2 die your data will still be good.

Good luck!  I hope you will come back to this idea and post an image of Aloysius, Angel and Aesop, the fish from tank A1.


Why isn't direct diagnosis of infectious disease through microscopes a common thing? I'm not sure if I am being accurate about this but from what I know about diagnostics (watching House MD etc), if a doctor has a suspicion of a pathogenic infection then he/she usually prescribes corresponding medication without doing some kind of a confirmatory test. But isn't it possible to just have a look at the blood sample under a microscope and then confirm it? I guess it can't be done for viruses because they need an electron microscope to resolve them apart but I guess normal bacterias can be identified using more commonly available microscopes.

The problem with this is that A) the infection may be local, and very few if any bacterial cells may be in circulation, and B) even if the infection is systemic, there could be as few as a couple of bacterium per million red and white blood cells, making visual confirmation impossible. More often, if the attending physician feels the need for a direct ID in order to prescribe the correct medication, a culture is taken from the site of infection or blood is drawn, and then subjected to one of any number of different automated ID systems and/or culture conditions to identify the particular type of bacteria present. This can be as simple as Gram staining to identify Gram positive vs. Gram negative bacteria (different types of antibiotics work on the two classes) all the way to a full identification (genus, species, strain) based on molecular sequencing, typically of ribosomal RNA.


What is the impact of sertraline on white blood cells? This simplified video and RT.com article discusses how the mechanics of the death of a white blood cell can be useful as an "alert mechanism" to other white blood cells of an incoming infection.

Also in the article it describes how this same notification mechanism might enable the transmission of certain types of pathogens and it has the following quote:

  "We found that a commonly used antidepressant can block this whole process and an antibiotic can promote this event,” said Ms Atkin-Smith.

The full report is available here.

Can anyone explain, (with a summary in layman terms) the impact of Sertraline on white blood cells?

Does taking Sertraline increase the risk of susceptibility to illness, or decrease it?

Short answer
While sertraline may theoretically affect the immune system, there is no evidence, as far as I know, that it negatively impacts immune status.

Background
In the article (Atkin-Smith et al., 2015) sertraline (a.k.a. Zoloft, an antidepressant) is shown to block the formation of ‘beads-on-a-string’ protrusions and apoptotic bodies after from dying white blood cells.

Generally, when cells die physiologically, they do not just disintegrate, they undergo programmed cell death called apoptosis.

Beads-on-a-string from a apoptotic monocyte. Source: (Atkin-Smith et al., 2015).

The authors hypothesize that these beads-on-a-string and apoptotic bodies may boost immune responses by containing antigenic material, or that they may contain a warning signal for other immune cells that a pathogen is on the loose.

These claims, however, are hypotheses.

There are many reported side effects of sertaline, but immune suppressant effects are not evident. The only side effects reported touching on it are, e.g., a fever and a sore throat. However, such general symptoms can be caused by a variety of causes and were not reported frequently.

Indeed, in a small study in HIV patients, sertraline showed no adverse effects on the immune system (Rabkin et al., 1994).

References
- Atkin-Smith et a. Nat Comm (2015); 6: 7439
- Rabkin et al. J Clin Psychiatry (1994); 55(10):433-9


Why do bacteria eat enamel? What causes tooth decay bacteria or acids?

I've been told that it is a combination of both but why would bacteria eat enamel?  There are much easier supplies of protein for bacteria to munch through (such as gums) and many of the elements within enamel are not needed for bacteria to respire. Is bacteria eating enamel a myth and if not why do they do it?

While I can't find any specific sources regarding bacteria eating enamel, I highly doubt this is what's happening in our mouths. I doubt this because your point is likely true - minerals in enamel provide no added benefit to the bacteria. I would ask a dentist about this to be sure though.

However, what is certainly true is that the acid produced by the bacteria in dental plaque is what causes tooth decay and gum disease. More specifically, S. mutans is the primary culprit behind dental plaque. Most notably is that S. mutans is an anaerobic organism and because it doesn't require oxygen to respirate, the pathway results in lactic acid as a by-product. This lactic acid is what makes enamel prone to demineralization and if untreated, can irritate your gums, causing gingivitis. It's also worth noting that not all bacteria will do this - not even all anaerobic bacteria that release lactic acid will do this. S. mutans is likely one of the few bacterial species that can survive in your mouth because of it's ability to withstand low pH environments in your mouth and form biofilms - able to nicely stick onto teeth.

S. mutans has no need to munch through enamel or gums. Much of what it breaks down for respiration can be easily obtained from the food and drinks that are left behind after a meal - mostly sugars such as sucrose.


Why do asparagine and glutamine have two different abbreviations? I'm looking at amino acid abbreviations and on every site I visit, asparagine and glutamine have two different abbreviations. Is there a reason for this? Do they represent different forms of the amino acid that may have different properties?

I'm looking at the abbreviations on this site as an example:
http://www.hgmd.cf.ac.uk/docs/cd_amino.html

On the page, asparagine has an abbreviation of 'N' and an abbreviation of 'B'. The abbreviation 'B' doesn't correspond to a codon so why is it there?

Glutamine also has two abbreviations ('Q' and 'Z'). The abbreviation 'Z' doesn't correspond to a codon either.

The abbreviation Asx (B) is used if it is uncertain whether the amino acid at a given position in a peptide sequence is Asparagine or Aspartate. Similarly, Glx (Z) is used when there is uncertainty between Glutamine / Glutamate.

These two pairs of amino acids can be ambiguous in peptide sequences because Asp/Asn and Glu/Gln differs only by a terminal amide (-NH2) group in the side chain, and this amide group can be spontaneously lost from proteins by a deamidation reaction. When this occurs, asparagine is converted to aspartate/isoaspartate, and glutamine to glutamate/glutamate. These cannot be distinguished from "real" aspartate or glutamate by classic peptide sequencing, nor by mass spectrometry, since their mass is identical. Hence, protein sequences obtained directly from protein frequently contains Asx/Glx entries.


Which phylum appeared most recently I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept of phyla. With this in mind, I'm curious which of widely accepted biological phyla appeared most recently, and what evidence do we have of their relatively recent appearance?

I'm most interested in animals, but I'd also welcome any information about other organisms.

In my view, we simply don't have good enough data to answer this question. The fossil evidence is too sparse prior to the Cambrian and the evidence that we do have suggests that the phyla were already too separated. Meanwhile, the depth of time and the different lifecycles and circumstances of the species involved mean that any "genetic clocks" we might use are likely to be too poor at keeping time and, indeed, different attempts have delivered different estimates of the time of divergence.


How is ATP involved in muscle contraction? The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP?

In my text explains this is the procedure for a contraction:

Ach released by motor neuron cross cleft and binds to motor end
plate
AP generated in response to binding of Ach gated channels and propagates down T tuble
T tuble triggers Ca2+ from sarcoplasmic reticulum
Ca2+ binds onto tropinin on actin filament and removes tropomyosin
This opens up sites for myosin to attach to actin using protein heads
Actin filament is pulled toward the center of sarcomere, causing contraction

I see that the action potential definitely needs ATP in order to be generated, aside from that I am surprised that the actual contraction via cross bridge binding does not seem to need ATP.

ATP prepares myosin for binding with actin by moving it to a
  higher-energy state and a "cocked" position.

  Once the myosin forms a cross-bridge with actin, the Pi disassociates
  and the myosin undergoes the power stroke, reaching a lower energy
  state when the sarcomere shortens.

  ATP must bind to myosin to break the cross-bridge and enable the
  myosin to rebind to actin at the next muscle contraction.

  The muscle contraction cycle is triggered by calcium ions binding to
  the protein complex troponin, exposing the active-binding sites on the
  actin. As soon as the actin-binding sites are uncovered, the
  high-energy myosin head bridges the gap, forming a cross-bridge. Once
  myosin binds to the actin, the Pi is released, and the myosin
  undergoes a conformational change to a lower energy state. As myosin
  expends the energy, it moves through the "power stroke," pulling the
  actin filament toward the M-line. When the actin is pulled
  approximately 10 nm toward the M-line, the sarcomere shortens and the
  muscle contracts. At the end of the power stroke, the myosin is in a
  low-energy position.

  After the power stroke, ADP is released, but the cross-bridge formed
  is still in place. ATP then binds to myosin, moving the myosin to its
  high-energy state, releasing the myosin head from the actin active
  site. ATP can then attach to myosin, which allows the cross-bridge
  cycle to start again; further muscle contraction can occur. Therefore,
  without ATP, muscles would remain in their contracted state, rather
  than their relaxed state.

Summary from: https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/muscle-contraction-and-locomotion-218/atp-and-muscle-contraction-826-12069/

Also this:

Essentially look up the cross bridge cycle (http://muscle.ucsd.edu/musintro/bridge.shtml)

I would also suggest reading it from the master himself here:
Huxley, A. F. "Muscular contraction." The Journal of physiology 243.1 (1974): 1-43.


How do point mutations arise from mistakes in DNA replication? Hi! I'm trying to make sense of this illustration (from the textbook Biological Science by Scott Freeman).

The general question is: How do point mutations arise from mistakes in DNA replication?

If you don't mind, however, I'd like to explain how I interpret the illustration so you can see the confusion. As the original molecule of DNA is replicated (in gray), a mistake occurs in the synthesis of the bottom strand in the new molecule (the noncomplimentary bases G and T have been paired together). Now, it seems like a second replication is required for the mutation to arise: the defective molecule is replicated resulting in two new molecules, one free of mistakes (because it takes as its template the top strand) and one "wrong" where the mutation is present.

But my doubt is, wouldn't the middle molecule already constitute a mutation? If a mRNA were to transcribe that sequence, the codon is already different from the original molecule. Must a DNA molecule be replicated two times for a mutation to arise (where the first time a mistake is made and a second where such mistake is, let's say, "consolidated")?

Thank you very much in advance.

Source of your misunderstanding

Your misunderstanding is very comprehensible as the figure is misleading.

The figure only shows a single event of replication. What you see as a second replication resulting into two double stranded molecules is NOT an event of replication. It actually represents the two possible outcomes from a 'mismatch repair mechanism'. The term DNA replication written on the figure should be replaced by Possible outcomes of DNA repair. The molecule that contains the G-T mismatch is therefore just a temporary state that will very quickly be changed to either the T-A state (bottom right of your figure) or to the G-C state (upper right of your figure). More information below.

DNA repair

  DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

The type of DNA repair that is of interest on the figure is called "DNA mismatch repair"

DNA mismatch repair

  DNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

There are specific enzymes to repair a mismatch such as the G-T mismatch represented on your figure. These enzymes can either repair G-T into G-C or into A-T. If the repair is A-T (lower outcome in the figure) then a mutation would have occurred. If the repair is G-C (upper outcome in the figure) then we are back to the original sequence and no mutation would have occurred.

Note that the probability of the two possible outcomes is different from 0.5 as these enzymes have ways to try to figure out which was the original strand and which was the newly replicated strand. You can learn much more about the mechanism of DNA mismatch repair on the wikipedia > DNA mismatch repair.


Are mitochondria alive? I'm working on an assignment for my IB biology class and some assistance would be highly appreciated. I've read several articles and I still haven't quite gotten the answer I'm looking for. I have to write a one page summary on whether or not Mitochondrion are alive or not.

Welcome to Biology.SE

Fields of interest

The assignment you have to write has a little bit to do with Biology and a little bit to do with Philosophy! The question of what is alive and what is not depends on the very definition of what is a living thing and this question is not of interest to biologists but only to philosopher.

How to nail this assignment

Therefore, for your assignment you will need to understand what a mitochondrion is (the Biology part) and to understand how do the different definitions of life apply to the mitochondrion (Philosophy part although you will need some knowledge in Biology to understand the relevance of these definitions).

What is a mitochondrion?

This question is too broad and cannot be answered here. Make sure to have a look at the wikipedia page. In short:

mitochondrion contain DNA
mitochondrion is the result of a bacteria that has somehow been internalized into a bigger cell (it is a symbiont). This is why today mitochondrion contain DNA. It is therefore not exactly an organelle like others. Note that plants, in addition to having mitochondrion, they have plasmids that are also consequences of a similar process of internalizing other form of life.
mitochondrion DNA evolve (of course)
mitochondrion are basically the energy factory of the cell.
mitochondrion are not able to live by themselves outside a living cell (to my knowledge).

Definitions of life

It is important to understand that the definition of life has absolutely no impact on biology and is nothing but a question of nomenclature.

There are a lot of definitions and I can't cover all of them here. You might want to have a look at this wiki page. The previous link lists the most common properties we think about when thinking about the definition of life.

Homeostasis: Regulation of the internal environment to maintain a constant state; for example, sweating to reduce temperature.
Organization: Being structurally composed of one or more cells — the basic units of life.
Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.[49]
Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.
Adaptation: The ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity, diet, and external factors.
Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.
Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms,"with an error rate below the sustainability threshold."

Related questions

The question of whether viruses are alive is a very common one. Here are two Biology.SE posts on the subject:

why-isnt-a-virus-alive
changing-the-definition-of-life


Can Mono-Cell or other organism self-replicate? I have a question regarding how organism replicate them self to create an other organism,

We know that in animal reign, we need a male and female that will generate a new being.

what I want to know is if there is a micro organism that can create another one without a partner of the same kind? and in that case how this organism can do that?

hope my question was clear!

Thanks!

The short answer is yes, there are single-celled organisms that can reproduce without another "partner". Probably the most famous example is that of bacteria.

What you're talking about is known as asexual reproduction. In bacteria, the process is known as binary fission, where one bacterium (known as the parent cell) divides into two organisms (known as daughter cells). These two cells will be genetically identical (barring any mutations) to the parent cell, because there has been no combination (for lack of a better term) of DNA, as there is in sexual reproduction.

The process works the same way it does in cells in multicellular organisms, such as humans: DNA "unwinds" (again due to lack of a better term) in the center of the cell, complementary bases are added to each of the now-separate strands (adenine with thymine, guanine with cytosine), the other parts of the cell are duplicated, and, gradually, the bacterium splits in two. The process can be very quick, compared to the nine months humans spend in the womb.

Asexual reproduction is not unique to single-celled organisms, though. While it is prevalent (and easy) in bacteria, some multicellular organisms reproduce asexually. Some plants are capable or this via self-pollination, and there have been some reports (albeit rather dubious) of certain "common" animals reproducing asexually.

There are advantages and disadvantages to asexual reproduction. One advantage is obvious: no mate necessary. As long as an organism has enough energy and nutrients to reproduce, it can. Also, the process is quick, and easy. There are some disadvantages, though. The big one is that there is no recombination from multiple DNA sources - that is, the resulting organism will have exactly (again, barring mutations) the same genes as its parent - for better or for worse. If an asexually-reproducing organism has a defect that still allows it to reproduce, chances are, its offspring will have that defect.

Some sources:

http://plato.acadiau.ca/courses/biol/Microbiology/Replication.htm

http://www.yourarticlelibrary.com/biology/asexual-reproduction-in-animals-characteristics-occurrence-and-types/11727/

http://www.mpipks-dresden.mpg.de/~mbsffe09/talks/Krug.pdf

http://www.britannica.com/EBchecked/topic/498542/reproduction


What are some features that do not make an individual better than others without this feature? If a mutation occurs so that this allele gives a noticeable feature that is present in this individual but absent in every other individual and this feature is of no benefit or detriment to the individual, I was thinking that this mutation will not make the individual better soothed to the environment or worse and so the gene may not die out but be passed from one generation to the next generation.

If this is so, I thought, there should be many of such “useless” gene present in today’s world. Other than the appendix (which has no function in humans) and subtle differences like eye color, head shape ( not too severe ones but like the ones we see everyday - different heads), which other examples exist?

Phenotypic effect of mutations

Most mutations have no phenotypic effect and therefore no fitness effect either (fitness is a function of both expected survival and expected number of offspring).

These mutations that have no phenotypic effects are therefore all neutral in terms of their fitness effect. Their probability to be passed on to at least one offpsring in a panmictic population of constant size $N$ is $\left(1-\frac{1}{2N}\right)^{2N} ≈ exp(-1) ≈ 0.36$. A mutation that is beneficial would have a greater probability and a deleterious mutations would have a lower probability. There are a whole bunch of equations for these but I don't want to get too "mathy" in this intro post.

Fitness effect of mutations

Among mutations that have phenotypic effects, some have no effect of fitness, some are deleterious, some are beneficial. The beneficial ones only represent a very small minorities of mutations.

Note that it is important to make the difference between a trait that seems to not be beneficial to you, while whether it actually is or is not beneficial. You cite things like eye color and head shape. Both of these traits can have very important on sexual selection. Try to date someone with a triangular head or with white iris! Also, if I am not mistaken, light colored eyes tend to let more light going through to the retina, hence light colored eyes are better adapted in environment where sunlight exposure is low. Head shape may have important impact too. For example, the jaw bones is an important contributor of the head shape and whether you have a strong or weak jaw is of importance (and the shape of the jaw is under sexual selection pressures).

Examples of neutral mutations

Most mutation that happen at non-coding, non-regulatory regions of the genome will be neutral.

Among the mutations that have phenotypic consequences but no fitness consequence, there are classical genetic markers (such as tongue rolling) that are likely free from any selection pressures. Note, that heritability for such trait is rarely 1.0 (see here for explanations). Maybe earlobes would be a good example, although there might have some sexual selection going one here.

Note also that as many mutations are recessive, the carrier of a single copy of the mutation may not be affected.

What is a gene?

You are using the term gene improperly. A gene is typically defined as a coding region. You might want to study a little the basis of genetics here. You should typically get used to the terms locus, allele and gene copy number. This answer can help you at this endeavour.

A small comment on the frequency of mutations

  If a mutation occurs [..]

Just to make sure you do not have a misconception about how frequent mutations are here, I would like to highlight that, in humans, at every reproduction event, the new born has about 10 to 100 new mutations that were not present in any of both parent. So, mutations are rather common!

Introduction to evolutionary biology

Your question is a very introductory question to evolutionary biology. You might want to have a look at a short introductory course such as evo101 by UC Berkeley.


If action potential is "all or nothing" then how are finely tuned signals sent from one neuron to another? If the action potential is an "all or nothing" phenomenon, then how is one type of neurotransmitter secreted rather than another? Let's say, for example, if a neuron received an excitatory post synaptic potential that initiated a graded potential that initiated an action potential, what specific signaling cascade or mechanism would denote the release of one excitatory neurotransmitter (say nor-epinephrine) over another (say dopamine) ?

how is one type of neurotransmitter secreted rather than another

Most neurons release a single major neurotransmitter. JM97 commented a link about cells releasing more than one, but that is talking about "extra" neurotransmitters are short peptides, different from the major neurotransmitters like glutamate, GABA, acetylcholine, dopamine, norepinephrine, etc - I think that link is very misleading in the context of your question. Those cells don't choose one or the other, they release their primary neurotransmitter plus the peptide.

However, there are lots of different neurons and lots of different TYPES of neurons, so some release one type of neurotransmitter, others release another. Typically this is denoted by refering to cells as "___ergic": GABAergic cells release GABA, glutamatergic cells release glutamate, etc. Those specific cell types express the proteins necessary to synthesize their neurotransmitters and transport them into synaptic vesicles, ready to release. The actual signalling cascade that results in vesicle release is pretty much the same across different neurons: the difference is in what is packaged into those synaptic vesicles.

  if a neuron received an excitatory post synaptic potential that initiated a graded potential that initiated an action potential what specific signaling cascade or mechanism would denote the release of one excitatory neurotransmitter (say nor-epinephrine) over another (say dopamine) ?

Simple: if the action potential is fired by a noradrenergic cell, that cell will release norepinephrine on all of its targets. If the action potential is fired by a dopaminergic cell, that cell will release dopamine on all of its targets. They are different cells.

In contrast to outputs, which use a single primary neurotransmitter, individual cells can receive inputs from many types of neurotransmitter. So a dopaminergic cell could receive GABAergic inhibitory inputs and also receive glutamatergic excitatory inputs, but it will only release dopamine on its targets.

If you have a network, and you wanted that network to release more dopamine on average, you would increase the synaptic weights of the excitatory inputs to dopaminergic cells: that is, increase the amplitude of EPSPs in those cells (you could possibly also reduce the inhibition).

In the title of your question, you asked how "finely tuned signals" can be sent. Tuning of signals isn't just about which neurotransmitter is released, but rather which cells that neurotransmitter is released on to. Individual cells can both receive 1000s of inputs and send outputs to 1000s of other cells. The patterns of those connections and the patterns of active cells are what determine the "message" - this is called "encoding".


What do you call that part of the muscle that connects directly to the bone? When you open up a chicken leg or a clam and you remove the meat, there is this little part that is connected to the bone and is not easily scraped off.

What is this part called and what mechanism does it use to connect to the bone or the shell?

The tendon is the part of the muscle that connects directly to the bone.

  A tendon (or sinew) is a tough band of fibrous connective tissue that usually connects muscle to bone and is capable of withstanding tension. Tendons are similar to ligaments and fasciae; all three are made of collagen. Ligaments join one bone to another bone; fasciae connect muscles to other muscles. Tendons and muscles work together to move bones.

The image was taken from the wikipedia link.


Why doesn't crossing over happen in mitosis? If there was crossing over in mitosis, then there would various nature of somatic cells. May be that's the logic, but what is the mechanism? Why are there no crossover events during mitosis?

It can actually on very rare occasions however, it is also highly problematic and generally creates deleterious mutations and can inactivate genes. Depending on the location of the cell and the cross-over within the genome, it can also contribute to the formation of cancer. For instance, in the case of retinoblastoma, if there is one mutated copy of RAS on one chromosome and a normal copy on the other and mitotic crossing over occurs, then you can potentially remove the protective nonmutant copy of RAS from one of the daughter cells. This cell is then one step closer to becoming tumorgenic.

Thus, one reason this may not occur ordinarily is to reduce the chance of causing such a cancer. As for why it does occur on the rare times it does, I am not certain as of the time of writing this.

Reference: The Biology of Cancer, by Robert A. Weinberg


What is meant by topographic barrier? There are three types of barriers, physical , climatic and biological barriers that can prevent the dispersal of organisms.

Topographic barrier falls in the category of physical barrier but exactly what should be considered as topographic barriers is not clear to me.

The source from which I actually came across the term says that mountain range is a topographic barrier like the Himalayan range separating the North-asian fauna (partly Palearctic fauna) from the Oriental fauna. But what else falls under topographic barriers is my question?

Whether something is considered a topographic barrier for an organism depends on the species being considered and its ability to traverse the terrain from one side of the barrier to the other. There's no blanket classification of what is considered a topographic barrier and what isn't.

For example, a certain mountain range may be a topographic gradient to a salamander (due to limited food, extreme weather conditions, etc.), but these same mountains might not be for a brown bear.


Are fluoroquinolone antibiotics (Cipro, Levaquin, etc) chemotherapy drugs? I read a claim (I can't find the source) that fluoroquinolone antibiotics are actually chemotherapy drugs, or maybe to be more specific, are "chemotherapeutic." Is this claim true? Additionally, if true, does this claim apply to all antibiotics, or only fluoroquinolones?

Short answer: Yes, fluoroquinolones are chemotherapy drugs
In layman's terms, fluoroquinolone antibiotics kill human cells as they divide. Fluoroquinolones are a class of drug called "topoisomerase interrupters." Every drug in this class is directly labeled as a chemotherapy drug except fluoroquinolones.
This is not well known by the medical community and is in part why irreversible damage from fluoroquinolone antibiotics is not well understood.
Long answer: Fluoroquinolones are definitely chemotherapy drugs, and they're dangerous
A refresher on how fluoroquinolones work, in case you slept through molecular pharmacology :
If you want you can skip this first section and instead watch YouTube: Fluoroquinolones: Mechanisms of Action and Resistance
How topoisomerase works
Bacterial cells have double helix DNA, meaning two strands twisted around each other. When bacterial cells divide, the two DNA strands are separated (untwisted), and eventually each side is turned back into a full double helix, making two copies.
If you think of a tightly twisted rope (representing double helix DNA) and start to pull the two ends apart, the rope will twist tighter and tighter and eventually you can't untwist it further. Nature's fairly primitive solution is an enzyme called topoisomerase.

topo-: dealing with topology, as in the structure of the DNA
-isomerase: a class of enzymes (enzymes are usually bundles of proteins)

The job of topoisomerase is to cut the the double helix DNA strand, untwist it, and then glue it back together.
There are several types of topoisomerase, which we'll come back to.
How fluoroquinolones kill bacteria
Fluoroquinolones bind to the glueing action of topoisomerase. So, as part of normal cell division, topoisomerase cuts a DNA strand, untwists it, then tries to glue it back together. However, fluoroquinolones block the gluing action ("plug the glue bottle"), so the cell literally cuts up its own DNA. Insidious, isn't it?
Don't human cells have topoisomerase?
Yes, since humans have two sets of DNA, let's focus on one at a time.
How fluoroquinolones kill human mitochondria
Human mitochondria are bacteria, and they do contain double helix DNA and topoisomerase. So why don't fluoroquinolones kill mitochondria? Trick question: they do, and it's worse than that.
Human mitochondria keep around backup copies of their mtDNA (we often call mitochondrial DNA "mtDNA" to distinguish it) to use when there are replication errors in DNA synthesis. Fluoroquinolones "deplete" mtDNA, meaning irreversibly destroy backup copies. The organelle desperately tries to pull in backup copies as it cuts up its own mtDNA during replication, and may die, or may become permanently damaged.
Insidious, isn't it?
Many other studies have proven that fluoroquinolones kill human mitochondria as they divide. Interrupting topoisomerase isn't the only way they kill mitochondria, but it's an important one.
How fluoroquinolones kill human eukaryotic cells
Human "eukaryotic" cells (cells with a nucleus, such as tissue cells) also have topoisomerase. So why don't fluoroquinolones kill eukaryotic cells? Trick question, they do:

Compared to an [actual DNA poison], ciprofloxacin produced comparable dose-dependent SCE frequency increases

(an SCE, "sister chromatid exchange" is a marker for how genetically damaged a cell is)
and

topoisomerase type II and DNA gyrase are physiological targets for [ciprofloxacin]

Insidious, isn't it?
Like mitochondria, topo binding is a small part of the kaleidoscope of how fluoroquinolones cause permanent cellular damage, but it's an important one.
As you can imagine, fluoroquinolones killing a cell's main source of energy (mitochondria), while also causing the cell to irreversibly destroy its own DNA lead to human cells dying as they try to divide divide
Even clearer: Compared to other chemo drugs
There are several oral chemotherapy drugs on the market, one of which is Topotecan (notice the topo-?). Here's how they work:

Topoisomerase I inhibitors:  Ironotecan, topotecan
Topoisomerase II inhibitors:  Amsacrine, etoposide, etoposide phosphate, teniposide

And, as linked in the earlier study, fluoroquinolones are topoisomerase II inhibitors. (They probably bind to other forms of topo, but we don't know for sure).
Even clearer: Fluoroquinolones are used for chemotherapy
There are a few
"novel" studies using fluoroquinolones as chemotherapy drugs. In this study, ciprofloxacin is used to target leukemia cells.
Why are chemotherapy drugs used as antibiotics?
When (non-fluorinated) quinolone antibiotics were first invented in the 60s-70s, we didn't know about mitochondrial DNA, and certainly not how fluoroquinolones affect mitochondria.
Don't fluoroquinolones have a good safety profile?
No.
Fluoroquinolones were released in the 70s, but the FDA warning for permanent nerve damage wasn't added until 2013. Because the symptoms of permanent fluoroquinolone damage are so outrageous (permanent nerve damage, tendons spontaneously rupturing, organ failure, psychosis, and dozens more). Doctors simply didn't know (and still don't know) to look for the symptoms, so they aren't documented.
There have been other fluoroquinolones that had "good" safety profiles, passed all medical standards, and then were promptly removed from the market after they started killing patients outright. One such drug, temifloxacin, was removed because it caused so many cells to die that the kidneys became clogged, killing patients.
The fluoroquinolones on the market are all able to, and have, killed patients through multiple mechanisms, but it's more rare, and the permanent damage symptoms are not connected by doctors.
All fluoroquinolones have the same core method of action, and all have a fluorine moiety allowing them to penetrate anywhere in the human body ("hard to reach" infections), so even though the current ones haven't been removed from the market, it doesn't follow that they are safe.
Why continue to prescribe them?
I sincerely believe that if doctors understood how fluoroquinolones worked, they would stop prescribing them, and use them only in life or death situations. The FDA has already advised never to use fluoroquinolones for "uncomplicated" infections, but this advice is not known nor heeded.
If only doctors read studies from over 10 years ago:

In view of the present genotoxicity, ciprofloxacin should be administered with caution.