To understand why satellite cells are genetically inactive in Barr body DAPI is used as a stain for DNA heterochromatic and euchromatic regions. The Barr body is heterochromatic.
In the slide of a normal human female cheek's somatic cells, there is apparently no other clear dark spot inside the nucleus than the Barr body against the nuclear inner membrane. - - I used an old microscope so my observation may be wrong as pointed in the comment.

How can you deduce from the given slide that the spot really contains inactive satellite cells that are not used genetically?
Why is the active X chromosome not visible by the same staining method? (It probably can be made visible by some other staining method.)

DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase.  In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus.  When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.

A great picture is here (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.

Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes.  The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.

I do not understand the first part of your question, though.  You cannot tell from a still image that the Barr Body is relatively inactive.  If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes.  If you clarify your question, I can answer better.


Power consumption of a ATP synthase in Watts Considering the ATP synthase to be a rotating machine, does anybody know its power consumption and/or power production in Watts? At least roughly, e.g. based on the average chemical energy produced per time unit?

There are tons of mechanistic studies of ATP synthase so you may be able to get a better answer from finding one of those. But here's a rough estimate based on thermodynamics and enzyme kinetics.

The $\Delta G$ of ATP synthesis/hydrolysis is about -50 kJ/mol. The $V_{max}$ is in the low hundreds (here is an estimate of 350 $s^{-1}$ for E. coli ATP synthase), giving you something like 17 MW/mol or 30 aW (3e-17 W) /molecule.

I did look briefly at some mechanistic studies, and found this reference of 80 pN * nM for the torque generated. That translates to almost exactly the same 50 kJ/mol (ATP synthase is very efficient). But of course you still need the $V_{max}$ (number of rotations per second) to get the power.


What's the highest temperature that algae can survive at? I know there are a lot of different species of algae and that each one has different environmental tolerances. I've seen data on different species:

brown alga Sargassum echinocarpum J. Agardh - grows well at 35°
Dictyopteris australis - grows poorly above 28°
halophilic blue-green algae A. fertilissima - temperatures of 47° stimulates germination

What's the highest temperature that growing algae or its spores can survive at? In other words, what temperature would guarantee that no algae could grow afterwards unless reintroduced?

Based on the habitat of Algaes, a classification called "Thermophytes" can bear high temperature. The Thermophyte algaes use to grow around hot springs and can live around 70°C.

Please find below the reference for all classifications and more details.

http://www.yourarticlelibrary.com/biology/8-types-of-algae-classified-according-to-their-habitats/7098/

http://www.biologydiscussion.com/essay/essay-on-algae/20891


What are the branches of system ecology? What are the branches of system ecology that scientists research in nowadays? Or what can system ecology can applied to, or be used?

I have read its Wikipedia page, but sadly it doesn't answer my question. The most relevant section of it is the "Closely related fields", but again, it doesn't answer my question directly.

From what I understand, system ecology is a sub-field of theoretical ecology. It uses thermodynamic in physics to explain a biological system, with the help of network thinking and some technique of visualization. I have presented this in detail what I understand on my website.

Related: How is the Energy Systems Language used in ecology?

What are the branches of system ecology that scientists research in nowadays? Or what can system ecology can applied to, or be used?

This field is often referred to as systems ecology or ecosystem ecology. It is the study of ecosystems. Thermodynamic principles are often used to construct food/system webs (networks) to understand cause and effect within the system. But I think systems ecology can be considered beyond just a numerical approach to include social (human) dynamics.

A great primer for systems ecology is that by Howard T. Odum:

Odum, Howard T. "Systems Ecology; an introduction." (1983).

  I have presented this in detail what I understand on my website.

After reading the post on your website I have some recommendations for complex systems science groups/hubs in which you can look for potential mentors/collaborators/ideas:

International Institute for Applied Systems Analysis (IIASA; Austria)
Santa Fe Insitute (US)
National Socio-Environmental Synthesis Center (SESYNC; US)


How to assemble three 60mer nts by pcr? Good morning,
I am new to molecular biology. The question might be silly but i would like to know the answer. I have three 60mer single strand synthetic oligonucleotide. Namely Tag 1 - 3. My goal is to assemble these three together by pcr. So i designed two primers having overlap of 18nts from each tag 1 and tag 2 and then Tag 2 and tag 3 ( i mentioned the orientation of my primers). What is the best way to assemble. I read about PCR- based two-step DNA synthesis. But i would like to know more about this.
If you have any questions please feel free to post. Thanks and looking forward for your valuable answers
[]

In order to assemble your TAG oligos by PCR you will need to redesign your primers so they are complementary to the TAG oligos as DNA polymerases work by adding nucleotides to the 3' end of a DNA strand.
Your design would look like this :

Now with this design you won't be able to assemble everything together as TAG-3 complementarity to primer 2 only presents 5' ends to be extended, which your DNA polymerase can't do. So you can either order the entire reverse complement of your TAG-3 oligo or design a primer 3 that would anneal at the 3' end of TAG-3 to amplify TAG-3.
With all these parts, you should be able to assemble everything in a single reaction, but depending on your downstream process you may have to purify the product of interest as the single reaction will generate intermediates (1, 2, 3, 1+2, 2+3).


What is meant by "catalytic amount of a hormone"? This textbook says:

  In the classic definition, hormones are secretory products of the ductless glands, which are released in catalytic amounts into the blood stream and transported to specific target cells (or organs), where they elicit physiologic, morphologic and biochemical responses.

What is meant by catalytic amount? Does it mean that amount required for catalysis? I know only renin which is catalytic and act as an enzyme, and many other hormones are non enzymatic so why the term catalytic is used in general sense?

The writer obviously means “small amount”, and has chosen his words badly as hormones do not themselves catalyse reactions.

The idea he is probably trying to convey is that a few molecules of hormone binding to their receptor can cause changes to many molecules within the target cell. This often (generally?) involves catalysis within the cell produced by the receptor activating an enzyme, so one can understand the line of thought leading to the misuse of this term.


Standard letter for 5-methylcytosine I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base.  At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U.  Is there a standard letter for 5-methylcytosine?  The only example I've found is this paper, which uses an italic C for 5mc, but I want a distinct letter.  The three candidates I've thought of are:

5 - for '5-methylcytosine'
M - for 'methyl'
B - Since methylation of U gives you T, which is one place earlier in the alphabet, so methylation of C gives B.

Well, don't use M or B, those are already taken (C or A, and not A, respectively).  You can see the full list here: http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html (The enWiki article on Nucleobases lists a few others but I would ignore those as 1. D is present in both and 2. they are rare and inapplicable)

5-methylcytosine isn't on there.  If you want to be pedantic about it, 5-methylcytosine is an epigenetic marker and as such is by definition not a genetic sequence; that remains simply a C and, genetically, the sequence is the same, despite the fact that it may indeed make a difference.

Most of the time people use m5C, so I'd go with 5 if I were you.  That certainly isn't used for anything else and if you must use a single character most anybody will know what you are talking about.


Identify this tuber like object found on beach Can anyone identify this tuber-like object I found on a beach in South Wales, UK? It's about 25 cm long and looks like a deflated football. Pretty spongy, saturated with water. I was hoping it was ambergris, but that seems unlikely.

It is spongy because it is a sponge, specifically a sea sponge. There are quite a large number of them native to the waters around england. I would guess Craniella cranium based on shape and location but I am by no means an expert on sponges.
Here  a cross section of a cleaned sponge

and sediment laden potato sponges after a hurricane.

you can see more images of collecting these here, http://www.vims.edu/newsandevents/topstories/archives/2011/irene_blobs.php

Here is a whole website dedicated to english sea sponges, http://www.aphotomarine.com/sponge_suberites_ficus_sea_orange_sulphur.html


phosphorylation of Glyceraldehyde 3-phosphate This question is related to something that happens when 3-phosphoglyceraldehyde is converted to 1,3-bisphosphoglycerate during glycolysis.

As I understand it, 3-phosphoglyceraldehyde is deprotonated by NAD+ and phosphorylated by a Pi group, which results in NADH + H. The extra H apparently comes from the Pi group (which I believe is called orthophosphate [1]).

Now, where does the Pi come from? is it just sitting in the cytosol?, does all Pi have a hydrogen? can someone clarify what an orthophosphate is, I never heard of that term.

Yes, the cytosol contains a high concentration of orthophosphate (in yeast, between 10--75 mM) so it is readily available for this reaction. The notation P$_i$ is commonly used because the orthophosphate ion can exist in multiple forms in water solution:

H$_3$PO$_4$ $\leftrightarrow$ H$_2$PO$_4^{-}$ + H$^+$ $\leftrightarrow$ HPO$_4^{2-}$ + 2H$^+$$\leftrightarrow$ PO$_4^{3-}$ + 3H$^+$

When we don't need to specify an exact form, P$_i$ is convenient as a shorthand for "some phosphate ion".

At the cytosolic pH (about 7.2), almost all orthophosphate is in the H$_2$PO$_4^{-}$ and HPO$_4^{2-}$ forms, which are roughly equally abundant. So yes, there is (at least) one hydrogen on orthophosphate available for the enzymatic reaction.

The term "orthophosphate" rather than just "phosphate" is common in biochemistry because phosphate also exists as polymers, including the di- and triphophates (in nucleotides, for example) as well as longer polyphosphate chains. These form are all referred to as "phosphates", while "orthophophate" specifically means the "monomer" P$_i$.


Why is cancer more lethal than (hypothetical)infections? I am a computer science student and I'm interested in algorithmic aspects of cancer! Once I heard that there exist more bacteria in human body than our own cells, I wondered that why bacteria, which divide faster than cell bodies, do not cause something like cancer in body? Isn't it evolutionary more probable for bacteria to gain aggressive properties and invade human tissues? Or maybe is it the case that bacteria really produce some lethal colonies like cancers in the body?

One difficulty with cancers is that cancer is a very complex disease  because of it's intra-tumor and inter-tumor heterogeneity. Isn't it more probable for bacteria to cause extremely heterogenous infections with regard to existing simple evolutionary models which are used to describe cancer?

Cancer is not inherently more lethal than bacterial infections. That's simply an artifact of the time we live in. Broad spectrum anti-bacterial drugs we invented in the 1st half of the twentieth century. Before that, most folks died of infections. Cancer was relatively rare because most folks didn't live long enough for cancers to become apparent.

Why do we have generic drugs for bacteria and not for cancer?  Largely because bacteria are not eukaryotes and we are. The biology of bacteria and human cells are so different that it's relatively easy to find drugs that dramatically affect bacteria, but not people. I say relatively easy, but still took several thousand years of human history to figure it out.

Because cancer cells are just variations on our normal cells, it's very hard to find something that kills the cancer cells, but not the rest of us. That's why chemotherapy makes folks so sick: the chemotherapy agent is killing, or significantly impairing, fast growing healthy cells along with the cancer cells. The most successful cancer drugs have identified rare metabolic pathways that are important to specific types of cancer, but not so important to healthy cells.


How long can one leave sample in lysis buffer for DNA extraction? I am trying to do some DNA extraction for my professor, and I make a lysis buffer with proteinase K. I did not have the time to continue the procedure so the hair and the buffer have been sitting together at room temperature for about 12 days. My professor stated it would be "fine" to continue on with my DNA isolation procedure, but I have my doubts.

Should I continue my DNA extraction( vortexing, boiling, centrifugation and collection of supernatant, storage at -20 degree Celsius) or would this be pointless at this time? My goal is to run PCR and then a gel.

EDIT:

Here is the composition of the lysis buffer:

In 20 ml of Lysis buffer:

final concentrations are $0.1 M$ TAE, $0.5M$ $\ce{NaCl}$, 0.2% SDS.

To $800 ul$ of Lysis buffer I added $5 ul$ of proteinase K at a concentration of $250 ug/ml$.

(Proteinase K was made via:  $ 0.0025 g$ up to $10 ml$ of TAE buffer( $1 M $))

This was in a $1.5 ml$ centrifuge tube that has been now sitting for 12 days.

It should be fine. Unless they have been contaminated with DNase, none of the components will damage or denature DNA. I've left purified plasmid DNA on the bench for weeks with no apparent degradation, so you should be okay (not that I recommend doing that on a regular basis). I would continue with the purification, according to your professor's recommendation, because you've already come this far. If worst comes to worst, you won't get anything, and you'll have to re-purify. However, the chances of your getting something are pretty high, so you may as well go with it.


A state model of sodium channels I am studying by myself Human Physiology.
I have encountered the following question:

In the following given model of sodium channel with 3 states open closed blocked (which I assume means inactivated), the rates of going from state to stated are given in the picture below.

a. Write matrix $Q$ for the system and find it's eigenvalues.
b. What does these values represent?

If anyone has an idea what is the required matrix I will be grateful.
Thanks!

There is no standard notation called Q (matrix).

However in this case I think the matrix that they are referring to is the state transition matrix (similar to the adjacency matrix as mentioned by Justas in the comments, but with rates instead of just the connections). Basically you have three states (lets call them A, B and C) and there is a rate for transition from one state to the other. You can also represent these rates in the form of transition probabilities.

You just represent this as a 3×3 matrix. Put zero where there are no such transitions (for example there is no transition from A to A or A to C):

$$\begin{array}{|l|c|c|c|}
\hline
 & A & B & C \\\hline
A & 0 & 10 & 0 \\\hline
B & 100 & 0 & 50 \\\hline
C & 5 & 0 & 0 \\\hline
\end{array}
$$

You can then calculate the eigenvalue for this matrix. How to calculate eigenvalues and what is their significance is off-topic in this site. You can easily find out how to calculate eigenvalues. Their significance is something that is not that easy to understand but you can read more about that and can perhaps ask a precise question in Mathematics Stack Exchange. Basically, they tell you how the system proceeds in different directions (denoted by eigenvectors).


Why do living fossils like crocodiles remain so constant and not evolve? Crocodiles have supposedly remained unchanged for millions of years, and several other species are considered as "living fossils". How do such species remain so constant over time given that they will have had so much time to accumulate new mutations?

Evolution is a process of change by four mechanisms; mutation, migration, drift, and selection.

You are correct in thinking that, because crocodiles have been around for a long time, they could have accumulated many new mutations in that time, relative to other more recent species. However, mutation is only one of the important mechanisms underlying evolution.

How different are ancestral and modern crocodiles?

It seems the appearance of crocodiles has been fairly unchanged since their occurrence ~85 million years ago (mya).

How can they remain so unchanged?

Genetic variation may have been low in the ancestral population, this would reduce the potential for evolutionary change, as most change would have to occur through new mutations. It seems the populations of ancestral crocodiles were quite small, such that a genetic bottleneck may have occurred (which would reduce genetic variation). Mutation rates seem to be relatively low in crocodiles (also see here) which would reduce the rate at which novel mutation occurs, reducing the potential for evolution.

Note that many mutations will be neutral in their effect (or "synonymous") so won't have an obvious phenotypic effect, so there may be substantial evolution at the genetic level despite the phenotypic similarity.

Low rates of evolutionary change could suggests some other things may have also played a factor. Given that the populations have been through multiple genetic bottlenecks, genetic drift could have slowed down rates of evolution eroding genetic variance, removing rare mutations from the population.

If selection has been fairly constant over time then there is less chance that changes will occur. If selection were to change and favour new adaptations then these are likely to spread, but if selection remains fairly constant over time then it will continue to favour the same mutations. After a long time of consistent selection it is likely that most mutations will be deleterious (have a negative effect) and be removed from the population by selection. Darwin suggested that living fossils could occur because the environment they are in has remained fairly constant (from this link).


Anatomy of nervous system's sensory pathways When I touch my hand on a hot stove, I feel pain. I'm interested in knowing all the main "endpoints" (components/parts of the body) that are involved in relaying this pain signal. As I understand it so far, they are:

Nerve (thermoreceptor)
Fibers
Spinal cord
Brain stem (medula => pons => midbrain)
???
Somatosensory Cortex

A special sensory nerve in my hand, called a thermoreceptor, receives a thermal input (the hot stove) and fires a pain signal to my spinal cord.

My spinal cord then sends the signal up into the brain stem, where the signal travels through the medula, the pons and the midbrain.

At this point the signal is somehow wired to my somatosensory cortex; the part of the brain that ultimately processes the signal and interprets it as "pain".

Have I identified all the key players here? What connects the midbrain/brainstem to the somatosensory cortex?

The key player you are lacking is the thalamus, which integrates a lot of stimuli, and pre-processes them before sending them to the cortex


What is the most reliable tumour suppressing gene for NSCLC? I was looking at some tumour suppressing genes that can be helpful in diagnosing lung cancer (particularly NSCLC - Non-small-cell lung carcinoma) at an early stage. I came across a few such as p53, etc. However, as a beginner (and someone who has never pursued higher studies in biology), I do not have much knowledge as to which is the most reliable and the most extensively documented tumour suppressing gene for NSCLC.

The first resource I would look at would be the TCGA publication on NSCLC which can be found at this location. The first figure shows the most frequently mutated genes. TP53 rises to the top as most frequently mutated gene in the cohort studied, however, one also sees on the list KEAP1, NF1, ARID1A, SMARCA4, RB1, and CDKN2 as commonly altered tumor suppressors TSGs. You will want to take into account copy number data and mutation data in the frequency count in cohort also. Another issue to check in the data set is stage of the tumors in TCGA. You mentioned 'early stage' in your query, but if all the samples in TCGA are recurrent then it may not be appropriate for your question. The cBioPortal resource allows you to look and manipulate the data and I encourage you to look at that resource. It is very well done and shouldn't have too much of a learning curve. You will be able to put in TSGs and get back the freq of mutations. They may also have information on stage so might be possible to filter for only those samples. There are also a couple of text-mining resources that you can ask queries through pubmed to get back gene lists or to link gene lists. One tool is Glad4U (search this name in google) which allows you to type a query such as: "tumor suppressor AND early stage NSCLC" and it will return a ranked list of genes. Ranking is based on co-citation. However, one must check the returned list to make sure the genes returned are TSGs. A listing of putative TSGs can be found here. The second resource is CoCiter v2.0. On the Gene-Term search you can rank the lists of TSGs against search terms and it will return a ranking of the TSGs most associated with your search term. Hope this helps.


What is a holocentric chromosome? I was doing this question that asked: "How many centromeres does a typical chromosome have?"

I thought one and the answer was:"One, except for holocentric chromosomes."

So then what are "holocentric chromosomes"?

I assume they would be chromosomes with more than one centromere, but then why do they need more than one centromere? And where can I get some more information on them? I tried googling but did not find much info on this.

In most eukaryotes, the kinetochore protein complex assembles at a single locus termed the centromere to attach chromosomes to spindle microtubules. Holocentric chromosomes have the unusual property of attaching to spindle microtubules along their entire length.

source


Can an insect poison itself with food? Is it possible that an insect poisons itself while eating "wrong" plants/fruits/... and have symptoms like pain (may hard to measure or detect) or orientation disorder?

Background:
I observed a physically apparently healthy caterpillar moving in circles (or rather changing its direction constantly and end up at the same point again) on the street and falling over in middle of moving or standing. My first and a bit naive thought was, that it may have eaten something wrong...

Indeed, many plants produce molecules which are poisonous to things that eat that plant (insect, mammal, bird) in the "hopes" of preventing that animal from eating them. In this sense, even eating the "right" fruit may be dangerous (if that individual plant happens to be an exceptionally vigorous producer of the poison, or because the eater is weakened for some other reason, or simply ate too much). I doubt insects would eat the wrong fruit that much, because evolution favors insects that can precisely recognize correct prey plants, at least in indigenous surroundings.

Indeed, many plant "flavors" that we humans enjoy (such as garlic and peppers) are likely such herbivore poisons that we happen to be immune to. In fact, almost every plant is actually poisonous - the question is, poisonous to which species?

Plant defense is a very actively researched topic these days, since it relates to things like agricultural efficiency and global food shortages (and besides, it's a very interesting phenomenon). Here is a review discussing what you ask about in more detail: http://www.plantphysiology.org/content/121/2/325.full

An addendum upon reading this question many months later: While evolution has perfected the ability of insects to recognize correct food, this has not been the case for man-made pesticides. I would guess that the caterpillar you saw is more likely to have eaten an artificial chemical (either pesticide or pollutant) than a "wrong fruit".


What is the difference between an antibiotic and an antibacterial? Concerning medicine, what are the differences between antibiotics and antibacterials?

An antibacterial is any compound that will kill or at least slow down the growth of strictly bacteria, a domain of prokaryotes.

An antibiotic is often used synonymously, but denotes a compound that kills or slows down the growth of any cellular pathogen, prokaryotic or eukaryotic. So, certain antibiotics can kill bacteria, fungi and parasites but antibiotics have no effect on viruses and prions.


Was lactose present in the environment before the evolution of mammals? Are there lactose sources other than dairy products in nature? I tried to search for it but I did not find anything. The question arose because I was wondering whether lactose-utilising enzymes in bacteria evolved only after the appearance of mammals.

Preamble

This is an answer to the motivation expressed in the question:

  “…whether lactose-utilising enzymes in bacteria evolved only after the appearance of mammals”

rather than that in the title. The presence or absence of lactose elsewhere in Nature will not decide this question.

Answer

The name lactase is applied to the mammalian enzyme that is able to catalyse the hydrolysis of the disaccharide, lactose, to glucose and galactose, allowing the digestion of this milk sugar by the suckling infant. However bacterial and plant enzymes that are normally referred to as β-galactosidases can also catalyse the same reaction.

The role of the β-galactosidases in bacteria such as Lactobacillus lactis that are found in a dairy environment may well be to hydrolyse milk lactose, as may be that of Escherichia coli, found in the human gut. However this is unlikely to be generally true for all bacteria. This is because β-galactosidases are found in a wide spectrum of bacteria, including extremophiles† which cannot possibly have had access to milk lactose.

β-galactosidases are generally members of a group of enzymes termed glycoside hydrolases and have been categorized into a number of families on the basis of sequence similarity. The enzymes in these families differ in their substrate specificity. To explain the existence of such enzymes in bacteria which do not have access to lactase it has been suggested that their natural substrates may be other disaccharides. This is actually the subject of a PhD Thesis by S.A. Shipkowski, who suggests that some β-galactosidases may actually hydrolyse β-1,4 galactobiose:

The significance of this is that the polysaccharide, pectin, found in certain plant cell walls, could be broken down by by other enzymes in the bacteria, yielding galactobiose.

Conclusion

Although the β-galactosidase in certain bacteria may be optimized to hydrolyse milk lactose, the gene encoding it is almost certainly derived from an ancestral glycoside hydrolases gene, the product of which predated the appearance of mammals and was used to hydrolyse other disaccharides derived from polysaccharides originating from various sources.

† It should be emphasized that the β-galactosidase from extreme thermophiles such as Thermus thermophilus KNOUC114 — isolated from a hot spring — hydrolyses lactose well. Indeed, its thermostablity has attracted interest in its development for use in the food industry (Ahn et al. 2012).


During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations? During bridge amplification, when sequences attached to adapters on the surface form "bridges" and are replicated, it seems like sequences with either end attached to the surface will be created.
For instance, in this link in figure 7, there are sequences facing both ways on the plate. In step 8, all the sequences are oriented in the same direction (pink end attached to the surface)
How are does this occur? How are the other sequences removed?

See this document on how Illumina sequencing works.

When you are doing a single end sequencing, the reverse strands produced after the bridge amplification + denaturation (step-7) are specifically removed (clipped at the junction of primer and the "insert" region). Furthermore, the free 3' ends are blocked (by chemical modification) to ensure that there is no unwanted priming.

For paired end sequencing, both strands are sequenced; so in one flow cell the forward strand is cleaved while in the other the reverse strand is cleaved.


What is the anatomical term for a two jointed leg? Allow me to apologize in advance for the layman's terminology.

I'm wondering what the anatomical term for a cat- or a goat-style hind leg is.

Cats, goats, t-rexes, and many many other animals don't have human hind legs (i.e., with one knee / one pivot point). They have two pivot points, with one bone going down, then another going back-ish, then another going down again.

I've googled and googled for the answer, but I'm completely at a loss as to what this is called! Is there any name for that style of leg? I'm sure there's a lot of variation inside the category, but there is a category, correct?

Welcome to Biology.SE!

I think you are talking about plantigrade, digitigrade and unguligrade.

Please note that the number of joints in mammals does NOT vary, but only the relative length (and shape) of the different parts of the leg.

A Plantigrade walks on the sole of the foot. 'Sole' translates to 'planta' in Latin hence the name.

Examples: Human, squirrel, raccoons, ...
Below is a chimpanzee skeleton

A Digitigrade walks on the digits (the toes).

Examples: dog, cat, hyena, ...
Below is a cat skeleton

An Unguligrade walks on the nails. 'nail' translates to 'ungula' in Latin hence the name.

Examples: cow, reindeer, goat, ...
Below is a cow skeleton


Australian Tree Identification Help I am looking at identifying a tree for a friend who lives outside of Melbourne.  Being from Tennessee in the US, we don't have anything very similar to this at all and it doesn't look like any of the US tropical trees that I know of either.  Can anyone help?
This is the far away view of the tree
Specific location: It was taken in the laneway behind a property in Glen Iris, Victoria just outside of Melbourne (Australia).

Ok, this is more complicated than I first thought. I am pretty sure that we have an eukalyptus tree here. The species is more complicated, but I think it is likely Eucalyptus baueriana or one of its subspecies. To check this further, more detailed images of leaves, blossoms are needed. Check this image (from here):


How to check if a fastq file has single or paired end reads I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method?

I checked wikipedia and MAQ but I want to know if is there a reliable document that describes all possible variants in sequence ID to check for single/paired end reads.

I am searching also for a library, better in Python, to achieve this.

Thanks

By now I got some interesting answers in this question on Biostars

Basically what I did is the following:

First of all, I checked if Sequence Id contains paired end notation. As described in this wikipedia page, for Illumina reads there are two possible notation for single/paired end reads:

@HWUSI-EAS100R:6:73:941:1973#0/1

If the last number is /2 in some reads then the reads are paired end; otherwise they can be single end.

The second notation is:

@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

If the first number in the second group is 2 in some reads then the reads are paired end; otherwise they can be single end;
Then I checked for multiple files. If a sample has two fastq files it is likely that the reads are paired end. It is to note however that with a single file it is not possible to exclude that paired end reads can be interleaved in one single file, even if it is not common (in my opinion);
The most general method is to cross check each single reads with the whole set of reads. If the first part of the sequence ID (in this case the field starting from @ and ending before the # - in the first notation - or the whitespace - in the second notation) is unique among all the reads (for each read) it is likely that the reads are single reads, otherwise - if can be found a duplicate for each reads - the reads are paired end.
In this case, on *nix systems it can be achieved with the following command (thanks to the biostars answers):

grep --no-filename @HWUSI-EAS100R:6:73:941:1973 *.fastq | cut -d' ' -f1 | sort | uniq -c | sort -rgk 1,1 | head

If the result shows in the first lines a result like this:

1        read1_ID

1        read2_ID

...

It is likely it is single end. Otherwise:

2        read1_ID

2        read2_ID

...

it is paired end.

I skim read BioPython API documentation but I cannot find something useful to do it.

Suggestions and corrections are welcomed.

Thanks


alpha tubulin molecular weight problem Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.

This is not so easy to answer, since alpha-tubulin has at 10 known genes in this family (data from Ensembl):

TUBA1A   tubulin, alpha 1a
TUBA1B   tubulin, alpha 1b
TUBA3E   tubulin, alpha 3e
TUBA3D   tubulin, alpha 3d
TUBA4A   tubulin, alpha 4a
TUBAL3   tubulin, alpha-like 3
TUBA1C   tubulin, alpha 1c
TUBA3C   tubulin, alpha 3c
TUBA8    tubulin, alpha 8
TUBAL3   tubulin, alpha-like 3

You can go on the site linked above and choose any of the proteins. I checked TUBA1A, and get a length of 451 amino acids and a weight of approximately 50,1 kDa.


Why can't we smell our own bad breath? Why can't we smell our own bad breath. Is there any way we can do that?

What you might be experiencing is olfactory fatigue, the temporary, normal inability to distinguish a particular odor after a prolonged exposure to it.

It's a form of neural adaptation, a change over time in the responsiveness of the sensory system to a constant stimulus. This adaptative mechanism might prevent the overloading of the nervous system.

However, some people (maybe most of them?) are able to smell their own breath. At least, I know I do. I can't point you to any statistics, but it might be an interesting research project, figuring out how many people can smell their own breath.


What exactly makes bananas go brown? I know that often oxidation processes are mentioned when referring to the color change from yellow to brown in bananas (specifically: those that you get everywhere in supermarkets, with no seeds).

However, I am really interested if there is a specific oxidative pathway that is generally followed in this process, and whether it has been examined.

The reason for this is the oxidation of phenol residues in the banana (for example in the yellow color) which get oxidized by the enzyme Polyphenol oxidase (PPO) to melanins. The scheme (the image is from this website on food browning) looks like this (you can of course also use more complicated substrates):

For further information, see these references:

Banana Polyphenoloxidase. Preparation and Properties.
Molecular cloning and characterisation of banana fruit polyphenol
oxidase

Polyphenol oxidases are widely found in fruits and cause most of the oxidative browning. See these articles:

Polyphenol oxidases in plants and fungi: going places? A review.
Enzymatic Browning, Polyphenol Oxidase Activity, and Polyphenols in
Four Apple Cultivars: Dynamics during Fruit Development


Distinction between primary and secondary tumor How can a primary tumor be distinguished from a secondary tumor? I tried finding it on the internet but it only said that they are found by means of immunohistology but I couldn't understand how.Please elaborate

The difference is pretty easy to understand. The secondary tumors is metastiesed tumor sped to enother parts of body. On the other hand the primary tumor is the source of the metastiesed.

I give you one example of this. On of the most common tumor of testicles is seminoma metastiesed to the peritonium, lungs, brain.

The secondary tumor is usually hard to distinguised with primary. But usually if there is specific antigen which can be recognised by antibody. The antibody is usually cultivated in mice. But this antibody have to be recognised by enother antibody. The second antibody to mice antibody is cultivated usually in rats. After that the secondary antibody is usually modified by fluorescent chemical. This is indirect immunohistochemistry. Direct is usually only the first antibody modifided by some fluorescent.

So first of all you have to do biopsy of that potential tumor. After that the sample is usually fixated by freazing and sliced by cryomicrotom. Than samples is usually put in to petry dish and poor with izotonic solution. Then the primary antibody is add. It take some time to react (find the antigen), thereafter is add the secondary antibody. To view the antibody you have to activated fluorescent by laser in fluorescent microscope. So if the fluorescent is in the sample, the tumor should be secondary.

Nevertheless is still hard to distinguish secondary tumor from the primery. Usually is up to experiencies with the tumors and how they are behave in body of patient. This is one of the reasons why is hard to treat the cancer.


Inward rectifying potassium channels during undershoot of action potential My professor said that inward rectifying channels help move the membrane potential back to the resting potential during the undershoot phase of the action potential. The membrane potential would have to be lower than the equilibrium potential of potassium for this to occur (inward potassium driving force), but the membrane potential never goes below the equilibrium potential of potassium during the action potential. So, when are potassium rectifying channels actively passing ions?

I hope I can maybe shed some light on this concept for you.  Rather than complicate anything more than necessary, let's start small and build. To directly answer your question, these channels can function as leak channels (so ions are always flowing through them at some rate) or can be open at select voltages (ions will only flow upon voltage-selective opening of the channel).

Here's a little more detail.  These channels are involved in a number of physiological processes (not only in neurons, but smooth muscle and cardiac cells as well).  One such process is, as your professor pointed out, to drive the membrane potential back to rest after you hyperpolarize the cell following an action potential.  I completely understand your confusion with this concept because in order to properly answer your question, I've gone through a number of resources to make sure I give the most complete answer possible.  Here goes:

Maybe the most important part!!!  These inward rectifiers were originally called “anomalous” rectifiers because, let's face it, they're goofy.  They don't do what you expect them to do (as you have pointed out).  Part of the reason is that there are molecular mechanisms that cause these channels to be blocked and preferentially permit an inward conductance, despite what you'd expect.  There's a decent review article on these channels that might help your understanding (the introduction is the most important part).  You can find it here http://physrev.physiology.org/content/90/1/291#ref-233.

Now I'll try to get into a different explanation that kind of oversimplifies things, but I believe might help.

Remember that the gradient is not solely electrical in nature, it is an electrochemical gradient.  Now you're probably thinking to yourself "I know that, dude, don't patronize me!"  I only bring this up because it appears your biggest concern is how the electrical properties of the gradient regulate K+ flow across the membrane (heavily considering the electrical driving force by focusing on membrane potential minus the Nernst potential for K+).  However, flip that thinking for a second.  Specifically, think about what happens during an action potential solely in terms of concentration.  Your rising phase is sodium influx to the cell (you go from lots of sodium outside the cell to lots of sodium inside the cell).  On your falling phase, sodium channels close and potassium channels open.  Thanks to the good ol' Na+/K+ pump, you have a gradient of little K+ outside the cell and a ton inside.  So what happens?  All that K+ rushes out of the cell (as you would also predict from the electrical component of your gradient now!).  That means you had a lot of K+ inside and a little outside, but you now have a lot outside and a little inside.  This goes on too long and you get an undershoot/hyperpolarization, but you have to get back to your resting membrane potential.  Enter the inward rectifiers.  These K+ channels open and (again, thinking solely about concentration) the K+ is going to flow down the gradient back into the cell.  If you throw in the electrical component, remember this:  Neurons exist in a multi-ion system which complicates things like reversal potential for a single ion.  This is a complicated subject that I won't get into, but it boils down to reversal potential being a different property from equilibrium potential, which becomes important in a multi-ion system.


Why don't all male animals kill a rejecting female? If a male animal is sure that the female animal will not reproduce with it, wouldn't it be mathematically optimal for the male to kill the female? (To ensure that no alleles of the "overreact-to-rejection" gene in other males can make use of the female as a reproductive resource)

I might be missing something very obvious here, but I can't seem to see why a gene for "kill-rejecting-potential-mate" wouldn't spread through the gene-pool.

The simple answer is most animals females can fight back. Its similar to the reason male to male fighting often evolves to become more and more ritualized. Fighting is risky, and the closer in size and capabilities the fighters are, the riskier it becomes. Behavior that tends to get you injured for little to no benefit tend not to get passed on. and there is little to no benefit in killing females for a male. Plus a female who is alive can change her mind later, so there is a direct benefit to the male for not harming her.

Now there are animals where a female will be bullied into mating to the point of risking injury or death. Those animals are very rare and have high dimorphism, they have males that are MUCH larger and more dangerous than the females, to the point the female is incapable of being a significant threat to the male. It is most common in animals that express harem polygyny. It also tends to carry the risk of inbreeding.

One horrifying example is hamadryas baboons. Males maintain a harem and threaten any female that even strays too far from the male. They even bite disobedient females.


Where is the aneurysm in this picture? I'm a curious person, I've never had any medical training, but I wish to know some more about aneurysms. Aneurysms are basically weakened spots in the elastic artery wall. This can eventually result in a blood-filled balloon bulging from the artery wall due to the high blood pressure in these vessels. Aneurysms can rupture and this can lead to brain damage when it occurs in the brain. Aneurysms can be detected by injecting contrast material into the bloodstream and making an X-ray (called an angiogram). Now I was reading a wikipedia article about aneurysms where I saw the following picture of an angiogram where reportedly an aneurysm should be visble:

Now, as I said, I know nothing about biology so I would really appreciate it if someone could download the picture and reupload it with the aneurysm circled.

Is it the really dark spot or the big soft spot to the right? Thanks!

Your image comes from the wiki page Aneurysm. The figure legend on the wiki page identifies it as:

  Angiography of an aneurysm in a cerebral artery

I am not an MD so I chose to first dig up a similar appearing cerebral angiography with the aneurysm identified (dark protruding spot indicated by the arrow):

Source: WestJEM, UC Irvine

Taking into account the normal vasculature as seen on this graph from UC Irvine, and given the similarity between the identified aneurysm in this angiopgraph and your wiki angiograph, I tentatively have identified the red-encircled structure in your original image as an aneurysm:


How do plants get their O₂ for respiration during the night? If I am not mistaken the stomata are closed during the night. As a result I have a hard time to imagine how the plant can get the O2 it needs for respiration during the night. I thought the plant could produce the O2 internally through some chemical reaction. Such reaction might include splitting H2O absorbed through the roots in two. Or maybe the O2 diffuses well enough through the plant tissues.

How do plants get their O2 for respiration during the night?

Not all plants have their stomata closed during the night. A notable exception are Crassulacean acid metabolism(CAM) plants that keep their stomata closed during the day and open it during the night. This is a common evolutionary strategy with Xerophytes.

There are also 2 other types of metabolic pathways namely C3 and C4. As a consequence we get what is called a C3 and C4 plant, which aptly represent the predominant metabolic pathway it employs.

Additionally plant cells, like all life, can produce energy without oxygen by Glycolysis. Furthermore, when stomata is closed, oxygen respiration is restricted, not blocked entirely. Finally it might be important to note that plant metabolism is reduced during the night.

Full disclosure, I am not a botanist. Please let me know if there are any glaring errors.


Sitting much, thrombosis and hypoxia I am thinking the more reasons why sitting much lead to thrombosis i.e. clotting of blood in blood vessels and then hypoxia in the deep tissues eventually.

What are the physiological mechanisms for this to happen?

One student said hormones.
It can be right, but I am thinking how.

Venous return from the limbs is largely facilitated by the action of neighbouring skeletal muscles compressing the veins and forcing the blood proximally past the valves which prevent back flow.  If you are inactive for a long time by sitting, or are sitting in such a way as to impede blood returning from your calves (i.e. with the back of your knees pressing into the edge of the chair) blood movement in this manner is greatly slowed.

Blood that is moving more slowly or turbulently has a greater propensity to coagulate and form a thrombus.  This is similar to the rationale for prescribing anti coagulants to patients with atrial fibrillation - the turbulent and slow movement of blood through their atria leaves them at greater risk of throwing a clot to the brain causing a cerebrovascular accident.

Hypoxia isn't really that relevant in the case you describe as arterial supply is unaffected (much higher pressure) meaning tissues do not become ischaemic. There is also collateral venous drainage from the limb although this can subsequently cause problems in the form of post thrombotic syndrome.  The most significant risk would be that of the thrombus breaking off and lodging in the lungs - a pulmonary embolism.


Definition of Linkage Desiquilibrium (LD) According to wiki, linkage disequilibrium $D$ equals

$$D = x_{11} - p_1\cdot q_1$$

where:

$$
        \begin{matrix}
        \text{Haplotype} & \text{Frequency}\\
        A_1B_1 & x_{11}\\
        A_{1}B_{2} & x_{12} \\
        A_{2}B_{1} & x_{21} \\
        A_{2}B_{2} & x_{22} \\
        \end{matrix}
$$

and

$$
        \begin{matrix}
        \text{Allele} & \text{Frequency}\\
    A_{1} & p_{1}=x_{11}+x_{12} \\
    A_{2} & p_{2}=x_{21}+x_{22} \\
    B_{1} & q_{1}=x_{11}+x_{21} \\
    B_{2} & q_{2}=x_{12}+x_{22} \\
        \end{matrix}
$$

According to Hartl and Clark, linkage disequilibrium $D$ equals:

$$D = x_{11}x_{22}-x_{12}x_{21}$$

Question

Can you please prove that these two formulations of linkage disequilibrium are equivalent (assuming that they are equivalent)? If they're not… Do we use different definitions? What are their respective meanings?


Are there free electrons in muscles, hair, or skin? Electric shock occurs upon contact of a (human) body part with any source of electricity that causes a sufficient current through the skin, muscles, or hair.

In metals many electrons are said to be delocalised (i.e, electrons are not bound to any of the atoms). Around one electron per atom is said to be unbound to atom in mettalic lattice. So there will be motion of electrons due to thermal energy, however due to their random motion, there won't be such a significant current produced. When electric field is applied across them there will be motion of electrons in a particular direction, causing significant amount of current. In case of insulators, due to bound electrons we can't expect current through them.

When our body becomes a part of electric circuit, current is said to pass through our skin, muscles, or hair. Does it imply that there are free electrons in skin, hair, or in muscles (like those in metals)?

Our body contains a lot of salt and which act as electroyte,so when we comes in contact of electric source then the electrolyte helps in the conduction of electric current through out body,


How Do Adherent Cells In Culture Attach To A Plastic Dish? I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are hemidesmosomes involved in anchoring the cells to the plastic dish? What (if any) other molecules are involved? What happens at the molecular level?

I doubt that hemidesmosomes are much involved in 3T3 adhesion, just because they are characteristic of epithelial cells and fibroblasts are mesenchymal.

You're on the right track, though. It's going to be the same basic processes as adhesion to the extracellular matrix. The major factors will probably be integrins and focal adhesion assemblies.

You're also raising an important point for in vitro work, which is that adhesion to plastic is a very imperfect substitute for ECM, and this probably has implications for the behavior of the cells. If you're interested in ECM-dependent processes like migration, adhesion, and invasion, consider coating your plates with collagen or Matrigel.


Most accurate depiction of cortical homunculus? I was looking at cortical homunculus and I realized there are several different pictures and they don't quite agree.  For instance:

http://wellbeing.media.mit.edu/2014/02/21/mindfulness-neuroimaging-and-neurofeedback/

http://nawrot.psych.ndsu.nodak.edu/Courses/465Projects11/PLS/4Thesomatosensoryandmotorcortices.htm

One area, for instance, are the feet, which I feel should have a fairly large (not as big as hands) area in the brain, mainly from the personal experience of having more sensations in feet, which like the hands has many nerve endings, though obviously much less fine motor ability.  But that's just my speculation, and I like an accurate depiction so I can start from there and make sense of this.  Thank you.

Be sure to distinguish exactly what the diagram is showing. Your first reference is sensory cortex mapping. The second reference is motor cortex mapping. The text of the second reference is admittedly confusing about this, a search for "Wilder Penfield motor cortex" verifies.

It seems reasonable the feet would show sensory response similar to the hands. Stepping on a nail is just about as bad as bumping your hand into one. Motor control is different. Muscles are not all innervated the same. In some of the large muscles, say in the legs, one nerve can control hundreds of cells. In other cases, particularily in the face, one neuron might control only six muscle cells. Thus a greater number of neurons, and a larger portion of the brain, is needed for control in these delicately controlled areas. It would make sense a greater part of our brain would be needed for motor control in our hands versus our feet.


What are some of the immediate challenges to break through before finding a cure for mad cow disease? What are the immediate challenges to break through in seeking a cure for mad cow disease?

I know that mad cow disease has no treatment as of yet.

The main problem is that Mad Cow disease is not caused by a "normal" pathogen but by a prion, a protein.

Traditionally, disease causing agents can be classified into viruses, bacteria, fungi, and parasites. Bacteria, fungi and parasites are all living organisms, alive in the traditional sense. It is, therefore, possible to design drugs that kill them.

Viruses are trickier, while not really alive in the traditional sense, they still have to make copies of their genetic material (DNA, or RNA in the case of many viruses) in order to cause infection. Therefore, drugs like ganciclovir that stop the formation of viral DNA can be an effective treatment.

Prion based diseases such as Mad Cow disease, Creutzfeldt–Jakob disease and Kuru, are not caused by a classical infectious agent but by a simple protein, a prion. Prions are misfolded versions of proteins already present in the host's body. When a prion interacts with the host protein, it causes this protein to adopt the same, misfolded, state as the prion. Protein function depends directly on the protein's structure, the way it is folded in three dimensional space. Therefore, the misfolded protein can no longer carry out its physiological role and disease symptoms occur.

Now, since the prion is just a protein, one single molecule, there is no essential life process that we can disrupt. We have to attack them using chemical agents that target the prion while not affecting the healthy, correctly folded, host protein. This is very hard to do.

The blood-brain barrier mentioned by Larry_Parnell is another problem. Briefly, the BBB, is a kind of fence that only allows certain of the various items circulating in the blood stream to enter the organism's brain. This is a wonderful defensive feature but it makes it much harder to design drugs that can enter the brain and target pathogens found there.


Why do mints make your mouth feel cold? Why do mints make your mouth feel cold?  And specifically, why does your mouth feel so cold if you eat a few mints and then drink a glass of cold water afterwards?

The feeling of cold from mints is caused by menthol. Menthol affects the TRPM8 receptor on skin and also in the mouth. TRPM8 is also a general cold receptor: so if you are in contact with menthol the receptor reacts just like when you are exposed to cold (Bautista et al., 2007).

The receptor is strongly activated at temperatures below 26 degrees Celsius (Bautista et al., 2007). Drinking water is usually colder than that. So if you ate mints and drink cold water afterwards, the receptor response is even stronger.


Did the Zika virus mutate? The Zika virus was already present and known to the world (mostly in Southeast Asia) before the current outbreak.

Why has the virus caused such an extreme outbreak?

Has it mutated from its ancestral form such as that found in Southeast Asia?

There is one main answer to this question: The Zika virus spreads so fast because it never emerged in this part of the world. Hence there is no natural immunity available in the population and a lot of infections occur. Once this "first wave" of infections is over, the level within the population will fall drastically. Some more information on this topic can be found here.

It is of course possible that the Zika virus has acquired a new mutation which adapts it better to humans and allows spreading much easier, but this is not yet known, since the situation in South America is still changing very fast with a lot of cases occurring and analysis going on. It still can be enough that the virus never emerged in Southern America and that there is no natural immunity available.

According to the paper in reference 1 (which is only a brief communication) the sequences of the envelope proteins of the virus are similar to the strains circulating in Asia and do not carry novel mutations:

The Surinam strains are the ones published in the paper mentioned above and are from South America. I haven't (yet) found any other analysis, but this will only be a matter of time. At the moment we cannot make a final statement on this although there is some speculation around.

Edit 23/02/2016: There is still no final conclusion available, but there is an interesting paper available on the Biorxiv-Preprintserver, which analyses the mutation rate in the genomes of the publically available strains. It can be found in reference 2.

Based on the available genomes, the author calculates the mutation rate of the Zika virus to about 10 Mutations/year. The virus is a RNA virus which have generally higher mutation rates than DNA viruses.

In the analysis he finds a number of non-synonymous mutations (mutations which lead to a basepair exchange), as seen in table 2:

Especially named is the M2634V mutation, but since this is in one of the envelope proteins, the author finds it relatively unlikely (although not completely), that this causes a much higher mutation rate.

In the Diskussion of the paper he writes:

  The sudden spread of Zika to South and Central America does not appear
  to have been due any particular change in the mosquito vector or
  anything to make the Zika virus itself more virulent. But rather from
  the fact that infected people are now able to fly rapidly from country
  to country, thereby spreading the disease extremely easily. This means
  there is little to stop the epidemic continuing to spread to further
  areas of population which have little, if any, herd immunity against
  the virus.

Edit (23.10.2016): There is now an interesting website which builds a realtime phylogenetic tree from the data published (it can be found here). The data also shows where in the virus the mutations occur:

References:

Zika virus genome from the Americas
ZIKA - How Fast Does This Virus Mutate ?


Methods for phage separation How can a mixture of unspecified phages be separated (into singular phage strains)? I.e, what are the main methods?

My research shows it can be done using CsCl centrifugation and affinity chromatography, but both seem laborious, the latter also requiring the phages to be already available in pure form.

Look up "phage purification." Basically, you add your phage solution on top of your host bacteria on a plate and incubate. As the bacteria grow, you should see plaques (clear areas in the bacterial lawn). Each plaque should be the progeny of one original phage, although sometimes two or more phages could be very close to each other on the plate and it will look like one plaque. So you have to take a sample of a plaque, re-plate on another lawn of host bacterium, and repeat this process for several rounds until the plaque morphology seems to indicate that there is only one type of phage present. Here is a good resource for phage protocols: http://phagesdb.org/workflow/


Just how light-sensitive is ethidium bromide? One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in both cases, but this second lab uses it up much faster.

Good question.

I found this reference in "Molecular Biology: A Project Approach"

  A phenomenon called photobleaching occurs when ethidium bromide (EtBr) -stained DNA is illuminated by ultraviolet light.... This decreased fluorescence is presumably due to the dissociation of ethidium bromide from the DNA.

Ethidium bromide fluoresces when it is in a hydrophobic environment, such as when its stuck between two base pair stacks in DNA- water quenches its fluorescence.

I also found this article citing the fact that sunlight can break down EtBr but only when a catalyst of iron and titanium dioxide is there to catalyze the reaction.

A lot of the original characterization of EtBr as a stain is very old, so I couldn't access it directly online... It looks like the compound itself is pretty stable, but UV can, somehow interact with it when its bound to DNA to bleach it out.


Why do epithelial cells arrest in response to serum? Primary epithelial cells, for example human mammary epithelium, fail to proliferate (arrest) in serum-containing medium. Therefore, a common growth medium for epithelium contains pituitary extract instead of serum (Hammond et al, 1984). This may be related to the fact that epithelium is normally not in contact with serum in the body.

On the other hand, many epithelium-like cell lines grow well in serum, and most tumor-derived cell lines are cultured this way. But it can be difficult to establish such lines from epithelial cancers: often, only fibroblasts grow out of tumor explants in serum-containing medium, while the (epithelial) cancer cells do not. In contrast to epithelium, fibroblasts increase their proliferation when exposed to serum, and this process is well studied (Iyer et al, 1999).

Why does epithelium arrest in response to serum? Are any mechanisms known? Is there any study of epithelium gene expression response to serum? Why is the behavior of epithelium so different from that of fibroblasts --- is there a physiological explanation, perhaps related to wound healing?
Is this true for all types of (human) epithelium?
Should we consider epithelial-like cells growing in serum to be adapted / selected? Have such cell lines then lost some part of the epithelial phenotype? Is this a serious artefact?

Any pointers to literature would be appreciated!

TGF-beta would be a good candidate. To cite:
"TGF-β inhibits G1/S progression in a variety of eukaryotic cell types. Among these, untransformed epithelial cells are particularly sensitive to the growth inhibition by TGF-β."
http://genesdev.cshlp.org/content/14/24/3093.full

Fetal bovine serum (FBS) contains a high level of latent TGF-β. Human serum as well has high level of TGF-beta (20-50ng/ml)

It is also possible that growth arrest is part of the induction of terminal differentiation by serum factor(s) such as TGFb.
"Type beta transforming growth factor is the primary differentiation-inducing serum factor for normal human bronchial epithelial cells."
http://www.ncbi.nlm.nih.gov/pubmed/2871553

Edit: got more reputation, so now I can post more than two links. Here is a review on TGFb signalling: http://genesdev.cshlp.org/content/14/6/627.full

Also a link to serum levels of TGFb:
http://www.ncbi.nlm.nih.gov/pubmed/16845225


If massive animals live longer, why do humans with gigantism die younger? What I mean is humans suffering from gigantism (type 1 neurofibromatosis, Marfan syndrome, X-linked dominant acro-gigantism, et cetera) rarely live more than 5 decades (50 years).
The same can be said to wolves: wild ones rarely live more than 9 years, and domesticated wolves (dogs) can live up to 20 years if they are small like chihuahuas, beagles, and toy poodles, and no more than 7 years if they are massive like great Danes, mastiffs, and Rottweilers.
But, at the same time, horses can live 3 decades (30 years), but hamsters only live 4 years.

In short many things determine life expectancy and the interplay between different factors will determine an individuals life expectancy and a species' average life expectancy.
How life expectancy links to size:

Among mammals there is an inverse relation between heart rate and life expectancy (mammals tend to average 7.3+/15.6 x10^8 beats per lifetime which appears to be a symptom of the fact that heart rate is a marker of metabolic rate and so there is a fixed 'metabolic lifetime' for animals (source). This is somewhat substantiate by metabolism variants in C. elegans and the link between metabolism and free radicals and DNA damage (source).
Larger animals are thought to have a slower metabolic rate by weight (not overall) due to scaling laws (see Kleiber's law) and how surface area and volume relate and change temperature regulation metabollic requirements.

Other factors that change life expectancy:

In breeding: a reduction in genetic variation caused by inbreeding (e.g. many dog species though the extent to which they are inbred will depend on the species) can lead to lots of underlying health issues that may reduce the lifespan independent of metabolic rate
Stress: Higher stress will reduce life expectancy
Nutritional abundance: reducing caloric intake may reduce metabolic rate and extend lifespan, though starvation will decrease lifespan

Gigantism:

Whilst the life expectancy for a species may be higher in general people with gigantism may live shorter lives than possible because of non-metabolic related reasons. For example many forms of gigantism are linked to hormones which promote cell division and growth which are also linked to forms of cancer.


Fibronectin glass surface adsorption Short summary

I'm having a glass surfaces and I want to adsorb proteins onto them. I have no problem, when I first adsorb fibronectin (human) onto some areas and afterwards any other protein. The second protein will only adsorb onto the remaining "free" areas.

But as soon as I apply fibronectin in the second place, it just adsorbs everywhere. And I want to avoid this.

More detailed Protocol

(direct microcontact printing):

Incubate a pdms-stamp with Protein-Solution #1 for some time and concentration
Dry pdms stamp and press onto coverslip for some time
Remove stamp and put a drop of Protein-Solution #2 for some time and concentration onto the coverslip

I varried already concentrations and times without noticeable success. I also tried adding some BSA to Fibronectin - also without success. All solutions are within PBS.

Further steps I anticipate:

Varying pH around the protein's isolectric point (Fibronectin: around 5.2)
Adding some detergens to fn-solution (e.g. Tween)
Variation of salt-content in fn-protein-buffer

My question

I'm wondering what the exact reason for the stickiness of Fibronectin is and which parameter is the best to vary? Did I miss something? Does Fibronectin stick to the other proteins or rather to "free areas" of the surface?

Please note: surface modification techniques (e.g. using epoxys) are no option.

I'm not sure, whether this topic perhaps suits the chemistry-community better. Feel free to move.

What is the exact reason for the stickiness of Fibronectin?

Fibronectin interacts with diverse substrates which reflects its non-specificiy and its interaction with hydrophobic substrates is better suggesting that the adsorption is dependent on hydrophobic interactions.

  Does Fibronectin stick to the other proteins or rather to "free areas"
  of the surface?

It can stick to both as you can see from the table. However, its binding to hydrophobic materials like polystyrene and PVC is the most efficient.

  which parameter is the best to vary?

Note that there will be a lot of free regions in the substrate. You cannot block all the sites unless you use a high concentration of fibronectin. So the best parameter to vary would be the concentration of fibronectin. You may also use fibronectin-BSA mixtures as their mutual binding is not that great (A stepwise method would be nonetheless better). You can also vary the adsorption time (see the figure below) but that is not as easily controllable as concentration. Since fibronectin does not bind to agar, you can also block some sites on your coverslip using molten agar (or agarose).

Reference:

Klebe, Robert J., Kevin L. Bentley, and Robert C. Schoen. "Adhesive substrates for fibronectin." Journal of cellular physiology 109.3 (1981): 481-488.


What is the mechanism behind plants losing their leaves? Do plants that lose their leaves (i.e., deciduous plants) do so because of external conditions (e.g., drought, cold), or because of an internal process?

Another way of looking at it: if you take a deciduous plant that loses its leaves during cold winters with long nights (e.g., Canada), and plant it in an environment where it is always warm and sunny (i.e., at the equator), would this plant continue to shed its leaves and re-grow them according to the seasons in Canada, or would it behave as an evergreen instead?

The process of a deciduous plant losing its leaves seasonally is known as abscission. It occurs when a layer of cells known as the abscission zone elongate and weaken, causing the leaf to fall off. It is mediated mainly by the hormones auxin and ethylene.

The functional purpose of abscission is to remove leaves when they are no longer producing a net gain of biomass. Leaves decrease in productivity during drought, decreased day length, and when under the effect of herbivory.

In some species (according to the day-length source), "When the daylength exceeds a certain 'critical' duration, growth may be
maintained continuously for at least 18 months under favourable temperature conditions, e.g., in Liriodendron tulipifera, Robinia pseudacacia". So, to answer your final question, some deciduous species (but not all) may indeed retain their leaves if they are grown in favorable conditions. One reason why not all deciduous trees retain their leaves even in favorable conditions is that internal ageing can also induce abscission: "In such species, growth is determined primarily by the endogenous ageing process and is only modified by environmental factors, including daylength"


Why would a bumblebee regularly hover over a arborvitae hedge? I have observed bumblebees hover over an a abrborvitae (Thuja occidentalis) hedge. A bumblebee will hover in a in one spot over the hedge for about 5-7 seconds, zip to another spot, hover for about 5-7 seconds, then another spot, then another. The bees will never land on the hedge. At any one time during anyone day, there will be only one bee hovering over the hedge. This behavior will go on like this all day.

Why do the bees do this?

Could actually be a male carpenter bee. They hover around like that waiting for females to pass by. If it is a male carpenter bee dont worry about it, they arent equipped with a stinger.


What is the impact of the invasiveness of the European Starling in North America? Currently there is a campaign to eradicate the European Starling from North America because of its threat to other species. Are there actual data regarding the extent of the ecological risk to native species, and are there data on the effects of the current eradication programs (are they working)?

Background

In North America, there an estimated 140 million European Starlings, or about 45% of the global total. The species was introduced to the continent over 100 years ago when only 120 or so were released in the New York area. Those few have quickly spread across the whole continent, competing easily with other native birds of similar type, especially for nesting holes, because they are naturally far more aggressive. It is currently listed in the IUCN List of the world's 100 worst invasive species. Annually, the US kills over 1 million of them with the sole purpose being extermination. There is even a specific poison commercially available. However I am having difficulty finding data to show how invasive the Starling really is in North America and the extent of the ecological risk to native species because of their presence. I would also be interested in data showing the impact of current control methods (do they actually reduce the impact on native species?).

First, for the record, I do not know the North American Starling situation well. However, I know of one study (Koenig, 2003) that failed to find strong effects of Starlings on other cavity nesters (i.e. looking at effects from cavity competition). When trying to control for other effects, only one species was potentially negatively effected by Starlings.

Starlings cause quite large economic effects though (Linz et al, 2007), and it wouldn't surprise me if this is the main reason for the control measures. The paper refers to a previous study which estimates that Starlings cause crop damage costs of \$800 million/year as well as \$800 million/year in health costs, due to disease transmission to livestock and humans (both figures from Pimentel et al., 2000).

So my feeling, based on a couple papers and some quick searches, is that the ecological impacts are uncertain (or to a large extent unknown) but that the economic impacts are quite large. Given the North American population sizes of European Starlings it would however surprise me a lot if there weren't any ecological effects on other species (negative and positive). These issues are hard to study though, especially without long-term data of high quality.


How does a drastic change to the genome persist and spread? I just read the article on songbirds in the November, 2019 Scientific American. The article explains that songbirds have an extra chromosome, called GRC (germ-line restricted chromosome) that other bird species don't have, and there's a hypothesis that this may have been partially or wholly responsible for the diversity of this group of species.

The following line caught my attention:

  Once the GRC originated in the last common ancestor of songbirds, members of that ancestral species that carried the GRC could produce fertile offsping only with mates that also had the GRC.

But when the mutation that created the GRC occurred, who did that bird mate with in the first place?

My belief is that most genetic changes are relatively minor, so they don't immediately result in incompatible mating. Speciation occurs as genetic changes accumulate over time. But the above quote implies that an entirely new chromosome is too drastic to allow interbreeding at all.

Wouldn't there need to be a whole bunch of birds who all had this extra chromosome at the same time to allow it to spread through the population? That seems unlikely to occur.

Am I just reading the line too literally? Could early birds with the extra chromosome mate with other birds, until the new chromosome accumulated too many changes?

It isn't necessarily true that individuals with different numbers of chromosomes are infertile. Even though common wisdom has it that horse (64 chromosomes)/donkey (62 chromosomes) hybrids are invariably infertile mules, that's not true; a significant number of fertile horse/donkey offspring have been documented.  Here is an example where the chromosomes were checked and confirmed to be 63 in the fertile mule parent.

Even more dramatically, the common shrew (a single species) has many different chromosome numbers as natural variability (at least 50 different chromosomal variants were identified in one paper) and this doesn't affect their interfertility.

So there are three general answers to the question here, though I don't know which is the most likely.

The extra chromosome arose and the original variant was very fortunate to have offspring; similar to the rare horse/donkey fertile hybrids.
The extra chromosome arose but had little effect on interfertility; similar to the common shrew. (The quote from the article in the question argues against this, but I don't know if it's a presumption made by the researchers, a presumption made by the writer, or a demonstrated fact.)
The extra chromosome arose in a single litter, so that several siblings shared it, and then interbred. Although incest avoidance is generally quite strong, animals that colonize islands or distance geographic areas (invasive species, often) commonly do interbreed this way.


Why don't mitochondria have plasmids? According to the endosymbiotic theory, mitochondria are descended from specialised bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm [ref].

And plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes [ref].

I was however taught that mitochondria have no plasmid and only have circular DNA. If the endosymbiotic theory is true, then how come mitochondria have no plasmid?

The mitochondrial genome is highly reduced; many mitochondrial genes have been transferred to the nuclear genome (see endosymbiotic gene transfer) and therefore the mitochondria are fully dependent on the nucleus to function.

Bacteria need not necessarily have a plasmid. Usually, all the important genes are present in the chromosomal DNA. Since the mitochondria have lost most of their genes and retain only a few genes that are highly essential for their function, the likelihood of retention of any plasmid DNA is very low. However, there are some reports of plasmid-like DNA in mitochondria (mostly in plants).

Handa (2008): in Brassica
Robison et al., (2005): in carrots
Collins et al., (1981): in Neurospora (a fungus)

Likewise, chloroplasts also harbour plasmid-like DNA (google-scholar hits).


BLAST 16s rDNA: Everything alligns to Bacillus sp I'm trying to identify and isolate Pseudomonas and Bradyrhizobium strains from rhizosphere and endophytic compartments of a tree. I plated the strains on selective media (King's B. for Pseudomonas and YEM for Bradyrhizobium) and purified the colonies grown by picking them and let them grow on separate plates. There is a lot of variety in morphologies.

When I had grown colonies of bacteria and was able to pick up single colonies I did a 16s rDNA pcr reaction on the colonies. After sequencing the 16s rDNA sequence I did a quick BLAST search to annotate the sequences and thus the bacteria to a species. But from all colonies till now (already 25 reactions sequenced) I only found that they allign best to Bacillus. I think this is strange because there should be a lot of variety according to their morphology.

Does anyone has a solution for this? Is it, for example possible to exclude the Bacillus group from the BLAST search? Or does this mean my colonies are still contaminated?

This is probably not enough information to answer my question but maybe you have experience with doing this and have some ideas.

Thanks!

As you guessed in the last sentence, it's hard to answer your question without some more information.

For example, how much of the 16S rRNA gene did you sequence? Most people just sequence the v3-v4 regions which are the most variable, but they only comprise a few hundred bases. Sequencing the entire 1500 bp gene gives more specificity when doing searches, but is also more expensive.

With regards to selection of colonies, do you know from the literature how selective your two different types of media are? We did similar studies with environmental E. coli including several rounds of screening and selection, and you would be surprised how much "junk" we got. If you're isolating from soil, Pseudomonas and Bacillus spp. are going to both be highly prevalent.

With that in mind, it is not enough to grow on selective media, do one transfer, and call it good. Really, you should have a screening method in addition to your selective media. Maybe some compound that yields fluorescence or a visible change to the surrounding media that you can use to differentiate your target bacteria from contaminants. Once you have your candidates, you need to isolation streak them onto fresh selective media. Then screen again and isolation streak again. Repeat this process 2-3 times, or until you have monomorphic, pure cultures. Only then should you start doing genetic/genomic testing on your isolates.

Hope this helps.


Species of dinosaur with longest fossile record (no birds!) There were many species of dinosaurs and many got extinct long before the whole clade disappeared. I am wondering which species has shown the longest fossile record. Since birds descend from dinosaurs, I excluded that case to preclude the easy answer! I fully understand the vagueness of my question, stemming from the uncertainties associated with the definition of species but I would think that at least some ballpark could be estimated?

Dinosaur biostratigraphy makes it not possible to answer your question through all of history. 8Ma is the highest longevity species I found in a biostratigraphy table. Dinosaurs are faster evolving than crocodilians who have 1/3rd as big a genome as a mouse and 1/6th that of a shark. Adaptive genus existed for 5-30 million years, and well known clades exist for 20-500 Ma.

The most complete geological formations often only cover small spans of history. Generally you will find that paleontologists have few species, and more often groups and genus represented by 10-20 species fragments.

The Hell Creek Formation covers 2 million years of history, and has revealed 400 species, of turtles, dinosaurs, metatherians, mammals, turtles, and a very rich image of life at that time, and 90 percent of the geological time scale is represented by only a fragments of fossils.

So, you won't find a good answer for species, perhaps the best way to find out the longest lived genus (i.e. like a dragonfly, all species are in the same family) is by doing some google tricks:

For genus i can find this:

Plateosaurus 214–204 Ma

Thyreophorans group 199.6–66 Ma

Gryposaurus genus  84-73 Ma

Plesiosaurus genus 199.6–175.6 Ma

Gorgonopsians 265–252 Ma

Dimetrodon 295–272 Ma

Carcharodontosaurus 112-93

Pterosaur 228–66 Ma

Mussaurus : 215–203 Ma

Lesothosaurus : 199–189 Ma

Spinosaurus : 112-93

Kronosaurus genus 125–99 Ma

scorpion 430–0 Ma.

Dragonfly     325–0 Ma

brittle star 499Ma-present

crocodilians 200-0

some shark genus: 100-0

snapping tortoise 100-0

horeshoe crab 455-0

nautilus 488-0

Fossil fields are incomplete, so the HellCreek time period is very well represented with lots of tyranosaurus, and other time periods are incomplete.

Animals with small genotypes Crocodiles and turtles evolve very slowly, and it gives you an idea of evolution speeds prior to the arrival of mammals, who seem can adapt faster than all previous larte animals.

crocodiles have less than 1/3 of the genes of a mouse and a human
tortoises have 2/3rds and so do horseshoe crabs
dragonfly have 1/6th the genome size of a mouse
sharks have twice as big genome


What are the positive effects of wrongful antibiotic use on a viral infection? I categorically accept that bacteria differ from viruses; so antibiotics DON'T help in viral infections. I also read this and this; so no need to explain this. I've read about the negative effects (eg exacerbation of antibiotic resistance); I ask only about the positive effects here, and NOT for reasons to exploit antibiotics for infections not due bacteria.

Yet I myself have witnessed that some people with viral infections feel better after wrongly taking antibiotics? and so asked about this first on Cognitive Sciences SE.

Initially, I suspected only some placebo effect, but this enlightened me on the side benefits of antibiotic consumption for a viral infection and motivated this question, now that my original question on psychology has revealed the relevance of biology.

There are indeed antibiotics which have immunomodulatory side-effects, these are mostly from the class of macrolide antibiotics (erythromycin, clarithromycin, roxithromycin, azithromycin) and to some degree from the tetracyclines. Beta-lactam antibiotics (as Penicillin or Ampicillin) have not been shown to be immunomodulatory, but they are among the most commonly used. See reference 1 for more details.

The biggest effect has been shown on pulmonary diseases such as cystic fibrosis or diffuse panbrochiolitis (see reference 2).

Although the exact mechanism of action is not known, Macrolides are know to downregulate the inflammatory cascade and that the reduce the strong cytokine expression of some viral infections. However, these regulatory effects are relatively weak if you compare them to the anti-inflammatory properties of corticosteroids. So the question here is if the advantages are really sufficient compared to the problems, which an unnecessary use of antibiotics may cause. See reference 3 and the references in the paper for more details here.

Antibiotics may be useful to fight bacterial secondary or superinfections which accompany a virus infection.

References:

Immunomodulatory Properties of Antibiotics
Macrolide activities beyond their antimicrobial effects: macrolides
in diffuse panbronchiolitis and cystic fibrosis
Macrolide Therapy in Respiratory Viral Infections


Does having to urinate imply that you are becoming dehydrated? This question came up after I read another question that coffee does not dehydrate you, but instead acts as a mild diuretic.

Does having to pee imply dehydration?

Allow me to elaborate: When you have to pee, that liquid is already in your bladder, right? If so, it is not in use by cells. However, since that water must have been previously absorbed in the body in order to be filtered through the renal system, having to pee indicates that you are less hydrated than you once were.

So in the case of coffee, while it doesn't directly dehydrate you, doesn't it indirectly dehydrate you by causing you to pee?

There are two parts to answer this question. "How does my body know when to pee? Do diuretics affect that, or my hydration?"

Does wanting to pee imply dehydration?

In summary: Not necessarily. Your body might have plenty of water, but the bladder is full. Alternatively your body might be dehydrated, but the caffeine and normal body functions have filled the bladder and you'll need to pee.
Caffeine as a diuretic.
Caffeine belongs to the Xanthines, and inhibits reabsorption of Na+ by cells, and increases flow rate of filtered fluid through the kidneys. This reduces water content in your body. In other words diuretics do dehydrate you, specifically caffeine will. Coffee and tea (very low doses of caffeine) are mild diuretics.
Bumetanide, Furosemide, and Torsemide are examples of stronger diuretics, and hydration should be monitored closely.
On the other hand, the colour of your urine may indicate your hydration.
The below image is a crop of this Cleveland Clinic infographic.

How does my body know when to pee?
The bladder is hollow and slightly elastic, so as it fills with urine it expands. A healthy bladder can hold up to 2 cups of urine comfortably for several hours. When the bladder approaches its maximum capacity, signals are sent to the brain, letting the body know that it is time to urinate.
But it's critically the kidneys that are controlling the production of urine.
Caffeine increases the production of urine from the kidneys, and fills the bladder quicker. However, the increase in production of urine from a cup of coffee is more than offset by the water in the coffee.


How was the heritability of IQ tested? I have read that IQ is highly heritable.

How could this be tested?

For honest testing, it seems to me that only children who were abandoned should have been tested, to exclude education effect. Was it really done?

UPDATE

Intelligence is one of the traits, that can be inherited both by genes and by education. You can't educate your children to have blue eyes, but you can educate them to count or to read.

So, to study heritability of intelligence, educational inheritance should be excluded.

I know that usual way to study heritability is to compare variability for monozygotic and dizigotic twins. Being sufficient for other traits, this method is highly insufficient for intelligence (which is obvious). Having identical perception system, monozygotic twins will respond identically to an education, so they will be more closely educated, even if IQ is completely independent of genes.

So, to study IQ heritability, subjects should be studied under different education conditions. I.e. they should be abandoned by parents and/or adopted separately.

My question is: was this done or not?

If not, then the question is, how education effects were eliminated?

Also I would like to know, if my reasoning about why just studying twins is insufficient is wrong.

I don't really know what you mean by "abandoned children".  Adopted children?  Children in the wild?  Have you read the Wikipedia article on the subject?  If you want to know how it was studied, just take a look at the references, it's pretty straightforward.

Heritability simply means how much variation in a trait is due to genetics, which is usually easiest to test in monozygotic twins.  Here's a good example where they did just that - they compared identical (monozygotic) and fraternal (dizygotic) twins raised apart or separately, finding:

  General cognitive ability yielded a heritability estimate of about .80 in two assessments 3 years apart as part of the Swedish Adoption/Twin Study of Aging. This is one of the highest heritabilities reported for a behavioral trait. Across the two ages, average heritabilities are about .60 for verbal tests, .50 for spatial and speed-of-processing tests, and .40 for memory tests. For general cognitive ability, the phenotypic stability across the 3 years is .92 and stable genetic factors account for nearly 90% this stability.

Here's another example doing basically the same thing.  The rest of the enWiki article gives a good breakdown of all the various factors involved in making this such a complex issue, as well as what was studied.


What is the role of acetylcholine in blood pressure regulation? What is the role of acetylcholine in the cardiac cycle and in blood pressure regulation?

I hope this answers your question:

So the heart is an electrically excitable tissue: it pumps due to action potentials that start  from specialized heart cells called nodal cells and these nodal cells spread the action potential to surrounding heart cells. These nodal cells are found throughout the heart and they make up what's called the conducting system. These nodal cells don't need neural or hormonal input for them to spread action potentials, they have this mechanism to spontaneously start action potentials on their own called a pacemaker potential, BUT they can be influenced by neural (think sympathetic and parasympathetic) or hormonal input. These external inputs change the frequency (the pace) of the heart beat by influencing the pacemaker potential of the nodal cells.

The sympathetic nerve fibers send out epinephrine which cause the pacemaker potential to occur at a faster rate, that's why during exercise (when epinephrine is released... hopefully) the heart beats faster. Parasympathetic nerve fibers send out acetylcholine which causes the pacemaker potential to occur at a slower rate, thus slowing down the heart. What does this mean in regards to the cardiac cycle? It influences how much blood (the volume) is ejected during the cycle. The volume of blood that is ejected from the ventricles, called cardiac output (CO), which is also how many liters/min, is determined by 2 other factors: stroke volume (volume of blood ejected during each ventricle during systole) and heart rate (CO = HR x SV). And therein lies a part of the answer to your question: when heart rate decreases because of parasympathetic stimulation, cardiac output should also decrease, granted stroke volume stays constant.

I unfortunately do not know how acetylcholine affects blood pressure. I've read a paper of how acetylcholine induced relaxation in hypertensive rats, but I'm not sure of the mechanism, like how it affects systolic or diastolic BP.


Have there been any theories put forward as to the reasons behind Temperature-Dependant Sex Determination in reptiles? This applies to most if not all reptiles, but I'll write about leopard geckos since that's what I know.

Incubation temperature of the eggs makes a big difference in the development of the gecko. Obviously excessively high or low temperatures will kill the embryo, but inside the safe temperature range there are some interesting effects. The most well-known is Temperature-Dependant Sex Determination (TDSD).

Studies have been done and it is quite well-documented that:

Incubating eggs at the mid-point of the safe range results in predominantly male offspring.
Incubating eggs at the high or low end of the range both result in predominantly female offspring.

According to my gecko book, there are also some interesting effects regarding males that hatch from female-biased temperatures being more sexually active but less aggressive to females than the "macho" males produced at male-biased temperatures, females at female-biased temperatures being the most fertile and high-temperature females being more aggressive than lower-temperature females.

(Incubation temperature also affects colour - specifically melanin production levels. AFAIK it's not known whether this is a direct effect of the temperature or an indirect effect from the changes in sex hormones at the different temperatures. It's probably a different enough issue to warrant a separate question, though.)

Going back to TDSD, my question is: what theories have put forward to explain this sex determination? Evolutionarily speaking, how did this come about? Are males less likely to survive so they are only produced at safe temperatures? Does the optimal male:female ratio for propagating the species change in adverse conditions?

I'm not looking for random guesses. I'm interested in knowing if there have been any theories put forward from knowledgeable and reputable sources.

Welcome to Biology StackExchange!

Environmental sex determination is tremendously interesting.
It looks like the most common explanation is that temperature-dependent sex determination (TSD) is the original form of sex determination, and genetic sex determination has evolved multiple times in different animal groups since then. Reptiles are a mish-mash of different mechanisms.

If TSD came first, then the real question is not why did it evolve, but why is it still around. And the answer is likely because it works well enough. I couldn't find a lot of evidence that females make varying choices for next temperature, so in "real life" it might mostly be that plenty of males and females are always born. There is also recent evidence that genes affect when the temperature has an effect, so again, temperature alone is unlikely to drive sex ratios.

As far as possible advantages of TSD there is no definitive explanation that has held up to testing. It is possible that ideal female development has slightly different requirements than male development, so nest location choice by the parent may act to produce more females if the current environment supports them more than males. For instance, it has been shown that having more female offspring when temperatures are higher results in larger females.

Sorry to not have a simple answer for you. The whole idea is fascinating, along with other environmental triggers to development, like worker ant larvae becoming a winged queen if given the right nutrition, or butterflies that add "eyespot" pigmentation to their wings in wet years with increased predators.


Is there any evidence that supports glycolysis in mitochondria or chloroplasts? Glycolysis is known to be a part of cellular metabolism undergone by both eukaryotic and prokaryotic cells, whether under aerobic or anaerobic conditions. As the endosymbiotic theory states that mitochondria and chloroplasts were once bacteria that lived apart from eukaryotic cells, do they have any enzymes or compounds suggesting that they once did glycolysis?

A search of UniProt returns no reviewed, mitochondrially encoded genes involved in glycolysis. There are some unreviewed entries, but a brief perusal of the associated publications suggests to me that these have all been incorrectly annotated (as one may expect from unreviewed entries).

Interestingly, Rickettsia prowazekii, an obligate intracellular parasite and the modern species thought to be most closely related to mitochondria, also has no glycolytic enzymes:

  Genome sequences of organisms enjoying an endosymbiotic lifestyle are at risk. The activities of homologous nuclear genes may render genes of the endosymbiont expendable and as a consequence they become vulnerable to obliteration by mutation. Good candidates for such purged genes in Rickettsia and mitochondria are genes required for amino-acid biosynthesis, nucleoside biosynthesis and anaerobic glycolyis. These and other genes would have been deleted when an ancestral genome first lived in a nucleated cell. Once genes essential to a free-living mode are lost, the endosymbiont becomes an obligate resident of its host.

Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Alsmark UCM, Podowski RM, Näslund AK, Eriksson A-S, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.