downloading a reference genome for alignment I am currently working through the code example on the MATLAB website. It requires me to download the reference genome of Arabidopsis thaliana (thale cress) so I can use BowTie2 to align the Chip-Seq experiment data. I need it in a .fa file.

Since I am very very new to this, what is the database where I can use to download this reference genome? How do I search for something like this? Thanks

EDIT: spoke too soon. I think the NCBI website did it for me. Under the Representitive -> Reference genome section. Is this correct?

EDIT2: The answer was in the MATLAB page also. The bioinformatics toolbox provides a function:

% getgenbank('NC_003070','FileFormat','fasta','tofile','ach1.fasta');
% getgenbank('NC_003071','FileFormat','fasta','tofile','ach2.fasta');
% getgenbank('NC_003074','FileFormat','fasta','tofile','ach3.fasta');
% getgenbank('NC_003075','FileFormat','fasta','tofile','ach4.fasta');
% getgenbank('NC_003076','FileFormat','fasta','tofile','ach5.fasta');

Since you are using Bowtie, you want the indexed genome, see if that's not available here, instead of downloading the fasta and indexing it yourself.

http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn


As electrons are moving through the ETC, how is ATP produced for the active transport to even happen? A lot of websites aren't being specific and they are just saying that when electrons move from a high to low energy state during the ETC, "energy" is being released and that energy is used to pump (active transport) H+ ions through the membrane. I want to know more. Isn't ATP formed by adding a phosphate to ADP? If so, where do electrons moving through the ETC get that phosphate from? BTW, I'm not talking about ATP synthase, because you need H+ ions for ATP synthase and I'm not understanding how those H+ ions are being actively transported through the membrane in the first place.

ATP formation is done using the Complex V called as ATPsynthase (also called as F0/F1 particle) and the theory explaining this process is called as the Chemiosmotic Theory2.

During cellular respirationKreb’s cycle (in the mitochondria) and Light dependent Photophosphorylation photosynthesis (in the chloroplast thylakoids) a set of reactions establish a proton gradient across the inter-membrane space ( hereby referred to as IMS) of the mitochondria/chloroplast( if you remember mitochondria/chloroplast are double membrane bound organelles).

Just as in a battery/cell we have EMF(electron motive force) we have, in the IMS of the mitochondrion/chloroplasts, a proton motive force.

Since substances always flow from higher potential to lower potential, the IMS of mitochondrion/chloroplast having a high amount of protons is a region of high potential and lumen of mitochondrion/chloroplast is a region of low potential since there are less number of protons.

The only way protons can move from the IMS  of the mitochondrion/chloroplast to the lumen of the mitochondrion/chloroplast is via the complex V (also known as ATPsynthase).

The ATPsynthase is a lollipop shaped protein structure that is freely rotatable and it brings ADP & phosphate molecules close together so that a covalent bond can be formed in between them.

How does it exactly do this you ask?
So let’s summarise what all we have here:

ATPsynthase that can rotate about its rotor.
Proton gradient across the IMS ( high potential) and the lumen ( low potential).
The only way out for the protons is via the ATPsynthase.

Now we can see a link here.

So what happens is, there’s the F0 subunit of the ATPsynthase through which the protons are able to move across the membrane and during that movement the rotate the F1 subunit.
During this rotation shown in animation here  the ADP & the phosphate group which are present in the active site of the F1 subunit are brought near each other and due to atomic interactions a bond is formed.
The mechanical energy ( movement of protons across the membrane) is converted into chemical energy ( covalent bond) between the two molecules.
This is the process via which the currency of the cell, ATP, is produced.
Hope that answers the question.


Difference between the inactivation of neurotransmitters and hormones Neurotransmitters must be somehow removed from the synapse once they’ve produced a post-synaptic potential, whether it be through enzymatic breakdown, diffusion, reuptake or another mechanism. However, I rarely see such mechanisms mentioned when discussing hormonal communication. I assume hormones just diffuse away from their receptor and do not continually stimulate the cell. However, there does not seem to be an urgency in breaking it down. Why is there this urgency, then, in the case of neurotransmitters, but not with other first messengers, like hormones?

Short answer
Hormones act in the order of minutes or hours. Neurotransmitters in the order of milliseconds. Moreover, hormones are blood-born, neurotransmitters are confined to the synaptic cleft or in the extracelular space directy surrounding the neuron. Hence, their mechanisms of inactivation are different.

Background
The distinguishing feature of hormones and neurotransmitters is the fact that the former are generally released into the blood, while the latter are confined to synapses, or the immediate extracelullar neuronal space. Hence, hormones can be readily cleared by the workhorse of blood clearance: the liver. For example, adrenaline is rapidly (half life 5 - 10 minutes) metabolized mainly by the liver, followed by excretion via the kidneys. Diffusion then will draw adrenaline away from the receptors as blood concentration drops. The relatively slow time course is beneficial, as the effects of epinephrine includes metabolic changes, such as the release of glucose to power up the body (Sherwin & Saccà, 1984). This needs time.

In the synapse, there is no blood flow and inactivation has to occur through other means. Further, epinephrine in the above example is a fast acting hormone. Many hormones work on an even slower time frame. For example, a stress-induced cortisol peak can last for as long as an hour (Kirschbaum & Hellhammer, 2000). Neurotransmitter responses may last for a few milliseconds. For example, some pacemaker neurons may fire at rates of 40-50 Hz (Häusser et al., 2004). Hence, neurotransmitters have to be cleared from the synapse at least within 20 ms. To wait for the released neuroransmitter to passively diffuse out of the synapse is simply too time-consuming. Neurotransmitters act at an entirely different time scale.

References
- Häusser et al., J Neurosci (2004); 24(42): 9215-9
- Kirschbaum & Hellhammer, Encyclopedia of Stress, 3 (2000)
- Sherwin & Saccà, Am J Physiol (1984); 247(2-1): E157-65


Why are recombination rates increasing in mammals? I have recently become fascinated with an awesome topic in biology and evolution that I feel is rarely covered in biology courses. That is, rates of meiotic recombination, or the the amount that an organism's genome is reshuffled before it is passed on to the next generation, varies across species! And no one really knows why.
A recent paper by Segura et al which gathered average recombination rates for males across a dozen or so mammals and showed that there is a trend of increasing recombination rate with mammalian divergence.
Why is recombination increasing through mammalian evolution? Is there any reason to believe that there is something special about placental mammals which would drive increased recombination?
There are some catches to this study such as low sampling of marsupials and monotremes and low power for most of species wide recombination rates, ie the average recombination rate of cells in a single individual. But I can see how getting samples from multiple tigers would be difficult.

If rates of meiotic recombination DIDN'T vary across species - THIS would require an explanation! After all, evolution creates diversity, not homogeneity.

I can only wonder that more recombination would allow for a faster diversification. The more DNA you shuffle, the more distinct each individual offspring may be (though I'm not 100% sure). The recombination rate has an energetic price, so not all animals recombine so much their DNA like later mammals. I.e. they needed a selective pressure to justify paying that price.

Perhaps it was useful for a group rapidly occupying the "vague niches" left by dinosaurs? This make sense, since the primary mammalian irradiation occured in the beginning of the Cenozoic era, right after the Cretaceous mass extinction that killed most big animals, including the biggest dinosaurs.

Unfortunately I have no references on the subject, it is just what makes sense to me, given evolutionary logic.


meaning of the "reads" keyword in terms of RNA-seq or next generation sequencing I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be found here and I've seen a word RNA-seq read. Altough I searched a lot to learn about, I can not find the definition of it, the thingsI found was about performance issues of techniques rather than explanation of the word. So, is there anyone who can simply explain me what is the meaning of this word as well as RNA-seq technique?

In RNA sequencing, the RNA is fragmented, DNA is synthesized complementary to the RNA fragments, which is  followed by a complementary strand synthesis. Fragmentation can be done after the cDNA synthesis too.
This DNA is then amplified to form a cluster that is sequenced. Most Next-Gen sequencing approaches sequence a short segment of the DNA (it has improved with experimental and technical optimization).
A read refers to the sequence of a cluster that is obtained after the end of the sequencing process which is ultimately the sequence of a section of a unique fragment. If an RNA is expressed in high copies then there will be more reads coming from it; reads can be redundant as well.

Courtesy


Mesoporous silica particles as anti cancer drug delivery method If this question is a little off topic for Biology, I'm sorry. I've recently read a lot about mesoporous silica nanoparticles as a promising drug delivery method. The huge range of customizability of the particles, coatings, contents, etc. can pretty much tailor them to be effective in delivering most drugs to most target locations in the body (or to specific cells). The research is not new, and all the articles hail the method as a very promising way to treat for example cancer. However, as far as I know, these methods are not widely used today. Why? Is there some catch that I don't see?

I'm no biology expert, but if this is so promising, and the research is at least a decade old, some companies would have produced this (they already produce the particles) in terms of drug delivery. So why not? Is it a case of null-findings not being published? Is it actually used and I'm blind?

Thanks for your help!

edit: for those interested, here is a good review

Though I totally agree with your views towards nanotechnology, There is always two sides of a coin.

According to this article THE BAD (of Nanotechnology):

  Health:

  Nanoparticles have been shown to be absorbed in the livers of research
  animals and even cause brain damage in fish exposed to them after just
  48 hours.   If they can be taken up by cells, then they can enter our
  food chain through bacteria and pose a health threat like mercury in
  fish, pesticides in vegetables or hormones in meat.  The
  increasingly-popular carbon nanotube (20x stronger and lighter than
  steel) looks very much like an asbestos fiber – what happens if they
  get released into the air?  Being carbon-based, they wouldn’t set off
  the usual alarms in our bodies, making them difficult to detect.

  Environmental:

  If nanomaterials really are as strong as diamonds, how decomposable or
  persistent are they?  Will they litter our environment further or
  present another disposal problem like nuclear waste or space litter?
  In the distant future, will self-replicating nanobots – necessary to
  create the trillions of nanoassemblers needed to build any kind of
  product – run amok, spreading as quickly as a virus, in the infamous
  “gray goo” scenario?

Not only that Each country have a different point of view on the topic of nanotechnology in Health(or nano-medicine).

Government Response on Nanotechnology:

United Kingdom

In its seminal 2004 report Nanoscience and Nanotechnologies: Opportunities and Uncertainties, the United Kingdom's Royal Society concluded that:

  Many nanotechnologies pose no new risks to health and almost all the
  concerns relate to the potential impacts of deliberately manufactured
  nanoparticles and nanotubes that are free rather than fixed to or
  within a material.

They want to change the existing regulation to be modified on a precautionary basis because they expect that the toxicity of chemicals in the form of free nanoparticles cannot be predicted from their toxicity in a larger form.

United States

Rather than adopt a new nano-specific regulatory framework, FDA convenes an 'interest group' each quarter with representatives of FDA centers that have responsibility for assessment and regulation of different substances and products. This interest group ensures coordination and communication. A September 2009 FDA document called for identifying sources of nanomaterials, how they move in the environment, the problems they might cause for people, animals and plants, and how these problems could be avoided or mitigated.

Berkeley, CA is currently the only city in the United States to regulate nanotechnology, which is still being opposed.

European Union

The European Union has formed a group to study the implications of nanotechnology called the Scientific Committee on Emerging and Newly Identified Health Risks which has published a list of risks associated with nanoparticles.
Consequently, manufacturers and importers of carbon products, including carbon nano-tubes will have to submit full health and safety data within a year or so in order to comply with REACH.

According to REACH(from Page 22, 4.2 Pharmaceutical regulation, PhD Thesis of Steffen Foss Hansen, DTU):

The application of engineered nanoparticles for medical use offers immense benefits
within areas like diagnosis, targeted drug delivery, and drug development and have been
marketed for more than 17 years (NanoRoad SME 2006, EGE 2007, Gaspar 2007).

Well-described and understood medicinal products containing nanoparticles in the form
of liposomes, polymer protein conjugates, polymeric substances or suspensions have
been given Marketing Authorizations within the EU under the existing regulatory
framework e.g. Regulation 726/2004 on authorization and supervision of medicinal
products for human and veterinary use, Directive 2001/83/EC on medicinal products for
human use, Directive 93/42/EEC concerning medical devices, Directive 90/385/EEC
relating to active implantable medical devices, and Directive 98/79/EC on in vitro
diagnostic medical devices (EP & CEU 2004, Council of the European Communities
1990, 1993, 1998, 2001).

There is no specific mentioning of nanomedicine in the EU legislation on medicinal
products and devices, tissue engineering and other advanced therapies. None of these
regulations or directives was written with nanomedicinal applications in mind and
although their scope covers nanomedicine they have been accused for being general and
non-specific and fraught with concerns and difficulties when it comes to dealing with
drugs more complex than traditional ones (Editorial 2007, D'Silva and Van Calster
2008).

The use of nanoparticles in nanomedicine has not been subject to much regulatory
scrutiny since existing laws and regulatory instruments are believed also to cover
medical products based on nanotechnology. The extensive testing requirements prior to
marketing of medicine may also contribute to the notion that the potentially negative
effects will be discovered prior to marketing, that patients are adequately informed
about negative side-effects, and that benefits outweigh the risks or the adverse effects,
should such be found to occur (EGE 2007, N&ET Working Group 2007) .


Where can I find trees preserved for hundreds of years? I assume there are climate conditions that cause trees to be preserved, since there are fossilized trees, however, it may be extremely rare to find a tree in a nascent state of fossilization.

Is it possible to easily find trees that have been preserved for 200-300 years? By a tree, I actually just mean a preserved stump.

Yes, this occurs fairly regularly in Alaska and British Columbia (and probably other places with low-elevation glaciers that interact with forested zones) where climactic oscillations have led to rapid advance and recession of glacial extent.

In Glacier Bay, Alaska, for instance, there are a number of interglacial stumps (you can see a few sites marked on this map). These stumps represent a forest that was established in the ice-free interim period between the Last Glacial Maximum (10,000-15,000 ya) and the "Little Ice-Age" (~500 ya). Thus, these trees have been preserved under the ice for a few hundred years and have only been uncovered recently (<100 ya). Many of the glaciers in Southeast Alaska are receding, so new stumps are being exposed every day.


What would the ploidy of a multinucleate cell be? If we have a haploid organism, and it undergoes karyokinesis without cytokinesis, would the organism be considered haploid or diploid?

Ploidy is generally defined in terms of the number of chromosomes in the nucleus, rather than the number of chromosomes in the cell.

Some examples in support of this:
- A paramecium has a diploid micronucleus and polyploid macronucleus
- Muscle cells are generally considered diploid even though they have multiple nuclei
- The additional chromosomes in mitochondria and chloroplasts are not considered to make cells polyploid, even if the organelle itself may be polyploid.

Thus, I would assess a cell such as you describe to be haploid, albeit with two nuclei.


How does noradrenaline result in rise of systolic blood pressure even when the cardiac output is decreasing? Systolic blood pressure[SBP] depends on the cardiac output. When Nor adrenaline is given there is vasoconstriction due to alpha-1 action on blood vessel, vasoconstriction results in increased total peripheral resistance and thus increases the diastolic blood pressure. The beta-1 action [increase in cardiac output] on heart by Nor adrenaline is counteracted by the reflex bradycardia  resulting in decreased cardiac output. Given the fact that SBP depends on cardiac output and the cardiac output is decreasing, why is there a rise in SBP on administering nor adrenaline?

Your question involves comparing an observed response to administration of noradrenaline/norepinephrine, which causes vasoconstriction thereby increasing the BP (during both systole & diastole,) to the hemodynamic/pharmacodynamic response of the cardiovascular system as a whole, which is decreased cardiac output & decreased cardiac work.  This is similar to asking why opening a finite water tank eventually slows down even though the pressure increases when you turn on the faucet.


Does pheomelanin have a useful biological function? Melanin is a natural pigment that is categorized into two main forms, eumelanin and pheomelanin. It's well documented in the science literature that increased eumelanin levels reduces the risk of developing skin cancer, whereas it was recently reported in Nature that pheomelanin may itself be carcinogenic. So my question is:

Does pheomelanin have a useful biological function?

I don't think that the role of pheomelanin is known yet. To produce larger amounts of it, you need mainly two conditions: A weak (or absent) MC1R signalling and the availibility of the amino acid cysteine. If MC1R signalling is strong, the preferred way goes into the direction of eumelanin. Its known for quite a while that pheomelanin produces reactive oxygen species which either directly cause DNA damage or do it indirectly by using up the cells storage of antioxidants. You can find more details in this review as well as links to a number of original papers.


How do beavers learn how to build dams? I was wondering whether all beavers, from all around the world, know how to build dams and lodges? Do they need to learn it from their parents? If you release a group of beavers in the wild that haven't been in contact with their parents, would they start to build stuff? or just hopelessly die/starve to death?

Question summary: is dam building learned or instinctive in beavers?
A blog post from 2011 references an article in the Juneau Empire titled Running water is sound of spring for beavers.  This article is no longer hosted on the Juneau Empire website, but archived versions are available.
Here's an excerpt (emphasis mine) --

Swedish biologist Lars Wilsson spent years studying captive and wild beavers, and he gained remarkable insights into their behavior. He raised beavers in an outdoor enclosure and in a large indoor terrarium ...
Wilsson initially captured four adult beavers and later he raised a number of beavers from infancy, some in small colonies with their parents and some completely isolated from adult beavers. He isolated the young beavers to see what beavers learn from their parents and what behaviors are instinctive.
He found that young beavers - who had never even seen a beaver dam - were able to build almost-perfect dams at the first opportunity.
The foundation of sticks and logs anchored to the stream bottom, the interwoven lattice of trimmed branches, the mud chinking, every aspect of dam building was hard-wired. Beavers do get more skilled at dam building as they gain experience, but the building behavior is instinctive.
Wilsson learned that the sound of running water is the cue for dam building and dam repair. In one experiment, he played a recording of running water, and the young beavers built a dam in a tank of still water in the terrarium. In another peculiar experiment, his captive beavers built a "dam" on a concrete floor against a loudspeaker that played the sound of running water.


Moss Transportation System In my biology textbook, it says that mosses are avasculer and do not have xylem like spermatophytes. So by what means do mosses transport nutrients ?

Mosses are able to transport water and nutrients internally through intercellular voids and cell-to-cell connections involving exchanges of cytoplasm, as well as externally across their surface. Labeling mosses as nonvascular plants is misleading because mosses in the Polytrichales order have highly specialized water and nutrient conducting systems which are reminiscent of xylem and phloem. But in general, a moss's main vascular system can be said to be its outer surface which is carefully designed to store and conduct water across the plant.

External Conduction

Moss cells absorb water and nutrients directly from their environment, so many of their nutritional needs can be met simply by ensuring water and its dissolved nutrients can spread across the entire surface of the moss plant. The water is able to spread through capillary action, aided by a carefully designed surface. Moss leaves are frequently appressed to the stem and have sheathed bases which create small places for water to climb along a stem. The leaves may also be covered in small bumps (papillae) which create capillary spaces. Rhizoids, which are somewhat like roots except typically only 1 cell thick, can also make good paths for water to flow across. Some mosses have their stems covered in rhizoids or paraphyllia to help conduct water. Sphagnum mosses have large cells across their leaves which exist mainly to absorb water like a sponge, and Leucobryum mosses have a layer of water holding cells on both sides of their leaves. Colonies of mosses often form compact mounds that allow for water to flow across the entire mound.

As far as I know, moss cells do not deliberately dump nutrients into the film of water on their surface in the hopes that it will be absorbed by other cells of the plant that need it more. But, when dessicated moss is rehydrated, solutes in the protoplasm may leak into the external film of water. These contents might be able to be reabsorbed by other cells of the moss, forming an incidental external nutrient transport pathway.

Internal Conduction

Water and nutrients are also able to flow through cells or spaces between cells from inside the moss. Experiments have shown that nutrients are relocated from old growth to new growth using cytoplasm-linked pathways in Sphagnum and Polytrichaceae mosses. Many moss stems and almost all seta (the stalk connecting a spore capsule to the main body of the parent moss plant) have special nutrient conducting parenchyma cells surrounding water conducting cells called hydroids. The central ribs of moss leaves also often show a similar pattern. Sometimes these chains of nutrient conducting cells in the leaves connect to the main conducting strands in the stem, but usually the leaf conducting strands come to an end somewhere in the stem cortex without connecting.

Mosses in the Polytrichales order have the most specialized nutrient and water conducting cells of all mosses. The nutrient conducting cells for mosses in this order are different enough from other mosses to be given a special name--leptoids. The vascular system in these mosses are not evolutionarily homologous to xylem and phloem, but serve the same basic transport purpose. In Polytrichum moss, water has been measured to flow 200 cm/h through the stem and organic compounds at 32 cm/h. These specialized hydroids and leptoids are what enables the tallest moss, Dawsonia superba, to grow up to 70 cm.

The water and nutrient transport architecture for mosses outside the Polytrichales is more variable and less specialized. Andreaeopsida, Andreaeobryopsida, and Sphagnopsida completely lack hydroids. Takkakia's hydroids are unique in that they are short instead of tall and transfer water through pores formed from plasmodesmata at their ends. Sphagnum has nutrient conducting cells, but they are not homologous to the nutrient transferring parenchyma cells of other mosses. Some mosses in families which typically have central conducting strands have lost that feature over time, and mosses which would normally have hydroids may fail to develop them if grown underwater.

Outside of the usual stem, seta, and leaf midrib conducting cells, it has been suggested that rhizoids and caulonemal cells also conduct nutrients due to similarities in cell organization to the nutrient conducting parenchyma cells. The cells that form the interface between the parent gametophyte and the sporophyte foot also transfer nutrients.

Sources

Chopra, R. N. Biology of Bryophytes. 2005. Chapter 11 "Conduction in Bryophytes".

Goffinet, B., and A. J. Shaw. Bryophyte Biology. 2009. Pages 60-70, 83, 301.

Ligrone, Duckett, and Renzaglia. Conducting tissues and phyletic relationships of bryophytes. 2000.


A good book for history of biology/biotechnology for lay people I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I guess that a book that covers most fields of biology cannot be compiled, but even more focused book would do.

Let me try to narrow it down: something like the greatest discoveries in the field of biology (like this article) would be an interesting book to read.

I am not sure how appropriate this question is for SE, but I am sure that I will get the best answer here. Besides, it would be great if lay people can be more excited about biology and contribute to the site growth.

Some that just come to mind, in random order:

One cannot skip reading:

Richard Dawkins - The selfish gene

And, obviously:

Charles Darwin - The Origin of Species

And, for those interested in the evolution of the brain (and its quirks):

David J Linden - The Accidental Mind
Oliver Sacks - The Man Who Mistook His Wife for a Hat

Not very DNA/evolution-oriented, but wonderful science books nonetheless:

Primo Levi - The Periodic table
And the neveraging must-read:
Isaac Asimov - A Short History of Chemistry


Why doesn't recombination occur in male Drosophila? "Males do not show meiotic recombination, facilitating genetic studies."

For a while I have known that this phenomenon occurs, this quote comes from the Wikipedia page on Drosophila melanogaster, and I frequently use this feature of Drosophila in constructing hemiclones for my own research in quantitative genetics.

But, until now, I have never asked why doesn't recombination happen? Why would this feature evolve?

Further, why is the absence of recombination sex-limited to males, why do females have recombination?

This is a venerable fact.  Exceptions in D. melanogaster strain Y-007 have been observed and D. ananassae has consistent male cross-overs, but this work dates back to the 1970s.

This Current Biology 2002 paper is not exactly new, but sheds some light on the issue in question.

  In male Drosophila melanogaster, meiosis occurs in the absence of recombination or a recognizable synaptonemal complex (SC).

The authors used a GFP-lac fusion to observe a series of sections of the male fly in meiosis with integrated lac - specific binding regions.  They see for the most part that the GFP bound segments of the DNA are not associated in cell division.  That is, homologous chromosomes physically associate during meiosis (via the SC) and in male drosophila, they do not.

It seems from more recent work, that the details of how this work is still being worked out but several gene regions and factors have been identified.  Suspected factors that help conspire to align the various homologous chromosomes are being looked into.  Take a look at the P.I.s biblio for more.

This isn't my main field, but as I understand it, many aspects of meiosis are still being mapped out.

As to the question of how this evolved and why; its definitely strange.
 It looks like there is a gender selected trait where the SC doesn't form in males.  Its easy to imagine a mutation that caused males only to lose recombination - the process is so complex its hard to imagine such a trait not showing up.

Still it's surprising to think that the trait has not only survived but become dominant in Drosophila all over the world.  To be a common traits to so many Drosophila species, it must have happened more than 10 million years ago.  Explanations of the advantages of sexual reproduction often include recombination.  Even the human Y chromosome has a self-recombination mechanism that reduces error in the coding regions.  As such, its hard to believe that this is not a huge disadvantage for the flies.  Still, if if it were such a big deal, you'd imagine Y-007 would have dominated and re-introduced the trait.

The only theory I can think of might be called 'lazy males'; that the males got the females to do one more thing for the offspring and it somehow outcompetes the sperm of the recombining males.  Lots of sperm are non-motile; that's a fact for humans, I have no idea what its like for flies that recombine.  Take a look at the variance in morphology as well - sperm are really crazy ugly sometimes and a good deal of the mating process is to help weed out the defective ones.  Without recombination, might it be that males produce viable sperm at a greater rate, helping them in sperm competition, which I'm sure is the case for fly mating - Drosophila are not monogamous too I'd guess?  Anyway that's not a researched idea, just a guess on my part.


Do desulfhydrase-catalysed reactions take place in animal cells? It isn't a homework question. I'm just stuck with desulfhydrase reactions and am unable to find enough information in the usual places.
Any external source on this topic would be helpful.

A desulfhydrase catalyzes the removal of hydrogen sulfide from a compound. So the answer is yes, but it's not the most-commonly annotated reaction for the enzyme cystathionine gamma-lyase.

I didn't know off-hand. Here's how I answered the question:

I searched Entrez Protein (or NCBI...whatever the thing's called) with the following terms:

(desulfhydrase) AND "Homo sapiens"[porgn:__txid9606]

And got three hits for isoforms of cystathionine gamma-lyase. I clicked on one of them and started reading. Key things I noted:

  EC_number="4.4.1.1"

  ...

  Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes
  the committed step of methionine biosynthesis. This pathway is
  unique to microorganisms and plants, rendering the enzyme an
  attractive target for the development of antimicrobials and
  herbicides.

So it's a good question because, if people normally characterize this enzyme in terms of Met biosynthesis, then we don't have a desulfhydrase. But I trusted the thing was annotated properly and that the comment above was just too medicine-oriented (as much biochemical literature is).

So to really understand the enzyme itself I searched MetaCyc for the Enzyme Commission identifier 4.4.1.1.

This let's me easily visualize the catalyzed reaction. And the annotation spells it out clearly:

  Enzyme Commission Summary: A multifunctional pyridoxal-phosphate
  protein. The enzyme cleaves a carbon-sulfur bond, releasing L-cysteine
  and an unstable enamine product that tautomerizes to an imine form,
  which undergoes a hydrolytic deamination to form 2-oxobutanoate and
  ammonia. The latter reaction, which can occur spontaneously, can also
  be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate
  deaminase.

  Also catalyses elimination reactions of L-homoserine to 2-oxobutanoate and ammonia, of L-cystine, producing thiocysteine,
  pyruvate and ammonia, and of L-cysteine, producing pyruvate,
  hydrogen sulfide and ammonia.


NaCl role in CTAB - DNA complex in DNA extraction I have a question about the role of NaCl in the DNA extraction process. So for NaCl concentrations under 0.5M, CTAB and DNA molecules can create complexes.
In those concentrations, proteins and other hydrocarbons are still soluble in water except the DNA-CTAB complex. If we raise the concentration of NaCl then the complex of CTAB-DNA will be soluble to water too. Correct me if I'm wrong until now.

So I don't understand something. Why do we use NaCl?

Let's assume that we don't add NaCl. Will the CTAB create complex with DNA or not? As I read CTAB creates ionic bonds with DNA (phosphate groups). So in this situation (without NaCl) CTAB must be able to create complex with DNA too.

So why did we use NaCl? Just to keep proteins and other hydrocarbons soluble in the water or there is something else that NaCl helps in this complex creation?

CTAB forms insoluble complexes with nucleic acids and can be used to selectively precipitate them from solutions, see this reference:

The isolation of bacterial nucleic acids using cetyltrimethylammonium
bromide (Cetavlon)

When you add NaCl in a concentration between 0.4 - 0.7M, the nucleic acids stay in solution, while polysaccharides and other substances, which may interfere with the DNA preparation do not. See this paper: "Rapid isolation of high molecular weight plant DNA."


How many Amperes to kill fruit flies and mosquitoes? As above. Making a homemade trap to kill them all.

I am not an electrician and may not be the right person to answer this. But I recently read this paper (Keller et al., 2016) and maybe this helps ... Keller et al. (2016) have a look at laser induced mortality in mosquitoes. It might not be fully adaptable to your needs (there is not much context in your question, though; I have no idea what kind of trap you are trying to build ... if it's going to be a fancy laser trap, the cited paper will be your perfect guide through the building process - however, you have to figure out the automatic camera detection (they are planning that, too) for yourself as they have not published that, yet).

Now, giving a concrete answer: Keller et al., (2016) found that lasers with 0.5W to 4W are sufficient for efficient mosquito inactivation. If you are planning to use a plug bucket (230V) this would be (0.5W/230V=) 0.002A to (4W/230V=) 0.017A. You could also set this up with a 9V battery. With a 4W laser this would be (4W/9V=) 0.44A. Using a lithium-based battery this would last for about (1000mAh/(4W/9V=0.44A)=1Ah/0.44A=) 2.27h total laser time.

I do not know if this easily translates to electric current, though ...


What is mRNA expression level? I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.

The RNA expression level is an estimate of the amount or proportion a given gene's RNA found in a sample of cells (such as a tissue sample) or even a single cell.

Expression is used because the RNA sequence is translated from DNA to RNA according to the signals within the cells.

There are various means of estimating this.  They often involve a sequence specific probe - a short length of DNA usually - which will bind specifically to the RNA in question.  The exclusiveness of the probe sequence, which is usually 20-45 bases long, to the RNA in question can vary and so this is a bit of an art sometimes.

Examples are qPCR (quantitative PCR), expression microarrays.  Both of these technologies have  many flavors and variants.

Another category of expression estimation include RNASeq - which will sequence all the RNA polymers in a sample and estimate all the sequences at one time.  The result is similar to a microarray, but RNASeq does not necessarily require the use of specific probes to an RNA to measure it, though it can.

These estimates are usually relative - except for careful qPCR perhaps.  The numbers are not usually interpreted as "X copies of the RNA" in the sample.


DNA dependent RNA polymerase How does a RNAP locate a specific gene? For instance, growth hormone has to be produced and the RNAP has to locate the gene. But the promoter (TATA box) will also be present infront of all cistrons. So how does the RNAP choose the specific gene? Are the promoters specific for specific gene?

It could be difficult for RNApol to access genes inactivated because inactivated genes are often tightly packed by chromatin. Many genes have enhancer elements(specific DNA sequences) as well as TATA, and transcriptional enhancers, which are proteins, would recognize enhancer elements in a sequence dependent manner and loosen chromatin structure to make RNApol access TATA sequences easily. Transcriptional enhancers also bind to the General Transcriptional Factor complex (GTF), which contains RNApol, therefore enhancers could bring RNApol to TATA sequences.
Many tissue specific and/or developmentally-regulated transcriptional enhancers are identified. You could say transcriptional enhancers regulate RNApol which to bind.

You can check this link and this.


Appropriate statistical test for a student lab? I am a HS Bio teacher and doing a microevolution lab involving candy. Essentially students use four candy types and push them together until one cracks (Nat Sel). They also do simulations of migration, mutation and genetic drift. They then calculate the "allele frequency" of each type per generation and look for changes. I want to have my students do a simple statistical test to see whether the change was significant or not from each evolutionary factor. I was going to do a chi square test, but someone told me that is not appropriate to this type of experiment.
So, can anyone confirm, is chi square inappropriate, and if it is..
Can anyone point me to a more appropriate test. These are high school kids with no stats background (and I have forgotten virtually all the stats I learned 20 years ago)...

To choose the right statistical method (it is more than just saying "use the t-test") you need to think about your experiment. A good starting point is this figure from Bitesizebio:

There are two relevant articles on that website:

Let’s Talk About Stats: Comparing Two Sets of Data
Let’s Talk About Stats: Comparing Multiple Datasets

Probably also interesting is the definition of statistical terms:

Let’s Talk About Stats: Understanding the Lingo


What is the length of anaerobic biodigestion stages? I have built an experimental portable batch biodigester to process organic garbage. A 50L drum filled half with garbage, half with water and with some cow dung added for inoculation, is connected from the top to a truck tire, boxed into another, larger drum.

I consider filling the bin within a week, based on the amount of daily garbage my home is producing. After a week, the bin is filled in with water and inoculated, and connected to the gas-holder.

How long would the biodigestion take in average before I can disconnect the bin and use the remaining slurry?

I have looked at existing information regarding the biodigestion process. The stages of biodigestion are explained in Chapter 4 of the Biogas Handbook sample I have:

  Aerobic
  Oxygen will inevitably enter with the raw materials put into the generator, and so aerobic bacteria use this oxygen up,
  meanwhile doing what they can to break the materials down. CO2 is
  released, and some heat is generated.

  Extracellular enzymes
  In this stage, anaerobic bacteria release enzymes that attack large molecules which are still outside their own
  bodies (extracellular), so these molecules will be broken down into
  “bite sizes.”

  Acid digestion
  The bite size molecules (still fairly large) are absorbed by the bacteria and digested. The main byproducts of this
  third process are simple molecules such as the short chain fatty
  acids, H2 and CO2. (We’ll get into the short chain fatty acids soon.)
  It’s interesting to note that at this stage, hydrogen gas, an
  excellent fuel, is evolved. Hydrogen does not often show up in the
  final biogas apparently because it is used by the anaerobic bacteria
  (in the next stage) in making CH4, methane.

  Gas digestion
  Now comes the part we’ve been waiting for. The fatty acids are now gobbled up by the last group of bacteria, who turn them
  into H2O, CO2, and best of all, CH4.

Alas, the length of these stages is not explained. However, Biorealis suggests the length of the Acid Digestion and Gas Digestion in a critique of conventional continuous-feed biodigesters vs. the two-phased biodigester it has developed:

  Conventional single-stage digesters are not only unstable, they are
  also relatively inefficient. For example, if the system is operated at
  a hydraulic retention time (HRT) conducive to growth of acidogens (2-3
  days), any methanogens present will be washed out of the system faster
  than they can reproduce, preventing them from ever becoming
  established. On the other hand, if the system is operated at an HRT
  conducive to growth of methanogens (20-25days), the faster growing
  acidogens will be maintained at the low growth rates of the endogenous
  growth phase - essentially at starvation level.

NB: I opted for a batch biodigestion system to avoid the complications mentioned by Biorealis here above and because Biorealis' two-phased biodigester is more expensive and less easy to build.

So far I have a rough biodigestion calendar of:

3 days of acid digestion
20-25 days of gas

But I still lack some information on the stages:

how about the length of the two previous stages mentioned in the Biogas Handbook?
on what do those stages depend and can I accelerate digestion somehow? (I already know about heat at 21°C, how about water ratio or anything else?)
how long does it take to digest a big chunk of food, say a 27cm² bit of carrot? (Important because I hope the garbage is completely processed before I toss the slurry in the garden as fertilizer)
in short after how much time can I confidently unplug the batch, knowing the biodigestion is complete?

Could you help me shed some light on the length of biodigestion stages? Thanks.

To give timescales for the different processes is very difficult because the speed (in g/d product yield) depends greatly on the number of bacteria, so first you'd have to modl the bacteria growth. I assume you don't want to go that road.

Also note that not all of the substrate is in the same state of fermentation at the same time, more so if you have bigger lumps. Like whole carrots.

One industrial batch-style fermneter I know of uses total retention times of 3-4 weeks, and they mix half the digestate into the fermenter again to provide for inocculum.


Why did we evolve to be able to see this specific set of wavelengths only? It is understandable that life didn't evolve the capability to sense all wavelengths of light, it simply didn't need it. My question is, why did it evolve the set of wavelengths it has, for example, the human visible range is 390-700nm, so why couldn't it be a different set of wavelengths, like, (say) 300-620nm? Is there a reason for it?

Well humans actually have a reduced spectrum compared to non-mammals. Reptiles and birds have 4 color sensitive cell types (cones), mammals lost two of these as modern mammals are descended from early mammals who were nocturnal. Primates evolved a third cone, (a mutant variant of one of the two they had before) Primates did this because many a frugivores and color is excellent for determining when fruit is ripe.


Topological property of DNA I was reading a course about DNA Supercoiling, and I stopped at this definition :

  [...] In the case of DNA, a topological property is one that is not affected by twisting and turning of the DNA axis and can only be changed by breakage and rejoining of the DNA backbone. (Source)

I didn't understand what they mean, can anyone clarify it please.

DNA supercoiling can be described numerically by changes in the linking number $L_k$, it's the most descriptive property of supercoiled DNA.

The linking number $L_k$ is equivalent to the sum of $Tw$, which is the number of twists or turns of the double helix, and $Wr$ which is the number of coils or writhes.

$$L_k = Tw + Wr$$

  [...]  If there is a closed DNA molecule, the sum of $Tw$ and $Wr$, or the linking number, does not change. [...] Since the linking number L of supercoiled DNA is the number of times the two strands are intertwined (and both strands remain covalently intact), L cannot change.

I don't know how to explain it more but I think the main idea is represented in the image below.

Edit:

From DNA Topology: Fundamentals :

There are two important features of the $L_k$:

$L_k$ is always an integer.
$L_k$ cannot be changed by any deformation of the DNA strands, i.e. it is topologically invariant. The only way to change it is to introduce a break in one or both DNA strands, rotate the two DNA strands relative to each other and seal the break. This is precisely the role of DNA
topoisomerases.

Related question: Reason behind formation of positive supercoils during DNA replication/transcription.

Sources : DNA supercoil and DNA Topology.


Do all animal cells have lysosomes? I know that white blood cells have lysosomes but what about other body cells? I mean, any other cell such as cells in the respiratory system.

You are probably referring to the process of phagocytosis, where macrophages engulf a pathogen by trapping it inside a vesicle called "phagosome", which then fuses with a lysosome, resulting in the digestion and disposal of the pathogen.

But in fact all eukaryotic cells have lysosomes. This is of course biology we are talking about, so there are many subclasses, different names, specializations and exceptions to the rule.

In plant and fungal cells, we find vacuoles, which serve a similar function as lysosomes in animal cells. There are also "lysosome-related organelles" with specialized functions in specific cell types (Marks et al. 2014).

The main role of lysosomes has been described in the recycling of macromolecular material. Their lumen has a low pH level (below 5) and contains a lot of enzymes specialized in degradation of e.g. proteins, nucleic acids etc. They can digest cellular waste products and material taken up by endocytosis. Nutrients can be reabsorbed into the cytoplasm.
Furthermore, research has proposed additional roles in nutrient sensing and metabolic homeostasis (Perera and Zoncu 2016).

That lysosomes play a crucial role in many cell types can also be seen in lysosomal diseases, which often result in severe effects in multiple organs (Ballabio and Gieselmann 2009, Saftig and Klumpermann 2009). In these diseases, lysosomes fail to degrade their targets, which impairs their ability to clean out cellular waste.

Here is a summary from the book "The Cell".


Why does something taste less sweet after eating something else that is sweet? Why does something taste less sweet after eating something else that is sweet, especially if you don't drink water in-between.

It's a general flaw (IMO bad design) in organic/neural sensor frameworks where inputs tend to be measured relative to previous experience rather than absolute quantitative.

This happens with weights as well. There have been plenty of experiments where people are asked to pick up a heavy weight and then a light weight, then record/estimate the perceived light weight. The next day, they pick up a medium weight and then the same light weight and record the perceived light weight.

The 2nd recording turns out "heavier" because of relative perception.

Suggestion: Computer-mediated nerves designed to measure in absolutes.


Is there already discovered non-carbon form of life? I have heard of some rumors going around about a living organism based on non-carbon. Is Has research been done with real form of life based on non-carbon? Or carbon-based life is only type of life what humans know of?

Carbon chauvinism

In a word, no.  There are some good chemical reasons to expect all life to be carbon-based.
Of course, it is no longer a silly fantasy to imagine an artificial intelligence that might qualify as life.  (Still FAAAARRRR in the future, though, if ever.)


Why does depolarisation by high intracellular K+ trigger calcium channels opening? I have learnt that in pancreatic beta cells, glucose being metabolised in the cell causes a high ATP level, which triggers ATP-dependent potassium channels to close. This means that potassium can't leave the cell anymore, which depolarises the membrane and causes voltage-gated calcium channels to open and release calcium into the cell to trigger insulin release. I don't understand why this happens, because both potassium and calcium being positively charged. Wouldn't this depolarise the membrane even more? I thought this would be unfavourable.

Ca2+ is very often the trigger to release neurotransmitter or, in this case, hormones. Ca2+ entry in the cell is important to activate the fusion of secretory vesicles with the membrane in pancreatic beta cells as shown in Fig. 1 (Thurmond, 2000). The function of Ca2+ entry is not so much related to its depolarizing actions.

Fig. 1. Ca2+-mediated insulin secretion. Glucose-stimulates insulin secretion by increasing the ATP/ADP ratio, which inhibits the ATP-sensitive KATP-channels, leading to membrane depolarization and opening of voltage-dependent calcium channels (VDCC), with a resultant major increase in cytosolic calcium, which, in turn, triggers exocytosis. SNARE proteins play a critical role in insulin granule secretion. The linking of the plasma membrane proteins syntaxin and SNAP-25 to vesicle protein VAMP-2/synaptobrevin-2 cause the docking of the vesicle, bringing insulin granules in close contact with the plasma membrane and calcium channels, after opening of calcium channels, the readily releasable pool (RRP) insulin granules located nearby are exposed to high level of Ca2+, resulting in RRP granule exocytosis. Source: Ren et al. (2007)

Ca2+ entry in the cell is potentially toxic and closely regulated. For example, internal stores are actively involved in the release and re-uptake of Ca2+ (Pian-Smith et al., 1988). Although Ca2+ influx will depolarize the cell further, it will not contribute substantially to the membrane potential compared to the effects of K+ and Na+.

References
- Pian-Smith et al., Endocrinology (1988); 123(4):1984-91
- Ren et al.,  J Transl Med (2007)
- Thurmond, Landes Bioscience (2000)


How can prokaryotes repair double strand breaks by homologous recombination if they're haploids? Title says it all, I must be going crazy.

Several answers to this question:

Much of the time what bacteria are doing to repair DSBs is actually non-homologous end-joining, which does not require strict homology. This is the more likely mechanism earlier in the cell cycle when copy number is more likely to be ~1.
If cells have completed DNA replication (later in the cell cycle), there are at minimum 2 copies of all DNAs present in the cell. These can be used for homologous recombination.
Bacterial chromosome copy number can be overreplicated in some situations, such that DNA replication is not synchronized to the cell cycle and is more than normal for a cell. In these situations copy number can be >2.


What is synaptic bias? In non linear model of a neuron there was a mention about bias (Bₖ) which was the summation of the synaptic weights.

I want to understand what synaptic bias is and their application/use in neuronal modelling.

Often artificial neurons are created with conventions that zero is "rest" and 1 is "threshold". The unit starts at 0, and when it reaches 1 it will send an input to all of its targets and be reset back to 0.

This isn't exactly how real biological neurons work, but its a reasonable approximation in some contexts (and can do real world computations).

Most of the inputs to a unit are variable, so you add some voltage to the neuron based on the synaptic weight. For example, one input with a weight of ".2" would move the cell 1/5th of the way to threshold by itself.

When people talk about a bias input, they are referring to an extra "always-on" input with a small synaptic weight. This can maintain a rest greater than 0 in a leaky integrate-and-fire cell; this allows for some more biologically relevant forms of inhibition (negative synaptic weights) to have an influence on the unit, by offsetting the bias input and pushing the voltage back to 0.

More often, I am familiar with using a bias input in networks that are not leaky. These networks just integrate until they reach threshold (although they may or may not get negative inputs). For these networks (or for a leaky network where the bias current is substantial relative to the leak), adding a bias input ensures that the network won't stochastically "fall asleep" due to a period of low activity. If the bias current is equivalent to ".02" units per cycle, for example, you would guarantee that the cell would fire once every 50 cycles with no other input.

There are some real excitable tissues that show similar behavior, but not due to a real bias input. Rather, there are intrinsic channels that slowly depolarize a cell. Some examples are in cardiac myocytes and the sinoatrial node making up the heart's "natural pacemaker", as well as in brain circuitry that controls breathing. The bias input is sort of a "made up" construct that is functionally, but not mechanistically, correlated with real biology.


Kinetic binding / unbinding constants of protein + mRNA ⇌ mRNP I wish to find an order of magnitude for the binding/unbinding constants of mRNA and RNA-binding proteins.

Suppose molecules A and B reversibly associate to give the complex C. Assuming the diffusion is large enough such that no concentration gradient exist, the reaction equation at equilibrium is:

➕[A][B] — ➖[C] = 0

with ➕ the binding constant (units: concentration-1.time-1), ➖ the unbinding constant (units: time-1), and [A], [B], [C] the concentrations of the molecules.

I found many papers assessing the equilibrium constant K = + / ➖ but I am interested in + and ➖ independently.

Ridgeway and coworkers designed a really neat microfluidic device for making these kinds of kinetic binding measurements on RNA and protein (Ridgeway et al. 2009). Their device works sort of like a stop-flow, and they used a FRET based scheme to detect binding and unbinding events. They took measurements for one particular rRNA/ribosomal protein pair and got (6 ± 0.4) × 105 M-1s-1 for the bimolecular on-rate kon and  (5 ± 0.9) × 10-3 s-1 for the unimolecular off-rate koff.

Ridgeway cites references 23,24,26, and 33 when talking about experiments with "similar constructs and buffer conditions", so those would probably be a good place to start looking if you want to assemble a diverse set of kon  and koff  values.


Statistical genetics: Allele frequencies that follow a Dirichlet distribution From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population.

  We consider a set of $I$ loci and let $K_i$ be the number of alleles at the $i^{th}$ locus. The extent of differentiation at locus $i$ between subpopulation $j$ and the ancestral population is measured by $F^{ij}_{ST}$ and is the result of its demographic history. Let $p_i=\{p_{ik}\}$ denote the allele frequencies of the ancestral population at locus $i$, where $p_{ik}$ is the frequency
  of the allele $k$ at locus $i$ $\left(\sum_k p_{ik} = 1\right)$. We use $\mathbf {p} = \{\mathbf {p_i}\}$ to denote the entire set of allele frequencies of the ancestral population and $\mathbf {\tilde p_{ij}} = \{ \tilde p_{ijk}\}$ to denote the current allele frequencies at locus $i$ for subpopulation $j$. Under these assumptions, the allele frequencies at locus $i$ in subpopulation $j$ follow a Dirichlet distribution with parameters $\theta_{ij}\mathbf {p_i}$,

  $$\mathbf {\tilde p_{ij}}  \space \tilde \space\space  \text{Dir}(\theta_{ij} p_{i1}, ..., \theta_{ij}p_{iK_i})$$

  , where

  $$\theta_{ij} = \frac{1}{F^{ij}_{ST}}-1$$

(I don't have much experience with Dirichlet distributions but I understand its definition and its usefulness in bayesian statistics).

Can you please help me to understand why $\mathbf {\tilde p_{ij}}$ follows this Dirichlet distribution?

Calling the $j^{th}$ parameter of the Dirichlet distribution, $\alpha_j$, I typically don't understand why they "chose" $\alpha_j = \left(\frac{1}{F^{ij}_{ST}}-1\right) p_{ij}$ and not, say just $\alpha_j = F^{ij}_{ST} p_{ij}$ or anything else.

Largely an informed guess based on properties of distributions rather than specific knowledge of statistical genetics: a beta distribution is useful for modeling the frequencies of two alleles at one locus. A Dirichelet distribution, which is a multivariate generalization of a beta distribution, would thus be useful for modeling a set of loci.

The flip side is to think of beta as just a special case of Dirichelet: if you only have one locus, beta works. If you have multiple loci, then Dirichelet.


How does lactulose cause the removal of ammonia from the colon? Lactulose is also used to reduce the amount of ammonia in the blood of patients with liver disease. It works by drawing ammonia from the blood into the colon where it is removed from the body.
[Source]

How is ammonia removed from the colon?
From the quote above it sounds like ammonia removal must be some other mechanism than absorbing it into the blood, correct?

Excess nitrogen must be excreted by the body and can come from nitrogen in the diet (e.g. amino groups from excess amino acids) or nitrogen-containing compounds produced by bacteria in the gastrointestinal tract (GI tract).
Normally the liver and kidneys are involved in excreting ammonia ($NH_3$) and ammonium ($NH_4^+$) from the body. Ammonia can be toxic in high concentrations, but the body can detoxify it through conversion to other nitrogen-containing substances (i.e. urea) or excrete the ammonia itself.
Ammonia in the blood is freely filtered at the kidney glomerulus and can be "trapped" in the urine flow by accepting a proton to become ammonium (i.e. $H^+ + NH_3 = NH_4^+$) . Because of the positive charge the ammonium ion is unable to passively diffuse back across the tubules into the blood. This is one mechanism that ammonia is excreted. In the liver, the Urea Cycle (see any basic or clinical biochemistry text for more information) is a set of enzymes that converts most of the excess nitrogen in the form of ammonia to urea, which is a non-toxic, water soluble organic compound that can also be excreted in the urine. The body uses these processes to dispose of excess nitrogen from amino acids as well as ammonia that is produced as a by-product of bacterial metabolism in the GI tract.
Some patients with significant liver disease (e.g. cirrhosis from either NAFLD, hepatitis or any other liver-damaging disease) have lost the ability to convert all the excess ammonia to urea. In these patients, an easy way to prevent excessive nitrogen uptake in the gastrointestinal tract is by treating them with lactulose. Lactulose is a carbohydrate that that is not digestible or absorbable by the body, but is osmotically active (pulls water into the intestinal lumen) and acts to speed up intestinal transit. Since lactulose works by speeding up GI transit it makes you stool more frequently (which is why it is very useful for constipation). For liver disease patients, however, the lactulose acidifies (i.e. decreases pH) the lumen of the intestines and ammonia is protonated to form ammonium, which effectively traps it in the intestinal lumen. A lot of the excess ammonium can then pass into the feces and decrease the amount of ammonia that the liver needs to process. This is similar to the mechanism of ammonium in the urine as mentioned above. Additionally, lactulose also decreases the amount of GI bugs that produce ammonia containing compounds as well, which also lessens the amount of ammonia for detoxification by the liver. (Lactulose can also be used for a treatment for small intestinal overgrowth). These GI bacteria metabolize dietary amino acids and other compounds in the gut for energy metabolism, which liberates nitrogen-containing compounds that can be absorbed by the intestines.
Edit: Here is a link for a great reference on NCBI that explains the mechanism of action of lactulose.


Glucose Carrier Proteins in Cell Membranes I'm using Campbell's Biology textbook, and it states that certain carrier proteins transport glucose across the cell membrane much faster than would occur normally. It states that the "glucose transporter" is an extremely selective protein, which doesn't accept even fructose, which is an isomer of glucose. However, another hexose, galactose, appears to me to be even more similar to glucose- it's just that one of the H-OH pairs is flipped. In comparison, though fructose is indeed an isomer, it's a ketose, but glucose and galactose are both aldoses. Given this, I'm pretty sure galactose is more similar to fructose.

My question is: is the carrier protein specific enough to carry only glucose and not even galactose? If it isn't and it's able to carry galactose, what would happen if galactose was transported into the cell in greater quantities?

Note: I'm a bio beginner, so please have some patience if my questions are nonsensical or my facts are incorrect, any corrections would be welcome.

First thing's first: there are many different kinds of glucose transporters (genes), even within the same organism. These genes share partial sequence identity in mammals, and are part of the SLC2A, or "GLUT" gene family. In yeast, there exist glucose- and galactose-specific transporters.

Often, not always, a glucose transporter type may be tissue specific. GLUT3 is expressed in neurons, in the placenta, and elsewhere. Compare this to the expression of GLUT1, found in red blood cells, and GLUT4, found in adipose and skeletal muscle tissue.

Each kind of transporter has various affinities for glucose (or other sugars for that matter), and various levels of permeability for similar molecules. This is what is called the specificity of the transporter. The rate at which sugars can pass through the pore of the transporter is called the frequency. Together, these properties define the function of a hexose transporter, and hence why there are different kinds with site-specific expression across the body.

In terms of regulation: GLUT1 is dynamically regulated based on available glucose (up-regulated during shortage and down-regulated during excess). This is not the case with GLUT4; instead, GLUT4 is insulin-regulated, so that muscles and fat tissues can uptake glucose for storage, which is a hormone-controlled process.

Here is a great webpage to help you understand the characteristics of hexose transporters, especially with regard to galactose, fructose and glucose.


How is Hypertonic Urine Produced in a Mammalian Kidney? I know that the ascending loop of Henle is impermeable to water and ions, and, by end of the ascending limb, the osmolarity of the tubular fluid is very low due to the active transport of ions out (e.g, sodium, potassium, chloride).

However, what if the person had to produce hypertonic urine due to dehydration or some other circumstance? Would the increase in osmolarity be done through a decrease in removal of ions in the descending limb, or has the distal tubule and collecting ducts got something to do with it?

The process of urine concentration in mammals occurs due to the interaction of the loop of Henle and its nearby collecting tubule. When someone is dehydrated, the kidney will aim to a maximal water reabsorption.
To concentrate urine, a maximal amount of ions will be reabsorbed. This is to maximalize the concentration gradient for water. However, the main driving force for water reabsorption is the urea concentration gradient (created by the loop of Henle). Then aquaporins will allow water to flow from the collecting tubule to the nearby medulla because of the presence of the neighboring loop of Henle. It is this proximity between the loop of Henle and the collecting tubule that allows such a high efficiency for water reabsorption.

Concentrating urine is not about leaving more ions in the water, it is about reabsorbing a maximal amount of water.


What is this dried animal for sale? I found this image on the Internet, which features an African youngster holding up an animal for sale to a potential customer sitting inside a car. It appears to be some sort of dried and disemboweled animal.

What is the identity of the animal?

The boy is holding a couple of smoked/barbecued cane rats, also known as "grasscutters".  These are commonly hunted as bushmeat in West and Central Africa and have recently been farmed as well.

You can see some similar photos here:

http://members.virtualtourist.com/m/p/m/178963/
http://westafricaadventure.blogspot.com/2011_04_03_archive.html
http://www.fionaleonard.net/2012/04/rodents-of-unusual-size.html
http://2summers.net/2015/01/23/pop-up-travel-cane-rats-in-ghana/


How are logarithmic trendline equations used to determine antibody concentrations in ELISA? For example, say you have plotted a standard curve and managed to obtain a logarithimic trendline equation like:  y = mln(x) - b

And you are working with data that includes:
a) standards,their concentrations and absorbance readings (taken twice - with mean absorbance and blank absorbance also calculated)
b)samples (and their absorbance readings) that you want to know the concentration of
c) all the samples have been diluted two fold

Would you simply just rearrange the equation y = mln(x) - c  to:
x = (y + c) / mln
and input y value as being the mean absorbance readings of the samples you want the concentration of?

Are there any further steps after this? Or any I have missed out?

Is there anything I need to do with the dilution factor?
Do I have to do mean absorbance - mean blank, to get the correct absorbance readings to input as y or are the mean absorbance readings themselves sufficient?

Thank you

If by ln you mean the natural logarithm, then no, you can't rearrange the equation in that way. Try this:

$$m\cdot \ln(x) - c = y\\
\ln(x) = y + c\\
\ln(x) = \frac{y+c}{m}\\
\exp(\ln(x)) = \exp\left(\frac{y+c}{m}\right)\\
x = \exp\left(\frac{y+c}{m}\right)
$$


Why doesn't yearly screening for lung cancer decrease mortality rates? In a large trial, screening yearly for lung cancer hasn't reduced mortality rates. Why is this? Isn't cancer best treatable when caught early? Is this because lung cancer is hard to treat anyway, because yearly is not frequent enough, or why?

There are a number of reasons, generally, why a screening test may fail to decrease cancer mortality rates:

The screening test may not be very good. I know this seems like an obvious one, but its something of a problem - a screening test will only reduce mortality if it catches cases that are both treatable and wouldn't be detected in time to treat using other methods. For example, it may be that even if caught slightly later by other methods, lung cancer is equally treatable (or equally difficult to treat).
Mortality from false positive tests and subsequent procedures in non-cases offsets any gain in survival among cases.
Diagnosis is only one step toward treating a disease. Even if detected, if a disease is not treatable or isn't treated, knowing you have the disease doesn't change your mortality risk.

In this case it appears that a chest radiograph isn't good enough at detecting lung cancer to manifestly improve mortality outcomes. The author's of the paper don't really specify why this is - though since they're just looking at lung cancer mortality, it's likely not #2.


Why did many species of Homo and their ancestors evolve in East Africa? One thing I find interesting about the theory of evolution is the idea that Homo Erectus and Habilis evolved in Africa, began to spread around the globe, then was superseded by Homo Sapiens Sapiens which also evolved in Africa. Why did the vast majority of Homo species evolve in East Africa first?  What was it about Africa which encouraged speciation more than other areas?

The question is based on a false opinion but I'll get back to that at the end.

Humans are still evolving

  Why did all species of Homo evolve in Africa first?

Humans are evolving all around the world. Evolution is not a thing that stops once we made the arbitrary decision of naming a lineage. When we first named humans, Homo sapiens sapiens, indeed the lineage was living in east Africa.

Humans is a lineage of Old World Great Ape

  One thing I find interesting about the theory of evolution is the idea that Homo Neanderthalis evolved in Africa

It would help if you could explain why you find that particularly interesting. It is possible that some falsy teleological view of evolution you may have might push you to make some unexpected conclusion from the idea that first Homo lineages lived in Africa (but might be wrong in your understanding of evolutionary processes). In any case, you can find an very introductory course to evolutionary biology here if you're interested.

If humans were a species of feline, it could have evolved elsewhere (it would look very different to what we currently call humans of course) but humans is a lineage of old world great ape. Old world great ape lived mainly in Africa. There is not much more to say about it.

  why Africa did Africa encourage evolution more than other areas of the world?

Africa is a continent. It is big! You can find pretty much any biome in the world in Africa (except toundra and taiga if I am not mistaken). Did the specific location where humans lived in Eastern Africa affect their evolution. Yes, the evolution of a population is always affected by its surrounding. For example, the presence of large game was probably a big selection pressure for cooperative hunting (but you can/could find large game everywhere).

It will be near impossible to answer in the general sense. A lot of things happened in human evolution. Even if you tackle down to a single trait, it will be hard to tell you what would have happened if the world would have been different because it was not. (WorldBuilding.SE welcomes questions like "if it was like that what would have happened?").

Origin of Homo lineages

There are a number of named Homo lineages, some of them have not lived in Africa. This include for example Homo floresiensis.


Fossil record of previously thought extinct animals I was watching this video from the Youtubers SciShow titled "7 Animals We Used to Think Were Extinct (But Aren't!)." Some of the extinct animals, were suspected to have gone extinct close to half a billion years ago, which leads me to believe that their fossils were obviously found in layers corresponding to those time periods and not in newer layers; however, since these animals are known to be still present today, I was wondering how it is possible that they do not have fossils in newer layers of the earth. Similarly, What caused the sudden stoppage of fossils?

I know very little about evolution, biology, and fossil records except from what is taught in high-school, and haven't taken a biology course in a few years, so if it is possible to get a simple answer that a biology ignorant person could understand I would greatly appreciate it! Thank you!

https://www.youtube.com/watch?v=e_TjrqWTV5s&t=187s

The formation of fossils is exceedingly rare. A number of unlikely events must all line up for us to find one. So there would be no reason to expect that we would find a fossil of anything but the most common and easily fossilized organisms. The probability of NOT finding a fossil is much greater than finding one.


Histone Deacetylase Inhibition So I am trying to brush up on my knowledge of HATs and HDACs.

I am reading the just the 1st paragraph of the background of this study

I remember learning that HATs turn things on on, and HDACs turn things off.

It says that sodium phenylbutyrate (PB), can epigenetically regulate gene expression by inhibiting histone deacetylase.

Does this mean that one of the effects this drug can have is turning the thing that turns things off to produce the effect of turning it back on? Similar to that of a double negative?

Thanks.

Yes, Sodium phenylbutyrate can upregulate the transcription of silenced genes by inhibiting the activity of Histone deacetylases (HDACs).
Histone acetylation performed by Histone acetyltransferases (HATs) helps in activation of genes, while deacetylation performed by HDACs is responsible for gene silencing. This makes HDACs a potent drug target to treat malignancies.

The inhibitors of HDAC regulate the chromatin structure which loosens the chromatin and hence effect the binding of transcription factors to DNA.  This binding modulates the expression of genes playing role in cell cycle and apoptosis, thus effecting cell growth and differentiation. (Reference)

But this is not similar to double negative. Double negative is term used in embryogenesis, where a particular repressor gene is activated in specific regulatory state. (Reference)


How large is the variability in human bone thickness, and is "big boned" a real thing or not? My girlfriend is arguing that there are "big boned" people, I read some articles that there is no such thing but she still didn't believe in me because she saw some articles too that big boned people exist. Am I missing something and is my girlfriend correct?

I know that some tall people or some people living in Europe or US have of course bigger bones that in some Asian countries because some Asians are really small. However, this is not how most people understand "big boned".

How large is the variability in human bone thickness in persons of the same height? Could this variation mean that a person might appear overweight, when they in reality are only having relatively thick bones (large diameter), so that the expression "big boned" might have some truth to it?

UPDATED

I'm asking about the most people perceive about the "big boned" thingy. Most people (like my girlfriend) sometimes touch chubby people and when they feel like it's not fat, they say "ohh, you're not fat, you're just 'BIG BONED'". I'm asking if there is a real health/scientific basis for that. Personally, I don't believe that 'big boned' is a real thing. However, it's hard to find information about this on the web.

Since the argument with my girlfriend was finished days after this was posted(sadly we were waiting for this but it took so long, we posted this question to have an answer right away) I'll just post here what I conclude about the "big-boned theory" based on searching through internet.

Let me site this link; that says,
"However, the initial findings of this study show that having big bones does not make you fat, being fat gives you big bones". What the link says, having more fats forced our body to increase the size of our bones for it to endure the stress brought by having heavier weight. Which means big-boned really do exists. (Damn lost the argument with my girlfriend because of this link)

Another site that says, "If your scale weight indicates that you’re overweight, it’s most likely because you’re carrying too much body fat.   Not because you’ve got 'big bones'". This site says that we cannot use the "big-bone theory" to reason out being fat. In the article, The heavier weight was caused mostly by fats and not by bones. Also the article says that tall person having 6'2 height will have of course bigger bones that a person with height of 4'2. Also the article says that "Still others definitely seem to have a larger “frame” as evidenced by a larger circumference of the wrist and ankles.  [NOTE:  The wrist and ankle joints typically do not have much fat or muscle, it’s mostly skin and bone.  So a person with a larger wrist would most likely have a larger bone circumference.]" (My girlfriend's face would be so happy to read this)

The last site that I would like to post here have chart to know if you're big-boned or not. The site also agrees that there is big boned

TL;DR

I lost, "Big-boned theory" is real but having heavier weight not mean your big-boned.

P.S. : Also instead of saying "ohh, you're not fat, you're just 'BIG BONED'" to someone just to make their feelings well, you're not doing it right! Just tell them the truth and tell them to do more exercise and have healthy lifestyle. :)


Body's decomposition Does a human body decompose in a completely sterile environment ? If yes, what decomposes it ? And how fast ? What happens in vacuum ? Can it remain exactly the same ?

Thanks

Does a human body decompose in a completely sterile environment ?

No it wont. Unstable molecules like ATP will quickly degrade spontaneously. The stable ones like many proteins and lipids wont degrade spontaneously. Enzymes are essential to degrade them and are to be supplied extraneously.

  What happens in vacuum ?

Body will dry up :P


What is this strange-shaped fruit? The fruit has form of a cube or icosaheder. It is green but quickly becomes black. The meat of ripe fruit is easily separated from the seed, is sweet and tastes as dried plum. The seed has strange icosahedrical form, like two pyramids connected.

The fruit is seen on Mediterranean coast of Israel.

Now I have the answer, and if you are reading this soon after eating the fruit you should probably seek medical attention.

Looks like Cascabela theviata which is in the Apocynaceae and the Wikipedia article makes clear that the fruit is also poisonous.


Laying eggs vs giving birth: is there a connection with internal vs. external ears? I have heard that "The animals who have their 'EARS' outside their body give birth to their young ones and the animals who have their 'EARS' inside their body lay eggs." Is this true? Are there counterexamples?

You are quoting from Imam Ali,

  "The animals who have their 'EARS' outside their body give birth to
  their young ones and the animals who have their 'EARS' inside their
  body lay eggs."

And in short the answer is that is wrong. Giving birth to live young is called vivipary. When a species lays eggs it is called oviparity. There are other mechanisms too.

  Ovuliparity: fecundation is external (in arthropods and fishes, most
  of frogs)

  Oviparity: fecundation is internal, the female lays zygotes
  as eggs with important vitellus (typically birds)

  Ovo-viviparity: or
  oviparity with retention of zygotes in the female’s body or in the
  male’s body, but there are no trophic interactions between zygote and
  parents. (Anguis fragilis is an example of ovo-viviparity.) In the sea
  horse, zygotes are retained in the male’s ventral "marsupium". In the
  frog Rhinoderma darwinii, the zygotes developed in the vocal sac. In
  the frog Rheobatrachus, zygotes developed in the stomach.

  Histotrophic
  viviparity: the zygotes developed in the female’s oviducts, but find
  their nutriments by oophagy or adelphophagy (intra-uterine cannibalism
  in some sharks or in the black salamander Salamandra atra).

  Hemotrophic viviparity: nutriments are provided by the female, often
  through placenta. In the frog Gastrotheca ovifera, embryos are fed by
  the mother through specialized gills. The lizard Pseudomoia
  pagenstecheri and most mammals exhibit a hemotrophic viviparity.

Though it is true that most typically we would associate egg laying with animals with ears "inside" such as birds and snakes, there are some examples that are not this way. Boa constrictors are one species which gives birth to live young rather than laying an egg and being a snake their ears are 'inside their body'. However I should point out that this is Ovoviviparity, not viviparity. For an example of a lizard with viviparity see the Pseudomoia lizard genus.


Is it possible for a person to eat so many carrots that one turns orange? I once read that Jerry Rubin (a famous 1960s activist) ate so many carrots that he turned orange. (This was in the East Bay Express, around twenty years ago.) I assumed it could be true, though he would have to eat hundreds or thousands of carrots; while a close family member thinks it's ridiculous. Is it medically/biologically plausible?

(I hope this question is appropriate to ask here--I'm new to this forum.)

Beta-carotene, the pigment that gives carrots their orange colour, can accumulate in the skin if taken in excess amounts. This condition is called carotenosis. Since beta-carotene is a lipohilic (fat loving: dissolves in lipids), its absorption is facilitated by dietary fats [1].

There is one report that says that excessive consumption of beta-carotene containing fruits and vegetables can lead to carotenosis [2].

Also have a look at this Scientific American blog.

Prince, Martin R., and Joan K. Frisoli. "Beta-carotene accumulation in serum and skin." The American journal of clinical nutrition 57.2 (1993): 175-181.
Wageesha, Nekadage Don Amal, et al. "Studies on hypercarotenemia due to excessive ingestion of carrot, pumpkin and papaw." International journal of food sciences and nutrition 62.1 (2011): 20-25.


Can IVF decrease the probability of trisomy in the fetuses of older mothers? Is trisomy mostly due to complications with fertilization?

If so, does in vitro fertilization reduce the probability of trisomy for the fetuses of older mothers?

If not, can zygotes be screened before in vitro fertilization?

Trisomy is due to non-disjunction in meiosis (the process in which eggs and sperm are created). This happens before fertilization.

Trisomies are more frequently seen in children of older women.  It's not fully understood why this happens, but it is likely related to the fact that the oocytes do not complete meiosis (and become eggs) until ovulation.  Here's an interesting paper that examines the physical causes of non-disjunction, but you might want to read up a bit more on meiosis (depending on your background) before tackling it.

You might screen for nondisjunction, but I don't think it's possible without killing the cells.  See the Wikipedia page on karyotyping, which explains how an amniocentesis might be used for a prenatal genetic diagnosis.  I don't know the regenerative capabilities of the human blastocyst, but if you had enough cells for a test, I don't think the blastocyst would develop normally.


Is this Heracleum sosnowskyi? There's a relatively big scare in local news about the Heracleum sosnowskyi plant, considering how dangerous it can be.

I was strolling through the park when I noticed these plants - the ones I photographed were rather small, but there have been a lot bigger examples in the park as well. For reference, I live in Poznań, Poland.

I have a feeling this isn't Heracleum sosnowskyi, but the only reason I'm thinking this is because it was in a local park where there are a lot of people / kids, and if there were any dangerous plants there there would be an uproar... but I'd rather be sure, thus I'm posting this question.

Is this Heracleum sosnowskyi?

No, I don't think it looks like Heracleum sosnowskyi. To me, the plant in your pictures looks similar to Angelica sylvestris (which is common in Poland), but there are many species in Apiaceae with a similar apparence and I'm not familiar with all of them. Species in the Heracleum genus has leafs that are "lobed" and all leaflets aren't as separated as the plant in your pictures (overall, the leafs of Heracleum look quite different), and the stem is usually "swollen" where the leafs connect (i.e. the leaf stems are swollen). Plants of Heracleum sosnowskyi (and H. mantegazzianum) are also much larger, and they often have a fussy apparence because of the bristle hairs.

Angelica sylvestris (picture from from wikimedia commons)


How does salinity affect the bonds of an enzyme? According to my textbook, "Too much or too little salt can interfere with the hydrogen bonds that hold an enzyme in its three-dimensional shape". I know that NaCl is held together by an ionic bond, meaning that one atom is strongly positive (in this case sodium) and one atom is strongly negative (in this case chlorine). I would guess the polarity of salt has something to do with its effect on hydrogen bonds, which consist of a hydrogen atom which bonds weakly to a strongly electronegative atom, resulting in a similar behavior to its ionization in glass of water, since water molecules are also polar and form hydrogen bonds with one another.

My question is, how exactly does salinity affect the bonds of an enzyme?

Sodium Chloride is not "polar". It is an ionic compound and dissociates into the respective ions in water (because of the latter's high dielectric constant).

Hydrogen bonds are similar to of dipole-dipole interactions (van der Waals) but much stronger and are therefore classified as a separate type of bond. However excess salt can lead to ion-dipole interactions (which are stronger than H-bond) that may prevent the formation of the hydrogen bond.

Ions such as Cl - can act as chaotropes (cause disorder)[ref]. K+ is also chaotropic while Na+ is kosmotropic (reduces disorder). However both Na+ and Cl - affect the entropy of water very slightly. So the effect of NaCl should be mostly due to ion-dipole interactions.


What evolutionary explanations are there for death? I know death and cancer doesn't hurt humans' reproductive success. It's not helping either.

Why do we die? Why dying humans (all of us) are common? What's the point of dying?

Death is not only for humans. All 'complicated enough' organisms die (with a notable exception of Hydra, though you may argue when it comes to the complexity). It is is easier to create a new organism from scratch than to repair both internal factors (free radicals, metabolic by-products, ...) and external (physical damage, exposure to toxins, ...).
Underlying causes of death actually can be evolutionary beneficial. For example, shortening of telomeres offers protection against cancer (on a cellular level), but also bounds lifespan.
So actually they may be evolutionary competition (within the same species) of young and old. Mutations helping young but harming older may be preferred to the opposite ones.


What is the difference between transport proteins and effector proteins in gram-negative bacteria? When considering pathogenic gram-negative bacteria, is there any difference between the function of  transport proteins and effector proteins? Or are they of the same functionality? Any reference would be very helpful.

Is there any difference between the function of transport proteins and effector proteins?

Yes. In this context, the term "effector proteins" refers to proteins that are inserted into a host cell on infection to modulate host cell processes. Effector proteins are inserted into a host cell using a secretion system. The proteins involved in the secretion system are transport proteins, but the effector proteins themselves have a wide variety of functions. They include enzymes, transcription factors, and protein-protein interaction partners, and they have been shown to regulate many host cellular processes, from metabolism, to vesicular trafficking, cell adhesion, and apoptosis.

You can read more about this here.  This review has an interesting perspective, and the Wikipedia page on Bacterial effector proteins isn't bad either.


How much oxygen does a brain consume? I am not a biologist - my background is in quantitative sciences, and I am trying to answer a rather quantitative question:
How much oxygen does a brain consume?
This however raises many sub-questions of purely biological nature:

How is the brain supplied by oxygen? (My naive understanding is that lungs tie oxygen to hamoglobin, which is then carried by blood to cells, which then ingest the oxygen, converting it to ATF. Is this correct? Does this apply to neurons as well?)
How much energy a neuron or the whole brain consumes per unit time? (e.g., per hour, in energy units or oxygen content)

I will appreciate explanations in laymen terms or references to accessible literature.

As has been commented, the answers to some of the questions here can be found in the literature. The nutrients and oxygen reach all tissues by the circulatory system — i.e. in the blood. And the link supplied by @trondhansen suggests a litre of oxygen a day. (I wouldn’t know — I never studied physiology.) However, as regards energy, I supply the following from the biochemistry text, Berg et al.

Brain. Glucose is virtually the sole fuel for the human brain, except during prolonged starvation. The brain lacks fuel stores and hence requires a continuous supply of glucose. It consumes about 120 g daily, which corresponds to an energy input of about 420 kcal (1760 kJ), accounting for some 60% of the utilization of glucose by the whole body in the resting state.

Note the correct form of expression:

the brain  / consumes fuel / to generate energy / to perform ‘work’

Glucose is the fuel, ATP is the chemical energy currency, and the work performed (as the text makes clear) is for the main (60%–70%) to:

maintain the sodium/potassium ion membrane potential required for the transmission of the nerve impulses.

(I am afraid that’s about as layman’s terms as I do. It does say on the label that this site is for students of biology.)


Estimation of cell count of E.coli culture Can I get some help with an estimation of a cell count in a culture of E.coli cells if we assume we begin with $10^6$ cells, that they divide every 30 minutes and they are incubated for 12 hours?

I do not know how to do the calculation with a start number that is not 2, if it was it would just be $2^{24}$. But how is it done when the starting number of cells is $10^6$?

Is it $(10^6)^{24}$?

Thank you!

You start with $10^6$ cells. After 30 min they double, so there are $2⋅10^6$ cells. After another 30 minutes they double again, so there are $2⋅2⋅10^6$ or $2^2⋅10^6$ cells. After three doubling periods, the number of cells is $2^3⋅10^6$. Doing this, the equation for exponential growth should become evident. All you must do now is determine the number of doubling periods in 12 hours.


Do conservation oriented genetic database exist? Are there any projects for the creation of the international genetic database of all endangered species, so we, at least, have a chance to clone them in the future if our current conservational efforts fail?

First, it isn't entirely clear to me why you would want such a database.  Essentially all sequences are available in one (typically all) of the big databases.

For example if I search the NCBI database for "extinct" I get this.  There will be many more sequences for species that are "only" endangered.

Second, having a genome sequence isn't sufficient for "de-extinction" of a species.  The reasons for this are beyond the scope of this question, but can be explored starting from this section of the wikipedia article.

You will likely also find this discussion to be of interest.


Where can I find SARS-CoV-2 genome sequences for the UK? I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not seem to have any UK ones either. I'm still waiting for my logon for Gisaid - looks like they may have some. Is there anywhere else I can try?

Oxford University's Bugbank project is designed to collect SARS-CoV-2 samples (and other microbial cultures) from UK Biobank participants for sequencing. Once completed this data will be available to researchers through the UK Biobank:

  We originally developed this system as a pilot study to determine the feasibility of prospective microbiological culture collection from UKB participants to create a microbiological biobank (‘bugbank’) for joint studies of epidemiological, human genetic and pathogen genomic risk factors for infection. In light of the COVID-19 pandemic, we have repurposed the system to provide near-to-real-time data on SARS-CoV-2 positive and negative test results for UKB participants.

Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank (2020) *

* Disclaimer: I have worked on this project.


İrreversible dopamine antagonist vs. Dopamine agonist Can a dopamine agonist reverse the effects of an irreversible dopamine antagonist?

No. Irreversible antagonism is, by definition, inhibition that cannot be reversed by the agonist. Let me summarize the basics. You can read about this in Goodman and Gillman's The Pharmacological Basis of Therapeutics, Chapter 3, but there are many basic biochemistry textbooks that will cover the same ground.

When an interaction between a ligand and a receptor is said to be reversible, it means that it can associate to form a ligand receptor complex, and then dissociate, leaving the system with free ligand and free receptor. In the most general case, when the ligand is bound, it changes the conformation and activity of the receptor, and when it dissociates, the receptor returns to its original conformation and activity. The effect of the ligand in the biological system is related to the proportion of bound receptors.

Irreversible ligands typically involve covalent bonding (e.g., aspirin, alkylating agents). When the ligand interacts with the receptor, it irreversibly alters the conformation and function of the receptor. Cell or tissue function is only returned to the free receptor state when the particular receptors that have had a ligand receptor interaction have been degraded and replaced by a new receptor.

One of the ways to test whether an interaction is reversible is to try to reverse it. Let's look at how you would do this.

Start by looking at the effect when an agonist binds. The agonist is reversible. When you add it to an assay that contains the receptor, it associates and dissociates from the receptor, but at any moment, some proportion of receptors is bound to agonist. This binding produces an effect you can measure. The effect is related to the overall proportion of receptors bound to agonist at any given time, which is related to the concentration of the agonist. When you increase the concentration of an agonist, more agonist binds and you can measure a greater effect. In this figure from Goodman & Gillman Chapter 3, you can see the log concentration of the agonist on the x axis and the effect measured in an assay on the y axis:

Now consider the effect of an agonist in the presence of an antagonist. Classically, a competitive reversible antagonist binds the same site as an agonist. When the antagonist is bound, it doesn't allow the agonist to bind. So run the same experiment as you did above (by increasing the concentration of the agonist and measuring the effect), but start with a solution that contains some fixed concentration of antagonist. Because an antagonist is competing for those same binding sites, there will be fewer receptors available for agonist binding, fewer receptor/agonist complexes, and a smaller effect.

If the antagonist is reversible, though, you can still get the same effect you got in the first experiment. You just have to increase the concentration of the agonist until it binds the same proportion of receptors. Since both agonist and antagonist are constantly associating and dissociating with the receptor, increasing the concentration of one of them will out compete the other.  In this figure (same source), you can see that in the presence of an antagonist (here, i, for inhibitor), it requires more agonist to get the same effect, but the maximum effect is still the same.

If the antagonist is irreversible you can't get the same effect you got in the first experiment, even by increasing the concentration of the agonist. The receptors have been permanently altered by the presence of the antagonist, and whatever portion of them had some interaction with the antagonist will either not bind the agonist, or will not produce an effect when bound. What you see in the assay here is that increasing the agonist concentration in the assay may increase the measured response, but you are unable to reach the same maximum response. Note here, the figure describes a pseudo-irreversible inhibitor (antagonist). This is just a term for an irreversible inhibitor that doesn't covalently bind the receptor, but has a strong enough affinity for the binding site that, based on the measurements, it looks like it covalently binds. Effectively, the inhibitor is going to sit there on the binding site until the receptor is degraded and will not be outcompeted by the agonist.