Quinone A, Quinone B, Ubiquinone, Plastoquinone: whats the difference? I am getting very confused about this. My understanding so far is that ubiquinone is used as an electron (and proton) carrier in oxidative phosphorylation in the mitochondria whereas plastoquinone is the carrier in the light dependent reaction in photosynthesis in chloroplasts. My guess is that these carriers are similar because it is a highly conserved carrier that was present in many of the original life forms (including those that formed chloroplasts and mitochondria).

My first questions are:

is the above distinction correct?
do we find ubiquinone and plastoquinone elsewhere in cells, other than in mitochondria and chloroplasts, or in other prokaryotes?

Then I am not sure about quinone a and b. My lecturer said that quinone b is present in photosystem II and it accepts the two electrons from the lysis of H2O and then it accepts two H+ ions from the stroma to enter the membrane of the thylakoid

But I have also read that it is plastoquinone which shuttles the H+ ions in the thylakoid membrane in the form of plastoquinol. So could it be that quinone B turns into plastoquinone on accepting the electrons, and plastoquinone accepts two H+ ions to form plastoquinol?

If so, how is the quinone B from photosystem II replenished?

Difference between Ubiquinone (UQ) and Plastoquinone (PQ)
Structural Difference: Structurally, UQ and PQ are very similar. They only differ in a methyl group and 2 substituents on the benzoquinone ring (Liu et al, 2016). See the image for comparison:

Functional Difference: Functionally, PQ and UQ are very different. I'll give some differentiation points:

PQ is located on thylakoids of chloroplasts (Millner et al, 1984), whereas UQ is located primarily on the inner membrane of mitochondria, though it is found in all cells and membranes (Turunen et al, 2004).

Half-life of PQ is 15 hours while that of UQ is 30 hours in spinach cells (Wanke  et al, 2000).

UQ10 influences expression of hundreds of human genes involved in different cellular pathways, and UQ10-mediated gene-gene networks are involved in inflammation, cell differentiation, and peroxisome proliferator-activated receptor signaling (Schmelzer et al, 2011).

On the other hand, the redox state of PQ pool controls the NADPH dehydrogenase complex activity and further influences on cyclic photosystem I (Ma et al, 2008).

Although UQ has more widespread effects than PQ, most of their effects are restricted to their corresponding organelles i.e. UQ mostly influences mitochondrial activity whereas PQ mostly influences chloroplast activity. This can be understood on the basis of endosymbiotic theory since mitochondria appear to be related to proteobacteria whereas chloroplasts appear to be related to cyanobacteria (Mereschkowski et al, 1905). These two are thought to be taken in by cells about 1.5 billion years ago. We can suppose that at that time, both these organisms had similar carrier molecules (since they are very crucial for metabolism). This can justify why UQ and PQ are so similar in structure. Thus, your way of distinction can be considered as correct.
Difference between Quinone A (QA) and Quinone B (QB)
Structural Difference: In many cases, both QA and QB are structurally identical. For example, both QA and QB are ubiquinone-10 in Rhodobacter sphaeroides (Laszlo et al, 2004). Thus, the main difference between the two is functional difference.
Functional Difference: The distinct physical properties of QA and QB, including redox potential, are controlled by interactions with the binding site environment. Studies have shown that the 3-methoxy oxygen of QB interacts with the reaction center backbone (specifically amide of GlyL225). This interaction pattern serves to break the symmetry of neutral UQ between QA and QB by locking the 2-methoxy dihedral angle of QB in a position conducive to electron transfer from QA to QB (Vermaas et al, 2015). In short (not going in further details), QB interacts with the amino acid residues in reaction center in such a way that QA and QB acquire large difference in redox potentials. Apart from this, since QB is more loosely attached to the membrane, it is easily detached on being reduced to QH2 for transferring high energy electrons taken from QA to cytochrome bc1-complex8.
Thus, it is hard to differentiate QA and QB on structural basis, although QB and QA have different redox potentials due to different environmental conditions. Also, it is hard to tell whether QA and QB are structurally similar in all organisms; it is only known that they both are UQ10 in Rhodobacter sphaeroides. So, there is no simple answer (yet) on whether QB converts to plastoquinone or not. But since, in Rhodobacter, QA and QB are UQ10, thus it is not possible to convert QB to plastoquinone by this species. On the other hand, in a photosynthetic bacterium Rhodopseudomonas viridis, both QA and QB are plastoquinone molecules (Deisenhofer et al, 1994). Here, there is no need of conversion of QB to plastoquinone since it is already a plastoquinone. This finding only strengthens the fact that it is not easy to give a simple answer on whether conversion of QB to plastoquinone actually takes place or not. A much similar reaction center, from a thermophilic cyanobacterium Thermosynechococcus elongatus, looks like this (Ferreira et al, 2004; Loll et al, 2005; Umena et al, 2011):

Talking about replenishment of QB, when QH2 reaches the cytochrome bc1-complex, it is oxidized back to QB. This oxidized QB can again participate in the process of transfer of high energy electrons. Thus, QB easily gets replenished in cyclic photophosphorylation.
References:

Liu M, Lu S. Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering. Frontiers in Plant Science. 2016;7:1898. doi:10.3389/fpls.2016.01898.

P.A. Millner, J. Barber, Plastoquinone as a mobile redox carrier in the photosynthetic membrane, FEBS Letters, Volume 169, Issue 1, 1984, Pages 1-6, ISSN 0014-5793, http://dx.doi.org/10.1016/0014-5793(84)80277-X.

Mikael Turunen, Jerker Olsson, Gustav Dallner, Metabolism and function of coenzyme Q, Biochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1660, Issues 1–2, 28 January 2004, Pages 171-199, ISSN 0005-2736, http://doi.org/10.1016/j.bbamem.2003.11.012

Wanke M., Swiezewska E., Dallner G. (2000). Half-life of ubiquinone and plastoquinone in spinach cells. Plant Sci. 154 183–187. 10.1016/S0168-9452(00)00200-4

Schmelzer C., Niklowitz P., Jürgen G., Okun J. G., Haas D., Menke T., et al. (2011). Ubiquinol-induced gene expression signatures are translated into altered parameters of erythropoiesis and reduced low density lipoprotein cholesterol levels in humans. IUBMB Life 63 42–48. 10.1002/iub.413

Ma W., Deng Y., Mi H. (2008). Redox of plastoquinone pool regulates the expression and activity of NADPH dehydrogenase supercomplex in Synechocystis sp. strain PCC 6803. Curr. Microbiol. 56 189–193. 10.1007/s00284-007-9056-x

Wikipedia contributors. "Symbiogenesis." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 26 Mar. 2017. Web. 14 Apr. 2017.

Laszlo Rinyu, Erik W Martin, Eiji Takahashi, Péter Maróti & Colin A Wraight (2004). Modulation of the free energy of the primary quinone acceptor (QA) in reaction centers from Rhodobacter sphaeroides: contributions from the protein and protein–lipid(cardiolipin) interactions. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1655, 93 - 101.

Vermaas JV, Taguchi AT, Dikanov SA, Wraight CA, Tajkhorshid E. Redox Potential Tuning Through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides. Biochemistry. 2015;54(12):2104-2116. doi:10.1021/acs.biochem.5b00033.

Wikipedia contributors. "Photosynthetic reaction centre." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 22 Oct. 2016. Web. 14 Apr. 2017.

Yocum, Charles Photosynthetic Reaction Centers, Univ. of Mich. 5 Sept 2008. Web. 14 Aug 2014


Why hypothyroidism causes body ache? In the condition of hypothyroidism the Thyroid Stimulating Hormone level is high in individuals. What signalling/metabolic pathway mediates this sensation of pain which is mostly experienced in feet and joints.

This isn't my field, and I'd love to see my answer surpassed by someone with expert knowledge.  But I should say a recent case report (Pantazis, 2016), though it dealt with an unusual situation, discusses some of the current thinking:

hypothyroidism is characterized by decreased synthesis and degeneration of collagen. Hypothyroidism also inhibits epimerase, which results in reduced chondroitin sulfate and elevated hyaluronic acid, hence weakening the matrix. Moreover, it causes accumulation of glycosaminoglycans (GAGs) in the extracellular matrix (ECM), being involved in the pathogenesis of carpal tunnel syndrome during hypothyroidism and predisposing patients to tendon calcification

THs have known effects at the cellular level on the proliferation and differentiation of bone and cartilage. The hypothyroid state appears to induce abnormalities in these tissues, which results in such clinical manifestations as epiphyseal dysgenesis, aseptic necrosis, possibly crystal-induced arthritis, and an arthropathy characterized by highly viscous non-inflammatory joint effusions primarily affecting the knees, wrists, and hands. Neuropathic and myopathic symptoms accompanying hypothyroidism may manifest as joint region abnormalities when in fact there is no underlying arthropathy.

These paragraphs cite three much older sources.  I don't see a tremendous amount of activity on this narrow issue in PubMed - the broader issue that this case illustrates is whether there are better ways of diagnosing and treating hypothyroidism to restore the balance more effectively; see Midgeley, 2019 for example.


How much time does it take a human body to replace all of its atoms? Mikel Vsauce (Vsauce youtube channel) said in his video that it takes about 5 years for the body replace all of its atoms, while in asapscience youtube channel they are claiming that it takes 10 years. I am confused and I can't find anywhere the precise time it takes.

Mikel's video (minute 1:14)
AsapScience video (minute 1:07)

Not all the atoms in the human body are replaced.

Carbon atoms in tooth enamel are not replaced after the enamel is laid down during tooth development. This was demonstrated in the 2005 Nature article "Forensics: Age written in teeth by nuclear tests", where the researchers showed that the amount of carbon-14 in tooth enamel can be used to accurately determine date of birth.


How does heredity work with Endogenous retrovirus? Q1: If someone in a species gets infected with an endogenous retrovirus, does that mean that absolutely all of their children will have that endogenous retrovirus? Or is it based on chance?

Q2: is there such a thing as an allele for the virus being there, and for it not being there? How does it work?

Q3: how can an endogenous retrovirus disappear from a species? And when it cannot disappear?

For a provirus to be heritable, the infection must occur in the germ line. The initial integration would occur at one site in the genome and thus the locus could be described as hemizygous. Inheritance would indeed be probabilistic, depending on whether an offspring inherits the provirus-containing chromosome or its uninfected homolog.

Eventually, the endogenous retrovirus (ERV) can become fixed or lost in a population by genetic drift and natural selection. Additionally, retrotransposition and, more importantly, reinfection can greatly increase copy number and allow ERV persistence despite a lack of fixation at specific loci. It should also be noted that more recently acquired ERVs exist that have not reached fixation in humans.

References and Further Reading:

Boeke JD, Stoye JP. Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements. In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997.

Belshaw R, Pereira V, Katzourakis A, Talbot G, Pačes J, Burt A, Tristem M. 2004. Long-term reinfection of the human genome by endogenous retroviruses. Proc Nat Acad Sci 101(14):4894–4899.


Why it is important to vaccinate a human newborn within 24 hours since birth? In Poland a newborn has to be vaccinated within 24 hours against hepatitis B and tuberculosis.

As I understand it is good to be vaccinated against both, I do not see the need to hurry so much.
Hepatitis B is transmitted sexually or by blood. The former vector is definitively unsuitable for a newborn, and the latter... Well, I do hope so far all Polish hospital adapted to Ignaz Sammelweis advice on antiseptics.
In case of BCG vaccine against tuberculosis (containing alive bacteria) there would be an additional risk if the newborn's immune system were in any way impaired which is unknown within first 24h. It is not that tuberculosis is common disease in Poland - is endemic (probably due to the obligatory vaccination indeed).

What possible biological benefits are there to vaccinate a newborn so early? Especially which of them prevail over possible risks of BCG vaccination?

In the US, infants are vaccinated against Hep B at birth and again a month or two later as well, because of the risk of maternal transmission. If the mother is known to be HepB positive, HBIG will also be administered.

  Perinatal HBV transmission can be prevented by identifying HBV-infected (i.e., hepatitis B surface antigen [HBsAg]-positive) pregnant women and providing hepatitis B immune globulin and hepatitis B vaccine to their infants within 12 hours of birth.

The reason for the HBIG is obvious, but it doesn't last for life. Therefore, the vaccine and its booster.

  Hepatitis B virus (HBV) infection in a pregnant woman poses a serious risk to her infant at birth. Without postexposure immunoprophylaxis, approximately 40% of infants born to HBV-infected mothers in the United States will develop chronic HBV infection, approximately one-fourth of whom will eventually die from chronic liver disease.

In countries where HepB is not prevalent, there is little cause to immunize at birth. However, it is too common in the US.

  Preventing perinatal HBV transmission is an integral part of the national strategy to eliminate hepatitis B in the United States. National guidelines call for the following:
  - Universal screening of pregnant women for HBsAg during each pregnancy
  - Case management of HBsAg-positive mothers and their infants
  - Provision of immunoprophylaxis for infants born to infected mothers,   including hepatitis B vaccine and hepatitis B immune globulin
  -Routine vaccination of all infants with the hepatitis B vaccine series, with the first dose administered at birth

The risk of HepB vaccine is low. The seriousness of the disease is high. It is not only the mother who might be a carrier. There are many unidentified carriers in the US. That makes the risk-to-benefit ratio low. Driving your newborn home in an automobile is probably more of a risk than the vaccine, but most people do so anyway, and do so many, many times over the course of the baby's life.

In the US, we do not routinely vaccinate against TB, so I cannot address that issue with any degree of expertise. The risk-to-benefit ratio is not as low as for HepB. It is given to children who are continuously exposed to someone (say, a parent) with active TB, or in certain communities where TB is very prevalent. Obviously, if the risk of SCID (severe combined immunodefficiency) is high, the risk of the vaccine is much higher, and some infants have died from it.

Discussing the risk to benefit ratio of all infant vaccines is too broad for this venue.

Separating Fact from Fiction in the Newborn Nursery: Hepatitis B Vaccine for Newborns
The benefits and risks of bacille Calmette-Guérin vaccination among infants at high risk for both tuberculosis and severe combined immunodeficiency: assessment by Markov model


What hydrolyses aspirin within the digestive tract and blood stream? I have had some further thoughts after my previous question regarding the buccal delivery of medication.  The active compound in aspirin (acetylsalicylic acid or systematically 2-Acetoxybenzoic acid)  is salicylic acid (2-hydroxybenzoic acid).

I understand that the hydrolysis reaction occurs as follows within the stomach - therefore in the body it is an acid hydrolysis:

N.B. The H2O is not shown in the diagram.

However having done this experimentally I know that in the lab to ensure a decent yield of salicylic acid I had to reflux the solution for several hours.  Yet the onset of action of aspirin tablets is much faster than this.  To me this suggests some enzymatic activity, but I have no idea which enzyme this is likely to be.

To follow on directly from my previous question, if the aspirin is absorbed directly into the bloodstream bypassing the stomach then what causes the hydrolysis in the blood stream and is it the same factor that increases the rate of hydrolysis in the stomach if the medication were to be taken orally?

Acetylsalicylate deacetylase is the enzyme responsible for this reaction.

  Precisely, the present investigation reveals that the hydrolysis of aspirin in liver, kidney and probably other tissues of
  rats is catalyzed by two highly substrate specific microsomal
  esterases, ASA esterase I and II active at acidic and slightly
  alkaline pH, respectively. The findings that ASA esterases have
  distinct organ distribution pattern and display responses to
  various inhibitors/activators that are different in many respects
  from those exhibited by cholinesterase and nonspecific carboxylesterase suggest that the latter esterases probably do not play
  a significant role in the hydrolysis of aspirin.

  From:
  Ali B, Kaur S (1983) Mammalian tissue acetylsalicylic acid esterase(s): identification, distribution and discrimination from other esterases. J Pharmacol Exp Ther,226,589-594


Are animals that live in areas where avalanches happen equipped to deal with that? Humans take courses to learn how to assess the risk of avalanches and how to deal with it. Additionally, they often use special gear to survive avalanches if they got caught in the middle of one.

What about animals that live in these areas like mountains with snow where avalanches occur (maybe wolves, deer, etc.)? Are they somehow aware of the risk? Do they handle it in any way (e.g. avoid especially steep regions) or able to manage getting out of it?

Most animals are not well adapted to deal with avalanches. For example, more mountain goats are killed by rock slides than by predators. http://www.nationalgeographic.com/lewisandclark/record_species_150_11_2.html

Meanwhile, a mountain at risk of snow avalanche must be deep in snow, right? At that point, there is very little food to be found; it's all buried. So there won't be many animals on the surface. Most of them would leave for more hospitable locations, or hibernate.


Why does ALS start in middle age? Amyotrophic lateral sclerosis (ALS) often starts at middle age, but I didn't find any suggestion why. Something seems to trigger the symptoms in middle age.

If I am not mistaken, the sporadic ALS is not genetic, but there are genetic variants. So these genes are with the person all his life. But why do the disease symptoms often start only in middle age?

Short answer
The causes of ALS are not well known. Some familial types are associated with toxic proteins, susceptibility to toxins and defective protein metabolism. My personal 2-cents is that metabolic and toxicologic defects tend to cause cumulative tissue damage over time, perhaps explaining the delayed onset.

Background
Amyotrophic lateral sclerosis (ALS), is a progressive, fatal disease characterized by the gradual degeneration and death of motor neurons.

In 90 to 95 percent of all ALS cases, the disease is sporadic, meaning that it appears apparently at random. Individuals have no family history of ALS, and their family members are not considered to be at increased risk for developing it.

About 5 to 10 percent of all ALS cases are inherited. About one-third of all familial cases result from a defect in a gene known as “chromosome 9 open reading frame 72,” or C9orf72. The function of this gene is still unknown. Another 20 percent of familial cases result from mutations in the gene that encodes the enzyme copper-zinc superoxide dismutase 1 (SOD1). In case of mutations in the SOD1 gene it is though that mutant SOD1 protein is toxic.

Other inherited forms are believed to change in the processing of RNA, that may lead to ALS-related motor neuron degeneration. Other gene mutations implicate defects in protein recycling. And still others point to possible defects in the structure and shape of motor neurons, as well as increased susceptibility to environmental toxins.

Source: NIH - ALS Facts Sheet


Stability of helical strands of DNA? The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). This means that the two strands are very highly negatively charged. What than stabilizes the double helix, preventing the natural electrostatic repulsion between the two strands?

[I am assuming that the phosphate groups are dissociated under physiological pH, correct me if I am wrong.]

There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as the ionic strength of the buffer is reduced (by increasing the repulsive force relative to the favourable energy term coming from the base-pairing).

When DNA is condensed these repulsive forces are masked by cations like spermine, and of course by histones.


Why is oxygen used up in eutrophication? This probably sounds pretty dumb, but wouldn't algae blooms produce a lot of oxygen? Although they would die out and decomposers would use up oxygen, is that more than what the algae produced?

Algae produce O2 in the upper layer of water but when they die they stop producing O2. They sink to the seafloor and most get decomposed by bacteria on the seafloor. In this process, bacteria use O2 contained in the bottom layer of water which decreases the dissolved O2 concentration in the bottom water.

These concepts (and much more!) are well described in the excellent open-access paper by Rabalais et al. (2010) Dynamics and distribution of natural and human-caused hypoxia. It also includes case-studies of areas affected by hypoxia and eutrophication around the world. A must read if you're interested in this topic!


Oxygen balence from growing plants for food I had thought photosynthesis and respiration where pretty much Oxygen and Carbon neutral per calorie.

http://news.mit.edu/2014/technical-feasibility-mars-one-1014

  If, as the project plans, crops are cultivated within the settlers’ habitat, Do found that they would produce unsafe levels of oxygen that would exceed fire safety thresholds, requiring continuous introduction of nitrogen to reduce the oxygen level.

Says that a closed system of plants grown to provide calories for human will end up with more oxygen.

Where does the imbalance come from? Where does the extra Carbon go?

If oxygen and respiration were carbon and oxygen neutral, there wouldn't be free oxygen at all. Plants would just respire all the oxygen they produce.

The extra carbon goes into the plants themselves. It isn't just what they use for energy, it is also what they are made of.

See also this question:

Are plants really oxygen neutral?

Plants are oxygen neutral when we take into account the decomposition of the plant, i.e. take the long-term view where the carbon making up the plant gets back to being CO2.


Please identify this moth from Bangladesh Sorry for bad resolution of the picture. This picture is taken from JU campus, Savar.

I think I have found the identification. It is a planthopper from ricaniidae family. Most likely Ricanula stigmatica.

Image source: https://en.m.wikipedia.org/wiki/Ricanula_stigmatica


How did giant sauropods satisfy their daily energy needs, considering their relatively small mouths? Gigantic sauropod dinosaurs had relatively small heads (and consequently small mouths) in comparison to their overall body mass.

In the book "Dinosaur Odyssey: Fossil Threads in the Web of Life" (by Scott D. Sampson) the author says (on pp. 218-219) that

  The sheer size of the biggest sauropods has long shrouded them in
  mystery. How could such gigantic animals with such small heads (at
  least compared to their body sizes) manage to consume enough food to
  sustain themselves? The mystery deepens when we look inside the
  mouths of sauropods. Cows are typical of big mammalian herbivores
  (e.g. elephants, deer, antelope, and the like) in possessing oversized
  teeth well suited for processing large amounts of fodder. Chewing
  serves not only to break food-items into bite-size chunks' it also
  grinds up the plant matter and begins the process of digestion by
  making the bits of vegetation more susceptible to chemical attack. By
  comparison, sauropods have puny teeth well suited to tearing or, at
  best, slicing, but not for grinding.

(emphasis added)

I don't remember Dr. Scott providing an explicit answer to the question "How could such gigantic animals with such small heads (at least compared to their body sizes) manage to consume enough food to sustain themselves?" but somewhere in the book he did mention that the earth's ecosystem may have been rather different back then.

However, since the book came out nearly a decade ago, I was curious on whether any other findings have been made since then.

How did sauropods manage to consume enough food to sustain themselves? Was it because of some differences in the ecosystem that are now lost?

Unlike mammals, saurischian dinosaurs don't have to chew their food. Like birds they have a gizzard to do that instead.

Look at a modern ostriches: they have a very small head because the head is only used to gather food not process it. Mammals process food in the head (chewing) so the head has to be large to support the muscles, teeth, and other apparatus for this. On the other hand, birds and sauropods use stones in the gizzard to grind up their food, so all that space is taken up in the torso instead of the head.  Ornithischian dinosaurs, which do chew, have large heads just like mammals.

Additionally since the mouth is not occupied chewing the time that would be lost chewing can be spent feeding instead. This can be a lot of time a cow spends 8 hours a day just chewing.

Source


Fruit identification - What is this green long fruit? I found this fruit in the South of France, but I have no Idea what it is. It's a green, hard fruit. I tried to cut it to see the inside (on the following pictures).
It fell from a big tree, but I don't remember much information about it.

Thanks in advance!

Could it be a Ceiba speciosa pod? We have a lot of Silk Floss trees near where I live and they grow these types of pods. When they are fully developed, they burst open and are filled with cotton-like floss and dark seeds. I have never seen an unripe one opened up, but it definitely looks like the ones on the trees. The trees themselves are easily identifiable as well. They are large with greenish trunks that have thorns growing along the surface. Also, if you had previously seen the tree with large pink-purple flowers, that would be a good indication.
https://en.wikipedia.org/wiki/Ceiba_speciosa


About modern dating techniques In a comment to this question, it was said that

  Radiocarbon dating won't work. For a start the tree needs to be dead, which since you're not using the rings I'm assuming it isn't. Also the atomic testing in the 20th century completely messed up the level of C14 in the atmosphere, so radiocarbon dating can't be used for anything that didn't die 70 years ago or more.

I did not know this. So, what kind of dating techniques biologists use today? :-)

In order to date the age of a tree, you have three solutions :

If you can cut the tree then you can simply count the number of rings. Note that for very old trees the central rings will have rotted and you will only have a lower bound on its age.

If some parts of the tree are dead, you can use radiocarbon dating to estimate the time of death with a relatively bad precision (the error is about 100 years which can be a lot for a tree)

You can estimate its growth rate (either using the width of the rings, or by doing multiple measurements for several years), and deduce the age from its size.


Identification of Sunbirds Location: Asansol-Durgapur region, West Bengal, India
Question:
Do they belong to the same species?
Note:

I presume the bird in Pic-1 is a male  Purple-rumped sunbird (Leptocoma zeylonica).
I think the birds in Pictures : 2-5 could be non breeding male Purple sunbird (Nectarinia asiatica) because they match very much with the Wikipedia description though the bird in Pic-2 has a short tail.
Pic-4 and Pic-5 capture the same bird.

The bird in Picture-1 is  Purple-rumped sunbird (Leptocoma zeylonica) according to this decription from wikipedia:

  The males have a dark maroon upperside with a blue-green crown that glistens at some angles, bright green shoulder patch and violet/purple rump patch which is generally hidden under the wings. The underparts are whitish with dark throat, maroon breast band and purple/violet patch in the throat which is visible in some angles.

The birds in Pictures 2-5 is a single species, non-breeding male of purple sunbird (Cinnyris asiaticus) according to this description:

  The male is glossy metallic purplish black on the upper parts with the wings appearing dark brown. The breeding male has the underparts also of the same purplish black, but non-breeding males may show a central streak of black on yellow underparts.

References:

Wikipedia
r/whatsthisbird


Why are there so many species of bats? I read that roughly 20% of all species of mammals are bats. Is there a good explanation for why bats have diversified so much compared to other mammals? Is it because bats' ability to fly allows them to fill niches that are completely out of reach (pun intended) of other mammals? If so, how is this reconciled with the coexistence of bat populations and bird populations?

Indeed, good question. There's tiny bats, large bats, and so many different species of them! A clue can be found in the observation that each bat species is almost always restricted to a small geographical region. With this in mind, it has been shown that an animal lineage's ability to diversify quickly in new environments depends largely on its diet. Bats have an incredible variety of dietary sources. Plant nectar, insects (there's so many different kinds of insects...), blood-feeding, and more! So, as you can imagine, bat species are restricted because they have specialized diets and because they are very good at taking up new diets over evolutionary time. Unfortunately for them, it restricts them to a geographical location much of the time. Geographical restriction is always a good starting point for speciation events, and there have been many in the bat clade. But why bats, specifically, you might ask? Well - it is argued (below) that it is due to the characteristics of their skulls, rather than their wings.

Dumont, E. R., Dávalos, L. M., Goldberg, A., Santana, S. E., Rex, K., & Voigt, C. C. (2012). Morphological innovation, diversification and invasion of a new adaptive zone. Proc. R. Soc. B, 279(1734), 1797-1805.


Why do T cells have MHC II receptors? I have seen the answer to this question which says that T cells do not express MHC II proteins which would make sense.
However, my textbook "The immune system" by Peter Parham disagrees. It says that T cells do gain MHC II receptors after activation.

*Activated T cells express MHC class II molecules, whereas resting T cells do not.

I cannot see why this is needed. MHC II molecules are for CD4 cells (helper T cells).
If the T cell presenting the antigen was a CD4 cell, then that seems useless, because this cell was already the one that could recognise this particular antigen - so why show it to others? The chance that another T cell that could recognise it too would be incredibly small no?
I guess I can see the merit of a CD8 T killer cell to show the antigen, as it could alert other CD4 T cells to come assist (although cytokines seem like a better method...)
So what is the purpose of T cells, in particular CD4, of showing MHC II proteins?

That's the description in my book which has the same image.
The book is: Janeway's Immunology (9th Edition)
Article discussing MHC Class II expression in humans:
https://doi.org/10.4049/jimmunol.168.2.763
Excerpt from the book:

The processing and presentation of pathogen-derived antigens has two
distinct purposes: inducing the development of armed effector T cells,
and triggering the effector functions of these armed cells at sites of
infection. MHC class I molecules bind peptides that are recognized by
CD8 T cells, and MHC class II molecules bind peptides that are
recognized by CD4 T cells, a pattern of recognition determined by
specific binding of the CD8 or CD4 molecules to the respective MHC
molecules (see Section 4-18). The importance of this specificity of
recognition lies in the different distributions of MHC class I and
class II molecules on cells throughout the body. Nearly all somatic
cells (except red blood cells) express MHC class I molecules.
Consequently, the CD8 T cell is primarily responsible for pathogen
surveillance and cytolysis of somatic cells. Also called cytotoxic T
cells, their function is to kill the cells they recognize. CD8 T cells
are therefore an important mechanism in eliminating sources of new
viral particles and bacteria that live only in the cytosol, and thus
freeing the host from infection.
By contrast, MHC class II molecules
are expressed primarily only on cells of the immune system, and
particularly by dendritic cells, macrophages, and B cells. Thymic
cortical epithelial cells and activated, but not naive, T cells can
express MHC class II molecules, which can also be induced on many
cells in response to the cytokine IFN-γ. Thus, CD4 T cells can
recognize their cognate antigens during their development in the
thymus, on a limited set of ‘professional’ antigen-presenting cells,
and on other somatic cells under specific inflammatory conditions.
Effector CD4 T cells comprise several subsets with different
activities that help eliminate the pathogens. Importantly, naive CD8
and CD4 T cells can become armed effector cells only after
encountering their cognate antigen once it has been processed and
presented by activated dendritic cells.


Name/term for mechanisms by wich the relative size/number of cells of some tissue/organ are preserved The cells of some organ or tissue are dividing and also dies (apoptosis). But this happens in somehow controlled manner so that the total size of the organ is approximately preserved or the total number of cells approximately stays the same. As far as I understand, this is somehow collective process, because cells in one side of the tissues should somehow coordinate the division/apoptosis processes with the cells of the far side. I have read in one book about cells, that such controlling mechanisms are purely undesrtood even today. Of course, such mechanisms work only approximately (or - to be more precise - they are more complex than just static preservation of the size/number), e.g. numberadipose cells can increase with time.

But anyway - my question is - what is the name/term for such controlling mechanisms and what are other important keywords/terms which I can use for searching more research papers about this theme?

I have specific interest in the control of those processes, e.g., with the aim to bound those processes for adipose cells and to encourage those processes for the muscle cell.

"cell cycle control" and Hippo-pathways mechanisms can be the answers, but I am still searching for the matter.

'Eutely' is the term used for organisms with a fixed number of somatic cells. I'm not aware of any term for sub-organismic structures.


Why are some housekeeping genes considered better? Whenever a PCR is done, we have to use housekeeping genes like GAPDH, to self normalise the values to account for different starting cDNA/DNA. Now there are many different genes like GAPDH, ubiquitin, actin etc.

Now when dealing with cells, I can understand that due to their immortal nature and frankly shocking number of generations undergone by them, the expression of the housekeeping gene may change.

Assuming that I am not dealing with cells and instead with animal tissues, does it matter which house keeping gene I select? Or in other words is GAPDH going to give me the same consistency between samples as something like 18s Ribsomal RNA or am I missing something specific?

Yes, it does matter. Gene expression varies a lot thoughout tissues and living conditions, so you need to test a variety of genes and choose the ones with the smallest variation in the expression between sample and control.

If you don't find any, you have to test other genes for this purpose. This is important, as this can severly affect the outcome of your experiment, since you normalize to the housekeeping genes. If these are not constant, it will cause problems. Have a look into the references, this helped me a lot.

References:

Accurate normalization of real-time quantitative RT-PCR data by
geometric averaging of multiple internal control genes.
The normalization of gene expression data in melanoma: investigating
the use of glyceraldehyde 3-phosphate dehydrogenase and 18S
ribosomal RNA as internal reference genes for quantitative real-time
PCR.
Normalization of qRT-PCR data: the necessity of adopting a
systematic, experimental conditions-specific, validation of
references.


Why in acute phorpyria? I am having confusing about treatment of phorpyria . I read it somewhere that for treating phopyria hemin and glucose is given IV . Please give me an easy explanation of it

Since porphyria is not one disease but many, I suppose that with "acute porphyria" you mean acute intermittent porphyria. The reason of the disease is an autosomal dominant mutation on the enzyme porphobilinogen deaminase, an enzyme that converts porphobilinogen to hydroxymethylbilane by a deamination reaction.

Now the heme is produced in many steps, and the enzyme above is important in the early steps of heme synthesis. In persons with porphyria, these heme precursors accumulate, causing toxicity. In acute porphyria the symptoms are mostly from the central nervous system. The figure under shows the steps of the biosynthesis of heme, and as you see at the upper right corner, defect in the enzyme porphobilinogen deaminase (PBG-deaminase) results in accumulation of porphobilinogen.

Glucose and other carbohydrates can help suppress disease activity, are given by vein or by mouth, and are part of initial treatment. Intravenous heme, however, is both more specific and effective than glucose and should be started if the patient’s symptoms fail to improve within 36 hours.http://www.porphyriafoundation.com/about-porphyria/types-of-porphyria/AIP [2015-05-02]

More about carbohydrates and the suppression of symptoms in porphyria http://www.porphyriafoundation.com/about-porphyria/diet-and-nutrition/the-glucose-effect-in-acute-porphyria [2015-05-02].


How to decide which is the correct scientific name for a particular species To start with, I am not a person having sound knowledge in biology. When I started my search for phyto-chemicals in a particular family in the plant kingdom, I got confused. The scientific papers use a particular name, and when I searched in these 2 websites, (just to name it) I got the message that some of the names are  "not resolved"  or "synonyms".

My questions are

Biologists do they accept  the names mentioned in  website 1? If not where can I find authentic names?
Who controls / monitors the name of these plant species?

When it comes to plants and animals, common names clearly differ from region to region.

A first effort to univocally classify them was done in the 16th century by Carl Linnæus (see my answer to this question for some historical background).

The nomenclature of plants is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN), and for animals from the International Code of Zoological Nomenclature (ICZN).

The fact that there are rules, however, does not imply that names are conserved over time, nor that there is a rule for everything!

As time goes by rules change, certain species may be assimilated by others, or a certain subspecies will separate and become its own, and at times name changing proposals even raise havoc in the scientific community.

In summary, it is important to remember that taxonomy poses rules that are there to facilitate talking about science. Those are not absolute rules, sometimes they are arbitrary, and therefore for certain species there is no univocal name (and surely there is no correct name).


Why don't protons diffuse out of the mitochondria during chemiosmosis? If the outer membrane of the mitochondria is very permeable, how do mitochondria maintain a proton gradient by pumping protons into the intermembrane space? Wouldn't they just diffuse into the cytosol?

Diffusion, is by definition (Ficks Law) describing movement along or against some gradient (here its concentration) even if the mechanism of transport differ: active, passive, facilitated. The setup of the electrochemical gradient across membrane, like any thermodynamic process is not perfect, there are always entropy losses. In this case, this manifests as the the diffusion of protons away from the membrane (one source, there are others). Note the connection between entropy of system (Mitochondria) and diffusion (the inefficient process) in this positive feedback process. I think its interesting as someone learning about this stuff to make these connections.

Recalling protons are being delivered freely into the environment (inter membrane space) by Electron Transport Chain. Some protons will diffuse away from membrane surface before they can be pumped back in since these highly charged species cannot passively diffuse back in. The chemiosmosis process, which is sustained by the energy input to drive ATP synthase, depends on maintaining a strong concentration gradient (separation) of H+ on either side of membrane. Since the outer membrane of the mitochondria is porous, it means the protons are free to diffuse out, and will do so because it is entropically favorable. This relationship is best described by $\ce{\Delta G = RTln(K)}$. Where $\ce{K=\cfrac{[B]}{[A]}}$ for a process $\ce{A \rightleftharpoons  B}$

Where A= Protons near membrane, B= protons diffused out. Having established that thermodynamically they (protons) will diffuse out[3]. It begs the question will they actually reach the outer membrane in a reasonable time.

Of course over long enough time they will. But over some meaningful scale like 1 second, the proton pump rate of ATP synthase, 100s-1 [5], how far can a proton get ideally?.
Back at the envelope calculation (ignoring any resistance effects from solvent, path, etc.) and using some approximate values (for yeast proteins and mitochondria):

From Fick's Rate Law, R,
$ \sqrt[3]{R} = \sqrt[3]{ D A \cfrac{[H^+]_c - [H^+]_m}{d}} = 14 \mu m $

So in 1 s an average proton ideally can diffuse 14 micrometers from the inner membrane, driven by difference in pH between membrane and cytosol. I think i maybe be fair to presume that based on this the mitochondria is leaking protons into into its near surroundings constantly. (for scale the mitochondria is about 100nm).

Hope that was helpful

VALUES:

Thickness of mitochondria,$d$, equal 0.014 $\mu m $ [4]

$\ce{[H^+]_m }$ at membrane = $\ce{-log[H+] = 10^(-6.8),  [H+] = 10^(-6.8)}$ [6]

$\ce{[H^+]_c }$ at in cytosol = $\ce{[H+] = 10^(-7.40)}$

Diffusion coefficient of H+ in aqueous media $D$ = 7000 $\mu m^2$ [2]

A (surface area from which diffusion is taking place) I set to 0.025 $\mu m^2$ (guess from average unit cell of crystallized structure of ETC Complex II in yeast).

REFERENCES:

D. Nelson & Cox (2012). Lehninger, Principles of Biochemistry, 6th Ed
https://esc.fnwi.uva.nl/thesis/centraal/files/f1163457446.pdf
http://www.ncbi.nlm.nih.gov/books/NBKhttp://www.atpsynthase.info/FAQ.html
http://www.ncbi.nlm.nih.gov/pubmed/9245766
http://www.atpsynthase.info/FAQ.html
http://jgp.rupress.org/content/139/6/415.full


What distinguishes Mendelian Inheritance from Non-Mendelian Inheritance? I'm having some trouble determining what exactly is the difference between Mendelian inheritance and non-Mendelian inheritance. For instance, I understand that chromosomal abnormalities such as Down's Syndrome fall under non-Mendelian inheritance because they concern chromosomes, not single genes. And I also understand that Mendelian inheritance concerns single genes, as in Sickle-cell anemia (which is an autosomal recessive disorder).

What confuses me is the fact that our textbook discusses dihybrid and trihybrid (concerning 2 genes and 3 genes, respectively) crosses under the Mendelian inheritance chapter, when to me it seems like these crosses are non-Mendelian because they deal with multiple genes. However, Gregor Mendel did in fact use the dihybrid cross to deduce the law of independent assortment, so I'm completely confused. Could someone please clarify this for me? I'm afraid that I'm maybe misinterpreting something.

You can discuss multiple genes within the framework of Mendelian inheritance; what you're probably thinking of, though, is the fact that Mendelian inheritance doesn't recognize the idea of multiple genes that contribute to a single trait.

For example, if there is a gene that controls petal color (blue vs. white, with blue = dominant) and a gene that controls height (short vs. tall, with tall = dominant), then Mendelian inheritance predicts that two short plants with white flowers will only produce short plants with white flowers.

But if there are multiple genes that interact to determine height in a complex way, that's outside the scope of Mendelian inheritance.


Preparation of normal DNA polymerase i don't need Taq polymerase. Just need normal DNA polymerase. So the main idea is preparation polymerase directly from Lactobacillus without using cloned vector. My idea is electrophoresis using agarose gel and calculating the isoelectric point of Polymerase based on protein sequence to know where they will migrate after electrophoresis. Is it possible for this idea ?

This is a very ambitious project for a DIY-er. To explain why, I'm going to use the example of DNA polymerase I from E. coli.

DNA polymerase I is the most abundant DNA polymerase in the E. coli cell, but nevertheless is still only present at around 300 copies per cell

  Ishihama Y et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics. 9:102.

This was the first DNA polymerase that was ever purified, in the laboratory of Arthur Kornberg

  (Enzymatic Synthesis of Deoxyribonucleic Acid : I. PREPARATION OF SUBSTRATES AND PARTIAL PURIFICATION OF AN ENZYME FROM ESCHERICHIA COLI Lehman, MJ et al. (1958) J. Biol. Chem. 33:163-170.).

In this paper a method of purification is described that starts with 60 litres of culture. There is also this statement:

  "One kilo of E. coli yields less than 10 mg of the purified enzyme."

I'm guessing that you have no experience of protein purification, so I'll just tell you that this is very discouraging: these days, with overexpression, people expect to get mg quantities of their protein from just a few grams of bacterial cells.

This is a clear illustration of why it is pretty much unthinkable for you to set out to purify an enzyme like this using small-scale methods, and explains why techniques of overexpression and the use of affinity tags have revolutionised protein purification.

And it gets worse: even if you did manage to purify some DNA polymerase I from a bacterial source you would find that it is actually not very good at making DNA. This is because as well as extending primers in a 5'>3' direction, it is is very good at degrading DNA in the same direction. In other words as the enzyme moves along a template molecule, copying it, it will degrade any existing DNA that it meets "ahead" of its direction of travel. This is why the most commonly-used form of this enzyme in research is the "Klenow fragment", a fragment of the polymerase that lacks the 5'>3' exonuclease activity. This fragment was originally made by treating DNA polymerase I with the protease subtilisin, but it is now expressed from an engineered polA gene. Klenow fragment polymerase was used in the original PCR experiments (it had to be added afresh at every cycle).

I don't know how much money you have to spend on your projects, but in fact these enzymes can now be bought relatively cheaply.  I don't think that you can expect to make them for yourself, without this becoming the actual project.

Finally, if you can get hold of a strain of E. coli with an expression plasmid for Taq polymerase then you really could make your own very easily - I've done this myself (but I no longer have the strain) and the heat stability of the enzyme makes the purification trivial. It would be much easier to use your own Taq with a heated water bath than to try to make DNA polymerase I. But obviously it depends upon what you are trying to do: Taq polymerase may be unsuitable for other reasons.


Dimerization of Immunoglobulin G I would like to know the specific determinants for formation of IgG dimers. My understanding is the stem of the antibody is a homodimer of two heavy chains, covalently bonded through two disulfide bridges called the hinge region. Is there any association between the constant region? My reading would suggest no but I have not found a specific reference as such.

For human IgG1 and 4, the only inter-heavy chain disulfide bonds are the two in the hinge region. IgG2 has 4 disulfides in the hinge, and IgG3 has 11:

There are intra-heavy chain disulfides in the Fc region, and of course there are non-covalent bonds between the two heavy chains (as well as the light chains) to maintain structure, but aside from the hinge region the only other inter-chain disulfides are between heavy and light.

Here is an interesting review of classical (determined in the 1960s) and non-classical (more recently discovered) disulfide bond formation and structure in human IgGs.


Does increased cell turnover cause cancerous mutations? If a certain set of cells or tissue are undergoing a lot of reproduction and repair cycles for some reason, does this inevitably lead to cancerous growths? If the mutation rate exceeds the normal 'background' mutation rate for the tissue will these extra mutations eventually cause cancer?

As user Luke said below; does an increased rate of replication increase the rate of mutations.

Increased cell turnover indirectly leads to cancer. Below is a direct quote from Human Molecular Genetics, 2ed. Chapter 9: Instability of the human genome: mutation and DNA repair.

Mutations can be induced in our DNA by exposure to a variety of mutagens occurring in our external environment or to mutagens generated in the intracellular environment. In the case of radiation-induced mutation, for example, Dubrova et al. 1996 reported that the normal germline mutation rate for hypervariable minisatellite loci was doubled as a consequence of heavy exposure to the radiaoctive fallout from the Chernobyl accident. However, under normal circumstances by far the greatest source of mutations is from endogenous mutation, notably spontaneous errors in DNA replication and repair. During an average human lifetime there are an estimated 10^17 cell divisions: about 2 × 10^14 divisions are required to generate the approximately 10^14 cells in the adult, and additional mitoses are required to permit cell renewal in the case of certain cell types, notably epithelial cells (see Cairns, 1975). As each cell division requires the incorporation of 6 × 10^9 new nucleotides, error-free DNA replication in an average lifetime would require a DNA replication-repair process with an accuracy great enough so that the correct nucleotide was inserted on the growing DNA strands on each of about 6 × 10^26 occasions.
Such a level of DNA replication fidelity is impossible to sustain; indeed, the observed fidelity of replication of DNA polymerases is very much less than this and uncorrected replication errors occur with a frequency of about 10^-9 to 10^-11 per incorporated nucleotide (see Cooper et al., 1995). As the coding DNA of an average human gene is about 1.7 kb, coding DNA mutations will occur spontaneously with an average frequency of about 1.7 × 10^-6 -1.7 × 10^-8 per gene per cell division. Thus, during the approximately 10^16 mitoses undergone in an average human lifetime, each gene will be a locus for about 10^8-10^10 mutations (but for any one gene, only a tiny minority of cells will carry a mutation). In many cases, a deleterious gene mutation in a somatic cell will be inconsequential: the mutation may cause lethality for that single cell, but will not have consequences for other cells. However, in some cases, the mutation may lead to an inappropriate continuation of cell division, causing cancer (see Chapter 18).

Here is another great paper that specifically addresses your question, linking increased cell division with the accumulation of both significant and insignificant mutations, which over time, lead to an accumulation of mutations needed for cancer to develop.


(Genetics) Is a silencer the same as gene silencing (heterochromatin)? Is silencer the same as gene silencing?
I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a silencer. Are they the same? Or is silencer an opposite of enhancer (repressor)?

You are a bit confused with your terms here. Remember, when you are talking about natural regulation of a transcriptome, you can control it at the level of the genome, transcriptome and the epigenome.

The Repressor protein is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. Depending on where it binds, it regulates at the level of the genome or transcriptome.

The Gene Silencer Region, is a DNA sequence in the geneome that  that allows repressor proteins to bind to it. It is usually very near the promoter of the gene that it wants to control. This controls the expression of the gene at the level of the genome to repress the transcription of the gene. There exists a few types (Classc silencers, negative regulators and polycomb response) but lets not get into that).

An example is the regulatory element in the classical Lac operon.

Gene Silencing as you call it is epigenetic in nature. I'll point you towards the wiki as it is quite big and diverse to explain it here:
http://en.wikipedia.org/wiki/Gene_silencing

you can read more about it here:http://www.ncbi.nlm.nih.gov/books/NBK26872/


What happens to the human ear as it naturally goes deaf? I was always told that when the human ear goes deaf to a specific sound (auditory frequency), then that sound is heard one last time, and upon fading away, will never be able to be heard again.

Is this in fact true? If so, why do we hear that sound (which seems to happen randomly and is somewhat loud for a split second) just before the ear becomes deaf to it?

Ultimately speaking, what exactly happens as the human ear naturally goes deaf?

Hearing loss is caused by different things, but your probably thinking of age-related hearing loss.

When people go deaf, it is be because "hair cells" in the ear break.

This breakage results from overly loud frequencies, or just random damage to cells over a lifetime.

If your last remaining hair cell that is tuned to a certain frequency after all the other ones have died gets killed somehow, it will depolarize and send an action potential to your brain telling it to hear that sound.

But that would be a very faint sound, since only one or a couple hair cells die off.

But in reality, it usually isn't that you hear a sound for the last time before going deaf, you have a faulty premise hear!

it's NOT like the ubiquitous "seeing the light" that happens when your heart stops.


Is the Hypothalamus part of the Central Nervous System or Endocrine System Sorry for a certainly naive question.
Some references (for example https://faculty.washington.edu/chudler/nsdivide.html) seem to to indicate that the hypothalamus is part of the Central Nervous System. Others (for example http://kidshealth.org/teen/your_body/body_basics/endocrine.html) place it in the Endrocrine System. I would have said it is part of both, but then I read the two systems are distinct. Could anyone explain me to which one it belongs and why?

Thanks,

Gilles

CNS refers to the brain and spinal cord. Its a very general term. Hypothalamus is part of the CNS structure but its unique in a sense that it secretes many chemicals into the bloodstream like glands hence part of the endocrine system! so they are both correct!


How do tea, coffee, and beer dehydrate you? For the long time I am trying to find out if the following is truth: They say that some beverages dehydrates. I heard that about tea (sometimes green, sometimes black, sometimes both), coffee, beer and more (for example coke).

How does hydration from these sorts of drinks compare to others (e.g. water)? Why do these drinks less efficiently hydrate?

Diuretics
These drinks contain minor diuretics. Caffeine is the diuretic found in tea and coffee. Alcohol is the diuretic in beer. Diuretic substances increase the amount of urine produced i.e causes dehydration. This is often offset by the water content of mild diuretics like tea, coffee, and alcoholic drinks.
Tea, coffee, and coke
Caffeine belongs to the xanthines, and inhibits re-absorption of Na+ by cells, and increases flow rate of filtered fluid through the kidneys. This reduces water content in your body. In other words diuretics do dehydrate you, specifically caffeine will. Coffee, coke, and tea (very low doses of caffeine) are mild diuretics.
Beer
On the other hand alcohol is an anti-diuretic hormone inhibitor that inhibits arginine vasopressin.


What is the big plant with white flowers on the photo? What is the 3m tall plant with white flower? It is from Central Europe and there is a creek near to it. I have a guess, but I want to know for sure...

Is the small one the same species?

More high res photos here:

https://ibb.co/cAaUMU
https://ibb.co/ih4Zo9
https://ibb.co/eJSyFp
https://ibb.co/gstS89
https://ibb.co/kQ2OWU

They both look like poison hemlock (Conium maculatum).  It can grow up to 3m tall and grows in moist areas including along creekbeds. One of it's common names is European Hemlock.  It is toxic to some domestic animals and humans.

Source: United States Department of Agriculture

Source: http://natureid.blogspot.com/2011/11/poison-hemlock-111211-elkhorn-slough.html


Would anything limit an "invasive species" T. rex introduction now besides equilibration with available prey or intervention by humans? In the video Two-and-a-half billion T. rex roamed Earth, study finds contains a short explanation of the results in Science Absolute abundance and preservation rate of Tyrannosaurus rex by the corresponding author of the paper.
I'd like to understand better what is known about T. rex's adaptability and range of environments where it was thought to flourish. It's hard to imagine what things were like back then, so using modern flora/fauna and climate distributions as reference points will help me to understand this better.
Based on that knowledge and reference frame, I'd like to ask about the following Gedankenexperiment:
Question: Would anything limit an "invasive species" T. rex introduction now besides running out of food or intervention by humans?
Would they basically thrive over much of the Earth's surface and eat all the other mammals? Or without a supply of dead and rotting dinosaur cadavers would these giant scavengers with excellent olfaction quickly deplete a small region and die of starvation?
Currently there is not likely enough DNA to reconstruct a full genome nor a scheme to build and incubate a dinosaur egg for it (as far as I know), so we are not at any risk of this happening in the near future.

Lots of things could impact a reintroduced invasive species.

Disease/sickness: although no close relatives are present that is not a guarantee,  many diseases jump species. Parasites likewise could cause problems, especially newer parasites the dino may not have a good defense for. Even modern Fungus could pose a problem for eggs.

Predators: While an adult t-rex is predator proof eggs and newborns are not. Rats and other small mammals as well as many birds have been the demise of many ground nesting birds.

Poisons: there are plenty of animals and plants that are poisonous enough kill a t-rex that the rex may not recognize as dangerous. Remember there are a lot of things around a t-rex did not evolve with. This is more dependent on location, a t-rex dropped in Australia might kill itself with its first meal.

Human stuff: I am not talking about humans killing them. I am thinking of the things humans make killing them. things like walking into power lines, eating weird plastic human garbage, car accidents ( a car moving at speed could easily cripple a rex), even something as simple as getting hit by trains


How to identify genes? You and me are different at DNA level. My eye color gene is different from yours. So, my DNA is different from yours. How can a scientist identify a certain gene in a chromosome (and its function) if chromosomes are different? How can we talk about "the" human DNA when nobody share the same (except twins)? Please, this is a practical question about how scientists identify genes, not a philosophic one (a question that bother me every time I read about discoveries in genetic)

First of all: We are not very different on the genetic level - the identity is somewhere around 99.6 to 99.9%. See here for details. If this wouldn't be like this, things like blood transfusions or organ transplants wouldn't work.

To identify genes there are different routes. "In the old days" (meaning before the possibility of massive high throughput sequencing or DNA microarrays), genes were usually discovered when they were connected to a disease which had a noticable phenotype. Researchers then tried to find out which protein or pathway was affected and from there went backwards to identify the genetic region. This way of discovery was relatively slow. An example for this kind of identification is the identification of the Mitf gene which is important for the development of pigmentation.

If you sequence DNA (doesn't matter here if these are complete genomes or only parts of it) you can identify genes based on homology with already known genes. You can also predict the presence of genes in a certain sequence based on regulatory sequences in the region before the gene (the promoter). These sequences are known and also highly conserved, so this gives a good estimate. Predicted genes usually need to be verified experimentally.

What is done today are the so called "genome wide association studies". Here you take a big cohort of people which all share one phenotype (for example blue eye color). Then you take a second group of people which do not show this phenotype and analyse their genomes (usually by sequencing or SNP genotyping). Then you compare the two groups to find the differences. Ideally you can then more or less directly identify a causative mutation which is responsible for the phenotypic difference between the two study groups. This usually needs also to be verified further.


What kind of fish did I see in waters off a tropical island in the Philippines? Found this while diving in the southern Philippines.

This is a Blackspotted puffer, Arothron nigropunctatus a commonly found fish on coral reefs in the Philippines. Although this species has a large color variation, the photos provided show common coloration (white body with black spots, a large black area around the dorsal ray). The white strip above the mouth is also a commonly found characteristic of this species, along with a face and snout that resembles a dog.

CC- Attribution - Photo by John E. Randall


What is this colourful insect with a large thorn? Someone sent me the picture so I don't have a lot of details. Is it a real insect or is it fake?

As @Kiritee mentioned this is actually a treehopper, due to thier unusual shape they are of long interest of naturalists.
This is a female Umbonia crassicornis.
Here's a female with her colourful nymphs captured by
C. D. S. Molinari
.

Facts:

The females have a pointed pronotal horn (spike), the males' are blunt, with a flat top.

The adults display variation in colour and size.

The pointed pronotal horn is an adaptation as the insectivorous birds mistake them as thorns (on stem) and do not consume them.

This is a variable species as to size, color and structure, particularly the pronotal horn of males (which is more angled posteriorly than the females' and often somewhat expanded apically).
This tall, essentially perpendicular thorn-like pronotum discourages birds and other predators from eating it, if only by mistakenly confusing it with a thorn.
Typically, the adult is green or yellow with reddish lines and brownish markings.
The range of this species is from Northern South America all the way to Mexico and Florida. Its preferred hosts are ornamental and fruit trees of subtropical regions.

Parental care: The females on sensing an intruder would rush to her nymphs and would charge the offender by kicking her legs, fanning her wings and sometimes even buzzing. The females communicate with the nymphs to ensure that they are in a group.
References:
Encyclopedia of Land invertebrate behaviour, Encyclopedia of Insects and Libraries of life

Picture References:

A female with eggs.
Two males (blunt top)
Original size

Good reads:

Thornbug to Thornbug-The inside story of insect song

Libraries of life (audio clips)


Identify Huge Mystery Beetle It is around 2 inches long, one inch wide, fat, hazel coloured with black specks and has short antennae. It's got a lot of cobwebs on its legs, since I found it in a corner in my house. It was found in North America.

It's a female Eastern Hercules beetle (Dynastes tityus). Unlike the male, the female doesn't have 'horns' as it doesn't need to fight in order to find a mating partner. It's the largest and heaviest beetle in North America. It belongs in Scarabaeidae or scarab beetles.

Source from BugGuide.com


Is it true that newborn babies don't produce tears while crying? Why? Well, I was just going through an article on eye, where in fun facts it was mentioned that newly born (for initial 1 to 3 months) babies do not produce tear while crying. Actually, I have found this true.

Now, I am wondering why is it so? Does any one know the reason behind this?

It is not completely true.  Babies develop the lacrimal system at 42 days, in utero.  The canals and ducts for tears are formed at 60 days [2].

At birth, tear production by the lacrimal gland is minimal. Normal tearing develops several days to 2 weeks after birth.[1]

Some 6% of newborns are born with a tear duct obstruction (in some online articles it stated up to 10%, but I think my source is more reliable).  The child still produces tears, but they can well up on the eyelid [2].
Other more serious abnormalities can cause this problem.  Duct cysts or hemangiomas can also cause tear duct blockages in more severe cases.  Various factors, such as anatomical abnormalities and problems with pumping tears increase the propensity for the disorder in children with Trisomy-21 [2].  As nico has alluded to in the comments, there may be a lag in the development of the physiology of tear production even in non-Trisomy-21 children.

[1] Thomas K. McInerny, MD, FAAP, ed. 2009. American Academy of Pediatrics Textbook of Pediatric Care. Elk Grove Village, IL. American Academy of Pediatrics, p1706.
[2]M. E. Wilson et al. (eds.), Pediatric Ophthalmology, 2009, pp. 276-284.  DOI 10.1007/978-3-540-68632-3_1.


Will sperm cells exhibit chemotaxis towards sucrose? I was wondering if sperm cells will exhibit chemotaxis towards sucrose? One of my friends told me that sperm cells die in presence of salts. So I guess sperms will move away from salt. Can someone give me any reference related to this area.

UPDATE (Answer for why sucrose?):

So I should have made things more clear. I was thinking to do an experiment by taking some sperm cells and its effects on sugar and salt and then to see it under a foldscope microscope. Since I am not a biologist, I wanted some guidance. The common available substances which came to my mind was sugar and salt.

If you google "sperm chemotaxis sucrose" you learn some things of interest. Notably, wikipedia's article on sperm chemotaxis indicates that the important chemoattractants for sperm (the things that attract sperm via chemotaxis) are various signaling molecules given off the by the egg.

It is not clear why you would necessarily think that sucrose would attract sperm or that salt would repel them. In the first case (sucrose), it is not obvious why sperm would expect to see sucrose. If I remember correctly, sucrose is actually pretty rare in animal physiology except as an energy source in plants that animals eat; and sucrose is largely broken down into monosaccharides before it even leaves the small intestine, so it's not like it's circulating in the body. For instance, a lab protocol for studying animal sperm chemotaxis suggests adding sucrose as a densifying agent that doesn't interfere with chemotaxis, suggesting that sperm are pretty independent of sucrose. In the second case (salt), it is not obvious that sperm would necessarily avoid the things that kill them. Those things may be correlated with doing their job! Most sperm cells are expected to die in the human reproductive strategy.

In plain terms: there are huge numbers of sperm which are competing really hard with each other to find and fertilize an egg, not to find sucrose or to avoid salt. The chemotaxis that sperm exhibit will tend to help them accomplish this goal. So it seems (according to wikipedia) that they follow the signals that say 'egg', not the ones that say 'sugar'.

Update:
Sorry, only just saw update on Q. Thanks for the clarification- sounds like fun! I've been curious about the foldscopes.

If what you want is to do an experiment, then I think you've actually got a great start with knowing first that salt interferes with their motility. That is a control experiment, e.g. the very first thing you should do, to make sure that the world works the way other people say it should. (First rule of experimental science: never trust anyone!). Look up a protocol which suggests a sperm-inhibitory concentration of salt (ideally kosher salt, not table salt which has a bunch of other stuff like iodine in it). Put sperm in that concentration of salt and then also in a medium where they should show chemotaxis (the protocol I linked to could be helpful here). See if you can reproduce the salt inhibition, ideally in a medium that is otherwise identical to the medium that allows chemotaxis.

Next, try other stuff. Unfortunately, chemoattractants are probably proteins/small molecules you can't buy at the supermarket. But you could try to get creative. I can't ethically recommend that you try to find a human source, because that gets weird pretty quick, though it is the obvious suggestion (I assume you are talking about human sperm). Potentially there is an animal source for such things which isn't too expensive.

However, you could say to hell with chemoattractants and chemotaxis, and try to just understand sperm motility. You could try other osmotic shocks, with simple cheap chemicals like glycine. It looks like there is some literature that calcium ions affect sperm motility. Or you could play with pH, using vinegar or lye, or temperature. I bet that all of those affect sperm motility (probably for the worse). Or you could try the effects of various weird hippie herbs from the health food store. It sounds like you are just looking for an easy, fun experiment, and if that's your goal then I suggest you try a bunch of things and see what happens. That way you're more likely to find something interesting.

If what you want is a more elaborate experiment, then I think it is worth your time to sit down and try to read up on how sperm work, and then design an experiment that really clearly tests a hypothesis. I am not an expert here, but the Yoshida article I link to looks like it has a good literature review.

Hope that helps.


How do I determine this logistic growth model formula? The Question

  Two yeast cells were placed into a special container to which food was
  continually added, to keep it at a constant concentration. All other
  factors were set for optimal yeast growth (for example, temperature,
  oxygen, and pH). The population was sampled every hour for 21 hours
  and the results of the estimated population size were recorded in the
  table below.

  Time (hour), Number of yeast cells

  (0, 2) (1, 10) (2, 15) (3, 20) (4, 40) (5, 60) (6,
  100) (7, 190) (8, 260) (9, 350) (10, 450) (11, 530)
  (12, 580) (13, 600) (14, 600) (15, 600) (16, 600) (17,
  600) (18, 600) (19, 600) (20, 600)

  What population growth model does the population appear to follow?
  Write out the mathematical equation it follows.

The Attempt

Looking at the values, I recognize the carrying capacity is reached at hour $13$ with $600$ cells, signifying a logistic growth model. The formula given to me for logistic growth is:

$\frac{dN}{dt} = rN[\frac{(K - N)}{K}]$

From what I have researched:

$dN$ = population size change
$dt$ = time interval
$r$ = (max) growth rate
$N$ = starting population size
$K$ = carrying capacity

So:

$dN = 600 - 2 = 598$?
$dt = 21$ hours
$r = $?
$N = 2$
$K = 600$

Plugging the values in gives me:

$598/21$ = $r2[(600 - 2)/600]$

Update 25/01/19

With some help, I have discovered how to determine the r/rmax value and have the following formula:

$r = (90+100)/2$
$r = 95/hour$

$dN/dt = 95N[(K - N)/K]$

With $N= 2$

$dN/dt=95(2)[(K-2)/K]$

and if $K$ value is carrying capacity, $K = 600$

$dN/dt=95(2)[(600-2)/600]$
$dN/dt=190(598/600)$
$dN/dt=190(0.997)$
$dN/dt=189?$

However, the question asks me to "Write out the mathematical equation it follows." So am I supposed to leave a value unknown?

The growth of the yeast can be studied with a Logistic model (i.e. differential equation) as follows:
$$
\frac{dX}{dt}=\mu X \left(1 - \frac{X}{X_{max}} \right)
$$
This is an ordinary differential equation that tells you how the population of yeast is changing with time (in fact is telling you how the concentration of Yeast $X$ changes with time).
The two parameters in the equation are the specific growth rate $\mu$ and $X_{max}$ the carrying capacity following the Verlhust model.
We could also write the equation following your notation:
$$
\frac{dN}{dt}=r N \left(1 - \frac{N}{K} \right)
$$
where $r (\mu)$ is the specific growth rate, $K (X_{max})$ is the carrying capacity, and $N$ is the number of elements in the population.
Note that this is a dynamic model that you need to solve (i.e. integrate the differential equation) to be able to compare with your experimental data. This model tells you how any population of this time behaves not only your Yeast in the mentioned experiment.
The solution of this model is the following Logistic equation:
$$
N(t) = \frac{K}{1+\frac{K-N_0}{N_0}e^{-rt}}
$$
Where $N_0$ is the initial number of Yeast cells.
If you fit this equation (i.e. with least-squares) you get the following values for your experiment (with their 95% confidence intervals):
K =       603.6  (594.3, 612.9)
N0 =      2.108  (1.179, 3.036)
r =      0.6729  (0.6196, 0.7262)
And the following curve.

$r$ is the growth rate (in $hr^{-1}$) that is related with the doubling time by the following formula:
$$
t_d = \frac{ln 2}{r} = 1.0301 hr
$$
Check also this answer about growth models


Probability of all alleles represented in a sample I'm trying to wrap my head around some formulas presented in the 1992 paper from Chakraborty Sample Size Requirements for Addressing the Population Genetic Issues of Forensic Use of DNA Typing, but I have not been able to.
Specifically, the right hand side of formula (16) and it's relation with formula (13).
$1-\sum\limits_{i=1}^{k}(1-p_{i})^{2n}$ (13)
$[1-(1-p)^{2n}]^{r}\geqslant1-\alpha$ (16)
Formula 13 indicates the probability, for a locus with $k$ segregating alleles whose frequencies are contained in the vector $p$, that all alleles are represented in a given sample of size $n$, and the right hand side of formula 16 indicates the probability of $r$ alleles to be represented in a given sample of size $n$.
First of all, why, based on 13, the expression inside the summation indicates the probability of an allele of frequency p, to remain unobserved in a sample of size n?
I tried to understand this from the Hardy-Weinberg equation but did not have any success.
Second, Why to take the expression in (16) to the r'th power?
Which biological concepts am I missing?

I'm going to strictly answer the questions, rather than step through the proof, because it involves a lot of formatting that I'm not familiar with.  Other folks are welcome to edit this!
Equation 13
This equation assumes a diploid genotype, given by the $2n$ power with $n$ individuals.  For anything with greater ploidy than mono-, it's mathematically simpler to determine the probability that an allele is not present.  As an example, see this calculation of a triploid Hardy-Weinburg equilibrium equation.  Using this simplification,
$P(single$ $allele$ $not$ $present)$ $= (1$ $- P(allele$ $present))$ ^ $(ploidy)$ ^ $(n)$
$= (1$ $- P(allele$ $present))$ ^ $(ploidy$ * $n)$
With $k$ segregating alleles, each allele has its own non-presence probability.  The probability of total non-presence is $1 - (sum$ $of$ $P(each$ $non$-$presence))$
Equation 16
In this equation, the author describes the probability that all alleles are present at a given frequency.  These allele presences are independent of each other and therefore multiplicative.  Since $P(allele$ $present)$ is vectorized, this product can be simplified to $^r$


Are there any ways to force DNA-origami to create a geometric shape from non-nucleotides (not from DNA)? I mean, can we create with the help of DNA-origami figures that would not consist of DNA, but, for example, carbon? Is it even possible?

I interpret your question to ask this:
Can DNA origami be used as scaffolds for the guided assembly of other non-DNA structures?
Yes.  From what I've read, two- and three-dimensional DNA structures can be used for nanoparticle assembly and as a nucleation factor in the crystallization of proteins and minerals.  You can find these examples and more in a lengthy review from 2017.1  Specifically, read section 6.6, Programming the Structure and Conformation of Non-DNA Materials.

Fan Hong, Fei Zhang, Yan Liu, and Hao Yan. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem. Rev. 2017, 117, 20, 12584–12640.


Which of the two mitochondorial membranes relate to bacteria according to the endosymbiotic theory? I seached for endosymbiotic theory in Wiki and I found this about endosymbiotic theory:

  Symbiogenesis, or endosymbiotic theory, is an evolutionary theory
  which explains the origin of eukaryotic cells from prokaryotes. It
  states that several key organelles of eukaryotes originated as
  symbiosis between separate single-celled organisms. According to this
  theory, mitochondria and plastids (e.g. chloroplasts), and possibly
  other organelles, represent formerly free-living bacteria that were
  taken inside another cell as an endosymbiont, around 1.5 billion years
  ago.

But I couldn't find any answer for my question, so I decided to ask:

According to this theory and differences between inner and outer mitochondria and plastid membranes, which membranes (outer or inner membranes) of mitochondria and plastids (e.g. chloroplasts) relate to bacteria?

And why do mitochondria need to have a double membrane?

The inner membrane is that of the engulfed bacteria. The bacterium would have been phagocytosed by a larger cell. Hopefully you can see in this image the smaller cell being engulfed in the membrane of the larger cell:

[ source ]


Why do fat people and thin people get hungry at the same time? Say a fat person and a thin person take breakfast at the same time. Around lunchtime, they'll both be hungry. Why? After all, the fat person theoretically has lots of body fat the body can consume instead, so the fat person does not have to feel hungry.

I am not sure your statement is true, fat and thin people may not always get hungry at the same time. You cannot simply compare these two categories as they contain subcategories including people "feeling hungry" because of disorders related to their mental health, physiology, diseases,...

The term you are looking for is "appetite regulation" and reading the wikipedia page will give you an overview of this subject and why your question is too broad to be answered. https://en.wikipedia.org/wiki/Appetite#Regulation


How much natural genetic variation is there between bacteria of the same species? There are lots of questions about how and why there is genetic variation between organisms of the same species, but I haven't been able to find a numerical value for the expected amount of genetic variation.

Let's say we have two different samples of MRSA252. We sequence these samples and get the full genomes of ~3 million base pairs each. What percentage of these bases would we expect to be different (assuming there is no sequencing error)? I figure it will be about 1%, but I haven't been able to find a source.

I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria. An academic source would be much appreciated.

I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria.

Yes indeed it will.  Bacteria are a huge domain of life; you might as well ask for variability between all plants or between all animals.  Bacteria can live in very different environments, and the whole things is made more complex by widespread horizontal transfer.

Still, for bacteria, you can't do much better than E. coli, and boy are they a mess.  Here's a paper from 2010 that blew my mind.  The authors sequenced 61 E. coli genomes and found:

  ...that any given E. coli genome sequenced will have only roughly 20% of its genes part of the E. coli core, and the remaining 80% are not found in all other E. coli genomes.

20% variability within a species.  20%, one species.  E.coli is an extreme example, but still, species is a stupid concept.  Here's a 2006 paper finding that plenty of unique Campylobacter proteins simply aren't in plenty of Campylobacter species.

On a more broad scale, here's an excellent (and free) paper you should look at.  It examines islands of "microdiversity" among various species, finding that some species are easily 50%-75% different.  A simple way to estimate this is too look at gene number for bacterial species, which should make it clear that some of these bugs vary by up to an order of magnitude.

In short: A lot.


How to design the primer when you don't have GC? I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that region with PCR.

For some reason I am not able to amplify the region. I designed my primer by Primer 3 plus and manually, but it is not working. The main reason is that I don't have GC pair in the primer.

Is there any other way to fix the problem?

My primer concentration is 200nm.

Without the sequence information I can only give very general advice.

1) Pick a different location — primers generally work best when they have something close to 50% GC content.

2) Make sure the 3' ends of your primers aren't complementary.

There is detailed advice on how to design effective primers available online including:

from MIT
Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR methods appl, 3(3), S30-S37.


Why do bulls-eye rashes look like they do? People infected with Lyme Disease often present with an erythema migrans ("migrating redness") rash. Most often, these rashes are in the shape of a bulls-eye.

Rash image.

Presumably, this is a reaction that many of our bodies have to the Borrelia burgdorferi pathogen.

Lyme disease also sometimes presents with different-looking rashes, and other pathogens also sometimes produce a bulls-eye-looking rash. CDC Link on Lyme Disease Rashes and Look-alikes.

What causes the bulls-eye shape of these rashes?

Thought process: A gradient of redness from the site of the tick bite makes sense--an immune response might be strongest at the bite site--but I'm still stumped on why there would be a spot of redness surrounded by a no-rash-ring surrounded by a rash-ring.

Note: If I remember correctly, external links to images are usually frowned upon. Although the images linked in this post aren't super graphic, I decided to make them external links for the sake of anyone who is sensitive to medical images.

The spreading of the rash is caused by dissemination (migration) of the Lyme spirochetes (Borrelia) through the skin out from the initial site of infection.

The spirochetes trigger a immune reaction that involves macrophages entering the skin and releasing pro-inflammatory factors.

The clear areas (when present) apparently represent areas where macrophages have been cleared from the skin and thus are no longer triggering a inflammatory response.

The different patterns associated with the rashes can be explained by differences in how fast macrophages are cleared from the skin.

Reference:
Vig, D. K., & Wolgemuth, C. W. (2014). Spatiotemporal evolution of erythema migrans, the hallmark rash of Lyme disease. Biophysical journal, 106(3), 763-768.


The smaller the cell the greater its surface-to-volume ratio? I read in a book that the smaller the cell the greater its surface-to-volume ratio (the surface area of a cell compared to its volume).

And larger cells have limited surface area compared to its volume.

How is this possible? I don't understand.

This is a basic property of geometry: for any given shape, area will be generally proportional to the square of the length, and volume will be proportional to its cube. (this isn't true for all shapes by any means; the "generally" refers to the principle that length, area and volume are 1, 2 and 3-dimensional properties respectively, not that all or even most shapes behave this way... although a lot of the shapes that happen to be common in the Universe do. See end of the answer).

For example, if a sphere has a radius of R, its surface will have an area of 4*Pi*R², and its interior will have a volume of 4/3*Pi*R³. This means its surface-to-volume ratio will be 3/R, which is inversely proportional to R, meaning when R increases it will decrease and vice-versa.

Like so:

\begin{array} {|l|l|}
\hline
R~(\sim length) & R^2~(\sim surface~area) & R^3~(\sim volume) &  1/R~(\sim surface~area / volume) \\
\hline
1 &   1 &   1 & 1~(= 1/1) \\
\hline
2 &   4 &   8 & 1/2~(= 4/8)\\
\hline
3 &   9 &  27 & 1/3~(=9/27)\\
\hline
4 &  16 &  64 & 1/4~(=16/64)\\
\hline
5 &  25 & 125 & 1/5~(=25/125) \\
\hline
\end{array}

Put another way, if your shape is growing in 3D then whenever you add a bit of length you'll tend to add much more area (because area is increasing along two directions of length) but you'll be adding even more volume (because volume is increasing along three directions of length), and more volume than area means the area-to-volume ratio becomes smaller.

It helps that cells are convex and can often be approximated as spheres, so the rule absolutely applies to them. It's different with squiggly shapes, or cases where you aren't growing along every axis (for example this principle is true if you increase a cylinder's radius and length, but not if you just increase its length; at that point length, surface area and volume are all increasing along a single dimension and thus all at the same rate; check the equations to see this). You often do find such squiggly, long or thin shapes in nature, and this is often an adaptation to get around the surface-to-volume decrease issue. Examples include your intestines, or the interface between the placenta and the uterus.


Does using CRISPR/Cas9 knockout need to add donor DNA in the process? I am new to this technology and don't quite understand how it works. Hope someone can give some suggestions! Thank you.

Short Answer:
No, for CRISPR/Cas9 knockout you do not need to add donor DNA.

Little bit more detail:
CRISPR/Cas9 allows you to cut at a given position (defined by the gRNA). This will lead to double strand breaks (DSB).

If you do not add any donor DNA, the cell's DNA repair mechanism will try to repair the double strand break. Since these CRISPR/Cas9 mediated DSBs usually have a blunt end it is really hard for the DNA repair mechanism to fix it. If will often introduce an error, for example by missing a basepair (or several) leading to a frame-shift mutation. This DNA repair mechanism is called Non-Homologous End Joining.

If you do add donor DNA it will contain both the sequence you want to introduce (say a green fluorescent protein) and homologous sequences on both sides of the double strand break. In other words, if you want to cut the sequence ATCGCA exactly in the middle you will get ATC and GCA. You want to insert AGA. The donor plasmid must then have the sequence ATCAGAGCA. As the cell now has the homologous regions, it will use the Homology Directed Repair mechanism.

The sequences are for illustration only - in reality a gene is usually several hundred basepairs and it is recommended to have much longer homology regions.


Is the amount of cholesterol the body produces affected by how much cholesterol you take in with food? In the past I've been told multiple times that if you don't eat foods containing cholesterol, your body will increase its production of cholesterol to balance out the lack of nutritional cholesterol. On the other hand, if you eat sufficiently much cholesterol, the body will adapt its production of cholesterol in the other direction.

What evidence is there to support this statement?

Here's a study in which they measured a decrease in endogenous cholesterol synthesis after various amounts of dietary cholesterol: Dietary Cholesterol Feeding Suppresses Human Cholesterol Synthesis Measured by Deuterium Incorporation and Urinary Mevalonic Acid Levels (Arteriosclerosis, Thrombosis, and Vascular Biology, 1996):

  The objective of this study was to measure the response of cholesterol
  biosynthesis in subjects to three different amounts of dietary
  cholesterol: 50 (low), 350 (medium), and 650 (high) mg cholesterol per
  2800 kcal. Individuals with low (n=7), normal (n=12), and elevated
  (n=11) plasma cholesterol concentrations consumed in random order
  solid-food test diets (15%, 55%, and 30% of energy as protein,
  carbohydrate, and fat, respectively) at each dietary cholesterol
  level. The three diets were consumed for 4 weeks each, and each
  dietary phase was separated by a 4-week washout period. During the
  final week of each diet, 0.7 g D2O was given per kilogram of body
  water and deuterium incorporation into the erythrocyte cholesterol
  pool was measured for 24 hours. Urinary mevalonate levels were also
  determined in samples obtained during two consecutive 24-hour periods.
  Both techniques provided measurements of whole-body cholesterol
  biosynthesis. In all subjects the cholesterol synthesis rate as
  measured by deuterium incorporation was significantly lower (P<.05)
  after the transition from low- to medium- and low- to high-cholesterol
  diets. Urinary mevalonate excretion decreased after the change from
  the medium- to high- (P<.05) and low- to high- (P<.01) cholesterol
  diets. Although correspondence between the two methods was poor, they
  both indicated some suppression of cholesterol synthesis by dietary
  cholesterol. The response of cholesterogenesis to different amounts of
  dietary cholesterol was related to the rate of synthesis under
  depressed conditions of the low-cholesterol diet. These findings
  indicate modest downregulation of synthesis in response to dietary
  cholesterol in humans, independent of plasma cholesterol levels.

  Metabolic responses to increased dietary cholesterol potentially
  include reduced endogenous synthesis, decreased absorption, and
  increased biliary excretion of cholesterol.

In some people, who are cholesterol hyperresponders, dietary cholesterol does not effectively suppress endogenous cholesterol synthesis, so it results in elevated blood cholesterol levels (Comprehensive Biotechnology, 2011). In one study, a decrease in dietary cholesterol intake resulted in a decrease of blood cholesterol in hyperresponders but not in hyporesponders: Endogenous cholesterol synthesis, fecal steroid excretion and serum lanosterol in subjects with high or low response of serum cholesterol to dietary cholesterol (Clinical Nutrition, 1986):

  In this study we addressed the question whether hypo- and
  hyper-responders to dietary cholesterol differ with regard to the
  flexibility of endogenous cholesterol synthesis after changes in
  cholesterol intake. Whole-body cholesterol synthesis was measured as
  faecal excretion of neutral steroids and bile acids minus cholesterol
  intake. In addition, we determined serum concentrations of lanosterol,
  a precursor of cholesterol and a possible indicator of cholesterol
  biosynthetic activity. The study was carried out with 2 hyper- and 4
  hypo-responders; these subjects had shown a consistently high or low
  response of serum cholesterol to a decrease in dietary cholesterol in
  two previous experiments.

  The subjects received controlled high- (on average 697 mg of
  cholesterol per day) and low-cholesterol (109 mg/day) diets for
  periods of 4 weeks in succession; cholesterol was the only dietary
  variable. The two hyper-responders again showed a significant decrease
  in serum cholesterol. There was essentially no decrease in serum
  cholesterol in three of the four hypo-responders. The decrease in
  cholesterol intake caused an increase in cholesterol synthesis in five
  out of the six subjects.

In conclusion, in most people, dietary intake of cholesterol does not increase blood cholesterol levels because of decreased absorption and endogenous synthesis and increased excretion of cholesterol.