How to choose right volume of DNA and SYBR Green I'm testing fluorescence level of a sample having dsDNA, SYBR Green and milli q water but I'm facing difficulty in choosing right volume of dsDNA and cons level of SYBR Green.

Details of sample: dsDNA:1000 nano mole, SYBR Green:1X (1000 times diluted from original stock)

Sample_1: dsDNA (3ul) + SYBR Green (5ul) + milli q water (27ul)

Sample_2: dsDNA (3ul) + SYBR Green (5ul)

Result: In first sample I haven't got any signal but in second case I got( But I want 5 times higher then what I got).

Please tell me how it work and how these things depends on each other. I'm not a biologist if possible suggest me resource as well.

I had to look it up online, but I eventually found here an important information: the detection limits of SYBR Green.

  dsDNA at 300nm transillumination: 60 pg
  Oligonucleotides at 300nm transillumination 1-2 ng

You should first check the size of your DNA of interest, and from its size figure out its approximate molecular weight (for example using this online calculator). Then, you should check that 1000 nmoles of your DNA corresponds to a mass greater than 60 pg. If not, you should increase the amount of DNA in your assay accordingly until the mass introduced in the assay exceeds the detection limit of SYBR Green.

Now, do you know the concentration of your DNA? In other words, how did you choose to use 3 uL of DNA? How do you know that these 3 uL contain enough material? (1000 nmoles as in your protocol, or better, that this is higher than the detection limit in terms of mass).

Also, did you use the 1000X stock solution of SYBR Green without intermediate dilution? If so, the final concentration of SYBR Green is much larger than the final 1X you want, in both of your samples:

sample 1: 5 uL of 1000X SYBR Green in a total volume of 3 + 5 + 27 = 35 uL means that the final concentration is 1000X * 5 / 35 = ~143X.
sample 2: 5 uL of 1000X SYBR Green in a total volume of 3 + 5 = 8 uL means that the final concentration is 1000X * 5 / 8 = 625X.

What you need is either use 1 uL of 1000X stock solution of SYBR Green + whatever amount of DNA that will be above the detection limit + buffer to adjust the volume to 1000 uL final (which will bring the SYBR Green to 1X final), or make an appropriate intermediate dilution of SYBR Green so that its final concentration is 1X by following the sample preparation as described in your question.

The sample preparation you describe here yields a composition that is way off the one suggested by your protocol, at least for the SYBR Green. Until you try again with proper final concentrations, do not conclude that it didn't work. :-)

Good luck with your project.


Concentration gradients across membranes with different ions I'm trying to gain an intuition for the dynamics of across neuronal membranes. The overarching idea here is they are controlled by ion concentration gradients across the membrane (which we can describe mathematically).

I'm looking for someone to delineate every present concentration gradient across neuronal membranes that are relevant here(involving $Na^+$, $Ca^{2+}$, $K^-$, and $Cl^-$).

It's unclear to me what creates a concentration gradient:

Are the concentrations of each type of ion independent from eachother, i.e. in a world without charge, diffusion across the membrane is individual to the concentration of each ion, or, is mediated by the net concentrations of mass (which makes less sense)?
Is the flow of ions across the membrane driven by net charge on each side, or the charge concentrations of each individual ion?

I try to answer your two questions briefly:

Ion gradients are dependent on charge, but there exist independent transport mechanisms, extending diffusion. Trans-membrane transport proteins can specifically move only one sort of ions. Also symport or antiport exists, that can depend on gradients of other (e.g. non-charged molecules). In addition, the mentioned inorganic ions can form chemical bonding to organic ions for example, which neutralizes the electrical charge.
Beside an electrical potential, also chemical (concentration) potential can act as force on ios. In addition active transport, inactivation as mentioned above and other factors have an influence on the molecule flow.


What is the name of this bug? I found this bug in my garden in India this morning.

That is a tortoise beetle (Family Chrysomelidae (Leaf beetle), subfamily Cassidinae). It looks very much like the Indian Green Tortoise Beetle Chiridopsis bipunctata. https://indiabiodiversity.org/observation/show/338651
I am almost sure it is in the genus Chiridopsis.


What is this tree that displays sycamore like characteristics but appears to be too small? I have been wondering about this tree:

It's bark/leaves make me think it's a sycamore, but it seems too puny. I don't think they'd plant a sycamore there... What is it?

The tree is in a park/residential area in Orange County, Southern California.

Reasons I think it looks Sycamorish:

Alternate leaves
3 lobes
Mottled/patchy/peely bark

https://www.thoughtco.com/identify-maple-sycamore-yellow-poplar-sweetgum-leaves-1343480

This is very likely a London planetree (Platanus × acerifolia), a hybrid species of Platanus often planted in cities.

 Source: Cuyamaca College

 Source: Wikimedia

The tree is a hybrid between Platanus orientalis and Platanus occidentalis (the sycamore tree), and has characteristics intermediate between the two species.

Smaller (heights of only 20-30 m vs 30-40+ m for parent species).
More deeply lobed leaf than P. occidentalis but less so than P. orientalis
Seed balls typically two per stem (one in P. occidentalis, 3-6 in P. orientalis)

Note: seed "balls" = aggregate of many small seed-like fruits called achenes

VERY OFTEN PLANTED IN URBAN AREAS

Because it's very tolerant of atmospheric pollution and root compaction

Description:

Leaves: alternate, simple, 3-5 lobes, maple-shaped, 10–20 cm long, 12–25 cm wide
Bark: pale grey-green (or brown), smooth and peeling (sometimes not peeling)


What is functional dissection? Reading [1] I found the sentence:

  Consistently, functional dissection of mouse and human wild-type and mutant RAS isogenic leukemia cells demonstrated induction of methotrexate resistance but also improved the response to vincristine in mutant RAS-expressing lymphoblasts.

I did not find a definition online yet. What is the meaning of functional dissection in this context?

[1]   K. Oshima et al., “Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia,” Proc Natl Acad Sci USA, vol. 113, no. 40, pp. 11306–11311, Oct. 2016.

The term 'functional' in this context implies a type of analysis that is able to provide a mechanistic understanding.

The authors first describe their exploratory approach, by which they identified some genes and their mutations that are associated with patient relapse in acute lymphoblastic leukemia. Then they proceed to intervene in the system, by expressing mutated KRAS in mice. When they did that, they observed several hallmarks of relapse in those mice. Hence they can conclude that a mutation of this gene is involved in the mechanism that underlies relapse.

Thus the way these authors use the term 'functional analysis'/'functional dissection' is in contrast to a correlational approach.

The underlying assumption is that by isolating parts of the system and studying their properties and their effects we will be able to understand the physical world. This is a philosophical (metaphysical) thesis called reductionism, which is arguably the prevailing view in the natural sciences.

The first use of the term "functional dissection" I could find is in a 1971 paper on the immunological response of small molecules. Their goal in that paper was to dissociate (or dissect) the effects of small molecules, such as a bovine glucagon, on antibody specificity versus antibody production. They have found that different parts of this molecule were responsible for antigen specificity (all antibodies recognised the N-terminal) and cellular immunity (mostly the C-terminal of the molecule was associated with DNA synthesis).


Where do plants obtain the metal ions needed for biological processes? Enzymes employ metal ions (e.g. Mg, Cr, Mn, Fe, Co, Ni, Cu, Zn) for catalysing certain reactions.

Let's consider planting a seed. Where will it obtain these metal ions from? Just from water?

Many ions are absorbed by the plants via the action of bacterias. Fe or B for example require chelating action from microbes. P and S need to be oxidised to enter the plant as well.
Source: Le sol, la Terre et les Champs - http://www.sangdelaterre.fr/index_135_151.html


Why can't we always create a vaccine against a virus when an ELISA test to detect it is possible? Before precising my question, here are some facts that I presume to be true:

A vaccine works by injecting the antigens of a virus into the body to train the immune system to recognize the virus and to be prepared to fight it if it shows up.
The ELISA test indirectly recognize the presence of a virus into a blood sample by testing the presence of the antigens of the virus and the antibodies that fight against it.
One of the reasons there are still no vaccine against HIV is because this virus has a very high mutation rate.
The ELISA test is used to detect the presence of HIV.

I have the feeling these facts contradict themselves and I would like to know where I am misleading.

Indeed, if we have an ELISA test for HIV, we should be able to create a vaccine because we know the antigens of the virus and we can inject a harmless version of them into our body, right?
Apparently, the answer to this question is no because the HIV virus has a high mutation rate and the antibodies produced thanks to the vaccine won't be able to fight every mutation of the virus (that's the answer that gave me my former biology teacher in high school). But if the HIV has a high mutation rate, how can we be able to produce an ELISA test for it?

I found the question quite interesting and will to provide a concept and a speculation although I could not answer the question to my own satisfaction (edits to this regard are welcome)

Currently (2020), the advanced form of ELISA tests for HIV are designed to simultaneously detect both the HIV P24 antigen (produced by the virus) and anti-HIV igG and igM antibodies (produced by the body in response to the virus). Refs (CDC: What kinds of tests are available, and how do they work?)(HIV Diagnostic Testing: 30 Years of Evolution)

While it is easy to detect known viral antigens like the p24 capsid protein in a diagnostic, it is not straightforward to use the same antigen as a vaccine and expect the host to mount an immune response that neutralizes the viral infection, although attempts have been ongoing. Possible scenarios could be that the binding strength of the antibody to P24 might be good enough for detection, but not enough for immunity or that recognizing and binding to P24 does not inhibit the infection. Coming to the evolution/mutation question, since both the p24 antigen and a few antibodies are being detected, it is unlikely the virus would mutate so as to evade the ELISA for all the targets.

The first point in Charlie's answer might be getting at this but it did not come through clearly.


Suggestions for an experiment? I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly substantial.
I'm interested in anything cell/DNA/molebio related with a mathematical connection. I >would prefer something other than mere statistical analysis, maybe something like >differential equations.
I have access to standard undergraduate lab equipment; assume that I'm able to procure all necessary materials and that I'm capable of performing the experiment. Thank you for the help.

As per the suggestion of shigeta below, I leafed through the links, and found gene circuits interesting. So, what exactly is a gene circuit, how are they modeled, and what are they used for?

This is a bit hard - most possible answers you still aren't going to like, but I'll give you three suggestions.

It sounds like you want to take something with a mathematical model and try to modulate it with molecular biology.

It seems unlikely that I can really give you a specific project, but there are four sources  I will recommend you look at.

I think I'd suggest the further limiting assumptions:

you want to work with E coli - its the easiest and most readily available organism to work with.
you want to work with a system that is self contained within a single plasmid - so it relies only upon 2 genes to act, 3 at the outside or you will have issues getting it all to work.
you want a mathematical system that already has a well fit model that  you will peturb.  building a new model might be a bit of a big first off project.  (but who am I to tell you what to do - these are just suggestions).

The First suggestion I have is Jeff Hasty at UCSD.  He has focused a lot on oscillating gene circuits.  He has simple systems that might be reproducible with a small lab, most recent work that combines a GFP oscillator with LUX is pretty cool. Both oscillators and LUX are independently good systems to work with. .  I've been a science fair judge and I can tell you, just reproducing one of his systems would be an impressive lot of work

Another body of work to look at is Adam Arkin. He has looked at lots of circuitry component candidates.  Articles such as "The hunt for the biological transistor" might get you thinking.  This is a broader body of work, and so it might take a while to get an idea from it.

Third, if this is boring to you and you want to look more broadly, you can look through the iGEM competitions.  These are projects with oscillators and bio synthesis systems which sometimes have mathematical models associated with them.  The big advantage here is that you might be able to start or join an iGEM team and then some or all the plasmids will be made already - mol bio gets very expensive if someone doesn't gift you some materials.


QTL mapping in Drosophila I have already googled it before but yet unsuccessful in finding the whole topic with intuition. Please help.

A guide to an associated book would be greatly valued.

First you need two, hopefully homozygous, strains that differ in some measurable quantitative trait. In worms it has been done with lifespan; in mice injected with ethanol it has been done with long-sleep and short-sleep periods. The two strains need to differ in their RFLPs. For flies there are probably lots of behavioural traits one could use.

You set up a cross, and then mate individual brothers to sisters, and keep repeating this breeding pattern for multiple generations to establish recombinant inbred lines. After 10 generations they are basically homozygous, and you take the individual lines and assay them first for the trait you are scoring, and second for the molecular markers. The results of the molecular mapping let your draw the haplotype along each chromosome, so you know which parental strain contributed which portion or each chromosome.

The results of each quantitative trait scoring let you classify each recombinant inbred line into one of the two parental phenotype classes (or if it is a multi-locus trait then you may get some intermediate lines).

With those two results you will be able to correlate the absence, or presence, of molecular markers along the chromosomes, with the quantitative trait you are studying.

If it works you will be able to narrow in on a genomic region that co-segregates with the trait. If there are multiple genes involved you may be able to assign a probability or LOD score to different regions.


Melatonin production - requires nighttime, or just full darkness? Is melatonin properly produced in daytime sleep in full darkness? Or does it require only nighttime sleep?

Additionally, what other biological implications are there, if any, to daytime sleeping? Melatonin production is the only biological implication I could find so far.

The immediate thought came to my mind was relation between Melatonin and Serotonin. Because both hormones have sleep related function. I read that both are light sensitive. Melatonin is produced by pineal gland in brain whereas Serotonin is at gut and CNS.

Light dependence(Wikipedia) of Melatonin is explained here where they say blue light produces more Melatonin and wavelength of light <530nm will have effect on Melatonin production. If the light intensity is more then Melatonin will not be produced. So what they say is if there is darkness(artificial) or dim light environment then this hormone will be produced and induces sleep. Almost everywhere they explain Melatonin whose production is sensitive to light.

(But even in the afternoon when there is bright light some of us feel sleepy which is mainly due to Serotonin released after heavy meal which is produced from tryptophan. This will again effect the sleep. It is obvious that without food we can not sleep at night. So Serotonin and Melatonin are interrelated as explained here Link1 and Link2).


Is there any advantage to one blood type over another? All humans can be grouped into ABO and Rh+/- blood groups (at a minimum).  Is there any advantage at all to one group or the other?  This article hints that there are some pathogens that display a preference to a blood type (for example Schistosomiasis apparently being more common in people with blood group A, although it could be that more people have type A in the areas that the parasite inhabits).  Is there any literature out there to support or refute this claim or provide similar examples?

Beyond ABO-Rh, is there any advantage or disadvantage (excluding the obvious difficulties in finding a donor after accident/trauma) in the 30 other blood type suffixes recognised by the International Society of Blood Transfusions (ISBT)?

I'd imagine not (or at least very minimal) but it would be interesting to find out if anyone knows more.

I've been doing a little more digging myself and have found a couple of other advantages:

Risk of Venous-thromboembolism (deep vein thrombosis/pulmonary embolism (1)).  Blood group O individuals are at lower risk of the above conditions due to reduced levels of von Willebrand factor(2) and factor VIII clotting factors.

Cholera Infection Susceptibility & Severity.  Individuals with blood group O are less susceptible to some strains of cholera (O1) but are more likely to suffer severe effects from the disease if infected (3).

E. coli Infection Susceptibility & Severity. A study in Scotland indicated that those with the O blood group showed higher than expected infection rates with E. coli O157 and significantly higher fatality rates (78.5% of fatalities had blood group O).(4)

Peptic Ulcers caused by Heliobacter pylori which can also lead to gastric cancer.  Group O are again more susceptible to strains of H. pylori (5).

Whether blood group antigens are displayed on other body cells or not has been linked to increased or decreased susceptibility to many diseases, notably norrovirus and HIV.  This is fully explained in the article that I was above summarising - "The relationship between blood group and disease" in addition to extended descriptions of the other two answers.


By What Mechanism Does Heat Cause Muscle Relaxation? Heat is commonly used "loosen" muscles, but what exactly is happening to relax the muscle? It wouldn't make sense that increased blood flow alone would relax muscle.

Read this it was very helpful to me as a Reiki Practitioner who wants to know how the heat generated by my hands on therapy with my patients for Hospice brings such relaxation to them.
http://healthyliving.azcentral.com/effects-temperature-muscular-contraction-11504.html


Like other animals, why humans don't have species & breeds? Like other animals, why don't humans have species & breeds ?
 Even my pet dog is one type of breed, but we (humans) lack breeds & species?  What is the main reason?

If you with 'humans' refer to our genus Homo (which is often the case), we do have multiple species, see wikipedia for an overview. The difference to many other organism groups is just that all species except Homo sapiens are extinct.

Also, taxonomic ranks below the species level - such as breed, subspecies, population and race - are very poorly definined and are usually used in different ways in different taxonomic groups. It is therefore difficult to draw one-to-one comparisons between these types of ranks across taxonomic groups. It is even relatively meaningless to compare e.g. taxonomic families between taxonomic orders, since they are used in such different ways, and compared to ranks below the species level taxonomic 'order' and 'family' have much clearer definitions.

However, if you with breeds of dogs are referring to distict phenotypes (which is basically what they are), you can easily see that some human populations also have distict phenotypes, so in this sense they are similar.

The reason why the concept of human races is largely obsolete and controversial (along with breeds) is clearly our human collective history of racism, nazism and eugenics.


Voltage-gated Potassium channels in the action potential of cardiomyocyte? There is one type of potassium voltage-gated channels open in Phase 1 too.
Some call them early repolarization channels.

I am not convinced that the channels are different in different phases: 0, 2, 3 and 4.

I think all these potassium channels are voltage-gated.
However, they probably differ in some places.
I am not sure if one type of channel can be open in all these five phases.

Which types of potassium channels are open during the action potential of cardiomyocyte?

Two main types of action potentials occur in the heart . One type, the fast response, occurs in normal atrial and ventricular myocytes and in the specialized conducting fibers (Purkinje fibers of the heart)and is divided into five phases. The rapid upstroke of the action potential is designated phase 0.The upstroke is followed by a brief period of partial, early repolarization (phase 1) and then by a plateau (phase 2) that persists for about 0.1 to 0.2 second. The membrane then repolarizes(phase 3) until the resting state of polarization (phase 4) is again attained (at point e). Final repolarization (phase 3) develops more slowly than depolarization (phase 0).

Genesis of the Upstroke (Phase 0)

The action potential amplitude (the potential change during phase 0) is dependent on [Na+ ]o.
The Na+ channels open very rapidly or activate (in about 0.1 msec), thereby resulting in an abrupt increase in gNa . However, once open, the Na+ channels inactivate (time course ˜1 to 2 msec), and gNa rapidly decreases.

Genesis of Early Repolarization (Phase 1)

In many cardiac cells that have a prominent plateau, phase 1 is an early, brief period of limited repolarization. This brief repolarization results in the notch between the end of the upstroke and the beginning of the plateau . Repolarization is brief because of activation of a transient outward current (ito ) carried mainly by K+ . Activation of K+ channels during phase 1 causes a brief efflux of K+ from the cell because the cell interior is positively charged and [K+ ]i greatly exceeds [K+ ]o . The cell is briefly and partially repolarized as a result of this transient efflux of K+ .The size of the phase 1 notch varies among cardiac cells.

Genesis of the Plateau (Phase 2)

During the action potential plateau, Ca++ enters myocardial cells through calcium channels During the flat portion of phase 2 , this influx of Ca++ is counterbalanced by the efflux of K+ . K+ exits through channels that conduct mainly the ito , iK , and iK1 currents. The ito current is responsible for phase 1, as described previously, but it is not completely inactivated until after phase 2 has expired.
During the plateau (phase 2) of the action potential, the concentration gradient for K+ across the cell membrane is virtually the same as it is during phase 4. However, Vm is now positive. Therefore, there is a large gradient that favors efflux of K+ from the cell. If gK were the same during the plateau as it is during phase 4, efflux of K+ during phase2 would greatly exceed the influx of Ca++ , and a sustained plateau could not be achieved. However, as Vm approaches and then attains positive values near the peak of the action potential upstroke, gK suddenly decreases . The diminished K+ current associated with the reduction in gK
prevents excessive loss of K+ from the cell during the plateau. This reduction in gK at both positive and low negative values of Vm is called inward rectification. Inward rectification is a characteristic of several K+ currents, including the iK1 current For these channels, large K+ currents flow at negative values of Vm (i.e., gK is large). However, when Vm is near 0 mV, or positive, as occurs during the plateau (phase 2), little or no K+ current flows (i.e., gK is low). Thus, the substantial gK that prevails during phase 4 of the cardiac action potential is largely due to the iK1 channels, but current through these channels is greatly diminished during the plateau.

Other K+ channels play a role in phase 2 of the action potential. These are characterized as delayed rectifier (iK ) channels. These K+ channels are closed during phase 4 and are activated very slowly by the potentials that prevail toward the end of phase 0. Hence, activation of these channels tends to increase gK very gradually during phase 2. These channels play only a minor role during phase 2, but they contribute to the process of final repolarization (phase 3), as described later. Two types of iK channels exist, depending on their rates of activation. The more slowly activating channel is designated the iKs channel, whereas the more rapidly activating channel is designated the iKr channel . The duration of the action potential in myocytes in various regions of the ventricular myocardium is determined in part by the relative distributions of these iKr and iKs channels.
Genesis of Final Repolarization (Phase 3)

The process of final repolarization (phase 3) starts at the end of phase 2, when efflux of K+ from the cardiac cell begins to exceed influx of Ca++ . As noted, at least three outward K+ currents (ito , iK , and iK1 ) contribute to the final repolarization (phase 3) of the cardiac cell.
Restoration of Ionic Concentrations (Phase 4)

The steady inward leak of Na+ that enters the cell rapidly during phase 0 and more slowly throughout the cardiac cycle would gradually depolarize the resting membrane voltage were it not for Na+ ,K+ -ATPase, which is located in the cell membrane. Similarly, most of the excess Ca++ ions that had entered the cell mainly during phase 2 are eliminated principally by a 3Na+ -1Ca++ antiporter, which exchanges 3 Na+ ions for 1 Ca++ ion. However, some of the Ca++ ions are eliminated by an ATP-driven Ca++ pump.


Why Do Nerve Signals Get Crossed? First off, I don't know if this is a normal healthy thing to occur. There have been many times where I have an itch on say my arm and I scratch it, only to feel the scratching elsewhere on my body. I assume somewhere along the transit of the touch signals to my brain the signal gets mixed up and is processed incorrectly.

So my questions are:

Why does this mixup happen? (chemical imbalance, damaged nerves, etc..)
How does my brain correspond the touch to somewhere else? (what is the process behind it)

Well nerve crossing or misinterpretation of nerve signal by the brain does not happen all the time. In case it happens frequently then I guess it would be Multiple Sclerosis or might be Fibromyalgia syndrome. In multiple sclerosis, the Myelin sheath surrounding neuron when gets damaged causes certain problem with nerve signal transmission to the brain. But that is not the main cause. The main cause can be found in Neuropathy:

When nerve cells are damaged, perhaps by a temporary restriction in their access to oxygen, they too atrophy or shrink a little, thus the synaptic junctions widens.  Just like with a spark plug in your car or lawn mower, if this gap gets too wide, the spark cannot make the jump. A normal sized nerve signal cannot jump this enlarged gap either, so the signal either does not get through or it gets misdirected to another part of the body and is misinterpreted as pain.

So I can say that the nerve cells in the place where you feel real pain fails to transmit the signal to brain via its neighboring nerve cell instead that signal passes through some other node randomly (or it might take the same path every time you touch the pain area) and signal the brain which gets misinterpreted and make you feel that you have pain in the misinterpreted region.


Where do cockroaches go in the daytime? Urban parks in North America teem with sizable cockroaches at night. However, in the daytime they are nowhere to be seen. Where do they go?

I know that they tend to avoid light, but how do they go about finding a hiding spot? Do they just throw themselves into any superficial crack and stay still? Do they travel a substantial distance into storm drains, water pipes, tunnels and hollow walls until they are well out of reach of larger animals? Do they have a nest that they return to every night or do they just use whatever hiding spot is nearby?

And specifically for small urban parks, flowerbeds and lawns - do they dig tunnels in the soil? Do they nest in the trees? Or do they simply leave the park and hide in nearby buildings, sewers, and similar human-built structures?

I ask because while it is obvious they must hide somewhere, I have never actually "gotten the drop on" a sleeping or hiding cockroach in a park - or elsewhere - I've only encountered roaches that were scurrying out and about. Some nocturnal insects can be found by for instance flipping over wet rocks or digging up some soil, but cockroaches despite being large and numerous are nowhere to be seen. Are they just really, really good at hiding?

Basically, yes, cockroaches are very good at avoiding detection. Since you linked to the American cockroach (Periplaneta americana), I'll discuss that species in my answer. I've only twice, in my life, seen an actual cockroach. I don't know what parks you're referring to in your question or if it's that common.

By the time you start lifting up a rock or board to look for a cockroach during the day, it will have already sensed you coming and have left.

  They spend most of their time in narrow, tight cracks and spaces where surfaces touch them on both sides.
  (Cockroaches from the University of Minnesota)

  Cockroaches like to be touched.
  Roaches are thigmotropic, meaning they like feeling something solid in contact with their bodies, preferably on all sides. They seek out cracks and crevices, and will squeeze into spaces that offer them the comfort of a tight fit. And I do mean a tight fit. The small German cockroach can fit into a crack as thin as a dime, while the larger American cockroach will squeeze into a space no thicker than a quarter.
  (10 Fascinating Facts About Cockroaches)

When you understand how thin a crack can be for a cockroach to wedge itself into, you get a better idea how they hide during daylight hours in the outdoors. Many trees have rough bark with enough crevices for them to hide. They could fit in the thin spaces between the bottom of concrete sidewalk pavers and soil, under leaf mulch and many other spaces you may never have noticed before. It takes very little. Best places to look for them in parks would be around trash receptacles where people toss food they didn't finish eating.


Standard notation for crossings (female, male) Is there any standard for the notation of a crossing (hybrid) which tells me which part is the mother and which is the father?
Example
StrainA: egg cell
StrainB: sperm cell
Which notation is correct?
StrainA x StrainB or
StrainB x StrainA
or isn't there a rule for this?

For plants, seed (egg cell) parent is shown first and pollen (sperm) parent second.
The rule is mentioned in wikipedia,
http://en.wikipedia.org/wiki/Hybrid_(biology)
section : in plants.
Another mention of plant example:
https://www.rhododendron.org/v50n1p36.htm


How can both strands of DNA code for proteins with similar functions? It's not clear from the question but for example:

AAAAAAA

TTTTTTT

The top strand would create a different protein than the bottom, and with the huge amount of nucleotide in a gene, I think it's very unlikely that the same region on both gene could create proteins that are similar to each other, even though they're alleles of the same gene. This would also affect codominance/incomplete dominance, since I'm assuming that only one of the strand would create a functional protein.

You are confusing the the forward and reverse strands of DNA as two alleles. They are not. Remember you have a double stranded DNA from each parent. Each of those two pieces of double stranded DNA represent alleles for a given locus.

For the example you gave, you can have different genes that overlap the same region of DNA. One is on one strand and a different gene is on the other. The DNA is read 5' to 3' so we think of one strand as forward and one strand as reverse.

See embedded pic for examples from this publication about different kinds of overlap and whether they are conserved across species.


Can scientists name themselves in the scientific name when they discover a new taxon? There are sometimes people names in taxonomy, like Myotis keenii was names after Mr. Keen who contributed to discover the species. So, if you discover a species and someone else is constructing the scientific name and names you, it's clear. But when you discover a species and you publish it in a paper, can you propose a scientific name that contains your name? Has it ever happened, or is it considered an unhealthy practice?

The answer is that in general, self-naming is severely frowned upon in the scientific community, but the act itself is not disallowed.

There have been at least two instances of self-naming recorded in literature, as stated in John Wright's book The Naming of the Shrew, page 34, where Jules Bourguignat named a species of snail after himself as Ferussacia bourguignatiana. The naming was apparently very poorly received (being referred to as taxonomic onanism), although I was unable to confirm this by locating the original citation.

Another example was given in the book on Sigismund Hochenwarth who named a species of moth (now Syngrapha hochenwarthi) after himself (original citation here).


Is it possible to move your arms above your head when handcuffed in the back? This move was seen in Pitch Black and i wonder if it is possible at all. Say you are handcuffed to a pole, hands in the back, and the pôle is a little higher than your head. You just want to do a complete loop with your hands, going above your head, so they end up in front of you and you are free of the pole.
Now, putting horrible pain aside, is it possible to perform this move alone?
If not, maybe with a small surface to rely on, for a lever effect?
Would it cause minor / major damage at all or just pain ?
I am also curious if performing this move slightly turned sideways help ( as much as you could at least, considering the situation). In the movie he goes one shoulder at a time.
Anyway, i hope im clear enough !
Exactly what i mean is this video at 1:35

This is not normally possible or would be extremely painful if done. But there are special cases.

  Atraumatic dislocation.
  This occurs when the shoulder dislocates with minimal force such as reaching up for an object or turning over in bed. Usually it will 'pop' back in itself or with a little help. Normally this type of dislocation does not need reducing in A&E. It can occur regularly throughout the day and will be associated with certain positions the arm is placed into. This type of dislocation is associated with people that have 'lax' joints, for example people who hyper-extend their knees and elbows and can get the palms of both hands onto the floor with ease.  This joint laxity is normal for these people and the onset of dislocation can be associated with a change in how the muscles around the shoulder are interacting with each other or a change in posture/ position of the arm. This can produce an imbalance in the control of the joint. Referral for appropriate physiotherapy is the initial form of management. The physiotherapist should look at the way in which the muscles and shoulder joint is moving and posture aiming to restore the balance. Treatment can 'cure' the problem as long as the exercises and advice is continued, but in some cases there is only minimal or nil benefit. At this point surgical intervention is indicated.
  Positional Non-traumatic dislocations.
  This group of people can dislocate their shoulders without any form or history of trauma. Some may have started out dislocating their shoulder as a party trick; others may have always had shoulders that just 'fall' out of joint. This type of dislocation is usually painless and can be put back in easily. Both shoulders are typically involved. The cause of this type of dislocation is usually a result of what we call 'abnormal muscle patterning' which means the strong muscles around the shoulder joint are not working in the correct order causing them to pull the shoulder out of joint with active movement in the particular direction such as lifting the arm forward above the head or out to the side and above the head.  The main treatment for this is physiotherapy that looks at re-sequencing the muscles in order to prevent further dislocations.  Occasionaly surgery in the form of thermal capsular shrinkage or plication may be neccessary.

Taken from here such people would be able to dislocate then get their hands in front and relocate.

The body can be trained to be quite flexible through training like gymnastics etc...


Insect Identification (even the family name would do) I found this insect in Bhopal,Madhya Pradesh,India could you please help me identify it??
I think it is some kind of beetle. Approximately 2-3 cm in size.

You've found a specimen of Coridius janus or cucurbit stink bug or red pumpkin bug (don't mix up with the red pumpkin beetle). They betong to the suborder Heteroptera (True bugs).

(picturefrom Wikipedia)

Also see:
projectnoah.org: red pumpkin bug

nbair.res.in: Coridius janus

indiabiodiversity.org: Coridius janus


Signaling between Organelles I'm confused about how organelles communicate with each other. I understand signaling between cells and the whole transcription and translation of DNA process. However, how does a motor protein know the destination of its package? How does a lysosome know when to break down a worn out organelle? How does the cell distribute ATP to the organelles where it's needed (how does it figure out where the ATP is needed?)?

There's no single common mechanism for intracellular communication, and some of the mechanisms (and some parts of some of the mechanisms) are known in much greater detail than other. For each of the processes you mention, we at least know that they proceed via very different mechanisms.

ATP distribution, for example, proceeds mostly by simple diffusion. ATP is a small molecule and is able to diffuse fast enough that it can move from one end of a cell to another in about ~20 ms on average [1].

Our picture of how ATP actually gets taken up by the various organelles is much murkier. For the case of the endoplasmic reticulum (ER), there is evidence that ATP is brought in via an ATP/ADP antiporter [2]. Transporting ATP via an ATP/ADP antiporter would have the effect of keeping the ratio of ATP/ADP stable in both the cytosol and the ER. It is reasonable to assume that similar mechanisms control ATP transport across other organelle membranes, but you'd have to dig into the literature to find out details.

References

1: Diffusion coefficients of ATP and creatine phosphate in isolated muscle: pulsed gradient 31P NMR of small biological samples

2: Transport and transporters in the endoplasmic reticulum


Studying the fruitfly nervous system I'm studying Neuroscience and Fruit Flies are a pretty big deal but I don't know as much as I think I should about them.  Are there and comprehensive sources that I could read?

I'd like a review of all the important parts of the nervous system, where they are, what they do, and how they connect.

Flybase is a generally useful source for Drosophila anatomy/physiology including the nervous system. From there I found this link which has some neuroscience-specific info.


Why aren't all animals cold blooded? At least, why don't all animals produce no more heat than the tiny amount that's a byproduct of walking or a bonobo climbing up a vine when the outside temperature is above 0°C? They won't freeze anyway.

After all, the amount of food controls the population size at whatever size makes each individual have just enough food, so shouldn't those with a lower energy demand be more likely to get enough food to rear more children? Shouldn't mutations that make a warm blooded animal able to thrive with a lower core temperature and produce less heat be selected for because there's more likely to get enough food to rear more children?

Also, shouldn't cheetahs evolve to produce extremely little heat in the day during rest even on not very hot days so they will be less hot and can chase their prey for longer? Have they already evolved that way?

If a species did evolve to produce less heat, would that also evolve to walk slower because it takes a lower speed to minimize the energy burnt per distance because they're producing less heat? I know there there will be a nonzero speed that minimizes the absolute minimum possible energy burnt per distance possible to evolve for that speed and a lower speed will actually increase the energy burnt per distance because the animal is walking for a longer time but the rate of energy burnt per time varies less rapidly with speed at such low speeds because of the energy burnt to fight against gravity.

Cold/warm blooded are misleading categories

The terms cold blooded and warm blooded is very misleading as it gives one the sensation that animals may warm up their internal temperature for the only reason of warming it up.

The terms homeo-, poikilo-, exo- and endo- terms are much more useful in thinking about control of body temperature. Have a look at this post and this post to understand these terms. Make sure to really read these posts to correctly understand these terms and how they interact.

Reformulating your question

What people, in general mean by cold vs warm blooded animals is whether they actively control their body temperature or not. That is cold blooded would mean exotherm while warm blooded would mean endotherm. As such the question becomes "why would any animal care about being endotherm if the body temperature won't go under freezing point anyway?"

Answer

Any metabolic pathway is affected by temperature. A change of temperature of only a few degrees can drastically affect the rate of chemical reactions. Homeotherm individuals (often homeotherm thanks to endothermy) are able to keep a quasi constant level of activity despite external change in temperature. It allow them to forage during hot and cold whether for example. This is a very important advantage but it often comes at the important energy cost. It is a trade-off between the benefit of homeothermy vs the energy cost of endothermy that will define the best interest of an organism.


Are there differing organelle to cytoplasm ratio in animal cells? Could anyone provide me with examples of cells with high organelle to cytoplasm ratios (heavily packed), and examples of cells with low organelle to cytoplasm ratios (sparsely packed)?

Yes.

The structure of a cell is highly related to its function. For example, a plasma B cell (a type of immune cell) contains lots of ER and Golgi because its job is to secrete antibodies, which are proteins, in your body. It has to create a lot of proteins, so a plasma B cell has a lot of organelles that help create, assemble and secrete proteins.

There are so many examples you can use.


Can/Have cancer cells be/been used in stem cell culture lines? Since Cancer cells have unlimited growth potential, can they be induced towards totipotency and pluripotency?
If so, can cancer cells be used in stem cell culture because of similar properties of unlimited replication?
Can they be used in cell lines to culture viruses even?

Cancer cells can be and are used in cell culture. HeLa cells were the first human cell line to be grown in culture and they were derived from a cervical tumor.

That being said, Cancer cell lines would not necessarily be used for stem cell work. They have sustained too many mutations to study the type of questions that stem cells are used to study, though as MattDMo points out, teratomas, tumors that originate from stem cells, can be used in stem cell research as a model for Stem Cells in culture. Also, they could never be used for therapeutic purposes.

As for viruses, HeLa cells were used by Jonas Salk to develop the polio vaccine, so cancer cells are used in viral research.

Edits in italics.


Are there cats with black skin? Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice.

I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?

Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.

Also, take an average cat - and shave for surgery:

Note pigmented skin matching dark stripes.


What is the ultimate source of ADP/ATP in humans? I am teaching myself Cell Biology from the internet. Despite my usually good Googling skills, I'm stuck in a loop with this question.

Q: What is the source of ATP?

A: ADP

Q: What is the source of ADP?

A: ATP

At first I thought that ATP synthase actually created ATP from scratch as intimated here:

  ATP synthase is an important enzyme that creates the energy storage
  molecule adenosine triphosphate
  Wikipedia

I then realise that ATP synthase doesn't create ATP so much as convert ADP.

My Question

Can humans synthesise ADP/ATP from scratch. If so, where are these phosphates made and if not what food source provides them and how? Also, where do we get the phosphorus?

Thanks

Phosphorus is a very common nutrient, found in high levels in proteins, which are in such foods as milk and milk products, meat, beans, lentils, nuts, and grains, especially whole grains. Phosphorus is found in smaller amounts in vegetables and fruit, as well. Adenosine can be found in many of the same foods, both as free ATP/ADP/AMP, and as part of the DNA found in all animal and plant-based foods (are there any other kinds?).

Adenine (the nucleotide base before the addition of ribose creates adenosine) is synthesized via the purine synthesis pathway, whose ultimate product is IMP, or inosine monophosphate. IMP is then converted to adenylosuccinate, then to AMP, which is then phosphorylated to ATP. It should be noted that, as is the case in most biosynthetic pathways, this one requires ATP to power it along, meaning it takes ATP to make ATP.


What is the origin of "melting" in molecular genetics? I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that they're referring to the separation of DNA from the double stranded form to single strands.

Maybe it's just because chemistry isn't my thing, but when I think of melting I think of a solid gaining enough energy to become a liquid. How did the term melting come to apply to DNA in this way? Does the term melting have a more general definition in terms of thermal chemistry?

The melting temperature (Tm) of a double stranded DNA tract is defined as the temperature at which 50% of the DNA molecules are dissociated into single strands (and 50% form duplexes). Sure, it has a different meaning than in physics... but it is a really common term in molecular biology and I doubt people will stop to use it anytime soon!

There is a vast amount of literature about the calculation of Tm, which is very important also for practical applications, such as designing PCR primers. This page has some explanations and references about the maths behind it.

I am not sure when the term first appeared, but it has clearly be used since the dawn of molecular biology.

DNA denaturation/renaturation dynamics were first studied in the '60s.

See for instance:

STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: BIOLOGICAL STUDIES - J. Marmur and D. Lane - PNAS, 1960

Although Marmur and Lane do not talk about melting temperature, we can find the term already two years later in this 1962 paper:

Effect of Concentration on the Formation of Molecular Hybrids from T4 DNA - Andrzej W. Kozinski and Michael Beer - Biophys J., 1962

Evidently the term was already common there, as they don't care to define it (it's even in the abstract).

Who first used it? I'm not sure, if anyone knows feel free to add a comment or edit the answer.


plant dormancy in different locations Say plant x has a dormancy period of y in location z, for instance in Sweden. We bring this plant to another location z', say France. Are there any results with respect to if/how the dormancy period would change? (I would assume such observations would be of interest to understand how plants adapt to/can cope with climate change.)

It might depend on the signal that the seed uses to end dormancy. Some seeds require 'vernalisation', that is a prolonged period of low temperatures, for them to germinate successfully.  If they don't have the cold period, they don't germinate because they 'think' that they haven't had winter yet.

Dormancy can also depend on the conditions that the parent plant lived under, so it is quite possible that if two plants were grown in different environments, their seeds would have differences in dormancy. This study looked at that effect in the 'model plant' Arabidopsis thaliana:
Donohue K., Dorn L., Griffith C., Kim E., Aguilera A., Polisetty C. R., Schmitt J. Environmental and genetic influences on the germination of Arabidopsis thaliana in the field. Evolution. 2005;596(1):740–757.

This paper gives a good review of Seed Dormancy and Germination in Arabidopsis from a few years ago:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243337/#i1543-8120-70-1-1-b60


Software to calculate Fst from sequence data I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations for example)

I've been looking at FSTAT but it doesn't run on MAC.

Do you have any easy alternative?

If You are familiar with R, try package adegenet. It contains very nice tutorials explaining its usage, including the very R basics. If You require graphical interface, install RStudio - very nice front-end for R. There are more possibilities how to calculate Fst in R, but adegenet is one of the most powerful genetic packages there.


Specific Neurons that Require Glucose I've been doing a bit of armchair biology lately, and have been interested in the metabolic flexibility of neurons. My understanding is that, besides glucose, many neurons can metabolize lactic acid or ketones. However, some reports point out that some neurons can only metabolize glucose, without ever indicating which, or in what regions of the brain. (It may be that the following exert is suggesting that each individual neuron is using a mix of fuel sources. I have not been able to find much via the Google.)

From the linked book:

  When changing slowly from a carbohydrate diet to an almost completely
  fat diet, a person's body adapts to use far more acetoacetic acid than
  usual, and in this instance, ketosis normally does not occur. For
  instance, the Inuit (Eskimos), who sometimes live almost entirely on a
  fat diet, do not develop ketosis. Undoubtdly, several factors, none of
  which is clear, enhance the rate of acetoacetic acid metabolism by the
  cells. After a few weeks, even the brain cells, which normally derive
  almost all of their energy from glucose, can derive 50 to 75 percent
  of their energy from fats.

Which neurons and regions of the brain can only burn glucose?

The source you link does not report that certain neurons only use glucose, and I am unaware of any reputable source that makes this claim.

Neurons do tend to use glucose as an energy source when it is available, and the brain does not tolerate sudden drops in glucose. However, as your source notes, other energy sources can be utilized given enough time to adjust, such as during starvation/fasting as well as suckling.

Cahill, G. F., Herrera, M. G., Morgan, A., Soeldner, J. S., Steinke, J., Levy, P. L., ... & Kipnis, D. M. (1966). Hormone-fuel interrelationships during fasting. The Journal of clinical investigation, 45(11), 1751-1769.

Hawkins, R. A., Williamson, D. H., & Krebs, H. A. (1971). Ketone-body utilization by adult and suckling rat brain in vivo. Biochemical Journal, 122(1), 13-18.

Nehlig, A., & de Vasconcelos, A. P. (1993). Glucose and ketone body utilization by the brain of neonatal rats. Progress in neurobiology, 40(2), 163-220.

Owen, O. E., Morgan, A. P., Kemp, H. G., Sullivan, J. M., Herrera, M. G., & Cahill, G. J. (1967). Brain metabolism during fasting. The Journal of clinical investigation, 46(10), 1589-1595.

Pollay, M., & Alan Stevens, F. (1980). Starvation‐induced changes in transport of ketone bodies across the blood‐brain barrier. Journal of neuroscience research, 5(2), 163-172.


Does cartilage connect to other cartilage? In the definition of a Ligament in Oxford states:

  A short band of tough, flexible fibrous connective tissue which
  connects two bones or cartilages or holds together a joint.

the wording of "two" prior to bones or cartilages sounds like it could be bone to bone, cartilage to cartilage, and bone to cartilage.

Are all of these combinations correct? If so, is there a good example where each one can be seen for reference?

A ligament can connect two bones:

Picture 1: Knee joint ligaments (source: Wikipedia, Creative Commons license)

A ligament can connect two cartilages or a bone and a cartilage:

Picture 2: Larynx ligaments (source: Wikipedia, Creative Commons license)

Ligaments can also connect internal organs:

Picture 3: Ligaments connecting abdominal organs (source: Wikipedia, Creative Commons license)


Is nucleoside-triphosphate delivery to RNA or DNA polymerase active or passive? Are nucleoside triphosphates (NTPs) actively delivered to RNA polymerase (similarly dNTPs to DNA polymerase) through some active chaperoned process, or are they so abundant in the nucleus that they rely simply on stochastic diffusion?

Are there any relevant papers on this process?

The amount of dNTPs is so important and sensitive the level of dNTPs should be optimum  not lower or higher. Lower amounts lead to insufficiency  and higher amounts lead to increased mutation rates. Also, this optimum amount of dNTPs should last for a couple of minutes to supply dNTPs needed for replication. The delivery of dNTPs is due to molecular signalling & stochastic diffusion.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847218/

"Eukaryotic cells contain a delicate balance of minute amounts of the four deoxyribonucleoside triphosphates (dNTPs), sufficient only for a few minutes of DNA replication. Both a deficiency and a surplus of a single dNTP may result in increased mutation rates"

http://onlinelibrary.wiley.com/doi/10.1111/j.1349-7006.2010.01719.x/pdf

"Optimization of intracellular concentrations of dNTPs is critical for
the fidelity of DNA synthesis during DNA replication and repair
because levels that are too high or too low can easily lead to
increased rates of mutagenesis"

http://www.nature.com/ncb/journal/v14/n7/full/ncb2540.html

"Production of deoxyribonucleotide triphosphates (dNTPs) is essential for DNA synthesis during replication and repair, and abnormal or imbalanced dNTP levels increases mutation frequency. Pagano and colleagues now demonstrate that the SCF-cyclin F ubiquitin ligase controls dNTP production during the cell cycle and following genotoxic stress"

http://www.ncbi.nlm.nih.gov/pubmed/22234185

"alterations in dNTP pools are associated with increased mutagenesis, genomic instability and tumourigenesis"


Allergy vs. Immunity What is the difference between these two phenomena in our organism: allergy and immunity? Both cause producing of antibodies which struggle against antigens. Is it true, that allergy always leads to destruction of tissues and organs? If yes, why does destruction take place in case of allergy but not within immunity?

First line of wikipedia > Immune system

  The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease

First line of wikipedia > Allergy

  Allergies, also known as allergic diseases, are a number of conditions caused by hypersensitivity of the immune system to typically harmless substances in the environment.

In other words, the immune system is here to defend the organism against diseases. However, sometimes this immune system misinterprets a harmless substance and start triggering an immune response against it. Such immune response against harmless substance is called an allergy. An allergy is hence a defect of the immune system. There are other defects of the immune system though, such as autoimmune diseases.


How to use swiss-mod to predict the secondary structure and 3D structure of a protein? I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling.

I'm getting confused with how and when to use Jpred, swiss-mod, and PDB. So far, I got the sequence from scanprosite, put it into swiss-mod, but what next? When does jpred come in?

3D structure.
Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what the SWISS-MODEL server does, and I think it automates the BLAST alignments from PDB). If there are no similar structures, you can resort to ab initio modelling if you have a reasonably straight forward globular domain, otherwise you might need to draw in additional expertise.
There are so many specific factors that need to be taken into account for a project like this. Depending on what the model will be used for, different questions are relevant.
Secondary structure.
You will need a few different secondary structure predictors to make it convincing and then you will need to check that your secondary consensus matches your 3D structure. If they don't match you need to think about "why not?"
If there is a difference it usually indicates that some 3D interaction is involved in the folding, so your 3D model usually trumps the sequence structure predictions, but do check your 3D structure against the secondary structure predictions.
Secondary structure prediction is more useful when a 3D structure is not available and modelling one is not an option.


Does our brain emit any kind of waves? I am currently trying to start a research project, and this is the most important question that needs to be answered. I cant't move ahead without knowing the chemistry of the brain.

Cells in the brain communicate with each other through electrical (and chemical) signals. The electrical signals from millions of neurons add up, and can be detected from outside the skull. This is called electroencephalography.

The signals that are strongest when measured in this way are often periodic or oscillatory (i.e. wave-like), because similar electrical signals from many neurons support each other if they are active synchronously. In contrast, when neurons are firing in a disordered way, then their electrical signals can partially cancel each other out when measured from outside the skull.


A molecular marker for global protein synthesis I know that protein synthesis is governed by a lot of factors (I'm mostly studying the mTOR pathway), but I'm looking for some kind of marker that will indicate the global protein synthesis rates.

I know there are tissue-specific markers (like actin/myosin in muscle) but I'd like something more that is ubiquitous and is proportional to global protein production (maybe a muscle can make more or less myosin depending on whether there are some factors).

I assume protein synthesis factors (like mTOR, S6K1 etc.) are quickly regulated, so they cannot be used as markers.

So, what would serve as the best molecular marker?

The answer will not satisfy you. The truth is no protein marker will do.

On one hand you seem to be looking at some individual, representative protein, which you could measure by immunoblot. But most proteins are in scant concentrations, just as many as required for their job, and go up and down depending on their specific roles, rather than on general metabolic trends. Even if some general control mechanism increases protein synthesis across the board, in a cell proteins are 20% actin, 20% tubulin, 0.0001% 4E-BP and 0.0001% p70-S6K (made-up numbers for the sake of example), any 1% total protein increase you'd like to measure would be 200,000 easier to detect in tubulin than in p70-R6K. In order to be a marker of general control of protein synthesis, the marker protein you'd want to measure should be a plentiful protein, with little to no specific control.

On the other hand, those are the characteristics of a house-keeping gene. So you won't be able to normalize such a "representative" blot! Normalizing house-keeping by house-keeping, you will have pretty much no change.

Embrace labeling experiments. Even there, the right normalization is debatable. If anything, the fact that everyone does those, rather than looking at protein X, should be an indication of how much you will struggle to prove points about protein synthesis rate using anything else.


Microinjection method in C. elegans I have a question about the experiment that using microinjection to inject RNAi into the C. elegans. To prepare the dsRNA for injection, fist have to clone the gene of interest from the worm genome DNA and insert into a plasmid that has either T3 or T7 promotors. To clone the gene of interests, one has to design the primers. There is a paper descripting the protocol of the microinjection. Here is the link to the paper: http://labs.bio.unc.edu/goldstein/dudleygoldsteinmmb05.pdf
It is said that the primer for clone need to add sequence of T7 Promotor, but why? and why just add partial not complete sequence? why is it in the second step of PCR? Is it required to add the restriction enzyme site to both primers? Why?
Also in the feeding experiment, the plasmid(insert) is transformed into the HT115 strain and use IPTG to induce the expression of dsRNA. However, the microinjection is using dsRNA to inject the worm. So after cloning the gene of interest and insert into the plasmid, is the dsRNA expressed in the vitro before injection? And how? Thank you!

What they're doing is called two-step PCR. In step one, some gene-specific primers with tags amplify genomic DNA, but the product has adapter regions now added to each end. In the second step, you add primers that complement the tag/adapter region and have T7 promoter sequences at the ends. Your second product will have the adapter region, and the T7 promoters on the outside. The paper you provided shows they just modified the process: the first product is the gene of interest flanked by part of the T7 promoter, and the second product is the gene of interest, the T7 promoters, and restriction sites for cloning.

Design and implementation of high-throughput RNAi screens in cultured Drosophila cells

It looks like from what they know, adding the partial T7 in the first step is just optimization for their procedure. You want to add those restriction sites to wherever you can imagine you want your insert cut by the endonuclease. In a ligation step for inserting the gene fragment, you'll have cut your plasmid open with the same restriction enzyme you use to cut the insert, so that it ligates in nicely.

The HT115 strain has some nice properties you can read about here like a lack of RNase III that would degrade dsRNA, so it's suitable to produce the actual dsRNA inside of, and for the feeding experiment this is fine. For microinjection, they're using in vitro transcription kits to get dsRNA from the PCR product, which should be a gene of interest flanked by T7 promoters and restriction sites. T7 polymerase will simply transcribe everything downstream of it's promoter, so we don't have to worry about the restriction sites except for the feeding experiment.

MEGAscript® T7 Kit

The above kit comes with a T7 enzyme mix, NTPs, DNase, reaction buffer, a stop solution, precipitation solution, etc. You should be able to follow the manufacturer's direction and get 100 µg RNA per reaction, according to the webpage. Then you purify the dsRNA. It's literally just T7 polymerases transcribing whatever is between the two promoters into dsRNA -and for that kit, linear DNA does work- and then you degrade any DNA, leaving you with the dsRNA.


Rate of Diffusion Through Cellulose Membrane From what I understand, the larger the molecular size, the slower the rate of diffusion and vice versa. However, after doing a lab (similar to this one) about diffusion through a cellulose membrane, my instructor said that despite substances having different molecular sizes, the rate of diffusion (thru the membrane) will be the same. Could someone further explain or did I hear incorrectly?

I think that your instructor was wrong.
For the type of experiment that you describe the dialysis tubing (cellulose acetate with pores) is acting as a semi-permeable membrane which can block the diffusion of a polymer (starch) but will allow the passage of a small molecule (glucose). The molecular weight cut-off of the tubing was probably 10 kilodaltons or greater, so glucose (180 daltons) would diffuse through the pores without hindrance, as would sucrose (342 daltons). But would the monosaccharide and the disaccharide move through the membrane at different rates?
This table gives values for the diffusion coefficient (D) of these two sugars as:

glucose 6.7 cm² s⁻¹ × 10⁻⁶
sucrose 5.2 cm² s⁻¹ × 10⁻⁶

The time τ to travel distance L by diffusive movement is given by
τ = L²/6D
Here all that matters is that τ is inversely proportional to D, so we can estimate that glucose 'diffuses' approximately 30% faster than sucrose.
Bulk diffusion is, of course, driven by a concentration gradient: if you were to start with, say, 0.1 M each of glucose and sucrose in a dialysis tube the glucose should reach equilibrium with the surrounding liquid faster than the sucrose.


Is Webmedcentral a reputable scientific publisher? I am a student, and I have written a paper (in drug discovery) which I want to publish. While searching for possible journals I came across Webmedcentral.

Is Webmedcentral a reputable scientific publisher?
What is the impact factor for this journal?

I checked this site and its journals in Scopus.com based on its "ISSN 2046-1690" but nothing was there. they are fast in submitting and publishing but it is not some thing great by it self. I think maybe its better to find some where better to publish your article(s).


How was gene therapy able to cure diseases through the transformation of actively dividing cells? I thought that gene therapy, when performed on target cells that regenerate themselves constantly, can be effective for a limited time only. I.e., the effect gradually wears off after a while, depending on how fast the target cells renew themselves. In other words, the patient needs to continue receiving gene therapy every so often to keep getting desired effect.

On the other hand, when targeting cells that do not divide/renew, such as an eye, gene therapy can and actually did cure blindness once and for all, and the patient no longer needs gene therapy injections.

So what about the other diseases that gene therapy allegedly cured? I think they include blood disorders like hemophilia and some serious immune system disorders? I thought they mainly involved cells that do regenerate, like bone marrow and liver?

Short answer
Both dividing and non-dividing cells can permanently be modified with gene therapy by using vectors that incorporate their payload in the host's chromosomal DNA

Background
Vector-based gene therapy can be applied by using vectors, such as modified retroviruses or adenoviruses, that incorporate their payload in the host's chromosome.

Whether the transformed cells are replicating yes or no, the parent as well as any possible daughter cells will carry the new DNA. For example, immunodeficiency has been treated successfully with gene therapy, but the first trials resulted in blood-bone cancers, because the stem cells started to proliferate uncontrollably, hence dividing cells definitely can be permanently transformed. In fact, when germ line cells are transformed in this way, even the offspring of the host will inherit it.

Sources
- American Medical Association
- Learn Genetics
- Utah University


What kind of bird is this? Found in southwest Michigan.  It appears to have fallen from a nest.

The body shape does seem to indicate it's some kind of heron/egret (12 species, of which, have been previously found in Michigan [according to Wikipedia]).

The seemingly large size from your picture (please edit with actual or best approximation of size), the tufted feathers on the head, white face, and the start of a black line on the anterior edge of the eye all suggest that this could be a great blue heron.

Great blue herons are typically grey (not the dark almost black of your specimen), but I did find some photos with nestlings /fledglings with darker plumage, including below:

 Source: Wikipedia


Parents are Rh +ve and child Rh -ve Suppose the two parents of a child have blood groups A+ve and O+ve, and the child has O-ve type. For blood group, there are two alleles. Since the child has O, the father must have one 'A' allele and one 'O' allele.

Does such a reasoning hold for the Rhesus factor too? Should I interpret that both the parents have one + allele and one - allele?

Rhesus antigen (Rh-D) is inherited in an autosomal dominant pattern.  Therefore you are correct in your reasoning.

Simple problems like this are often best worked out using Punnet Squares, shown below for the scenarios you have considered.

Because the inheritance pattern is dominant, if either parent was homozygous (DD) for Rh-D then 100% of their offspring will be Rh+ve.

In order to have a rhesus negative child, neither parent must be homozygous for the D allele.  You are correct that one possible scenario is a matching pair of heterozygotes:

In this situation 3/4 of the children are rhesus positive and 1/4 rhesus negative.

There is an alternative where one parent is Rhesus negative and the other positive.  In this case there is one heterozygous parent and one homozygous negative parent:

In this scenario, half of the children are rhesus positive and half rhesus negative.


Is there an enzyme for the transformation of the hydroxyl group? I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme.

The substrate is aromatic hydroxyl group. Product should not have hydroxyl group.

How should these types of queries be searched for?

It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products.

ReBIT allows you to query enzymes by your molecular structures of interest using their SMILES code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.

If you're seeking to do a more extensive search, I would suggest BRENDA. There you can search for reaction substrates and reaction products and even both. Both strategies may provide you with an enzyme that does the transformation chemistry that you're looking for.

Lastly there is always ENZYME, The Enzyme Data Bank. There you can search for chemical compounds. I did a search of coumarin and there are a few hits but they are for methyl-transferases and hydrolases. A more extensive search may give you a few leads.

Most of the concepts that I just suggested are explained in the following review: De novo biosynthetic pathways: rational design of microbial chemical factories.


What are the differences between Signaler and Primer pheromones? I have searched few authentic books and have found the following difference between them.

Signaler pheromone induces fast reaction in the recipient and the Primer induces slow reaction.

But I did not find any book that discriminates their function.

P.S. I have read Wikipedia and I'm not counting on it.

A good example of a primer and a signaler pheromone could be in the recently discovered pheromone system in pennate diatoms (unicellular algae). When diatoms reach a certain size as a result of successive divisions (they get smaller with each vegetative division) both mating types start to produce a first pheromone that provokes cellular responses in their mates: 1) to stop dividing vegetatively and 2) to produce either another pheromone (a cell attractant, by one of the mating types) or to induce a sensing system to locate their mates. So, the 'Primer' pheromone would be the first, and the 'Signaler' the second pheromone, i.e. the attractant. A similar system exists in fungi. The evolutionary explanation is likely that organisms don't need to invest in pheromones and their associated repertoire of sex genes when mates are not present.

References:

Metabolomics Enables the Structure Elucidation of a Diatom Sex
Pheromone
Pheromone signaling during sexual reproduction in algae


Fe in bacteria light-harvesting system Reaction Center Is the Fe in the reaction center of bacteria light-harvesting system bounded or free atom?

After reading the comments in the first answer, I believe OP's question is this:

  What kind of bond occurs in the Fe of the reaction center of bacteria light-harvesting system?

Before continuing, it's worth mentioning that an ionic bond is a kind of bond, and that atom would not be considered free (whatever that means) even if its bonds were only ionic ones.

However, to make things here even more unequivocal, the bonds of that Fe are covalent bonds (thus, that atom is not free under any definition...).

According to the Protein Data Bank in Europe, this is the x-ray high resolution structure of the photosynthetic reaction center from Rhodobacter sphaeroides at pH 10, zoomed at the portion that contains the Fe (link here):

You can see that the Fe has 5 bonds, thus summarised:

  [SQUARE_PYRAMIDAL] - HIS 190L - HIS 219M - HIS 230L - GLU 234M - HIS 266M

And what kind of bond are those?

According to the same PDBE entry, they are covalent. Have a look at the color code in this page: http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2uxj&ligandCode3letter=FE

Here is a screenshot, in case the link above doesn't work. Have a look at the 5 red bonds (red represents covalent... not very legible, I know):

Source: Protein Data Bank in Europe


Why are some fungi poisonous? There are many poisonous fungi in nature. For example Amanita Phalloides.
What reasons could a fungus need poison for? Some species, like venomous snakes, use poison to kill other species as prey. But what about fungi? I can't think of any purpose for poison in fungi. If poison has no real function in fungi shouldn't evolution get rid of it?

The same reason some plants are poisonous: to stop animals from eating them.

The visible part of the fungus is called, rather misleadingly, the fruiting body. It exists to produce and spread spores and thus produce the next fungal generation. Getting eaten, rather obviously, inhibits its ability to do this. Being poisonous discourages animals from eating the fruiting body and thus permits it to complete its life cycle.


How many proteins are in the Earth's proteome? Humans alone have thousands of proteins. With that in mind, it seems like the total number of proteins among all species would be very large.

Are there any available estimates for how many proteins exist on earth in all organisms? I'd also be interested in how many of these are unique proteins as opposed to proteins that are very similar to other proteins, i.e an estimate of non-redundant proteins alongside the redundant proteins.

Current records
According to Uniprot, there are 85,381,808 protein records, and with the UniRef90 filter (i.e removing records that can be represented by an entry with at least 90% sequence similarity), there are 42,424,511. However, these databases are moving targets and will change over time. We will sequence more species, find novel splice isoforms, and various other methods will expand the databases. Indeed, the databases will be truncated also from time to time as some hypothetical proteins may be based on genes that turn out to not code for proteins after all.
In 2007, a study estimated that the earth's proteome would contain around 5 million sequences, and that the majority of these would be elucidated by 2012. I suspect this is a very thorough study, however, a lot has changed in the last 10 years. This estimate is actually less than the nearly 9 million species estimated in more recent studies.
Approximate estimate
So let's do some back of the envelope maths. Let's assume the article estimating nearly 9 million species is about right, and that we've only catalogued some 1.2 million. But UniProt isn't even close to this number.UniProt contains 25477 scientific names in it's controlled vocabulary. So for 25 thousand names, we have 85 million protein records. What if we had 8.75 million names?
Let's assume:
$\frac{Predicted~Proteins}{Predicted~Species}=\frac{Known~Proteins}{Known~Species}$
We can rearrange this to:
$\frac{Predicted~Species~\times~{Known~Proteins}}{Known~Species}= Predicted~Proteins$
Generous estimate (Uniprot, 335527 proteins per species):
$\frac{8750000\times{85381808}}{25477}=2.932413e^{+10}$
Conservative estimate (Swissprot, 41 proteins per species):
$\frac{8750000\times{554241}}{13408}=3.616952e^{+7}$
For the sake of completeness let's assume the number of <90% identical proteins will remain around half that value. We can say that there might be around $1.8e^{+7}$ to $1.5{e}^{+10}$ "unique" proteins, less than a trillion ($1e^{+12}$). Given the absurdly generous 335 thousand proteins and very stingy 41 proteins per species, we can be fairly certain that if there are indeed 8.75 million species, the number of proteins will fall between those estimates.
The biggest assumption here is that the proteins have a linear relationship with species which is unlikely to be the case, and at the generous estimate we are pretending that there are no proteins in UniProt that don't have species annotation. As for Swissprot, this only includes proteins that have been manually curated, so this ignores many proteins that are safe to assume exist and typically only covers proteins that are of interest to scientists.

A minor correction to your question, the UniProt lists ~20 thousand protein coding genes in the human proteome, not millions. Those protein coding genes are subject to various post translational modifications and isoform splicing, so there will be more final proteins than 20k.


Can neurons take oxygen from air? Why can't/don't neurons take up atmospheric oxygen or at-least dissolved oxygen (like amoeba does) to survive and do all life processes outside animal body ???

Short answer
Neurons, and in fact all cells in the body, utilize water-dissolved oxygen to fuel their energy metabolism.

Background
The brain, and tissues in general, obtain their oxygen through passive diffusion (Fig. 1). Water, carbon dioxide, and oxygen are among the few simple molecules that can cross the cell membrane by passive diffusion,  or osmosis (source: Estrella Mountain Community College).

The body uses hemoglobin to transport oxygen (Fig. 1), because passive diffusion would take too long, especially in oxygen-hungry warm-blooded animals like humans.

Gaseous exchange in fluid medium is mediated by hemoglobin. source: Kokyo


Affinity Column of membrane bound receptors I understand affinity columns can be used to study the ligand/enzyme affinity. But is an affinity column able to be used for membrane bound receptors? I

This is a classic reference where Stanley Cohen and Graham Carpenter used an affinity column made out of the epidermal growth factor (EGF), and used it to purify the EGF receptor: JBC 1980


Don't the radioactive labeled molecules of dNTPs or DNA harm themselves or their surroundings? I'm reading some papers for the first generation sequencing methods and some earlier than them, like Ray's Wu first time DNA sequencing from a λ phage virus cohesive 5' ends. Ray Wu, like Maxam-Gilbert and Sanger, used 32P / 3H to label either dNTPs or DNA molecules.

But what happens if you add such radioactive materials inside a test tube with DNA and other molecules like DNA Pol I? For example,  32P emits electrons at 1.709 MeV. Couldn't these high energy electrons harm the DNA or Pol I molecules (bonding destruction), that are present nearby at the time of reaction?

It's worth considering how many high energy electrons are actually released compared to the number of molecules in the tube. For instance, I routinely work with $^{32}P$-labeled DNA, and measure the specific activity of samples by scintillation counting. For me, a very hot stock sample of labeled DNA (~1000x more concentrated than I would use in an experiment) will register on the order of $10^8$ disintegrations per minute (dpm). That means each minute, about $10^8$ beta particles are emitted by decaying phosphorous atoms inside the sample. But the amount of DNA molecules in that same tube is about 50 pmol, or about $3 \times 10^{14}$ molecules.

So if each of those beta particles were absorbed by a DNA molecule in the same sample, thus damaging it, that would be a rate of self-damage of $10^{-6} min^{-1}$. Of course, most of those beta particles actually make it out of the tube, so the actual rate of self-damage is much lower still. Since we're probably interested in measuring processes on much shorter time scales than this self-damage rate, it becomes negligible.


What is the effect of a pure-oxygen environment on a plant? Just read What's the effect of oxygen deficit on plants? ; and wondered whether the opposite would have any effect on a plant.

That is to say, if a potted plant were placed under a bell-jar and the air within replaced by pure oxygen would the plant starve? If the environment/soil were loosely radioactive, would it make a difference?

As hinted in other answers, the key problem with a pure oxygen environment would be the inability to photosynthesise caused by the absence of carbon dioxide.
The overall equation for photosynthesis (the process in which energy from the sun is harnessed to fix inorganic carbon dioxide into organic molecules that  are of use to the plant) is:
6CO2 + 6H2O → 6O2 + C6H12O6
The carbon dioxide required for photosynthesis is obtained from the atmosphere by diffusion through stomata on the leaves.  Therefore if the atmosphere contains no carbon dioxide (i.e. in the scenario you suggest) photosynthesis would not progress, meaning glucose used by the plant in respiration would not be replaced.
This would eventually lead to the cessation of cellular respiration due to a lack of reactant.  This would cause the plant to die.


Are cryovials really better than regular tubes for cryopreservation? What is the rationale for using cryovials instead of regular, sterile centrifuge tubes for the storage of mammalian cells?

With a good aseptic technique and without touching the cap directly, there should not be a significant risk of contamination in regular microcentrifuge tubes. Is the plastic quality fundamentally different (in terms of leaching chemicals etc)? Both kinds of tubes are usually made of polypropylene so it's not obvious how they would otherwise differ.

There may be a difference when storing things in direct contact with liquid nitrogen (as regular tubes may leak), but many cells can be stored for years in a -80°C freezer, a temperature at which most molecular biology tubes are perfectly stable.

I do not have data to back this up, but can say that from experience, cryo vials are a much better solution for storing your valuable cells. First, their plastic is thicker, meaning they’re more sturdy and can handle a deep freeze much better. The killer feature is the screw caps, which means that they will never pop open accidentally due to mishandling or temperature changes (which has happened me with samples in microcentrifuge tubes). These screw caps also allow much more efficient storage in expensive cold conditions (liquid nitrogen will be best for cells long term) and easier retrieval from boxes that are freezing cold.

Microcentrifuge tunes may suffice but cryo vials exist for a reason.


What does genetically tractable strain mean? I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this kind of data, I wanted to have a look at some work that was already done. I found this interesting article: Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.
I think that it could be a good starting point. However, it is not easy to understand the whole article for me and I suspect
that the source of this difficulty is mainly due to the fact that I do not know what "Genetically Tractable Pyrococcus Furiosus Strain" means.
Searching in Google I found this article: Systematic evasion of the restriction-modification
barrier in bacteria, that explains:

Bacteria that are recalcitrant to genetic manipulation using modern
in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems.

Then it tells also that:

A strain that is not amenable to alterations of its genome or to the introduction of new genetic information during genetic engineering is termed genetically intractable.

Therefore, from this short explanations, I have an idea of what genetically intractable means. But, I still wonder why in the first article that I mentioned, the scientists should have been interested in sequencing such a genome (genetically tractable) and in comparing it with the one that was firstly sequenced (the so called reference strain) ? Moreover, what does genetically tractable mean?
Indeed, in the case of the first article, the following description is reported:

The best characterized of the Pyrococcus species is P. furiosus, the first to be isolated (19) and the first to have its genome sequenced (49). This organism has been studied by numerous “-omics”-based approaches, including transcriptomics by tiling (59) and DNA microarrays (14, 35, 51, 54, 57), comparative genomics (8, 33, 60), proteomics (32, 42), metallomics (11), and structural genomics (25). In many ways, it has become one of the model hyperthermophiles, a status recently sustained by the development of a genetic system for the organism (37). This was based on isolation of a variant in a lab strain population, designated COM1, which was highly efficient in taking up and recombining exogenous DNA in both circular and linear forms. The COM1 strain was obtained by targeted gene disruption of the pyrF. locus (PF1114) using a plasmid designed for double-crossover recombination (37).

Then what they do is:

The genome sequence of COM1 has now been determined, and comparison with the published sequence of the P. furiosus reference strain (49) (NC_003413) revealed a surprisingly large number of changes.

Thus, I do not understand (both in the case of this article and also in general case) what genetically tractable means (the description given by the article is not sufficient for me to understand) and why are we interested in doing the alignment between the reference genome sequence and the genome of genetically tractable strain ?
Sorry if my question could be trivial but my biological backgrounds are really poor. I reported the extracts of the articles because they give me an idea of the answer but, to be honest, I do not have fully understood them. Therefore, if you can explain me also those extracts, it would be great. Thank you in advance.

You've already basically got the idea of "genetically tractable": if we can readily modify an organism's genome using known techniques, then it's genetically tractable.
That's a moving target, of course, because the set of available techniques is constantly expanding, so this is more of a pragmatic definition than a taxonomic definition. It's a notion that's quite important, however, because it's far harder to study an organism or to develop applications if you can't manipulate its genome.  If you can manipulate genetics, then you can make knock-out strains, introduce new functionality, and apply many, many other powerful and useful biological techniques.
So now to the last part of the question: assuming you've now got a tractable strain, why compare it with the reference strain? Well, if you're working on engineered applications, you probably really don't need to (other than from curiosity).  If you want to use the tractable strain to study things about the original, reference form of the organism, however, then you need to know their differences in detail, in order to have some idea of how much your results obtained by manipulation of the tractable strain are likely to inform your understanding of the reference form.


Meaning of "auto" in trans autophosphorylation? Why this process called "auto"?
Is it because each tyrosine kinase receptor subunit of the RTK dimer has the ability to phosphorylate tyrosine or other amino acid residue present in other subunit of the RTK dimer's cytoplasmic tail? Is it because no new set of kinase enzyme is needed to phosphorylate them?

Receptor tyrosine kinases are proteins which float around in the cellular membrane. Upon binding of their ligand, the dimerize (two units form a dimer). This releases the kinase domains and the proteins start phosphorylating themselves over cross (meaning part a phosphylates part b and vice versa). This looks like in this figure below (from here, it is an interesting article):

Besides ATP this process needs no further co-factors so the "auto" refers to the ability of the RTK to phosphorylate itself upon activation. See more about autophosphorylation here.


Need help identifying multi-colored grasshopper I was out hiking with my friend when we ran across what I presume to be a grasshopper. It didn't seem very startled by our presence, and we were able to get some pretty cool pictures. I've been having trouble finding out what species it is. I was hiking near Albuquerque, New Mexico, and the grasshopper was about 1 - 1.5 inches in size. It was about midday when I saw it.

It's what's called a Rainbow or Painted Grasshopper (Dactylotum bicolor).

You can learn more at Bug Guide Species Dactylotum bicolor (where the picture is found) or Wikipedia' article on Dactylotum bicolor. The colour and pattern is very unmistakable.


Is agriculture really a net contributor of greenhouse gases? A lot of scientific studies and credible sources indicate that agriculture is one of the major contributors of greenhouse gases. The exact numbers seem to vary a lot, I've seen everything from 8% to 45% of global greenhouse gas emissions.

What makes me unsure how to really interpret these numbers is the fact that the process of growing feed to feed livestock, raising livestock, and then eating that livestock, is a cycle. The very same plants that the livestock is eating has during the course of its growth acted as a sink, i.e. absorbing carbon dioxide from the air. This is totally different from pumping oil out of the ground and burning it, which is (in the relevant short term) only production of greenhouse gases, without the sink.

I would assume that any serious study on greenhouse gases would factor in the entire cycle of absorption through animal feed and release back into the atmosphere, yet none of the studies I have seen say exactly how they arrived at the emissions.

Aside from the fact that oil is used in agriculture, when only considering the actual gases released from animal farming vs plant farming, it doesn't really make basic sense to me that there could be a net production of greenhouse gases - where did the surplus come from?

The issue is that it is not always a cycle, when you drain wetlands or burn forests to make more farmland that's not a cycle that is permanent change. A change that can continue having effects for centuries. Then of course you have petroleum fuel used to run tractors and the production of fertilizer which are often not cycles either but pure extraction.

One of the reason the number varies so much is because of disagreements about what falls under agriculture, does the fuel used to run a cargo ship moving bananas count? How about mining equipment used to extract minerals used to make fertilizer? Many simply forget to include things like peat bogs or changes in soil bacteria.

For instance draining a peat bog releases tremendous amounts of carbon, as a functioning net carbon sink is changed into a carbon producer. Sometimes this happens as water is diverted to farmland but often it is done just on purpose to get more farmable land. Exact impacts vary from place to place leading to wide ranges of estimations further complicating it.


Help me identify species of fruit fly? I found this fruit fly in Pune/India. It was about 1 cm in size. I explored info on several species in same region, but they were different in appearance, especially that black spot in middle of body.

This insect might be Bactrocera dorsalis.

It looks similar to this species based on the characterstic yellow spots, shape of the abdomen, as well as the light brownish orange stripes on the abdomen.

I had arrived at this conclusion by reverse-image searching the second picture that you have posted and observing the thorax and abdomen patterns. This image shows a very similar pattern as shown in your second picture:

The Wikipedia article has quite some stuff to say,

  Bactrocera dorsalis is a species of tephritid fruit fly that is endemic to Southeast Asia, but has also been introduced to Hawaii, the Mariana Islands and Tahiti. It is one of the major pest species in the genus Bactrocera with a broad host range of cultivated and wild fruits.

Considering that you had found this insect in Pune, it makes a lot of sense to conclude that this is, in fact, the insect that you have found.


Why does closing one eye in bright light allow me to open the other? I often find it physically painful to open my eyes past a squint after stepping out into the full summer sun. However, if I close one eye entirely, I can keep the other open without pain. This seems odd. Naively, one would assume the pain results from too much light entering the eye and doing some sort of damage to the interior, but if this were true, closing one eye would have no effect on the other. Does the fact that it does imply the discomfort is actually related to (e.g.) the sum-total of information reaching the optic chiasma?

A couple of factors play into this. First, you're halving the number of nociceptors that are signaling the brain. Second, there is a psychosomatic effect. Your brain continuously combines the visual data from both eyes to form one image. With one eye closed, your brain combines the brightness of both inputs to form an image that is roughly half as bright as reality. As a result, your brain not only ignores a portion of the nociceptor signals from the open eye, but it also doesn't assume the presence of pain like it normally would.

I've no publicly accessible sources to cite, as this is something I learned in my EMT class. Someone actually asked your same question in class


what benefits does lab procedure Realtime PCR have in gene silencing experiments? RT-PCR performed in gene silencing but mechanistically what are the benefits of this procedure?

RT-qPCR amplifies mRNA molecules present in a cell, if you have the right primers for it. The whole point of RNAi (the "gene silencing" that I think you're referring to) is downregulating the expression of a specific gene, so you'd expect the mRNA transcript of said gene to be not present (rather, present at very low concentrations at any given timepoint) if indeed the interference has worked.

Therefore, after RNAi has been performed, you can check by qPCR that there are indeed very low levels of the specific mRNA present in the cell. You might want to also perform a Western Blot against control cells transfected with scramble siRNA (where nothing should be downregulated, think of it as an "empty" siRNA), to check that protein levels are indeed much lower than in "regular" cells.