Does tremor frequency generally increase as Parkinson's disease progresses? I've been trying to research this question, but most if not all the on-line journals require costly subscription, and the studies that are posted look at tremor frequency with regards to other factors.

My question has to do with the tremor frequency, starting at early onset to later stages of Parkinson's disease - over the course of the disease, and without drug treatment (such as L-dopa), does the tremor frequency generally increase?

Frequency of tremor typically remains constant for the person. Levadopa (sinemet) does not change the frequency.

Typically the tremor frequency will be in the range from 3Hz to 7Hz.  There is a common phrase when dealing with PWP (Person With Parkinson's Disease). If you have seen one PWP, you have seen one PWP.

Currently I am part of a study by the Micheal J Fox Foundation using Pebble Watches and Smart phones to monitor PD.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1014720/
Hughes AJ, Daniel SE, Kilford L, Lees AJ (1992) Accuracy of clinical diagnosis of Parkinson’s disease: a clinico-pathological study of 100 cases. J Neurol Neurosurg Psychiatry 55: 181-184.

https://blog.getpebble.com/2014/08/25/mjff-intel-parkinsons/


How to predict Protein-Protein Interactions from a pair of gene symbols? I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The existing PPI webservers I've looked at (ClusPro and HADDOCK) require that I use PDB ID's as input. Unfortunately, PDB ID's don't always exist for the gene symbols I'd like to compare. I believe I need either:

a way to generate PDB files myself (perhaps with a folding program?) and then connect/upload them to a PPI webserver.

or

a way to find the most similar sequence that does have a PDB ID and upload it to a PPI webserver.

Am I understanding my problem correctly? Are there resources that can help with 1 or 2?

This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need some experimental data on the structure of your proteins.

If your proteins have not been structure determined, the next best thing is some kind of homology model, that is, a prediction of your protein structure based on a known structure of a homologous protein. These can be more or less accurate, depending on how close the homolog protein is. If specific domains are interacting, it may be enough to create a model of the domain only.

There are online tools available for homology modeling, for example swiss-model from the expasy site. This is not an automated process though --- creating an accurate model requires some skills. You should read the publications describing these tools and make sure you understand the process and error souces, and perhaps contact an expert if in doubt. Good luck!


Why do plants produce so many hybrids as a kingdom? Why do plants produce so many hybrids? I have read that they are the largest kingdom of organisms to do so. Does this have something to do with polyploidy events?

Yes, it has very much to do with the poliploidy events. Specifically if you look at the grasses, most grasses that are diploid (eg., AA, BB), cannot hybridize, but in some rare events when they form polyploid (AAAA, BBBB), they can readily hybridize to form fertile progenies (AABB).


Hardy weinberg equilibrium and Wright Fisher model Is the hardy weinberg equilibrium derived by using a model similar to the Wright Fisher model, just without assuming genetic drift and finite pop size? Both seem to use the same assumptions except Wright Fisher takes into account finite pop size and genetic drift. What is the model used to derive Hardy-Weinberg equilibrium called?

Welcome to Biology.SE

When you talk about the 'Wright-Fisher model' I suppose you are referring to the 'Wright-Fisher model of genetic drift (WF)'  involving the use of a binomial distribution.

You are correct that the two models make very similar assumptions. However those assumptions are generally speaking found in a large set of different models just because they often simplify the math. I think it is quite wise to consider these two models as very much independent.

Shared assumptions

Both the WF and the Hardy-Weinberg model (HW) assume

non-overlapping generation
panmictic population
absence of selection, migration and mutation
random mating
no sex-ratio bias

Of course, violation of some of these assumptions are relatively easy to model but such complication is often not taught in intro classes to population genetics.

Wright-Fisher model derivation

Let $2N$ be the total number of haplotypes, where $N$ is the population size. I here just assumed a diploid population but derivation for a haploid population is just as easy. Let $k$ be the number of occurrences of allele A, so that the frequency of the allele A is $p=\frac{k}{2N}$. Assuming sexual reproduction only, the number of occurrences of the allele A in the next generation is

$$k' = {2N \choose k} p^k (1-p)^{2N-k}$$

Quick side note: Effective population size

The variance of this distribution is $var(k') = 2N p (1-p)$. The variance of the allele frequency in the next generation is therefore $var(p') = var(\frac{k'}{2N}) = \frac{1}{4N^2} var(k') = \frac{2N p (1-p)}{4N^2} = \frac{p(1-p)}{2N}$.

Replacing $N$ by $N_e$ and solving for $N_e$ yields

$$N_e = \frac{p(1-p)}{2 var(p')},$$

which is the definition of the effective population size $N_e$.

Wright-Fisher model assumptions

The WF does not per say assume a finite population size, it is just that when the population size is infinite, the model loses all of its appeal!

Hardy-Weinberg model derivation

See here for a more complete discussion

The derivation of Hardy-Weinberg genotype frequencies is simple enough to not rely on any pre-existing model. Let's consider the simple version of the HW model, the one with a bi-allelic locus. The two alleles A and B exist at frequency $p$ and $1-p$ respectively. Imagine you have to draw an allele from this population. The probability to draw a given allele is equal to its frequency. Now draw a second allele. Assuming the population is large enough or assuming that selfing is allowed, the probability of drawing a given allele is still the same at the second draw than at the first draw.

As such the probability of drawing the allele A twice is simply $p p = p^2$. Similarly the probability of drawing the allele B twice is simply $(1-p)(1-p)=(1-p)^2$. The probability of first drawing the A allele and then the B allele is $p(1-p)$ and the probability of first drawing the B allele and then the A allele is $(1-p)p$. If we don't make the discrimination between AB and BA genotypes and just call them all AB, then the frequency of the AB genotypes is $2p(1-p)$. Of course $p^2 + 2p(1-p) + (1-p)^2 = 1$.

Hardy-Weinberg model assumptions

It is common to say that HW assume infinite population size. This is correct if you make from HW the interpretation that the genotype frequencies are exactly at $p^2$, $2p(1-p)$ and $(1-p)^2$ and that no evolutionary change will occur. But if you interpret HW as indicating the expected genotype frequencies from which deviation exist, then you do no make the assumption of infinite population size. Under this second interpretation, one can test deviation from HW expectations with a binomial test (or most often, when the population size is large enough with a $\chi^2$ goodness-of-fit test).

Related post

Solving Hardy Weinberg problems is very related and offers a good tutorial.


Anatomical differences between herbivores and omnivores What are differences of herbivores vs omnivores? I do not mean dietary differences (obviously), but physical ones.

E.g., afaik herbivores have a much longer digestive tract than carnivores; then there is the difference in teeth, possession of carnivorous instincts or lack thereof, etc.

But where is the distinction between herbivores and omnivores? Is there a clear distinction at all, or is the border between the two groups somewhat fuzzy? Or are omnivores merely herbivores who are less picky?

EDIT

As pointed out in the comments, the last sentence seems to ask for dietary differences. It is not meant to; the only difference I am aware of is dietary, so it asks whether there are any anatomical distinctions, or the dietary is the only one. I.e. are they anatomically similar, and not distinguishable in the same way herbivores and carnivores are; hence are they herbivores that simply do not mind eating non-plant based food in a while?

I hope this serves to clarify.

EDIT 2

I realize that this question is quite broad, so while I am trying to get a good view of the bigger picture, partial answers will be more than welcome!

"Is there a clear distinction at all, or is the border between the two groups somewhat fuzzy? Or are omnivores merely herbivores who are less picky?"

On second thought, I'll tackle those questions.

The "border" between herbivores and omnivores is very fuzzy among mammals, birds and at least some reptiles. Amphibians are a treat - they're all carnivores. Among reptiles, snakes are exclusively carnivorous.

Most lizards are also carnivores, though there are some herbivores. I'm not even sure about omnivorous lizards, though.

Omnivores are all over the map. If some are described as herbivores that are less picky, others could be described as carnivores that are less picky.

Note that certain species can be herbivores, carnivores or omnivores in certain parts of their range or during certain seasons. For example, bears may feast on salmon or ungulate calves when they're available but spend most of their time foraging for plants and small animals.

The most familiar omnivores include humans, pigs, raccoons and (some) rats, so you might look for some similarities between these species. Humans and raccoons are plantigrade, for example (as are bears - and rats, too, I believe). Humans, pigs and rats are known for their intelligence. Pigs and rats are very popular in medical research, for some interesting reasons.

Another thing to note is species that defy their group's general dietary tendencies. For example, the giant panda and palm nut vulture are herbivores, whereas other vultures are carnivores and most bears are omnivores - except for the polar bear.

There's another general rule; omnivores may be more rare in habitats that are lacking in plants. I don't think any marine mammals are considered omnivores, for example. All cetaceans (whales and dolphins) are carnivores, as is the sea otter. However, sirenians (manatees, dugong, etc.) are all herbivores.

That might give you something to work with.

EDIT: To my surprise, there are some good resources comparing omnivores and carnivores. Check out The Comparative Anatomy of Eating. The source might look a little flaky, but it looks very accurate to me. (It uses some of the same examples I did. ;))

To my surprise, there is apparently a closer correlation between carnivores-omnivores than herbivores-omnivores. But bear in mind that this article apparently focuses on mammals. Thus, differences in jaws and teeth can hardly be applied to birds.

Regarding my comment on omnivore intelligence, see Intelligence, Evolution of the Human Brain and Diet, though I can't vouch for its accuracy. Intelligence can be related to diet; it takes more brainpower to capture active prey than sneak up on a clump of grass, for example. This would suggest a preponderance of "intelligent" organisms among carnivores.

Intelligence can also be related to anatomical differences, like bipedalism, opposable thumbs and binocular vision.

In fact, most of the animals that are renowned for their intelligence appear to be carnivores or omnivores. Exceptions include gorillas, orangs, gibbons and the giant panda.

While whales, wolves/dogs, squids and octopuses are carnivores. Crows and ravens - regarded as among the most intelligent birds - are omnivores, as are humans, chimpanzees, pigs and at least some rats. As far as I know, pigs are generally regarded as the most intelligent ungulates (hoofed mammals); they're also among the few that are omnivores. (I can't think of any other omnivorous ungulates offhand.)

Pigs are also more compact than other ungulates, with stocky bodies and short legs. In fact, there don't appear to be many long-legged omnivores (among mammals, at least). Similarly, most (if not all) long-legged birds are carnivores (or insectivores, vermivores, etc.).


Why doesn't local anesthesia affect muscles? While having a dental surgery, I've got this question that why I can still talk, open/close my mouth, move my lips and so on while I can't feel anything at all in my mouth?

If the local anesthesia interrupts the alert that goes through brain, how is the muscle still functional? Is it some sort of one-way interruption which only disables the alert that go "from" the nerve "to" the brain? Or are there different nerves for this task?

@Nicolai's answer is not entirely correct.

Background

The most common local anesthetics are all the "-caine" drugs - like novocaine, lidocaine, - and even cocaine has some of the same pharmacology, as well as other effects (in movies this is why cops might rub some white powder on their lips - if it's cocaine, it will make their lips tingle; this is not standard training for non-movie police; also not advised for drug sellers or purchasers, because for exactly this reason cocaine is often cut with other -caines or other compounds that give a tingly feeling).

What all of these drugs do is to block voltage-gated sodium channels. These are the channels that propagate action potentials through axons and excitable dendrites. Other local anesthetics that aren't used in the clinic, like tetrodotoxin from pufferfish, block the same types of channels. At sufficient concentrations, local anesthetics block all nervous activity: unlike @Nicolai's answer, they do shut down nerves (as a brief note for terminology: nerves are bundles of axons containing many many individual fibers).

So back to your original question: how come the muscle isn't impaired during dental surgery?

Geometry of innervation of the face

Take a look at this picture of the nerves innervating the facial muscles and the muscles themselves: https://bmc.med.utoronto.ca/cranialnerves/wp-content/images/c_07/Facial-vii12_labelled768.jpg (note: I wasn't able to find a good image that has a license allowing me to reproduce it here; if someone finds one and wants to edit it in, please do - thanks!)

They mostly come in from the sides of the face, and so they are further away from the site of local anesthetic injection. The muscles themselves also extend further away. It may be that the muscle is partly anesthetized, but you don't realize it.

Limited diffusion and location of injections

Diffusion of local anesthetics is limited because they actually act inside cells, and only the unionized form can diffuse across cell membranes. Once inside the cell, the tend to be ionized and therefore get "stuck". Therefore, they don't typically diffuse nearly as far as other compounds of similar size, especially lipophilic compounds.

The nerve endings that sense pain, on the other hand, have to be at the surface of the skin/mucous membranes. That is, they are exactly where the local anesthetic is being injected. The objective of local anesthesia is often to inject enough to affect only those surface tissues, trying to spare the deeper tissues.

Effects on nerves

However, it isn't too uncommon to overdo it and to paralyze the underlying muscles or nerves. Even nerves far away can be affected, for example see this paper discussing cases where the local anesthetic travels near the eyes and impairs eye movement. There are also other non-dental procedures where block of a particular nerve is the intended result: this can be seen as an alternative to general anesthesia. One example is the use of an epidural (essentially into the space around the spinal cord) injection during childbirth or surgery. The extent of paralysis depends on the dose, however, and usually the intent is to avoid major paralysis and use other drugs like opiates to assist in preventing pain.


Effects of smoking tobacco compared to inhaling other smoke How much less dangerous is breathing smoke from burning wood and coal compare to smoking tobacco?

Edit:  Sorry.  I should have made the question clearer.

If this were an experiment, it would be set up like this.  Subject 1 is a control, so he is exposed to smoke from burning tobacco for a year.  Subject 2 is exposed to smoke from burning maple leaves for a year.  Subject 3 is exposed to smoke from burning pine needles for a year.  The other subjects continue in this fashion, being exposed to smoke from many different sources.  The rats are examined for lung cancer through this year and for the remainder of their lives.  What would the expect results of this experiment be?

(at an epidemiological scale)
WHO on tobacco

more than one billion smokers worldwide...
Tobacco kills nearly 6 million people each year.

WHO on indoor air pollution

Around 3 billion people still cook and heat their homes using solid
fuels in open fires and leaky stoves. About 2.7 billion burn biomass
(wood, animal dung, crop waste) and a further 0.4 billion use coal...
Nearly 2 million people a year die prematurely from illness
attributable to indoor air pollution due to solid fuel use.


Are there examples of Apis mellifera of different colors? Re: my previous species-identification question,  What species is this gray bee? I'm still curious: Are there any recorded/reported cases of either albino Apis mellifera, or at least with substantially different pigmentation/color? Is it possible that only part of a colony gets this trait?

I've been reading a little more, and found a partial answer.

Not sure about albinoes, but Wikipedia lists a few different colors, arguably substantially different:

Under Apis mellifera subsp. ligustica (the Italian honeybee),

Leather
Bright yellow (golden)
Very pale yellow

Under Apis mellifera caucasia (Caucasian honeybee),

Dark with brown spots at times

In fact, both photos below are reported as Apis mellifera, here and here respectively.


How can I change the payload of a bacteriophage used to transform E. coli? I was looking at bacteriophages and how they're used to transform E.coli. While the whole process of how a bacteriophage works makes sense theoretically, I wanted to know how one goes about changing the default payload of a bacteriophage with the payload of interest (engineered plasmid) in practice?
Clarification:
payload - Genetic material that the phage inserts into the bacteria
default payload - Whatever genetic material the phage inserts into the bacteria naturally
payload of interest - Engineered plasmid that I want to insert into the bacteria

I am currently using a 'phage integrase' system to insert my gene of interest into P. putida and it is definitely a seamless process with high efficiency so I highly recommend it!
As for your question, the method through which we integrate the gene of interest using the phage integrase system is simpler than you think. We do not change the payload of a bacteriophage. We simply electroporate with two plasmids, one that expresses the BxB1 integrase and another plasmid that has our gene of interest that we want to integrate into the genome of P. putida. This integration is highly efficient, and it operates through a serine recombinase that recognizes specific attP and attB sequences in the plasmid that contains my gene of interest and native genome of my engineered strain. This method is significantly more efficient for engineering certain strains (typically non-model organisms) for genome integration purposes.
References for additional information on the system for your review:
Here is a paper that describes how we use the phage integrase system to effectively edit the genome.
https://www.sciencedirect.com/science/article/pii/S2214030116300438
Here is the paper that discovered and characterized the mechanism this system operates through.
https://www.sciencedirect.com/science/article/pii/S1046202310003142?via%3Dihub


PCR and large-scale PCR I have performed PCR with 50 μL, which showed a clear band in the gel electrophoresis. I then performed large-scale PCR with 3650 μL, which showed an unclear band in the gel electrophoresis. What can be reason for this? Could it be plasmid loss even though there is a band, just a very unclear one? It should be mentioned that the single PCR was performed in the summer, and the large-scale was performed now

I made the large-scale in a falcon tube and then moved the mixture to PCR tubes each containing 50 μL, so the PCR conditions should be the same as the single PCR amplification

If all reagent concentrations and cycling conditions are the same, I suspect that you did not sufficiently mix your large-volume reaction prior to dispensing as 50 μL aliquots.

It should be mentioned that the single PCR was performed in the summer, and the large-scale was performed now

If you were using the same polymerase and primer stocks for the small- and large-volume reactions, were the stocks properly stored in the interim? Recombinant DNA polymerases in glycerol buffers have shelf lives of months to years depending on the supplier specifications and storage conditions, though you should expect some decreased activity after several months.


Transcribing DNA to mRNA with introns I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem:

  Given the following DNA sequence, 5'-GGATCGTGCCACCATCCACCATCGTTA-3', if two introns are in bases 3-9 and 15-22, what is the mRNA transcribed? Give the answer 5' to 3'. Note that the first base is base 1.

And here are the steps that I took:

5'-GG ATCGTGC CACCA TCCACCAT CGTTA-3' (remove the bolded)
5'-GGCACCACGTTA-3' (new string)
take reverse complement
swap T's with U's

Is this correct? Or where am I going wrong?

I think the only place you are going wrong is in getting confused about strands ("take reverse complement").

5'-GGATCGTGCCACCATCCACCATCGTTA-3'   << coding strand
3'-CCTAGCACGGTGGTAGGTGGTAGCAAT-5'   << template strand

The coding strand has the same sequence as the transcribed RNA (apart from T>U), so the primary transcript is:

5'-GGAUCGUGCCACCAUCCACCAUCGUUA

Then, positions of introns:

5'-GG AUCGUGC CACCA UCCACCAU CGUUA

and after splicing:

5'-GGCACCACGUUA


How to interpret a phenotypic frequency density plot I just read a paper that ran an evolutionary agent-based simulations aimed to test how genetic preparedness and social learning affect survival in various environmental conditions (changing environment, danger level, etc.). The full paper is here.

I'm a psychology student, and quite new to this area of literature.
About the graph, I get that density refers to the population density of different strategies at the end point of the simulation, but what does x-axis stand for?

I cannot find any specific mention about the x-axis in the paper, so I presume the graph is a standard one that does not need elaboration.
Could someone explain to me how to interpret the graph?

Judging from the first section of the Results part of the paper, it looks like the x-axis represents a continuum between two divergent phenotypes.  At one end is parental learning, and at the other end is social learning.  The density (y axis) represents the proportion of the population that displays a given balance between the two extremes.

Generally, density plots are a normalised way of presenting observations, such that the overall area underneath each density plot is equal, regardless of the number of actual observations making up any given plot.


At what stage is the nervous system developed enough to interpret neuronal signals as 'pain'? According to this article in Live Science, one of the reasons the fetus can't feel pain until 19 weeks is because the nervous system isn't fully developed.

But according to this article, the heart starts beating at day 16.

And according to this article, the nervous system controls the rate beating of the heart.

Then my question is, **how can it be assured that the nervous system isn't developed until 19 weeks, when the nervous system controls the heart beating rate since day 16?

First, there is some confusion on your part about heart cells and pain perception. Heart cells generate an action potential intrinsically; they do not need the central nervous system to beat (your second article explains this; read the part about the importance of calcium.) So yes, long before a fetus can feel pain, the heart is beating, because there must be circulation of nutrients throughout the embryo.
Secondly, the vagus nerve and sympathetic nerves can affect heart rate (the former by slowing it down when firing). These nerves start to reach their endpoints late in week 4 of development. So 19 days is not correct.

Cardiac sympathetic system
Although the primitive human heart starts to beat at 21 to 22 d, heart development continues to day 50, and it is near the end of this period, during the fifth week, that thoracic neural crest cells migrate from the neural tube through the somites and form aggregations (ganglia) near the dorsal aorta. [emphasis mine]

To experience pain, however, requires maturation of certain parts of the brain, most importantly, part of the thalamus and the cerebral cortex:

Current theories of pain consider an intact cortical system to be both necessary and sufficient for pain experience. In support are functional imaging studies showing that activation within a network of cortical regions correlate with reported pain experience. Furthermore, cortical activation can generate the experience of pain even in the absence of actual noxious stimulation. These observations suggest thalamic projections into the cortical plate are the minimal necessary anatomy for pain experience. These projections are complete at 23 weeks' gestation.  [emphasis mine]

Fetal surgeons and anesthesiologists often use 20 weeks as the time at which a fetus can start to feel pain, because that is when the fetus reacts to stimuli that would be recognized as pain if applied to adults (e.g. recoiling from noxious stimuli.)
One must recognize that recoiling from noxious stimuli does not prove what the fetus is perceiving. But it's a step in the direction of protecting the fetus from unnecessary pain.
Autonomic cardiac innervation: Development and adult plasticity
Can fetuses feel pain?


How does CpG island methylation lead to gene silencing? I see often the blanket statement that CpG island methylation can lead to gene silencing.  However, I have been unable to find a straightforward explanation of the mechanism by this.

Is it a purely physical block of binding for transcription factors?  Does the methylation create a tertiary structure that is compacting the DNA?  Does it recruit histone modification factors that compact the chromatin?

Please feel free to cite literature so I can go read the papers.

CG methylation has long been associated with gene silencing due to the generally negative correlation between gene promoter methylation and transcription levels.

When CG methylation occurs in the promoter or enhancer region of animals (where these 'CpG islands' tend to be), methylation seems to impede (to some extent) transcription factor (TF) binding.  That is the baseline mechanism for gene repression.  The altered chemical properties of the DNA make it less favorable binding site for its cognate TF.

In some cases, methylation clearly prevents TF binding.  For instance, some TFs bind DNA to block methylation, which facilitates access of another TF or set of TFs to the bound DNA (for instance, this paper by the Schubeler lab about NRF1).  In the case of other TFs, their binding is less reliant on methylation state, possibly due to the strength and breadth of the binding site (for instance this work from the John Stam. lab about CTCF).

Methylation also can affect nucleosome positioning and stability in some contexts; the nucleosome effects are poorly understood currently  because nucleosomes and methylation likely feedback on one another.  See this work from the Zilberman lab for an example.

The role of a higher-order repressive structure forming is arguably not obvious yet; for instance, histone H1 bining does not appear to be heavily influenced by methylation state (although this is somewhat contentious because there is often a positive but weak correlation at repressed elements in the genome between H1 and methylation--for instance just pubmed 'h1 chip' with reviews and read a recent one).  More certain is the relative change in location of methylated promoters within the nucleus to a place of transcriptional 'silence' (inactivity).  These repositioning phenomena are under intense investigation; you can learn more about this by googling for 'nuclear topology and gene repression' or something like that.

hope this helps


Identifying an insect looking like a crumle Recently a little insect crawled over the carpet. First I did not notice, as its appearance is quite similar to the coloring of the carpet. Then I understood that it is not a rolling crumble, as the window and the door were closed.

I took it on an ordinary sheet of DIN A4 paper, but have not the slightest idea, what kind of insect it is. It makes the impression to have taken a shower of water and dust in a row.

What's that insect called?

The second photo gives an idea of the size, as it shows a drinking glass turned upside down.

Note: The place this insect was encountered is in eastern Germany

Looks like the nymph of a masked hunter.
They carmouflage in dust and sand.


Were there any vertebrates with 6 or more limbs? My question is actually a bit more broad than what's in the title, but I don't know how to put it succinctly.  When I was trying to find the answer to that question, I found that all known terrestrial vertebrates are ultimately descended from a species of lobe-finned fish that had 2 sets of bilaterally symmetric fins (which excludes the dorsal and ventral fins), which were the basis for the limbs of its tetrapodal descendants.

The best way I can think of to phrase the question is: Does paleontology has any evidence of a vertebrate that had 3 (or more) sets of bilaterally symmetric limbs or lobe-based fins?  I'd like the focus to stay away from ray-finned fish, even though they're vertebrates and related.

This is not the common question, which is whether there is or can be a mammal/reptile species with more than four limbs.  The essence of that question's answer is that mammals and reptiles both evolved from a common ancestor species that were tetrapods, and that it's extremely difficult to change the genetic floor plan in the necessary way without causing fatal problems (along with other evolutionary issues).  By and large, this common question is so common that it chokes out the type of question that I have, making my amateur attempts at further research difficult to impossible.

I've not read it but this SE question Why don't mammals have more than 4 limbs?
though not a duplicate (it asks about mammals not all vertebrates) may have some elements in its answers pertinent to your question.

And the question Why are there no vertebrates with more than four limbs? has been asked in Quora where it has 7 answers you may find useful.

Also this discussion thread Why can insects have 6+ limbs, but mammals only have 4? in reddit.

  Does paleontology has any evidence of a vertebrate that had 3 (or more) sets of bilaterally symmetric limbs or lobe-based fins?

You sent me far down the rabbit hole with this one, for reasons that escape me my instant response was 'yes the Coelacanth' but as you correctly point out that has only 4 paired fins.

As seen from The origin of tetrapods our limbs came from fins, Coelacanth is a good example of the likely early beginnings of Tetrapod limbs, they occasionally use them to 'walk' on the seabed.

The image provided in this National Geographic article Coelacanth Rediscovered gives a much clearer picture of it's 'limb' structures.

Latimeria chalumnae, the coelacanth (SEE-lee-uh-kanth), thought extinct until a biologist identified one off the coast of South Africa in 1939.

I've trawled Google for early chordates looking for examples of more than two pairs of fins & haven't been able to find any, it seems the earliest paired fins appeared in (or shortly before) Ostracoderms & from there continued in an unbroken line to the tetrapods & our limbs.

Paired fins don't appear to have developed in chordates before then or to have ever developed into more than two pairs.

So to the best of my knowledge it appears that the answer to your question is no.

Other links.
Yunnanozoon
Myllokunmingia
Haikouichthys
Evolution of fish


How do animals perform detailed active camouflage? We often see videos of octopuses and chameleons changing their color to suit their surroundings. If it was a simple color change from white to red, it'd be understandable, but some of these animals can change colors while incorporating a lot of detail.

How do they process so much information and mimic it. Is this a subconscious action, or do they actually draw a picture in their head and then 'print' it on their bodies? Does this ability come from birth or does it get better over time?

Some of it is voluntary and some involuntary and is detailed in this book. Chameleons have chromatophores (pigment containing light reflecting organelles in cells) which help in their colour change and many factors like age, health, etc does affect it. And no, they do not form a picture on their head and print it on their bodies.


Can assimilated energy be simply lost from a trophic level? I was reading Environmental Studies By B. S. Chauhan and there a diagram of a model of transfer of energy.

NU = Not used energy has been shown, energy that was neither stored or exported to the next level.

I wonder what physiological process causes this loss of energy at all trophic levels?

In this diagram, since this is the only loss between trophic levels (along with  respiration and NA within each trophic level), NU represents dead organic matter, that is not transferred along the food chain. In other words, this represents dead leaves that are not eaten by herbivores, hares that die of old age and not predation, and foxes that are killed by falling rocks. So NU is the amount of energy that goes directly into the  decomposer community (another flow to decomposers is coming from matter that is excreted by herbivores and predators), since this diagram only includes primary producers, herbivores and predators.

NA, on the other hand, represents energy that is consumed by the next trophic level but not assimilated (Not Aassimilated). So this represents faeces etc.


Species ID: Buckyball-like fungus Previous research

A friend of mine shared a link of some beautiful fungi: http://imgur.com/a/Dii3H. I was intrigued by the curious critter below -- it seems to have honed the power of buckyball geometry, presumably much before we Humans ever did (search: Buckminsterfullerene to learn about a feat of chemical engineering).
Google reverse-image search almost got me the answer I needed, but no species name.
I've asked friends on Facebook with no answers yet.

Question

What is the name of this species of fungus?

Related Questions on Stack Biology

Here's a related Species Identification question of a fungus: Puffball mushroom species ID? (by @rg255)

EDIT: I'm an idiot... the Imgur had species names, thus answering my question, post-mortem. Thanks @skymningen for pointing that out.

Looks very similar to Clathrus ruber fungus.

Be careful, it is poisonous.


Is it possible to have sleep paralysis while sleepwalking? At least from a conceptual level, these two disorders don't conflict. The effect of sleep paralysis is being conscious while having the inability to consciously direct motor functions. Sleepwalking is the unconscious direction of motor functions. So combining the two, the effect would be that you are consciously aware of yourself and your surroundings while you are also unconsciously moving about, outside of your conscious control.

Therefore the only way the two wouldn't be possible together is if their activation conditions were mutually exclusive.

From wikipedia

  Sleepwalking occurs during slow-wave sleep (N3) of non-rapid eye movement sleep (NREM sleep) cycles. It typically occurs within the first third of the night when slow-wave sleep is most prominent. Usually, it will occur once in a night, if at all.

https://en.wikipedia.org/wiki/Sleepwalking#Causes

  The first of these stems from the understanding that sleep paralysis is a parasomnia resulting from dysfunctional overlap of the REM and waking stages of sleep.

https://en.wikipedia.org/wiki/Sleep_paralysis#Pathophysiology

So from a small amount of searching it seems it is not possible, unless SWS, REM, and the waking stages of sleep can all be overlapped.

While it is hard to completely rule out this convergence ever happening (perhaps cases haven't been reported), it is highly unlikely due to the specific stages of the ultradian sleep cycle at which sleep walking and sleep paralysis occur [Ref. 1]. Sleep walking during non-REM sleep would have to continue through the REM stage in order to see intrusion of sleep paralysis that occurs at the exit of REM to wake [Ref. 2].

A key feature of REM sleep is deep muscle atonia that paralyzes the body and prevents among other things one from acting out dreams [Ref .3]. Thus, if a person sleep walking were able to enter REM before returning to bed, the sleep walking / other unconscious motion itself would cease.

I do question your reasoning that the combination of these two parasomnias would result in being:

  consciously aware of yourself and
  your surroundings while you are also unconsciously moving about,
  outside of your conscious control.

because the intrusion of sleep paralysis would in fact lead to muscle atonia and prevent one moving about. This is not to say that terrible things have not occurred where muscle atonia has failed while the subject remains asleep/unconscious; this falls under the fascinating category of REM-behavior disorders (where people act our their dreams - including violently hurting themselves and their partners), which judging by your question I think you will find interesting! [Ref. 4].

References:
[Ref. 1]: sleep stages
[Ref. 2]: sleep paralysis
[Ref. 3]: muscle atonia
[Ref. 4]: rem-behavior disorder


Degenerate primer design for DIG in situ hybridization New to molecular and have learned to design primers from google/youtube so any info would help

Would someone be willing to share their protocol for degenerate primer design?

Breakdown:
Trying to design degenerate primers to amplify/clone specific GPCR genes from an unsequenced genome of a particular fish.

I'm using Ensembl and Genbank for sequences of closely related fish but the complete gene has only been sequenced in 2 other fish species.
I use ClustalOmega for alignment. Is it okay to just use 2 other species for generating degenerates?

1) are there any other good databases for gene sequences?

If the gene is supposed to be well conserved then you can use the sequence from the related species.

For protein coding genes target the ISH probe to the coding region which is more likely to be conserved.

What you can also do subsequently is to:

amplify the CDS
do 3' and 5' RACE
Clone in a plasmid (do a blunt end or TA cloning)
Sequence the insert
Design exact primers

  are there any other good databases for gene sequences?

EMBL and DDBJ


Why isn't Bubonic Plague as virulent as it once was? Although I am admittedly not anywhere near an expert on any topic, I still have a hard time understanding how Black Death and Bubonic plague are one in the same. Since plague still exists, with news stories about it every once in a while, and especially in places like India, why doesn't it spread with anywhere near the rate it did during the Middle Ages?

Obviously global society in general is much more sanitary than it was then, people also tend not to live in close quarters with animals today as they did then, however in places like rural India and China this lifestyle still takes place and plague still exists, so why aren't there large out breaks of plague in these areas if it indeed is Black Death?

Is it possible that Black Death has been miscategorised due to various historical circumstances and scholarly errors?

The identification of the Black Death with plague is now fairly well-established - see this paper (open access) in which PCR and protein detection were used to detect the presence of Yersina pestis in human skeletons from plague-related mass graves across Europe.

Outbreaks of plague do occur in rural environments, see this WHO page for some details. The WHO plays a role in responding to these outbreaks, as long as they are notified by the relevant countries. Plague infections respond well to antibiotic treatment.

There has also been a recent outbreak in Madagascar. According to the epidemiologists we are still in the midst of the 3rd plague pandemic, which started in China in the mid 19th century.


Reporting observation of a bird outside its seasonal presence Last summer I saw this bird in the countryside of Bulgaria (Dobrich area) and I think this is a specimen of Great Grey Shrike (Lanius excubitor).

By looking more in detail the distribution of that bird (I checked in few books including the Collins Bird Guide in French edition), I noticed it is present in Bulgaria but only in winter season. However I took this pictures in August 2017.

First, is it really a specimen of Lanius excubitor?

And if yes, should it be reported in some way?

I know some other countries have reporting tool on Internet but I have no clue about observations in Bulgaria.

It is NOT a Great Grey Shrike (Lanius excubitor).

It is a young Lanius minor Lesser Grey Shrike (which breeds in Bulgaria).
I say young (born the same year) because of the white tips of the feathers (they are new) and not so extended black mask (which probably induced you into the ID mistake).

I attach a picture of young Lesser Grey Shrike for comparison.

Generally you can report your observation on ebird.
There is a team checking the unusual observations (although for Europe at least many mistakes are not picked up).


PCR processes number of amplicons produced Beginning with 600 template DNA molecules after 25 cycles of PCR how many amplicons will be produced?

This is a theoretical consideration, as PCR depends on a number of factors as optimal priming, salt concentration, enzyme activity, available dNTPs and so on. Ideally the number of DNA molecules is doubled with every cycle. So the general formula to calculate the number is:

$ n \times 2^{cycles} = $ number of DNA molecules at the end of the PCR

n is the number of molecules set into the reaction

So for our 600 DNA molecules with 25 cycles this would give:

$600 \times 2^{25} = 20.132.659.200$ or roughly 20.1 billion molecules of DNA.


Plant identification: San Francisco, USA I am taking a biology lab class and I need to identify all these plants which are from the San Francisco area.

My question is how can I find the right keyword to find their names on internet? Or can you recommend any book that I can find in library?

I'm going to refrain from giving you the answers because the point of the assignment is to  learn how to do it yourself.

You should likely start  by using a dichotomous key (likely provided by  your instructor).

You could also try  searching the Jepson California eflora or CNPS Identifying Native Plants for online keys.

Check out  the California Native Plant Exchange website if you don't know the name of the plant but know the general area where you saw it.

If you don't know what general type of plant  you have,   you should try keying  the plants to family  first  to get better search terms.  Try here.

If you don't know plant terminology  used  in  these keys,  try  "Plant Identification Terminology: An Illustrated Glossary" (Harris & Harris, 2001)


Why do dogs come in all shapes, but cats are generally all the same? Minus hair and fur, cats (the domestic kind) seem to be just scaled versions of the same thing.  Dogs on the other hand can have long necks, short necks, long bodies, short legs, long ears, short ears.....

Until recently, cats were not extensively selectively bred, but were allowed to roam freely and therefore interbred randomly.  Darwin pointed this out, contrasting cats to species that were routinely "enclosed":

  On the other hand, cats, from their nocturnal rambling habits, can not be easily matched, and, although so much valued by women and children, we rarely see a distinct breed long kept up; such breeds as we do sometimes see are almost always imported from some other country.

In contrast, dogs and some other species were selectively bred for certain characteristics "each good for man in different ways":

  The key is man's power of accumulative selection: nature gives successive variations; man adds them up in certain directions useful to him. In this sense he may be said to have made for himself useful breeds.

Why were cats not selectively bred, while dogs were? This gets to be somewhat speculative, but it's clear from looking at dog breeds that many of the different breed functions need to have a larger animal than a cat, as well as one with different personality: Herding sheep, hunting foxes or badgers, fighting bulls, etc.  Cats' function for humans has traditionally been to hunt mice and rats, a role for which they're already beautifully adapted.

(There are a number of small dog breeds, of course, but these parallel cat breeds in that many are ornamental, or else originated as rat-hunters.)


Reverse evolution to gain back lost traits Many animals return to shapes similar to their ancestors like mammals and reptiles growing fins and fish tails or animals losing limbs they just grew and so on.

But I notice that once an animal loses a feature it doesn't actually grow back... they con only mimic it, no reptile or mammal has fins but only limbs that look like fins... and no aquatic mammal or reptile seems to regrow back their lost legs or arms.

No animal seems to regrew its ancestral gills even though they live 100% of their lives inside deep waters.

If some organs can be so useful to have back, with evolutionary pressure at maximum, why don't they ever return?

What blocks animals from re-evolving something they lost?

Back evolution

Evolution do not strictly keep a history of how they were before. There is no way for a population to specifically produce mutations to reverse previously fixed mutations in order to evolve back in time. This has sometimes been called Dollo's law but very few people actually use this term today.

Note however that a population may have kept pseudogenes or specific developmental pathway or case of atavism that make the evolution of some traits similar to previously existing trait "easier". A very nice example of such mechanism is the case of Membracidae (treehoper).

Example of Membracidae

insects have evolved flight once. The first flying insect had 3 pairs of wings, one pair on each of the 3 segments of the thorax. Today, there exist no insects with 3 pairs of wings. In all lineages descendent of this flying ancestor many have no wings and many have 2 pairs of wings only. Here is a schema showing a typical insect with 2 pairs of wings.

As you can see there is no pair of wings on the first segment of the thorax (called prothorax) as it has been lost through evolution. Note that the diptera (true flies) have lost a second pair of wings (the one on the metathorax which has been replaced by halters).

Membracidae (treehoper) is a family of wingless insects. They use previously existing developmental pathways and previously existing genes (Prud'homme et al. 2011) for developing wings on the protothorax but instead of making wings, they make all kind of funny shape for defense purpose. Here are a few examples


Eating rarely but a lot, or often but little I wonder if it matters if an average person eats the same amount of food distributed between a few (2-3) meals during the day, or constantly having small snacks.

I'm interested in several aspects of such food consumption:

How does it affect appetite?
How does it affect fat accumulation?
Are there any notable side effects caused by either way of eating?

Eating many small meals or eating large meals is irrelevant. The only thing that matters is getting the right amount of calories needed for your body to function properly.
Fat accumulation does not happen if you do not go over your daily calorie limit.
After a big meal your food is not only stored as fat but as a polysaccharide form of glucose called glycogen that is stored in the liver and or muscles for later use.
Therefore, there is no better way to eat, it depends on what size you like your meals to be as long as you stay within your calorie range.

See http://www.choosemyplate.gov for more information.


What is the relationship between the light and dark reactions of photosynthesis? My main concern is why are the dark reactions (those that produce hexose) needed? As far as I understand, the sole purpose of photosynthesis is to synthesize carbohydrates, which are only used for energy storage. So, why don’t plants store energy directly as ATP (by photophosphorylation) and not as carbohydrates? (Of course, that would be too bad for other creatures.)

Elaborating my question:

Plants use chlorophyll to convert light energy into chemical energy of ATP and NADPH by photophosphorylation and chemiosmosis.
Then plants use the ATP and NADPH to synthesize glucose by the Calvin cycle.

So, what is the need of step 2? Why don‘t plants just use that ATP and NADPH for their metabolism?

PS: although @David has provided a nice answer to the current form of the question, the selected answer by @christian still remains selected since it answered my original query i.e. why excess ATP is not feasible for plants instead of why synthesis of carbohydrates is important. Any further answers/comments shall address the latter one, although none of them can be selected as correct since the latter query is not the original one.

ATP is a bad medium for storing energy as detailed here.

  ATP has a molecular weight of 507 Da
  Glucose has a molecular weight
  of 180 Da, and contains the same amount of energy as 31 ATP molecules


Do eye's muscle share the same nerve? When I try to rotate my eye, both of my eyes will rotate the same amount and in the same direction (obviously).

I'm wondering if it is possible to control each eye separately. I've never seen anyone that can do this (except some pics on the internet which I'm not sure if they are digital edits simply for fun).

Is it possible? If not, why? Is it because they are both controlled by the same nerve? Or is it simply because we are not used to it and it's super difficult (but possible)?

Each eye is controlled separately. Three cranial nerves emerge at the brain for each eye to control the so called extraocular muscles. That we usually move both eyes in one direction is due to that our brain is trained that way. Nonetheless, we sometimes move each eye individually, for example when looking at an object that is very close to our face (convergence). I wonder that you have not noticed it on yourself, since it is a pretty common eye movement. Further, you can train your brain to perform other, rather unusual movements, as you can see in this video.


What's the therapeutic index of Pethidine (Meperidine in the US)? What's the therapeutic index $\left(\frac{LD_{50}}{ED_{50}}\right)$ of Pethidine (Meperidine in the US) via the intravenous route for humans or whatever species you can find? The therapeutic window $\left(\frac{TD_{50}}{ED_{50}}\right)$ for humans will suffice if accompanied by the therapeutic index for pethidine via IV of another species.

Pethidine is an opioid painkiller with approximately $\frac{1}{7}-\frac{1}{8}$ the strength of morphine and a definite influence on monoaminergic neurons.

I imagine it'd be in the neighbourhood of 30-100, like most opioids that have been implemented in medicine.

Closest I reached:

Source: Page 105, The Complete Recovery, By Anthea Hatfield Google Book


Why can't cats run longer distances like dogs? Cats can run about nearly 30mph. Their stamina, though, is for short distances. Why can't they run longer?

Can cats be trained to run longer distances like dogs? For instance, could their resistance improve by stair case training (running many times up and down the stairs)?

Cats, both domestic and wild are, for the most part, ambush predators that catch their prey with bursts of speed. Lions and cheetahs do run down their prey, but not over long distances. Wolves chase their prey over long distances, sometimes for hours. This is a classic case of trade-offs. Humans have modified the behavior of domestic cats and dogs, but both still rely on the characteristics of their ancestors. You can build cat muscles with exercise, but you can't make them "dogs".


Is it possible to grow brain tissue in vitro? Can we make a super-brain this way? I wonder whether such experiments were conducted? Is it possible to create a "biological super-computer" this way?

This is actually not an unheard of idea among neuroscientists and is an aspect of much research.  Brains in general have amazing computational powers and abilities that allow them to circumvent the limitations of computation which is usually based on a Turing Machine. Neurons pursue highly parallel architectures and exhibit cognition or even emotions or do highly sensitive signal processing, which has heretofore been unapproachable with computational methods such as Machine Learning.

As such many researchers are focused on understanding the brain or at least the brain's structure to augment or produce computation.  Here are a couple of examples of neuron arrays flying virtual or real drones....

The ethical issues aren't great concerns because neural cell networks can be encouraged to grow differentiating from easy to grow cell lines like fibroblasts.

Another approach to augmented computing is to interface directly into a living brain. Model brain organoids are a popular topic of interest and could one day be used to interface to other computational systems.  There are of course many devices that try to interface to the brain via electrical fields in the same way EEGs work.

there are connectome projects that are trying to understand the neural connections between cells that are so important to brain development, with the theory that the topology of these networks might enable even computers to perform like brains.


Can the word phalanx also be used to describe the finger bone plus the soft parts around the bone? I was talking in an SE chatroom about fingers, and not being a native English speaker, I had to look up the word used for the part of a finger from the tip to the closest knuckle. I came across the word "phalanges", but the Wikipedia article specifically refered to this as phalanx bones, i.e. just the bone and not everything around it. Can this term also be used to describe the bone plus all of the softer parts around it like the muscles, blood vessels, skin and nail? If not, is there a more commonly accepted biological term for the bone plus the soft tissue around it?

It's a great question, and in my humble opinion, the answer is:

Phalanx (plural: phalanges), (also Cambridge and MedicineNet) is the term for one of the bones (only) in the fingers or toes and not for all the "meat" around it. The Google images search for phalanges is quite convincing.

Someone on https://english.stackexchange.com/ might know a word for the whole bone + "meat" part of the finger.


Genetics: pedigree following a rare trait autosomal recessive I have two questions pertaining to this pedigree
I believe it to be an  autosomal recessive trait.

The probability that individuals IV-1 and IV-2 would give rise to an affected individual would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24
Suppose individual IV-2 was unaffected. The probability of his marriage giving rise to an affected child would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24

I worked on this problem for the last hour or so and figured up question 1 to be 1/2 and question two to be 1/4. I don't feel this is correct. I feel like I am missing something. If you don't mind showing the calculations for how you came about an answer that would be greatly appreciated.

Question 1

Okay, so I'll go through my own process for you here step by step, moving down the tree.  Here's an annotated version of your diagram with my own thoughts (it's been a while since I've done this but should hopefully be accurate):

Generation 2:  As you realised, the trait is autosomal recessive so the female (II:2) has the genotype aa.  The male is considered wild type unless informed otherwise, giving him a genotype of AA.  I think you had worked all this out, but they are shown in red on the diagram.

Generation 3: Using the two genotypes of the parents from II (red), we know that all the progeny in generation III are carriers - i.e. Aa genotypes.  This is indicated for III:6 in orangey-brown.  I think you also worked this out successfully.  However in your original chart, III:7 is noted as Aa.  III:7 is from outside of the affected family and would therefore again be considered to have be wild type and therefore instead have the genotype AA - shown in purple.

Generation 4: In order to work out the potential genotypes of IV:1 we have to do a cross between the two parents III:6 and III:7 - which works out as follows:

        |          Male          |
        |     A            a     |
        |------------------------|
F       |                        |
e     A |    AA            Aa    |
m       |                        |
a       |                        |
l     A |    AA            Aa    |
e       |                        |

As you can see, there is a 50% chance of IV:1 being healthy AA and a 50% chance of being a carrier Aa - shown in green.  As IV:2 is affected, we know his genotype is aa (pink).

Generation V:  Now for answer to your first question.  If IV:1 had the AA genotype then the child could never be affected, reducing the odds to 50% immediately. Of this remaining 50%:

        |          Male          |
        |     a            a     |
        |------------------------|
F       |                        |
e     A |    Aa            Aa    |
m       |                        |
a       |                        |
l     a |    aa            aa    |
e       |                        |

50% of the offspring would be affected.

Therefore the probability of V:I being affected is $\frac{1}{2} \times \frac{1}{2} = \frac{1}{4}$

Question 2

The second question seems very odd to me.  If IV:2 was unaffected in the literal sense of the word they would be wild-type AA.  This would make the probability of them having an affected child as 0.

As this isn't one of your options, I assume they mean that IV:2 is a carrier (Aa).  We are this time therefore crossing either AA or Aa (IV:1) with Aa (IV:2).  Again, if IV:1 is heterozygous dominant (AA) none of her children will be affected.  This means the odds are again reduced by a half.  In the case that she is heterozygous Aa then the cross becomes:

        |          Male          |
        |     A            a     |
        |------------------------|
F       |                        |
e     A |    AA            Aa    |
m       |                        |
a       |                        |
l     a |    Aa            aa    |
e       |                        |

Giving 25% healthy, 50% carrier and 25% affected.

As you're looking for affected children: $\frac{1}{2} \times \frac{1}{4} = \frac{1}{8}$


Can sexual reproduction create new genetic information? Is there a small chance that in sexual reproduction a new allele forms in the off-spring that was not present in either of the parents, or are the alleles in the offspring always from at least one of the parents?

Is new genetic information ever created during sexual reproduction, or only through mutations during an organisms life time?

Homologous Recombination not only shuffles different mutations together, but similar sequences near each other from gene duplication events and from regions with highly repetitive sequences can recombine and cause gross changes in the sequence of the genome in hot spots.


Does DNA being circular or linear directly affect the speed of DNA replication? Let's say we have two DNA molecules of equal length, one belonging to a prokaryote and the other to an eukaryote. It's known that replication of the eukaryotic DNA is faster in this case. One clear reason for this is that linear DNA has multiple origins of replication whereas circular DNA only has one.
Now back to the real question: Does it matter for rate of replication whether the DNA is circular or linear? Does it contribute to eukaryotic DNA replication being faster in our specific case?
One thing I found in an old revision of this Wikipedia article is as such:

One reason that many organisms have evolved to having linear chromosomes is due to the size of their genome. Linear chromosomes make it easier for transcription and replication of large genomes. If an organism had a very large genome arranged in a circular chromosome, it would have the potential problems when unwinding due to torsional strain.

What I make out from this is that the rate of replication isn't directly affected. It's more closely related to avoiding other issues that arise from eukaryotic DNA molecules being typically longer than prokaryotic ones. But in our case where we declare both DNA to be of equal length, I'm assuming circular vs linear has no bearing on the rate of DNA replication.
So am I correct on my assumptions?
Edit in response to the answer below:

It's known that replication of the eukaryotic DNA is faster in this
case (where DNA molecules are of equal length) because eukaryotes
have linear chromosomes whereas prokaryotes have circular ones

If it makes sense to form a sentence like this, presenting linearity as the cause, then it's enough to satisfy my definition of directly affected in this case. For example, it's easy to make this claim if you present the number of origins of replication as the cause. I looked at the textbook you mentioned and the quantity of origins of replication is in fact mentioned this way.
Conclusion:
I went ahead and did a bit more reading in that textbook. What
I've understood is: An eukaryotic linear chromosome has multiple
replication origins rather than a single one in order to compensate
for its much larger size. So while the shape might be a factor
(possibly, not certainly), the primary and "direct"
reason is the difference in size, not the shape.

I am not sure if I well understand what you mean by directly affected.
I will list some possibilities below (For reference you can see any genetics textbook, I use, Genetics: A conceptual approach by Pierce, but I guess any textbook would do).

Porkaryotic polymerases (usually processing circular DNA) have a higher nucleotdie per second speed than eukaryotic polymerases (processing linear DNA). Does this mean that shape directly affects speed? In this case I would say no. It's just a difference between prokaryotic and eukariotic polymerases. Some prokaryotes have linear chromosomes and their polymerase will still be faster than eukaryotic polymerases.

One prokaryotic chromosome has only one origin of replication, while one eukaryotic chromosome has several of them, so that eukaryotes parallelize even in a single chromosome. Does this mean that shape directly affects speed? In this case, I would say yes. Due to steric effects, the shape of the chromosome has to do with the ability of having several origins of replications, even if the lengths are the same. Edit: After Ved's comment, I realized that this is also not necessarily true. Not all circular chromosomes have one single origin of replication; archaea have circular chromosomes with more than one origin of replication

Linear chromosomes are easier to unwind. Does this mean that shape directly affects speed? I would say, yes for large chromosome and no for small chromosomes. Edit: After David's comment, I realized that I am not really sure that linear chromosomes are easier to unwind. A Wikipedia entry states this, but I gave a look at the paper they referenced and found no real statement about this.

Importantly, if the DNA molecules you compare are one prokaryotic and one eukaryotic and they are very short, I would bet my 5 bucks on prokaryotic (circular) being faster, because in absence of all the parallelization the eukaryotic DNA polymerases are slower than prokaryotic ones.


Do the recent findings of an ape-like creature in Europe with human-like teeth change the Out of Africa narrative? http://www.telegraph.co.uk/science/2017/05/22/europe-birthplace-mankind-not-africa-scientists-find/

Two fossils of an ape with human-like teeth were discovered in Greece, and Bulgaria, and they are about 7.2 million years old.

Does this change the narrative of the 'Out of Africa' theory?

Have scientists in the relevant fields commented on this yet?

Does this change the narrative of the Out of Africa theory?

Not at all since the Out-Of-Africa hypothesis is about the African origin of all modern humans (Homo sapiens), i.e. that the species originated in Africa and then spread over the rest of the world. It is not about where possible, early ancestors may have originated. The ape from the article, Graecopithecus freybergi is claimed to be one of the oldest Homininesa, but that does not change the claim of the Out-Of-Africa hypothesis.

Reference

a Fuss, Jochen, et al. "Potential hominin affinities of Graecopithecus from the Late Miocene of Europe." PloS one 12.5 (2017): e0177127. https://dx.doi.org/10.1371/journal.pone.0177127


What is the mechanism behind sympathic effusion of serous cavities due to nearby abscess? Patient with left perinephric abcess which does not ruptured have reduced breath sound that is mostly due to plural effusion revealed by CT scan which was sterile. I found this called sympathetic effusion , Why it named as this and what is the mechanism behind it ?

The left perinephric space is adjacent to the left subpleural space so inflammation can spread from the former to the latter.

Diaphragmatic inflammation then results in a left exudative sterile pleural effusion. It's called sympathetic since it's not infective.

https://radiopaedia.org/articles/perirenal-space

https://emedicine.medscape.com/article/1979032-clinical#b4


Corneal transplant and HLA matching Is HLA matching/ blood grouping required for corneal transplants ? I think,it shouldn't be, because cornea is avascular.

I tried searching on the net but most of the references are old and controversial. So please provide a reliable and latest reference for your answer.

Cornea is considered as an "immune-privileged" site and tissue, neither HLA nor blood grouping is required for allogeneic corneal transplant.

In terms of reference:
This could be one: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802514/


Why do so many parasites infect definitive and intermediate hosts rather than just one host? Many parasites infect multiple host species, with one host species being the definitive host (where the parasite reproduces), and the other host species being the intermediate host (where the parasite grows to maturity). (Further details described as "complex life cycle" at https://en.wikipedia.org/wiki/Parasitic_life_cycle ) Why is this complex life cycle so common? Why wouldn't more parasites adopt a simpler life cycle of just one host?

I knew that there were some parasites that infected more than one kind of host species, but now that I am looking into it, it seems like a majority of internal parasites have this kind of life cycle. Does anyone know why?

Several reasons have been proposed.

  We suggest that complex cycles in helminths without penetrative infective stages evolve by two essentially different processes, depending on where in the cycle a new host is inserted. In ‘upward incorporation’, a new definitive host, typically higher up a food web and which preys on the original definitive host, is added. Advantages to the parasite are avoidance of mortality due to the predator, greater body size at maturity and higher fecundity. The original host typically becomes an intermediate host, in which reproduction is suppressed. In ‘downward incorporation’, a new intermediate host is added at a lower trophic level; this reduces mortality and facilitates transmission to the original definitive host.

--Evolution of complex life cycles in helminth parasites

  Despite these advantages to omitting hosts, the majority of digenean trematodes have a life cycle with three hosts, suggesting strong counteracting forces that maintain hosts in the cycle. Such forces have been proposed to be higher growth and fecundity (Parker et al., 2003), an increased probability of finding a mating partner (Brown et al., 2001), and higher transmission rates (Morand et al., 1995; Choisy et al., 2003; Parker et al., 2003). ... we propose here that maintaining a second intermediate host in the life cycle can be advantageous for the individual parasite to increase the intermixture of different clones and therefore decrease the risk of matings between genetically identical individuals in the definitive host.

--How a complex life cycle can improve a parasite's sex life

Also see The evolutionary ecology of complex lifecycle parasites: linking phenomena with mechanisms.


What are centromeres *really*? I've gathered that a centromere is a a region*  where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark regarding its physical structure and functioning.

At what point during DNA replication is the centromere created, and how is it created? How does it hold the chromatids together (what are its components)?

Specifically:

When it is being created (presumably during cell division) how is the positioning  of the centromere controlled? Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot: a section of DNA that 'says' "Right part of centromere, to be attached to left part"?

Secondly, after their condensation into chromosomes (e.g. during prophase), are the sister chromatids physically intertwined around each other** for the purpose of joining, or are they simply adjacent?

Is there a 'loop' in the centromere slung over the adjacent chromatids to join them?
If they are intertwined, how is this achieved during DNA replication, whilst the non-centromere parts of the sister chromatids are not intertwined?

How does the centromere break down to allow the chromatids to separate (e.g. during meoisis 2 and anaphase)?

On a somewhat unrelated note, what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?

*(i.e. there is not a separate physical object dubbed 'the centromere', rather it is a collection of objects in a region)

**(That is, considering no other molecules than the chromatids, if you were to pinch the top and bottom ends of the left and right chromatids and pull them apart, could you separate them without them locking together (basically, do they intersect knot-theoretically)?)

There are many questions in your question. I'll try to answer each question pointwise.

  Which flags are used by the enzymes in the process of making the
  centromere to tell them that it is the right spot

There are some centromere associated repeats in the DNA which mark the site for centromere assembly. There is no particular consensus sequence of this repeat. However, this study says that in certain cases stable chromosomes are formed in the absence of centromeric repeats.

  are the sister chromatids physically intertwined around each other for
  the purpose of joining, or are they simply adjacent?

They are joined by proteins called cohesins. Cohesins looks like rings which form around the sister chromatids. During anaphase, the anaphase promoting complex (APC) activates an enzyme called separase, which in turn degrades cohesin.

  what in the centromeres do the spindle fibres attach to, and how do
  the tips of the growing fibres notice it to head it its general
  direction?

Centromeres serve as a site for the assembly of kinetochore. Kinetochore is a multi-protein complex which forms contact with the spindle fibres (specifically, K-fibres. Refer this previous post). An essential component of kinetochore is the motor protein dynein which makes the kitetochore to crawl along the spindle fibres, towards the pole. The wikipedia article on kinetochore is quite descriptive and you can refer that for details.


Are there official criteria for an experiment to be considered statistically robust for publication in a decent scientific journal? For a high school project, I investigated the effect of breathing meditation on teenagers. 15 students were asked to follow specific directions and meditate for 10 minutes a day for 8 weeks. Each week, their heart rate, ventilation rate, maximum lung capacity and blood pressure were measured with 5 trials. These measurements were also done prior to the meditation regimen.

My question is, to publish an experiment in a scientific paper, must there be a specific number of participants, trials, or time-length of the experiment?
This is to talk about in the discussion part of my report.

Please let me know what you know!

There is no single measure for "robustness" and a lot of it boils down to the field. Usually physics has a very high degree of precision: p value close to 0. For instance, the Higgs boson was a confidence level of 5 sigma, while biology or psychology is going to usually have more leeway: maybe 2 sigma (Sigma).

However, there should be no (statistical significance) criterion to publish. The idea that only positive studies should be published has led to biases in available data in a number of fields (Fighting publication bias: introducing the Negative Results section). Negative results are very useful to us as robustness of a theory is often evaluated using meta-analyses. If a person fails to publish their results because it does not robustly justify their theory, then the data available to perform a meta-analysis is diminished.

Clearly, you want the study to be properly run and you want the method to be reasonable. A garbage study, regardless of the statistical significance measured, is going to be looked upon negatively.

That being said, if your topic is something that has been researched a number of times, a small study is not going to be looked at very well, as there is already "better" information available. The study should provide some kind of new insight into the topic.


What is needed for a G-matrix? I have been doing a lot of reading on quantitative genetics and the G- (and B-) matrix lately. I get the principle behind performing the analysis now but I am still not sure how to do it. I'd like to be able to try it out with some dummy/old data in R to see how it is done.

Let's pretend I have measured 5 traits of Drosophila (Wing length, lifespan, eye pigmentation, bristle number, and fitness). Could I construct a G-matrix for the population from this data and also get a B-matrix to measure the selection on the traits?

Aims of the post:

1) What information (trait measurements, fitness scores etc.) is needed to construct G- and B- matrices?

2) I would like to find print or online material that would guide me in actually implementing this method. It seems like there is an awful lot of papers saying that G-matrices are great, but no one actually says how to do them in real life...

To construct the G-matrix you need additive genetic variances and covariances for all traits, so you normally need results from breeding experiments (e.g. phenotypic midparent-offspring data), that you can do parent-offspring regressions on. Don't know any good online sources but see Balding et al. 2007 p. 534ff for some info. I've seen methods that claim that the G-matrix can be estimated directly from phenotypic data from unrelated individuals (e.g. Zintzaras 2011) or from genomic info e.g. SNPs (Vattikuti et al. 2013), but are not familiar with these and do not know how reliable they are.

A clear background on using mixed models to estimate the G-matrix, including examples/tutorials, can be found in Wilson et al (2009).

Or did you have something else/something more specific in mind?


What percent of biology study is dedicated to species-specific subjects like ecology and evolutionary biology? I'm thinking of studying biology, especially ecological and evolutionary biology. Could you give an estimate for me, what percentage of current standard biology study at university contains information about these subjects, and not theoretical biology? What percentage of the study is dedicated to species-specific subjects?

I'm thinking of studying biology...

Did you have gone through the basic (school) level of biology and chemistry? otherwise the concepts may become hard to handle.

  especially ecological and evolutionary biology

Ecology and evolutionary biology is in fact highly information-dependent area.

Ecology is the study of habitat, lifestyle and interrelationship of different organisms. So there will come the role of different organisms in ecological relationships.

But there are other parts like statistical calculation of gene frequencies, energy uptake, etc. These parts will contain lesser amount of species-specific information.

Evolutionary biology too; have various fields and aspects, and could be studied in various ways.

If you need to study about evolution of a certain genera with fossil evidences; or estimate  the evolution of biochemical pathways; a lot of species or genus-specific information may require.

Whereas there are generalized areas, such as basic principles of evolution, its mechanisms, statistical models, etc.

(update coming soon...)


Why can blood group O be given to all blood groups? The blood of persons of blood group O contains antibodies against antigens A and B. The red blood cells of persons of blood group A have A antigen on their surface. If someone with blood group A receives blood from a donor of group O, then anti-A antibodies in the donor blood should attack the A antigens on the recipient's red cells. Shouldn’t this be a problem?

Good question! Let's start with an overview and explanation of the ABO blood grouping system (Dean, 2005):

Blood groups, antigens and antibodies: Subjects with blood group A carry the A antigen on their red blood cells (RBCs) and have antibodies to antigen B; subjects with blood group B have the B antigen and anti-A antibodies, blood group AB carries both the A and B antigens and have no antibodies, and finally folks with group O have no antigens but both antibodies.

Blood groups and transfusion: Circulating antibodies in a person's blood will attack transfused RBCs from unmatching blood groups. These antibodies fix complement and cause rapid intravascular hemolysis, triggering an acute hemolytic transfusion reaction that can cause disseminated intravascular coagulation, shock, acute renal failure, and death (Dean, 2005). As people with blood group AB have no antibodies, they can receive all blood groups without issues. People with blood group O can only receive RBCs of blood group O, because they carry both antibodies. Blood group A can receive A and O, and blood group B can recive B and O. Hence, blood group O can be received by all other groups, and is therefore the universal donor.

Typically, literature on transfusion deals with the haplotyping the antigens of the donor RBCs. The question whether the antibodies in the donor's blood with blood group O would start attacking cells in recipient with blood group A, B and AB is, therefore, a very good question. And the answer is: yes, they will. Why then is O still the universal donor as they have both anti-A and anti-B antibodies?

First, whole blood is not used for "routine" blood transfusions (Torrens University Website). Instead, blood component therapy has largely replaced the use of whole blood (Patient.co.uk website). For routine transfusions, only the fraction containing packed red blood cells is transfused (Mayo Clinic website). Hence, in these cases, the blood plasma containing the antibodies is (virtually) removed after centrifugation. Since O-type red blood cells contain no antigens (Dean, 2005), and the plasma with the antibodies are not transfused, it can be donated to everyone, barred that the rhesus factor matches.

Secondly, even if plasma is transfused, antibodies in the donor's plasma are a minor problem, because of the small amount of antibody present in the donated plasma, which is further diluted on transfusion into the recipient's circulation (Dean, 2005).

Reference
- Dean (2005) Blood Groups and Red Cell Antigens. Chapter 5.The ABO Blood Group


What's a "constitutionally small penis"? I'm reading some urology papers and came across one involving penis growth (Kim & Song, 2008); here's an intro passage that I'm confused about:

A total of 58 patients with constitutionally small penises, without chromosomal anomalies and gene-associated syndromes, intersex, and hypospadias, were included in this study. The average patient age at their first visits was 10 years and the average follow-up period was 2.2 years.

What's a "constitutionally small penis"?
Edit:
I've read the paper in detail and I don't see where the authors distinguish between a small penis and a "constitutionally small" penis.
Would a "constitutionally small penis" be the same thing as a "micro-penis"?  If not, then where do we draw the line?
References
Kim, K. S., & Song, G. G. (2008). Penile Growth After Puberty in Patients with a Constitutionally Small Penis. Journal of Pediatric Urology, 4, S63. doi: 10.1016/j.jpurol.2008.01.174

"Constitutional" refers to the physical state of the concerned individual (Merriam-Webster).

In biology, it most probably means a trait that is not pathological or environment induced.

This is in the context of size of babies:

  Small for gestational age (SGA) can occur following a pathological
  process or may represent constitutionally small fetuses.

  From: Ananth & Vintzileos (2009)

  Between18-22% of infants SGA by population
  standards are reclassified as normally grown by customized standards
  and as the perinatal mortality of these reclassified babies is similar
  to those who are normally grown they can be considered to be
  "constitutionally  small.".

  From: McCowan et al. (2018)

  In most cases, it is difficult to differentiate between
  constitutionally small head size vs pathologic microcephaly, and
  available data regarding prenatal diagnosis of microcephaly are based
  on small numbers of cases of varying etiologies.

  From: Ultrasound screening for fetal microcephaly following Zika virus exposure.
   American Journal of Obstetrics & Gynecology, Volume 214, Issue 6, B2 - B4

Regarding constitutionally small penis: Since the article you mentioned is the only source (scientific or otherwise) of this term, I would believe that it is based on the population average (of possibly South Korea from where the authors are). Moreover, since it is not defined rigorously, it is most likely an arbitrary classification.


Help identifying a fly by its remains I recently hiked in a swampy forest in the Yaroslavl region(Eastern Europe) near lake Plesheevo and came across a clearing. Although the area was swampy and verdant, there was a 5 meter wide "bald spot" on the ground which looked like sand. Near that spot there was a lot of buzzing (which I initially mistook for the buzzing of wasps), and soon I found myself covered in these black flies.

The flies clung to my fabric hoodie, at least one tried crawling in my hair, and one tried to find its way into my eye.
I tried shaking them off, but they seemed to be able to cling very firmly to my clothes. (later I discovered that even dead flies were really hard to remove from fabric)
At that point I panicked, quickly retreated, and spent a good 15 minutes extracting every single one of them from myself and my garb.

When I came back, I took a picture of the carcasses of two flies that found their way into my pocket and silently passed away there from unknown causes. Unfortunately, I didn't get to take a picture of a living fly because I was too agitated at the time.

Their length was approximately 0.3 inches and when squashed, they produced yellow spots on my clothes.

I tried identifying them, but didn't have much success. They seem to look like a variety of horse-fly (or a dear-fly), but I think none of them actually bit me. Also, strangely enough, my clothes were sprayed with insect repellent which they seemed to either completely ignore or were actually attracted by.

They look very much like Hippoboscidae. https://en.wikipedia.org/wiki/Hippoboscidae
This family are parasites of birds and mammals, but I am not aware that they are vectors of any diseases to humans. So don't worry. One member of the family is a wingless parasite on sheep (Melophagus ovinus)


Why haven't prey evolved the ability to always outrun their predators? I can understand why some prey can't outrun a recently evolved species. However, since cheetahs have existed for so long, why haven't its prey evolved to always outrun it, driving cheetahs to extinction. Is it because the cheetah population size is so much smaller than the population size of most of its prey species that its prey species are under very weak natural selection to outrun cheetahs? Is it that those that can run faster have more other biological costly traits?

There are (at least) three important factors to consider here; evolution under selection requires genetic variation upon which to act, selection can act on covarying traits causing trade-offs, and adaptation also occurs in the predator. A lot of this is covered elsewhere on this site (including the effects of the other mechanisms of evolution), but little specific reference is made to predator-prey co-evolution.

Adaptation and genetic variance

One of the mechanisms of evolution is selection, and adaptation occurs when species evolve as a response to selection. For a response to selection to occur there must be genetic variation within the trait, such that the genes an individual carries affect the individuals fitness. For example, there may some genes which give the carrier better muscle structure for fast running, and this increases survival which, in turn, increases reproductive output. The importance of genetic variation is often overlooked, but is highlighted by the breeders equation. Genetic variance can arise by novel mutations, or can exist as standing genetic variance.

Selection on covarying traits

Selection is seldom, if ever, a univariate process. That means fitness is not determined by a single characteristic, so fitness in a prey species may be determined by the speed at which it can run, but also its metabolic rate, stamina, ability to acquire nutrients, the way it provisions nutrients for growth and repair etc.. Genetic covariance between traits (induced by linkage or pleiotropy) can impact the response to selection, because any selection acting on a covarying trait can cause affect the adaptation occurring in the focal trait (strengthening, weakening, neutralising, or even reversing the direction of response). Therefore, if running speed covaries with other traits it may be difficult for selection to increase running speed. Think about athletes, I doubt Usain Bolt could run 10,000 metres as fast as Mo Farah and vice versa, because there is a trade-off between speed and stamina.

Adaptation in other species

If selection did cause speed to increase in the prey species then that would strengthen selection for increased speed in the predator. This is called an evolutionary arms race, where the adaptive the evolution of two species interacts causing adaptation and counter-adaptation. For example, genes which allow faster running might spread through a population of gazelles (prey) because carriers are more likely to outrun the lion (or the other gazelles), but this will increase selection on lions (predator) to increase speed (or adopt other strategies) which will spread genes to make the lions faster (use other strategies); the result being adaptation and counter-adaptation between the gazelle and lion populations.

There is a little series here about Butch Brodie and his studies of coevolutionary arms races between garter snakes and toxic newts. It would be good to read on the Red Queen Hypothesis, which describes how species, under interaction with other species, must continue to evolve just to prevent extinction. Also worth noting that prey species often have more than one predator species (and predator species often have more than one prey); interaction and coevolutionary networks are complex. What may be adaptive in some interactions may also be maladaptive for other interactions (see specialist and generalist, and selection on covarying traits).


Signaling through G protein Coupled Receptors? There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a experiment through which we would be able to identify specific Gs or Gi proteins in cell lines?

EDITED ANSWER

Based on comments and responses my original answer to this question received I have decided to edit the answer and respond to some questions.

Since I work on proteins, I tend to favour protein based approaches specially when wondering about the presence of a protein. This is simply the case because protein is what is important functionally (purely talking about protein based problems/questions here and not talking about RNAi stuff here) so what I have experienced editors require for majority of papers, they want to see some sort of protein work. Now I'm aware that is not always possible since the antibody (Ab) might not be very specific or sensitive specially for low expressing proteins. If a protein is highly transient that makes the problem even worse, which is why many people resort to mRNA expression to make deductive reasoning for the presence of proteins although that makes a number of assumptions about how the mRNA is processed and whether the relationship between mRNA expression and protein expression level is linear but thats another discussion. So all I'm trying to say is that it's important check for the presence of a protein using Ab based techniques, which are immunohistochemistry (IHC) and western-blot (WB).

So my primary recommendation is to use Gi and Gs species specific (non-cross reactive) antibodies to check for the presence of your proteins of interest and always use Ab heavy chain control for IHC and a negative control for your WB using a sample that you know doesn't express your proteins of interest, if thats available. IHC also tells you some spatial information and whether Gs and Gi are both present in the same cell line or not and if they co-localise etc etc! Obviously check for Ab availability and if its compatible for IHC or WB procedures.

The other method that is feasible is if you know your two different cells express only one of the Gs or Gi exclusively, you can look at their specific inhibitors and add it to some of your cells and the chances are if the dose is high enough it will cause the cells to die since Gs or Gi are crucial for cell function. You can probably get away with an experiment like this using wells in a 24 well dish so you don't have to use that much media or drugs. But with stuff like this it might not work and you might get off-target effects so just do this as a complementary test. For your drug test always do a DMSO control since the chances are that's what the drugs are dissolved in and if not just use whatever solvent the drugs are dissolved in and add them to your cells in your control experiments.

Now the other possible and commonly used method to check for the gene expression of protein and subsequently infer its presence as a protein is to use a reverse transcription based PCR, such as RT-PCR although it doesn't have to be real-time as correctly mentioned in the comments. Please note that I'm not at all an expert in this and do check my answer in this section since I haven't personally done reverse transcription based PCR. As far as I'm aware, the basic procedure is to extract cellular mRNA, which can be performed using kits such as RNeasy or a similar product (I'm not promoting any products here and these are just what I have came across!). The protocols come with the kits and available online, and tells you exactly what min/max cell number/RNA levels should be present and how your cells should be (pelleted) before processing. Another method for RNA extraction is CsCl but thats pretty messy and complicated and requires high expertise to get it right but I know its inevitable for certain situations but for cell processing, a kit will do. At least RNeasy protocol states it enriches for mRNA and selectively exclude other types of RNA. Once you have your cellular mRNA you can proceed to reverse transcription using the appropriately designed primers for your gene of interest using a thermocycler. Again I'm not sure what tools to use for designing the primers for making cDNA from mRNA and what to look for (apart from the fact that make sure your primers are specific) as I only do regular PCR but would welcome any edits! Once you get from mRNA to cDNA, you can then run them on your (Ethidium Bromide or whatever DNA staining based) agarose gel and see if your amplicon is present and is the correct size (again based on the primers you have chosen you would know what the correct size is) and hence whether your gene is expressed or not. At least RNeasy kit says you do not need to use DNase digestion to get rid of any DNA before reverse transcribing your mRNA as most of it gets cleaned up when using the kit but you have that option. Now regarding the next-generation RNA sequencing I do not know anything about them so would again welcome any edits but seems unnecessary since you only want to know if the gene of interest is expressed so don't need any sequence info but thats an option too (although I imagine a little expensive?). Just to mention something very obvious, it's important that the species, which your lines have been generated from are sequenced or you have good sequence information about the Gs and Gi genes in your lines otherwise designing primers would be guess work. Its always best to see if anyone has done what you are trying to do and ask for their primers as most people are happy to share reagents.

Now you have probably noticed so far that my methods are quite biased towards molecular biology approaches and that's simply because that's what I know more about, however a great suggestion was to use cAMP levels as an indicator for Gs or Gi expression. Again I'm not an expert in this since I haven't ever analysed small molecules but I imagine that involves something like a HPLC, which you need to discuss with a chemist/biochemist how to extract and clean up your cells from everything and leave only the cAMP. There is probably a procedure/kit/biosensor for it but I will avoid getting into it as I know virtually nothing about this. However I have a note of caution for these types of indirect experiments. I have no idea what your cell lines are and how well they are characterised but since lines have all sorts of mutations and deletions and insertions in them, it's not a good idea to make inferences from cAMP levels. Since considering cAMP presence is quite important for cellular function, their absolute levels in a cell line is not necessarily a good indicator of whether one cAMP production regulator is present or not and I'm sure if you do something like this you open yourself to major criticism by any journal editor/referee. What will be a good idea though in any future experiments you do with these cells is to over express Gs or Gi and see their effects on cAMP production but I just don't recommend using cAMP levels as a sole indicator as to whether Gs or Gi is expressed or not.

If everything else fails and you got tired and wanted to wash your hands off this identification task, you can always lyse your cells and send them for mass spectrometry (MS) if there is such a facility at your institute. It's crucial that the species, which your lines originate from are characterised in terms of their global protein sequences since programs such as Mascot query the raw spectral data against databases such as UniProt to get protein coverage and subsequently protein hits. Also before you go ahead with you MS experiments, just speak to the facility manager and ask for guidance as to what lysis buffer is best to lyse your cells in and what components should not be in your lysis buffer and how sensitive their machines are and how likely you are to get detection and what your protein concentration should be. I think the best machine to use is Orbitrap and as a general rule, the higher the protein amount, the more likely you are to detect it. Since cell lysate is pretty messy and the MS machine columns can get saturated by abundant proteins such as actin, it would be best to run your lysates on an SDS-PAGE gel under reducing conditions (you can even do multiple loads by running your samples in the gel, switching off the WB machine, loading more samples and running them in the gel and continue doing this a few times. It works, I have done it myself but for pulled down samples which are a bit cleaner (less contaminants/unwanted proteins) in general). Once your gel runs through just cut the region of the gel corresponding to the molecular weights of Gs and Gi and send that for MS identification. This method (running your lysate through SDS-PAGE gel) gets rid of unwanted proteins that can interfere with the identification process. But MS is very expensive!

Again I would highly welcome any edits to my own edited reply! I'm here to help and learn.