texts: There are single wire pacemakers used for regulating heart beat. The wire will conduct pulse to the heart. How can one wire be enough? Where is the reference wire for the stimulation of heart?


texts: Carbon Monoxide and High-Oxygen-Affinity Varieties of Hemoglobin

texts:
I recently learned about the concept of "affinity" in regards to hemoglobin. For hemoglobin in humans, carbon dioxide has a lower affinity than oxygen, which allows gas exchange to occur in our lungs.

Carbon monoxide is problematic for us because it has an even higher affinity to hemoglobin than oxygen does. This means that our red blood cells will not exchange carbon monoxide for oxygen in our lungs.

My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?


texts: If you were to use an older sphygmomanometer and a stethoscope to record blood pressure, why would you hear no sound when the cuff was inflated to 160mmHg


texts: I see a swing bucket rotor for PCR trips and don't know what step is using? What difference if I use fixed - angle? In addition, Which step I can use swing bucket instead fix - angle in molecular biology (Example: extraction, purification,..) to improve centrifugation efficiency?


texts:
I snapped this picture on a walk in the Pacific Northwest last week, and, being new to entomology, cannot manage to identify whether this is a moth or a butterfly.

It seems to have the coloring of a moth, yet it was out around 4-5 PM, with the sun still shining brightly. Its antenna look like a butterfly's, but its face (particularly the eyes) seems to be that of a moth. The wings are folded up like a butterfly (in another picture of the lepidoptera), but they look quite drab for a butterfly. Any help?


texts: Genetic carrier Pedigree of Recessive Traits

texts:
A human male and female couple with normal colored ears discover that, in both of their families, their fathers (who have normal ears) each had siblings with red ears.  Red ears is a rare autosomal recessive disorder.  None of their grandparents had red ears.  Assume that the red ears in both families were caused by mutations in the same gene, that there were no new mutations within the pedigrees, and that the mothers of the couple were not carriers of the disease gene.

A) based on the information, what is the probability that the male in the couple is a carrier of the red ear disease gene?

B) if the couple had 1 child, what would be the probability that child would have red ears?

I was discussing this problem over with a friend and we got different answers.

A)I think the answer is 25%.  I multiplied 1/2 and 1/2.
B)6.25%.  I multiplied 1/4 and 1/4.


texts: Using nanodrop for analysing biological samples other than nucleotides

texts:
I am a 3rd timer postdoctoral fellow with some experience in molecular biology and biochemistry, but major skills in Zoology and Natural History. I am studying some natural extracts, and isolating compounds.

Some biological samples come in limited amounts (e.g. invertebrate haemolymph), hampering analytical methods that rely on larger amounts. For instance, establishing UV-Vis spectra of extracts is a usual non-destructive method for approaching unknown samples and estimating general parameters, done with a spectrophotometer.

The microvolume-scaled spectrophotometer system popularly known as 'Nanodrop' has been around labs since almost two decades now. Its use has been usually limited to fast purity & concentration estimations for DNA & RNA in molecular biology labs.

I am considering using the nanodrop to estimate parameter of other biological and chemical samples. The manual says most commonly used solvents are compatible with the system. I have however yet found no-one else who has tried using Nanodrop for different applications.

Please, anyone here who has experimented using a Nanodrop system with other biological samples and extracts could comment on the experience?


texts: recolonize earth desert with plants : which plants first?

texts:
if willing to recolonize earth desert , let's say sahara or any dehydrated and sterile land, without intensive human intervention, what would be the first plants / algae / fungi /bacteria to grow ?

what could be the strategy to slowly bring back biodiversity and trigger new water cycles ?


texts: How antibodies are produced in our body against intracellular proteins of infectious bacteria?

texts: When an infectious agent invades our body, then surface antigens of the infectious agent are detected by our immune system and B-cells get activated. However, we do have antibodies in our blood against intracellular proteins of the infectious bacteria. What is the mechanism which produces antibodies to intracellular proteins, which are never exposed to our immune system.


texts: Why are dreams sometimes remembered and sometimes forgotten?

texts: Why is it that sometimes, when we wake up, we are able to remember what we were just dreaming, but sometimes we don't remember any of it?


texts:
I recently watched the movie -"interstellar" and I came through the question that how can ageing be affected by space-time? Wherever I look, I get it as a fact that it's kind of ageing slows down in space, but I don't understand why.

How can space-time affect internal cellular metabolism? And if it is related to our biological clock, then can it be a sufficient explanation for this kind of drastic ageing changes?


texts: What is the difference between how motor function is controlled in cerebrum vs frontal lobe?

texts:
At least according to wikipedia, the frontal lobe houses the primary motor cortex, but in a different article about the cerebellum, it says the cerebellum controls motor function. So, do both parts control voluntary movement at once? What's the difference in the roles these two parts play in movement?

https://en.wikipedia.org/wiki/Cerebellum

https://en.wikipedia.org/wiki/Frontal_lobe


texts: what are examples of experimental designs on exposing materal for degradation

texts:
if one wanted to compare how sources of DNA would degradate in various conditions(environmental) how would they do this in an experimental fashion but also be best comparable to real world examples of Enviromental conditions? Sorry if this question is worded poorly, any suggestions would be appricated.

For example, if I were to expose my own blood to various conditions such as a wet enviroment versus a dry ennviroment, how would I best replicate these enviroments in real life(ie: bloodly water in a cup versus dried blood on a floor) without introducing confounding varables?

I would need some type of "standard" yes? And if so, then would using sterile controled conditions be appropriate, or should I literally be using these real world situations for "better" results?

I tired finding papers, but I guess my research methods are too poor to get anything useful.

EDIT:

My facilities I have access to are a small academic institution, I know basic autoclave use and have access to gel rigs and pcr machines. My samples do not have to be blood, it could be any human tissue or sample, like hair or spit. I suppose I would use the same sample, but kept in a sterile condition for a controo, maybe a petri dish?

I guess my mental protocol would be to try different degradation conditions and extractions, but starting with a boiling DNA extraction to see how effective a certain condition was compared to a control.

I could set up a time table of like 2 weeks to perform the experiment, and every 3 days or so, extract DNA from the control and the sample to then pcr with some human primers(I think we are using the fbi's CODIS primers that they use in foriensics, but only a subset due to cost) and then run an agarose gel to determine degradation( poorer resolution meaning more degradation I suppose?).

Another wuestion that popped to mind, for my time table and my DNA extractions, would I have to perform the pcr and subsequent gel elecrrophorsis as soon as I am done with my extraction, or could I store the extraction samples until I am ready to run a large batch of pcr tubes and a large gel? Would they degrade in a -80°C freezer?


texts: Is averaged molar CO2 and O2 output/input necessarily identical?

texts:
Do we take up identical amounts of oxygen to the amounts of CO2 that we output? Equivalently, do plants take up identical amounts of CO2 as they release O2? (moles, averaged over >24 hours)
I was interested in the contribution of room-plants in removal of (harmful) CO2. From theoretical knowledge of photosynthesis, the citric acid cycle and respiration chain, I suspect that a persons molar CO2 output is roughly identical to the O2 input, and in reverse for plants, as summarized by the net-equations:

Diverse sources mention that human needs around 0.8 kg oxygen per day, while realistic house-plant acquisitions produce no more than 10% of that. Paradoxically, while the effect of house-plants in O2 production was described as minuscule, plants were consistently highlighted for their efficient removal of CO2 from rooms. (I know that the ratio of CO2 to O2 is around 1:20, so absolute removal of CO2 has higher relative effect.)
As I personally cannot exclude a contribution of human secretion (sweat, unary..), and also I lack knowledge of the exact chemical composition of molecules that are accumulated during plant growth and storage (in bulbs or fruits), which may contain different ratios of oxygen and carbon, I cannot exclude that in/-output O2/CO2 ratios can deviate from perfect equivalence. But if so, by how much?


texts: What does enzymatic equilibrium in % represent?

texts:
I am studying an enzyme which can catalyse a chemical reaction in both directions. The paper I am looking at is mentioning a thermodynamic equilibrium of 1% in the synthase direction.

What does that mean more intuitively? I am mostly confused by the percent unit as I expected a constant rate without unit...

My guess would be that under these specific concentrations of substrates/products, the enzyme is catalising 1 synthase reaction and 99 inverse reactions for each 100 reactions it is catalising. In other words, the equilibrium constant K of the synthase reaction under these conditions would be 0.01.

Is that correct?


texts: Why can't primary RNA be used as a direct template for a protein?


texts: The PDB file format is explained here. My question is what "chain identifier" is exactly? What is the difference between two residues which have the same sequence number but different chain identifiers?


texts: Where to find E.coli gene expression data?

texts:
I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc.
I have tried GEO but it only gives a list and one should read all pages and samples one by one to see which conditions were used.


texts:
just like in the title my question is, is there any kind of paw/pads lines or paw muscle anatomy in animal hands? or its pretty much random?

example like mammary lines as bilateral structure that rules where mammary tissue can develop. is there similar thing like this for animal paw/pads? especially comparable to human hands?

prefferably include image (example like this mammary lines) if possible.


texts:
Motion after-effect illusions, such as the waterfall illusion, refer to illusions where fixating a screen which shows stimuli moving in a particular direction  elicits the perception of motion in the opposed direction when subsequently looking at a static image.

Here is an example: Video Motion After-Effect

The explanation is typically that adaptation effects lead to a saturation of the firing rates of neurons encoding the viewed motion direction.

So far so good - but why do we then perceive afterwards motion in the opposite direction, and not in any other direction where no adaptation has happened?


texts: This salamander was found in a small forest pond somewhat near the Oregon coast. In the area are many rough skinned newts and a small number of another type of salamander that I still can't find the species of. I'm guessing it is either the salamander species or a rough skinned newt.


texts:
I'll keep this question straight and simple:

Some succulent plants produce carotene, a red pigment, in response to great heat, turning their leaves red. The dragon blood tree (Dracaena draco) is among the succulent plants. Does it exhibit this behaviour too?


texts: How are elements like iron recognized and routed to the right places for use in the body?

texts: I asked this in Chemistry and it was suggested to ask it here. I wondered how the genome, which afaik does not contain iron or calcium as "reference" copies, nonetheless produces an organism that uses certain elements. If it create proteins which bind preferentially to iron or calcium, how then are such elements routed to sites where they can be bound? Are there proteins in addition to those which bind to elements that are responsible for routing? I should mention that I am a software developer and imagine mechanisms analogous to computer code.


texts: What is a typical value of the selection coefficient s?

texts: I am trying to gain an understanding of the real world effects of natural selection from the equations, especially comparing it with drift. However I have been unable to find any examples which give an estimated value of the selection coefficient for a population considering a particular trait. Could anyone link me to some studies that give an actual value for a selection coefficient? Thank you in advance!


texts: Why are the sympathetic and parasympathetic axons different, in terms of presynaptic and postsynaptic length?

texts: Does the parasympathetic system have a long presynaptic efferent axon because it takes a great distance to reach target organs from the brain stem or sacral region of the spine? Does the sympathetic have a long postsynaptic efferent axon (that reaches the target organ) since the presynaptic neurons are centrally located in the thoracic and lumbar regions of the spine? What purposes do these different axon lengths between the presynaptic and postsynaptic parasympathetic and sympathetic neurons serve? I'm looking for an answer that explains their benefits.


texts: Why is PEG important for efficient yeast transformation?

texts:
One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient transformation. How does it affect the take-up of the foreign DNA? Yamakawa et al (2) showed that PEG is essential for the recovery of the cells but I couldn't access that paper to read more about it.

1. R Daniel Gietz & Robert H Schiest (2007). High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method

2. Yamakawa, M., Hishinuma, F. and Gunge, N. (1985). Intact cell transformation of Saccharomyces cerevisiae by polyethylene glycol. Agric. Biol. Chem. 43, 869-
871.


texts: How DNA programs the first cell in womb into a human

texts:
Sorry if you see me silly. I am just a programmer happens to be curious about biology...

So far I understand how DNA make protein, how cell divides, how one composed of cells->tissues-> organs.

But, still a piece is missing in my knowledge.. Given the sperm entering the egg creating the first cell, and the nutrients from the mother... how do that very first single  cell diversify , multiply, transform to a human of many different type of cells, tissue and organs ? Is this all the diversification and
specialization of cells directed just by the "child" DNA alone ?

Also, how does DNA (along with living condition ?) decide the course of my life  (making me 1m tall at 6 y.o , have my hair black, my life expectancy etc..)


texts: Recent classification for parasitoid (ecological relationships)

texts:
I'm about to present an exam about ecological interactions in biological control. Although the position of some groups is clear, in the case of parasitoids they are included sometimes as predators, some others as parasites, while sometimes they are included like an own group. For example, in this paper they
 are included as parasites, but I wanted to know if there is a more recent reference or classification for these groups (Trophic strategies,
animal diversity and body size Kevin D. Lafferty and Armand M. Kuris).


texts: I use Rose bengal agar cloramfenicol for search yeast and molds for inclusion in petri plat. Which is the method correct for count? I'm not sure if i count everything or only the bigger one?


texts: Is it possible to lose weight doing brain exercise?

texts:
According to this article human brain consume a comparable amount of energy with skeletal muscle. So is it possible to do some brain exercise (calculate something in mind etc.) instead of physical exercise to lose weight?
More specific questions:

Is it theoretically possible?
Is there any real-life example?
What kind of brain activity require more energy?
Pros and cons (brain exercise vs. physical exercise)


texts: To what extent does loss of neurons in the substantia nigra affect movement?

texts:
There is a substance known as MPTP that is capable of crossing the blood-brain barrier. Once it does so, it is metabolized into a toxin called MPP+, which then selectively destroys dopaminergic neurons in the substantia nigra pars compacta of the brain, causing parkinsonism. This effect of MPTP was discovered when drug users were poisoned with it in the 1980s.

How much of an effect does this destruction of neurons have on movement? Were these patients completely paralyzed as a result, or did they retain some ability to move voluntarily?


texts: Why does centipede keep running into my hair and bite me?

texts:
After I moved into a new house in the suburban area, I was bitten by an unknown creature near my spine at mid-night. I felt painful and dizzy. However, after 15 mins, I no longer felt dizzy and the pain faded, so I did not see a doctor.

Serveral months later, the same thing happened again at mid-night, the creature ran into my hair (I have long hair) and bit the back of my neck. This time we figured out that it was probably a centipede, as it was red, had many legs, and ran fast.

Yesterday, a centipede ran into my hair again in the morning. Luckily, I felt something was in my hair and I manged to shake off the centipede, so it did not bite me.

Why does centipede keep running into my hair and bite me and what should I do?


texts: Do male mammals other than humans have nipples?

texts:
When I grew rabbits, I had a pair, one male and one female. And while the female's nipples were quite prominent, especially after giving birth, I don't remember the male having any nipples at all.

Do males of other mammal species, have nipples like human males, or is it a trait that's unique to Humans?


texts: A mutation question from the Indian National Biology Olympiad

texts:
DNA was isolated from wild type (Gal+) and mutant (Gal-) E. coli cells and separated by density gradient centrifugation technique. DNA from Gal- strain acquired a lower position. This indicates that the mutation is caused by:
(a) deletion (b) insertion (c) mis-sense mutation (d) point mutation

Me and my friends had an extended discussion on this question and we all agreed that since the Gal- strain acquired a lower position, it was obviously more dense than Gal+ strain. Now, one of them claimed that if the volume were to remain constant, then mass is directly proportional to density hence the insertion mutation should cause increase in mass corresponding to a similar increase in density. I am not convinced by this explanation. They also said that, "Keeping the volume constant is a necessity since the experiment would lose its meaning otherwise". I am curious to know how far these assertions are correct.
After doing some research on this topic on the internet, I found a paper related to this question :
Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli
The answer given by the organizing committee of the 2nd Indian National Biology Olympiad was (b) insertion.
What could be the possible explanation for such an occurrence? Me and my friends are still unable to grasp the logic behind it even after going through different papers and books.


texts: How are the paranasal sinuses linked with the capillaries in the ear canals?

texts:
Sinus congestion often seems to be accompanied by excess pressure on the outer ears (as anyone who has shared a transcontinental flight with an infant can attest to) or fluid buildup in the canals.  An increase the capillary pressure within the ear canals would explain the pressure, but what is the physiological connection between the sinus pressure and pressure in the ears?

The most obvious answer I can think of is that any direct drainage from the sinuses would cause a backup of fluid into the Eustachian tubes.  This would only explain pressure coming from the other side of the eardrum, but is such pressure simply relieved by blood pressure transfer to the capillaries in the ear canal, or is there a non-trivial mechanism by, e.g., a vagal circuit which governs the relationship between the sinuses and the outer ear?


texts: Why are human feces riskier than urine with regard to spreading diseases?

texts:
I came across a Wikipedia article titled "Urine diversion". It explains different ways, including using special diversionary toilets, and treating the collection of human feces and urine separately as opposed to just flushing everything down the toilet, maybe something most people in well developed countries are used to. These sentences caught my attention:

Separate treatment of the two types of waste is justified since urine is nearly sterile and low in pathogens, provided an individual is healthy.[3] This means that urine can be readily utilized as a fertilizer or discharged with less risk to community.[4]
Human feces, on the other hand are high in pathogens, including up to 120 viruses and need to be treated well before it can be safely used in agriculture.
Urine diversion - principle (Wikipedia article)

So urine is nearly sterile and low in pathogens, however it qualifies that statement with the condition that the person producing that urine is healthy. I assume when they compare this to feces they do so with all other things being equal (ie., provided an individual is healthy).
It claims that there may be up to 120 viruses in feces, as opposed to urine which it characterizes as being relatively low risk. I assume that feces are riskier in transmission of diseases because it naturally contains more pathogens, but it doesn't explain what these viruses or pathogens are. I was wondering if someone could elaborate on the risks of feces over urine, and also, notwithstanding that it says that urine is relatively low-risk, what health issues can be caused by reusing urine.


texts: If certain cells or tissue in a specific part of the body are for some reason overworked; like the cases of severe acid reflux damaging the throat repeatedly and the cells in the throat having to do growth and repair a lot more than they would with a healthy person -- or problems in the stomach attacking the stomach lining a lot, causing 'extra' growth and repair; could these situations of 'extra' growth and repair cause various cells used in these processes to mutate with all the cellular division and replication required? And maybe some of these extra-growth-and-repair induced mutations might cause the apoptosis mechanisms to malfunction?


texts: Can anyone identify these bugs in the soil?

texts: I was checking the soil around my pineapple pear tree and found this living down in the dirt. My goal is to identify the insect so I can properly treat the soil in an organic manner.


texts: Why don't electric eels shock themselves?

texts:
Why do electric eels not stun or pain themselves when they discharge their high voltage shocks? While it is known that they use those high voltage shocks to track their prey (as discovered by my professor Kenneth Catania [1]), and there is most likely some form of cage effect provided by the water (until they come out for a more powerful sting to scare predators), and that when curled less current might return through their own bodies [3], it is not clear why there discharges do not interfere with their own central nervous system (cage effect) or peripheral nervous system (through which current would flow in parallel to the water and target)?

[1] https://www.nature.com/articles/ncomms9638

[2] http://www.pnas.org/content/113/25/6979.full

[3] http://www.cell.com/current-biology/fulltext/S0960-9822(15)01147-1


texts: Meaning of "Domain with function to find" (FIIND)

texts:
From NALPs: a novel protein family involved in inflammation.

FIIND - Domain with Function to Find.

What is the meaning of this name? Does it mean "Domain with an unknown function"?
I'm translating an article in which this domain is mentioned, and I found three different translations of the term into Russian: "Domain with an unknown function", "Domain with a search function", "Domain with identification function".
I think the first translation is the most logical one, but I'm asking just in case, because I'm not an expert in this field.

The NALP subfamily. Finally, a large subfamily of the CATERPILLAR proteins is composed of 14 NALPs (also called PANs36 or PYPAFs37; FIG 2.) and is characterized by the presence of an amino-terminal PYD. This modular architecture is found in NALPs 2–14 (short NALPs), whereas NALP1 contains an additional domain — which our group has designated FIIND (function to find) — and a CARD, forming a carboxy-terminal extension. With two notable exceptions (NALP1 and NALP3), the NALP genes are located in two clusters on human chromosomes 11p15 (NALPs 6, 10 and 14) and 19q13.4 (NALPs 2, 4, 5, 7, 8, 9, 11, 12 and 13) (TABLE 1). Interestingly, the 11p15.5 region is an important IMPRINTED region and has been implicated in the imprinting disorder Beckwith-Wiedemann syndrome and in various human cancers, including Wilm's tumour38.


texts: If every person between 15-60 had an immune system equal to the healthiest people, would this affect the spread of coronavirus?

texts: Has anyone calculated the speed or breadth of the spread of something like coronavirus (or any cold, flu, airborne pathogen) based on how well the population can master the virus with their immune system? Just as a simple example, let's say you shortened the window of contagiousness by 2 days. Would that have a significant impact on the spread of the virus?


texts: How to assess if biological measurements follow a normal or a log-normal distribution

texts:
I am using a dataset composed by $m$ samples and $n$ features (genes). Each data point is real number.

I want to understand how to preprocess data before analysis, in particular: do data points follow a normal or a log-normal distribution?

I thought about using qqplots and searching for different tests to assess the form of the distribution, but I have a doubt:

Do I have to assess the form of:

each sample distribution
each feature (gene) distribution
the whole dataset ($m$ samples x $n$ features (genes))

?


texts: What might earlier versions of caddisfly shelter-building behavior have looked like?

texts:
The caddisfly has an amazing ability to build armor for itself by using a self-produced underwater glue to hold together pebbles: https://www.youtube.com/watch?v=Z3BHrzDHoYo.

How could this behavior and the ability to produce the glue have evolved? The survival advantage of the current level of the caddisfly's ability is clear, but how were the incremental stages advantageous? How could it have developed its armor-building ability without a strong enough glue? And how could it have developed a stronger glue without the armor-building ability that would make it useful?

My guess would be that before it was building a full shell like it does now, it started just by holding a pebble or two to itself. Then perhaps the bodily fluid that is now used as glue gradually increased in stickiness and helped the organism keep hold of the rocks or keep them together. It seems, however, like any modest amount of increase in stickiness that could occur due to mutations wouldn't have been enough to keep the rocks together.


texts: For fish, does a bony skeleton have any advantages over a cartilage skeleton?

texts:
I have learned that two important lineages of fish are the bony fishes (Osteichthyes) and the cartilaginous fishes (Chondrichthyes). Many websites mention an advantage of the cartilaginous skeletons of sharks and other chondrichthyans: they're lighter than bony skeletons.

But it has been harder for me to find out if we know of any things bony skeletons do for fish that cartilage skeletons can't do, or don't do as well.

My research and hypotheses

I found an old Manual of Geology by Samuel Haughton (1865) that says

  [a bony] skeleton only affords an advantage over a cartilaginous skeleton by allowing a greater variety of points of attachment for the muscles of the Fish, and so admits of more powerful motions.

But maybe other people have discovered more things since this was written. Also, I'm curious if this is just a theoretical argument, or if we have actual evidence that bony fish are capable of using their muscles more effectively than cartilaginous fish.

I have three main hypotheses at present:

Haughton was right, and a bony skeleton is just more effective at serving as an attachment point for muscles.
Bony skeletons are more effective at protecting the fish.
There are no advantages to bony skeletons; bony fish just happened to evolve this way. (As far as I can tell, the early evolutionary history of fish has been a bit unclear and I haven't been able to determine if there is current consensus about whether bone or cartilage skeletons came first, and whether chondrichthyan cartilage skeletons are an inherited primitive feature or an innovation.)


texts: May have killed a cutting. Can dead plant cells be revived?

texts:
Ok. So, I went to New York City for the first time! My parents picked a hotel, and we had a good trip.

And even cooler, that hotel wasn't very far from a cool cedrus Atlantic a tree.

I got a cutting, but accidentally left in in the car today, and my mom went to work. The new growth has died. The old hardened-off growth still exists, but may or may not be dead.

It's evergreen, and it's not easy to tell.

So, assuming it is dead, and since it will be a long time till my next family trip, how could I bring one of the cells back to life, so I can generate explants?

Obviously this is very hard to do with animal cells, but could it be different with plant cells?

Could I just collect a bunch of dead cells, and pour atp solution on them?

Could I perform a nuclear transfer?

How could this be done?

And most importantly, CAN this be done?


texts: Online Database for PPG (Photoplethysmography) signals (both Infrared and Red light readings)

texts: I am looking for an online Database for PPG (Photoplethysmography) signals for SPO2 (oximetry) analysis. I have tried several sources but they only have single datasets labelled "PLETH" and not individual IR (Infrared) and Red Signals. Please help me find such database or let me know any workaround for this.


texts:
I'm not sure if this is physics, biology or chemistry related so I will start here.
I'm from a city (Baku, Azerbaijan) where crude oil is known to be extracted since ancient times. Oil is no longer being produced within city limits however soil is still heavily contaminated in some parts of the city.
Recently a major project has started to turn one of the most contaminated parts of the century old oilfield (see http://en.wikipedia.org/wiki/Black_City_(Baku) for more) into urban territory.
Developer promises that all contaminated soil is being removed and recultivated but I still have some doubts about it. I also don't trust official reports so would like to conduct my own investigation.
What is the health hazard of soil contamination? Are hydrocarbon vapors direct health hazard? Or may be it's radon that surfaces with oil? What and how to check? Would I be ok if I just check radioactive contamination with dosimeter/radiometer?

Edit:

You can ignore water contamination and direct contact with chemicals. I'm talking only about vapors during hot season.


texts:
I have to separate two proteins of 86kDa and 80kDa respectively, however, I just cannot get a decent separation even in 6% polyacrylamide gel. To make matters worse, these two proteins are isoforms and there is no commercially available antibodies to differentiate either one. I am pretty sure raising an antibody against one of the isoform is not an option for me.

I am tying with the idea of reducing the gel to 4% (I am pretty sure I am pushing it already) or a 2D gel (both isoforms seem to have the same IP though).


texts:
In the following diagram about chromosome inversion, I don't understand:

Why do we need to take the reverse complement from step 1 to 2? Isn't inversion just reversing the bases in the region?
How is the bottom diagram derived? For example, where does the ACCCCACTC come from? I thought it should be: GACTGCCGT for 5'→3' and CTGACGGCA for 3'→5' (inversion of the sequences in the second step).

http://web2.mendelu.cz/af_291_projekty2/vseo/print.php?page=315&typ=html


texts: What is this plant with white-spotted thorny leaves from Morocco? Photographed in spring.


texts: Is there more diversity in marine species?

texts: I was reading about how life emerged from oceans, and the following question occured to me. Do land species suffer from the founder effect and is there more (genetic) diversity in marine species? A quick google search pointed to the fact that a majority of species live on land. Is that a paradox?


texts: why dna polymerase 3 requires a primer for replication

texts: Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.


texts: Why do leeches lose septae due to parasitism?

texts: So I found this piece of information in my textbook without a proper explanation, and I can't seem to find the relation between the two.


texts: Does urea at different concentrations (5 or 0.5M) have different effects on proteins?

texts:
The problem is to explain why each additive gives rise to the distribution of the protein (RMAS) as shown in the Western blow below:

In each case, the homogenates were subjected to high-speed centrifugation and the supernatant/pellet fractions were resolved separately by SDS-polyacrylamide gel electrophoresis. The gels were blotted and probed with an antibody raised against RMAS.

I am specifically stuck on explaining the effect of the 0.5M urea vs 5M urea on the soluble and insoluble proteins represented by the pellet and supernatant respectively. My thinking is that at low urea concentrations (0.5M) the pellet protein is destabilised by urea and solubility increases showing a band. However, soluble proteins are denatured and show no band. However, at 5M urea, the pellet proteins are reversibly soluble and therefore do not show as a band whereas the soluble proteins are OK and so show a 'normal' band. I don't know if this is the right explanation, so could someone please explain it to me??


texts: Why must a planet be in a star's "habitable zone" to have life?

texts: I have seen many articles that talk about a star's "habitable zone" as the ring around it which is just the right temperature for planets to have liquid water, which is necessary for life. My question is, why does a planet need to have liquid water in order to sustain life? Who says that extraterrestrial life can't live off of some other kind of sustenance?


texts: How many organisms have ever lived on Earth?

texts: I've looked for some information on this, but couldn't find anything useful. Has there been any noteworthy attempt to estimate the sum amount of individuals of all species that have ever lived on Earth?


texts: Why do cell membranes let small non-polar molecules through but won't let small polar molecules through?

texts: If the hydrophobic hydrocarbon chain of the phospholipid prevents the movement of polar molecules through the membrane. Why does the hydrophilic phosphate head of the phospholipid not prevent the movement of non-polar molecules?


texts: How effective is it to rinse fruit, lettuce, tomato, ... with water?

texts:
The general rule I've seen stated is that to get rid of some nasty bacteria, one should rinse fruit and vegetable under running water before using them, especially if eaten raw.

Most likely the effectiveness of such a measure depends significantly on the details of how this rinsing happens.  So, by how much is the risk of health problems reduced in different cases (e.g. just bath the fruit&vegetable in a water bowl, pass them quickly under running water, bath them and scrub them, keep them for a minute under running water (moving them around and scrubbing them at the same time), ...).

Of course, assuming those fruit&vegetable have already been washed earlier (e.g. before we bought them).


texts: Optimal Growing Conditions concerning CO2 level (ppm) for aquatic plants

texts:
I know this is rather specific but I would like to know what level of CO2 concentration in the water is optimal for the highest possible plant growth rate.

I did an experiment where the growth rate increased with higher CO2 levels in the water of the plants. The highest ppm were 60 but I don't know if higher levels would keep increasing plant growth or decline due to high acidity of the water.

The specific plant if this helps would be limnophila sessiliflora

Any information on this would be much appreciated.

Jonas


texts: Why is urobilinogen reabsorbed from the gut just to be excreted via the kidneys?

texts:
The Wikipedia article on Urobilin states:

Bilirubin is... excreted as bile, which is further degraded by microbes present in the large intestine to urobilinogen... Some is reabsorbed into the bloodstream and then delivered to [the] kidney.

This process is puzzling to me since it doesn't mention any function or reason for urobilinogen to be absorbed into the body, aside from it being there so it can be removed by the kidneys.
The only reasons I can speculate are that:

Urobilinogen shares a transporter/receptor with a similar, useful compound.
It has a direct useful function when in the bloodstream, not mentioned on the wikipedia article or a few other sources I've skimmed.
High urobilinogen is harmful to the gut and it's necessary to remove it via the blood to the kidneys.
Urobilinogen is inherently able to diffuse across the intestinal barrier into blood as a result of its chemical structure

Is it one of the above, or some other reason I haven't taken into account?


texts:
(1) Is it possible to identify the snake in the picture below?

If (1) cannot be answered:

(2) In view of the pattern of colors, is it possible the snake in the picture below be non-venomous? If so, what kind of non-venomous snake?

Additional informations:

Size: 62cm.
Region: South of Brazil, noutrh of Paraná.
I do not have a picture of the head.

Pictures:


texts: What species of butterfly/moth is this please?

texts:
What species is this please?

It's really tiny. That's an oregano leaf.

Location: United Kingdom


texts: Is there a blood panel lab test that measures all the hormone-producing glands?

texts:
I understand that there are gland-specific hormone tests, such as:

Secretin: for the pancreas; and
Prolactin/ACTH: for the pituitary; and
PTH: for the payathyroid, etc.

However, are there any "composite" blood panels that test the "entire gamut/spectrum" of organs/glands, similar to what composite metabolic panels do for your cell counts?


texts: If alcohol is a depressant, why does it makes certain people more hyperactive?

texts:
Alcohol is by traditional definition a depressant from what I have been taught, ergo it shows down CNS responses.

However, why does alcohol then make some people act out and be more energetic than when they don't drink?


texts:
As far as I know for evolution to work mutations  are necessary. Mutations are the raw material on which natural selection works.

But mutations are always completely random and human beings have no control over it.Then my question is how artificial selection works? Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?


texts: Why don't raisins lose water when in air?

texts:
It is common that we soak raisins in water, and they acquire water by endosmosis. That means that the cells are permeable to water, right? Then why don't they lose water when kept in air? Or kept in sugar without any water?

EDIT: Also, take the example of peeled potatoes. Put them in a hypertonic solution, and they lose water, but when kept there, in air, they don't. How come?


texts: Overexpression by integration of an additional copy vs promoter exchange

texts:
In Becker et al (2011), the authors increase the expression of several genes through different methods. For some genes (e.g., lysA, ddh), they achieve overexpression by integrating an additional copy of the gene and its flanking regions. On the other hand, for other genes (e.g., lysC, dapB, fbp, and the tkt operon) they take another approach and instead replace the native promoter with a strong constitutive promoter (Psod or Petfu).

Is there an advantage of one technique over the other? Why was one technique preferred over the other one for certain genes?


texts:
I’m reading on hormones and the book talks about how peptide or amine hormones are easily broken down by proteases present in the blood plasma. This has led me to question the interactions between these proteases and the blood proteins of the blood (such as albumins and globulins). Does having proteases in the blood mean the blood proteins are constantly broken down? How do the blood proteins get anything done then? And what good do binding proteins do in protecting hormones during vascular transit when the binding proteins are also susceptible to blood proteases?

Edit: I’ve been requested to provide some quotes and references.

  Because water-soluble hormones can dissolve in blood, many circulate as free hormones, meaning that most of them dissolve directly into the blood and are delivered to their target tissue without binding to a binding protein.

The book goes on to say

  Water-soluble hormones, such as proteins, peptides, and amino acid derivatives, have relatively short half-lives because they are rapidly degraded by enzymes, called proteases, within the bloodstream. The kidneys then remove the hormone breakdown products from the blood.

These quotes were from Seeley’s Anatomy and Physiology, 10th edition.


texts: What is the most-stable gene identifier?

texts:
I've struggled in the past with designing data(bases) around gene-identifiers that evolve over time.  For example, UniProt and Ensembl change their identifiers for certain proteins/genes and the IDs go stale after a while (years).  HGNC seems possibly better for this?  What I'd like is to have a single unique identifier for each human gene that will remain stable for many years.  I know genes get re-classified occasionally, but you shouldn't end-up with a new identifier for the same locus.

Suggestions?

Thanks


texts: How to safely conserve my current DNA methylation marks?

texts:
I read the Wikipedia article on DNA methylation

Let's say I want to extract and then stock my current DNA methylation marks somewhere so that I can use it safely 20 years in the future for a medical procedure that doesn't exist yet.

What method should I use?


texts: Can a plastic degrading bacteria science fair project be recreated in a school lab?

texts: i am just looking for a science fair project and am fascinated by this topic. i was wondering if a project concerning the isolation of plastic degrading bacteria could be done in a school lab. I am in grade 10. Anything helps!


texts: Will a nucleic acid sequence deduced from a protein sequence be expressed from a plasmid?

texts:
I have a fasta file containing the amino acid sequence of glycogenin-1: https://www.rcsb.org/fasta/entry/6EQJ
I want to create a plasmid that produces glycogenin-1.
Is it possible to use the glycogenin-1 amino acid sequence to produce said plasmid? Or would one need the nucleic acid sequence to do so?


texts: Is this a worm or snake?How to get rid of it?

texts: Hi! I found this thing in my bathroom. I killed it but still it's friends keep on reappearing. It moves slowly , is it a snake? How can i get rid of them? I live in Mumbai, India. It's rainy season here and the size of animal varies from 5 cm to 15 cm approximately.


texts: This is more a question about the evolution of taste than about the chemical composition of vegetables. Why don't vegetables taste good despite being healthful?


texts: What's the relationship between oxygen consumption and ambient oxygen concentration for a lobster?

texts:
I was looking at a research paper by Thomas (1954) and came across a graph with ambient oxygen concentration plotted against oxygen consumption rate of a European lobster kept in water.

As we can see, this is a linear relationship, but I'm unable to figure out the reason behind this direct linear relationship.

I would be glad if anyone out there can suggest a possible reason, because just rote learning the graph is not something which should be done.


texts:
I heard most dolphins are born tail first. I have read many explanations from books and internet articles and they said that dolphins are born tail first to prevent them from drowning.

But now I don't get this explanation. There must be no air in the mother's womb, so the baby dolphin can't breathe either way. I think they get oxygen from the umbilical cord until it's disconnected.

If this is true, why would they drown if they are born head first? Why are dolphins born tail first unlike most mammals?


texts: Why do tails of some lizards break so easily?

texts:
When I was younger once I have tried to catch a ground lizard by its tail but,
unfortunately the tail got broken and the lizard ran away.

Why did the lizard's tail get broken so easily while other animals have stronger tails?


texts: Why is warm water comfortable, but warm air uncomfortable?

texts:
I friend of mine tried floating, where you lay in a bath kept at body temperature (98.6 degrees F).  He said after a while you don't feel the water at all.

This made me wonder why being in warm water (bathtub, spa, etc) is comforting, but a hot weather feels miserable.  Can someone explain the difference?


texts: Will daily sweeped ants eventually learn their path is a dead-end?

texts:
An ant colony (likely Lasius niger) made its way through one of our rooms, literally.  That is, they enter by a door and leave by the other, and vice versa.  Some carry eggs, but in both ways, so I'm not sure whether the nest is on one side or the other.

I sweep them outdoor everyday, but each night they repopulate the path.  Am I wasting my time or is there a chance sweeping makes them decide it's a dead-end ?

NB : Washing the floor didn't change anything.  I also tried to barricade with somehow large amounts of essential oil of Eucalyptus citriodora, but it didn't seem to help.  Anyway although suggestions to get them leave are welcome in comments, I'm genuinely interested in knowing if the sweeping strategy may have an effect or not.


texts:
I saw the chart in this post Histidine aromaticity. Since I'm not allowed to comment and post a question instead of an answer, I have to ask my question in a separate thread.

How can histidine be classified both as positively charged and hydrophobic?


texts: Does focusing on a certain part of the body increase electrical activity in that region?

texts:
I am batting around ideas for master's thesis topics and was wondering whether or not just focusing on an area of the body would cause of boost of  neuronic activity? Not sure whether this would fall under the rubric of a self-fulfilling prophecy of the mind, or some other secondary body function. I though it might be interesting to examine the relative differences between varying parts of the body and their respective degrees of responsiveness to intentional cortical activity, as directed by a person. If anyone has an answer please respond soon as I can't quite nail down how to search for a question like this online (finding specific phrases, etc.) Also, feel free top point me to any readings related to this (would-be) phenom.
Thanks!


texts:
They say a Moluccan cockatoo's screech has a decibel level of around 129 or even more (e.g., 135). That is almost as loud as a jet engine (140 dB at 100 feet).

How are they able to emit a screech that loud? Don't they hurt themselves?


texts: What is the location of the Hypoglossal nerve?

texts:
I kind of know where the hypoglossal nerve is located when I look at the diagram, but I'd like to know how far is the nerve from the skin and where is the closest area to the skin before and right after it's branching?

Is there any video or schema showing the location of the Hypoglossal nerve relative to skin and not the skeleton?

From this pic. I can't really tell the closest location of being able to detect the nerve near the skin.


texts: Is a large tumor is more likely to develop hypoxic regions?

texts:
It is known that cancerous tumors in humans can develop hypoxic regions where no blood nor oxygen arrive to some volume of its cells, creating a dead lump inside or around the tumor.
See Wikipedia - Tumor hypoxia.

  Are hypoxic regions and regions without blood supply are more common in large tumors than in small tumors?
  What is the likelyhood or frequency of hypoxic regions in small (< 2 cm) and large (> 4 cm) tumors?
  What is the typical size of an hypoxic region within a tumor?

The article in Wikipedia is too techincal and very hard to be read and understood, and doesn't have an explicit answer to my question.


texts: What makes an animal/species suitable for domestication/training?

texts:
Humans have domesticated all manner of creatures during the course of their civilization - dogs, horses, several types of cattle, varieties of birds, and perhaps others too.

A prerequisite for an animal to be domesticated, obviously, is that there be some return from the animal voluntarily, or otherwise. For instance, milk from cows/buffalos.

What I'm looking for is an answer to the question what ... characteristics must an animal fulfil to be domesticated/trained. Docile is, perhaps, one characterstic. Amenable to training may be another. What other characteristics must be fulfilled before one would venture to consider training/domestication of another species?


texts: No bands show up in gel electrophoresis, not even marker

texts:
I haven't seen any gel lanes in neither my PCR samples nor the marker itself when photographing them.  This is not my first time performing 1.2% agarose gel electrophoresis.

I see gel lanes when I take the gel out the apparatus, but when I go to photograph them:  nothing shows up.  I only let the samples "run" for 30-40 minutes (when I ran for an hour, the bands almost ran off the gel).

Tried using different markers:  no luck.

Re-added some more EtBr to better stain the gel:  no luck.

I am also keeping the lights off in the dark room, so I do not think I am exposing the film to light early on (errors still a possibility though).

What could I be doing wrong?  Am I taking the film out too early?


texts:
I am searching for source, that providing information about enzymes\proteins, in different types of cancers, that their amount in cell is significantly higher - comparing to normal, healthy cell.

Some pathways that exist in cancer in much more higher amounts.

For example - Telomerase.

Is there some sort of database for this information?


texts: What is the motivation behind the CCA -> CCU modification between SARS-CoV-2 and the mRNA vaccine when encoding the signal peptide?

texts:
The S glycoprotein signal peptide in SARS-CoV-2 and the mRNA vaccine is encoded by:
           3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3
Virus:   AUG UUU GUU UUU CUU GUU UUA UUG CCA CUA GUC UCU AGU CAG UGU GUU
Vaccine: AUG UUC GUG UUC CUG GUG CUG CUG CCU CUG GUG UCC AGC CAG UGU GUU
               !   !   !   !   ! ! ! !     !   !   !   !   !

What is the motivation behind the CCA -> CCU modification between the virus and the vaccine?


texts: Need either a [similar] ribosome to the following few | a heuristic for finding [similar] macromolecule given 20 others

texts:
Background :

Hi! I am running a small experiment dealing with structural heterogeneity of the ribosome, actually of ribosomes across all domains of life. It's entirely computational: I get cryoEM  samples(below) from PDB, parse the crystallographic profiles and see if I can enclose on physical clusters of proteins that persist across domains of life (i.e. uL4 reliably neighbors uL22 according to this ontology) and things like that.
So far I've been working with the following dataset of eukaryotic/eubacterial/archeal macromolecules and am feeling pretty shackled by it at this point.

Question :

I would be very happy to augment this dataset with any number of "similar" ribosomes to put through the algorithm, but I don't know much about exemplar species to draw from and decided to ask here if somebody would recommend some more or less well-studied species(or straight-up PDB IDs) that would make a good addition. If you could point a boy to where I can "just get more" that'd be even more awesome. I'm not a biologist by training so you probably know of some obvious resource I don't.

I have no other constraints on what the targets are. Thank you so much and stay safe!

 I realize that most of these listed here are like the go-to organisms in biological research.


texts: What are the exact differences between stereocilia and microvilli?

texts:
This is a question in an old exam of Histology. I tried to answer the question, and I've made many searching attempts, but without resulting in any fixed/exact information. In some articles on the web, I've read the stereocilia and microvilli have both actin core, and this website states that stereocilia doesn't have actin filaments! I'm just feeling lost at this point. And now, I'm just searching for an exact answer for that question.

Note : It may be a super easy question for you. So please note that I'm a novice self-learner at Histology.


texts: Why do crows sit on treetops even when it is cold?

texts:
It is cold outside: -1 degrees Celsius, wind 14 km/h and snow from time to time. I was wondering why crows (maybe birds in general in Northern Europe) are calmly sitting in relatively windy places even though there are plenty of potentially warmer places to go to. (see picture at the bottom).

My first guess was that it isn't cold enough for them However, I couldn't find support for this online, so it's not possible to know for certain.

NB1: This is my first post - let me know if something is inappropriate.
NB2: I am not a biologist, so please be patient.

I'd appreciate links/references where I could get information that gets closer to finding an answer to the given question.


texts:
I would like some help with the recognition of the snake shown in the image below. I was doing a fieldwork in a forest in Slovakia when I found it.

I was thinking it could be a water snake but I am no expert in snakes.
Does someone know what kind of snake is this?


texts: how is the plasma membrane repaired after endocytosis?

texts: When the vesicle is swallowed of course the lipid layer internalizes. My question is how will the top segment of membrane will bind back together when that vesicle took the membrane with it inside cytoplasm. Will the plasma of the cell decrease or they will repair back and how does the membrane know that a certain substance is outside and i have to internalize myself in order to swallow. The same thing with exocytosis: How does the membrane open itself and repair back and what will happen to the membrane of the vesicle which went out?


texts: Retrieve the associated annotation from Uniprot

texts:
I have a dataset that I extracted using Cytoscape and STRINGAPI
Hoz can I retreive the annotation of that network from uniprot  as it has more than 1k proteins . and doing it manually is not possible


texts:
I need to stop some protein from being active and searching for some universal way to do so. In mammalians.

With CRISPR it is possible to knock-out the entire gene. But it's a little complicate (need two gRNA for eg.). There are also another reasons, so I need to do this with only one gRNA.

So I am thinking about inserting some mutation.

My question: Is there way to make some mutation that will prevent creation of functional protein, with high efficiently - with one gRNA. And without need to know the active site of protein.

For example, frame-shift or mutation around start codon? Is it possible? If so, how can I do this? To where I need to send the gRNA?

Thanks.


texts: In protein-protein interactions what is the difference between a binding site and an interface?

texts: I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?


texts: Species Identification: Coniferous tree, Italy

texts:
I noticed it close to the place where I work, I live in Italy
Could you tell me the complete name of this tree?

Particular of the leaves


texts: Does finite rate of increase depend on mortality of individuals in a population?

texts:
As written in my lecture handouts, there two main factors in the Geometric Growth Model of populations:

$R_{0}$ is the expected lifetime reproductive output. This way, for unicellulars, for example, when time between division represents life time, if there is no mortality, $R_{0}$ is calculated as $R_{0}=1*2$, where 1 is 100% and 2 is the amount of daughter cells expected to be produced as a result of the mother cell split. We also define that for this isolated incident, $B$, the amount of births is 2, while the mother cell "dies", which leads to $D=1$.

The second factor is $\lambda$, which is the finite rate of increase, which in other words means that this is average per-capita multiplication factor per one time-step.
When we measure population growth in time-steps of 1 lifetime, we can conclude that $\lambda=R_0$. We actually look at $\lambda$ as at $\frac{N_{t+1}}{N_{t}}$, where $N_{t+1}=N_{t}+B-D$(1) and $N_t$ is the amount of individuals in the populations at time-step $t$. This way we define $\lambda$ using $b=\frac{B}{N_{t}}$ and $d=\frac{D}{N_{t}}$: $\lambda=\frac{N_{t+1}}{N_{t}}=\frac{N_{t}}{N_{t}}+\frac{B}{N_{t}}-\frac{D}{N_{t}}=1+b-d$.

All fine when we deal with ideal conditions, where all mother cells divide and there are no mortalities or mutations.

But suppose we're told that only 80% of the mother cells will divide, and the remaining 20% will die without division. In this case: $R_{0}=0.20*0+0.80*2$.

What I'm trying to understand, how will $\lambda$ be affected by this? Does $\lambda$ refers to ideal conditions only, or it depends on the natural situation?

(1) We ignore Immigration and the Emigration at this point.


texts: Do's and Don't's of Undergraduate Research?

texts:
I was fortunate enough to get a position as a researcher for the Mayo Clinic's SURF Program this year.  My PI's lab focus is on the the immune system's role in CNS axonal and neuronal injury, specifically through the lens of how innate and adaptive immune effectors interact w/ infected neurons.

Although I do research under a professor at my college and I volunteered for a state university lab during the previous summer, this is my first REU/SURF opportunity, and I REALLY want to make a good impression.  Here are my questions:

What are the do's and don't's in terms of being a skilled and efficient researcher?

Since I am still an undergrad, I know that I will be a less useful asset to the lab than a grad student or post-doc, but what can I do as an undergrad to not burden my colleagues and PI?

Thank you all for your help!  Wishing you all the very best!


texts: Is this formula for calulating the energy requirements of pets applicable to all animals?

texts: This website gives the formula: 70M3/4 = Resting Energy Requirement for pets in calories/day, where M is the mass in kilograms. Is this formula correct and accurate, and will it work for rabbits, mice, and guinea pigs?


texts: Why do alpha-gal allergies only occur after a tick bite if alpha-gal is already present in red meat?

texts:
I just read an NPR article about allergies to red meat being caused by tick bites. That stood out to me because I thought allergies are triggered by an initial exposure to some allergen. In this case, the allergen is alpha-gal, a disaccharide found in cell membranes of most mammals; humans and apes are a notable exception. The article explains that ticks might cause this allergy by transferring alpha-gal from other animals to us when they feed on our blood.

However, we also are exposed to alpha-gal every time we eat red meat. How are we protected from allergic reactions when we eat red meat but not when we eat peanuts? Why does that protection fail after alpha-gal is exposed to our bloodstream?


texts: How does Liebig's law affect the growth of specific characteristics on a plant

texts:
I am familiar with the law of minimum, that is that the growth of the plant is dependent on the least available nutrient/resource.

I visited a farm in which they purposefully shaded tabaco plants to guide the growth of the plant (e.g. to make the plant grow taller and wider leaves with better concentrations of nicotine). I am wondering if this applies to other nutrients/plants. Example: Does deficiency in nutrient X guide the growth of spinach with Y% more iron?


texts: What is the evolutionary purpose of white spots in nails and how can they be characterised due to Leukonychia?

texts:
Suppose you haven't hit your nails so the white spots are due to Leukonychia.

Are the discoloration i.e. the white spots due to lower porosity (less minerals absorbing) or some other factor? I cannot understand their physiobiological chareterisation and why are they created due to evolutionary terms? To show a person that he is lacking minerals? Or why do some people have them?


texts:
How do I sterilize/disinfect ordinary table sugar for lab use?
I'm using the sugar in an agar and I want it to be as clean as possible. Are there any effective, conventional ways of doing this?


texts: Radiation therapy is a very popular cancer treatment method. But can it have any risk for make a different cancer? Because i think that radiation exposure can make DNA mutation and thus increase the risk to cause cancer, so why we still use radiation to treat cancer? That's so contradictory.


texts: I want to know the name of this water plant?

texts: Above is an image of an unknown plant. It grows without any care.


texts:
i am looking for likely truncation sites to prove recombination in sequences. i have 4 sequences. i believe one to be the "real sequence" and the other 3 to be recombinants caused by cleavage possibly due to Arg c proteinase. I know my sequences overlap due to multiple alignments i have performed using UniProt and i have chosen the enzyme due to carrying out cuts on Expasy cutter. If anyone could point me in the right direction this would be much appreciated.
many thanks in advance


texts: What is the thinnest spot on the ilium called?

texts:
Is there a specific name for the spot on the human iliac fossa where the bone is the thinnest? (Or, is there a name for the thickness measurement of that spot, e.g. the left/right _________ is 2.1mm?)
Green arrow:

(image source: my own pelvis)
This point, for example (color maps thickness):

(image source: me)


texts: Are there any examples of information compression in nature?

texts:
As the title suggests, I am looking for any examples of naturally occurring information compression. Initially, I thought protein synthesis was such a form of compression, creating larger entities (proteins) from a small subset of chemicals (A,C,G,T(U) in DNA) via ribosomal translation. However, I was quickly disillusioned as the amount of information contained in DNA is not increased within proteins after their formation.

So are there any natural processes, whether in animal, plant or otherwise that exhibit information compression?


texts: Tiny light-colored bug ID in Amman-Jordan

texts: Can you please help me identify this bug I keep finding inside my home in Amman-Jordan. Mostly on the wall and once on the bed sheet. Too small to be noticed and too light colored. I used my flash light and zoomed with my mobile camera to be able to take photo.


texts: How does the brain's energy consumption depend on mental activity?

texts:
What is the impact of mental activity on the energy consumption of the human brain?

I am most interested in intellectually demanding tasks (e.g., chess matches, solving a puzzle, taking a difficult exam) versus tasks with a similar posture but less demanding (e.g., reading a newspaper, watching TV).

I heard that energy consumption stays remarkably constant regardless of the mental activity (and energy consumption can be explained by elevated heart rate due to stress). However, it seems to contradict techniques such as fMRI, where the change in metabolism is measured (unless the relative change is really small).


texts:
Pedigree analysis is a process of establishing a virtually correct inheritance pattern of a genetic condition in a proband's family. I call it virtually correct because in many a cases we assume the genotype of a parent to be something by weighing the genotypes of the offsprings.

Now in a given problem like in this one where the trait follows autosomal dominant inheritance pattern I have problem deciding the genotype of I-3.

My opinion:

The genotype of II-6 is AA'. (Obtained from a calculation which I have decided to not to mention as it will make it lengthy and complicated)

(here A=Normal allele on autosome and A'=Mutant allele on autosome)

II-6 receives allele A from mother I-4 (who is obviously AA) and allele A' from father I-3. Now the genotype of the father could be either AA' or A'A'.Since the probability of having a AA' female child becomes 100% if we assume the genotype of the father to be A'A' so the genotype of the father I-3 is A'A'.

But one of my instructor says that it cannot have a genotype A'A' because it is fatal and I am not convinced with his reasoning.

In Huntington's disease presence of one HTT gene is enough to cause death of the person. It is a dominant lethal allele. While in achondroplasia, an autosomal dominant disorder the mutant allele when present in two copies is fatal.It is a recessive lethal allele. A heterozygous person survives with symptoms of Achondroplasia.

So death is not always caused by two copies of a mutant gene of a dominant autosomal trait. It may be caused by only one copy of gene as in Huntington's disease or may not be caused at all(I've no proof of this. Its my assumption).

So in a pedigree where nothing has been mentioned about the lethality of the genes concerned we shouldn't assume them being recessive lethals. This is all I think. Am I correct?

Finally: Should the genotype of I-3 be A'A'?


texts:
I need to make RNA:DNA duplexes. I can make 100 to 200 ug of mRNA through in vitro transcription, and I know how to use reverse transcription to make a cDNA library, but I have questions with this.

The mRNA I make with IVT is all poly A RNA, and the reverse transcription kit I have says to use 5ug of total RNA or 500ng of poly A RNA. I need to make at least 10ug of RNA:DNA, which is 20 times the suggested limit for poly A RNA, so a direct scale up probably isn't practical.

I can't find a literature precedent for making such large amounts of DNA through reverse transcription, everything I have found that uses RNA:DNA duplexes used short strands that were chemically synthesized and combined, my mRNA is 1800 bases long, so I can't just order an oligo, I have to make it.

EDIT : I can't comment on my own question.

The duplexes will be about 1800 bases long, it's for firefly luciferase.

Trying to make the DNA for the duplex from the original DNA template presents other issues. While it would be easy to cut it out from the plasmid, it would be double stranded, and I would have to mix with the RNA and heat it up to dissociate everything and hope that the RNA bound before the DNA strands reassociated. I also think it would complicate my controls, because it would be harder to say that any expression I see after delivering these duplexes came from the RNA and not the DNA. Of course synthesizing the DNA from the RNA could also introduce that problem.

Some crude calculations suggests that the dNTPs are the limiting reagent for a transcript this size, and that even with 5ug of mRNA I should have enough oligo dT primer for the reaction. I right now I am running reactions from 0.5 to 5ug of mRNA, 1uL of primer, and 4uL of dNTPs, to make sure I have enough. Hopefully the gel will turn out ok.

EDIT: I got the results. So far it looks like 3.0ug of mRNA works the best. It has the darkest band, and looks like the right length. Less mRNA gives fainter bands that appear too short, and more mRNA gives slightly fainter bands that appear slightly too short. Also, I ran the reaction for 2 hours instead of 1.


texts: Do High Iron Stores (but within the healthy range) Make Sun Exposure Damage Worse?

texts:
Ultraviolet damage from sun exposure is related to the creation of free radicals. Iron is often involved in exacerbating damage by free radicals.

Having lower iron stores is associated with reduced risk of diabetes. Could having lower iron stores reduce UV-related damage from sun exposure?

=========================================================================

I add some references after being asked in the comments:

On iron and free radicals: Iron, Free Radicals, and Oxidative Injury

UV-light and free radicals: Ultraviolet light-induced free radical formation in skin

About high ferritin making diabetes worse:
"Compared with those in the lowest quartile, subjects with diabetes in the highest ferritin quartile were 55% (P = 0.029) more likely to have microalbuminuria."
Source

Elevated serum ferritin levels predict new-onset type 2 diabetes


texts: Why is a magnesium ion essential for ATP activity in enzymic reactions?

texts:
The Wikipedia entry on Magnesium in Biology includes the following:

  ATP (adenosine triphosphate), the main source of energy in cells, must be bound to a magnesium ion in order to be biologically active. What is called ATP is often actually Mg-ATP.

I don't understand why magnesium is essential for breaking the high energy bond in ATP?


texts: What determines testosterone exposure in womb, baby's genetics or mom's body?

texts:
I read this article which has the following quote:

  The ratio between index and ring finger is believed to be linked to exposure to the male hormone testosterone in the womb.

And I wonder what determines the amount of exposure to testosterone in the womb. Is it testosterone produced by the fetus itself, in which case the baby's own genetics is the answer, or does this exposure the article speaks of more likely refer to testosterone produced by the mother and exposed to the baby?


texts: Do homing pigeons fly straight home or follow certain "highways"?

texts:
Homing pigeons (Columba livia) have been prized for their navigational abilities for thousands of years. They’ve served as messengers during war, as a means of long-distance communication, and as prized athletes in international races. (Source)

Do all homing pigeons just pick a direction, and fly "straight" home, or do they all follow certain "tunnels" or "roads" to get closer to their home area, before heading home? (similar to cars getting on a highway between two regions)

Does any information about that exist? I'd be interested to know if pigeons released in the same area (with different target locations in one common direction) tend to do follow the same paths, or if it's just a chaotic crisscross.


texts:
I was looking at mongoose eyes in particular, but my understanding is:

Circular (human-like) pupils simply get larger/smaller depending on light levels, no change in "shape"
Vertical slit (cat-like) eyes get wider or narrower, from "almost a line" to "almost a circle".
Goats, mongooses, etc. have horizontal "bar" pupils — more-or-less straight edged across the top and bottom, with rounded (semicircular?) sides.

Do horizontal bar pupils, like those of a mongoose, change size in varying light levels? If so, how does their shape change? Do they get taller or narrower? Do the top and bottom become convex or concave? Does the radius of the sides increase? Does anyone have good reference pictures or diagrams?


texts: Is it ok if I define Genes this way in Biology?

texts:
Genes are found in chromosomes and their job is to show us the traits of someone (height/hair color)

I do know that alleles specify the height of the person (Tall/Short) and their hair color(blue/green), etc. So is it correct to define Genes this way in my exam?


texts: Identify caterpillars and, if possible, parasitoid (Sabah, north Borneo)

texts:
Someone on Twitter posted some photos yesterday of a lump of mud that, when knocked off a chair by accident, revealed a number of caterpillars:
https://twitter.com/solomilne/status/956135158381334528

I've uploaded one of the photos below. The assumption (which seems reasonable, but I suppose isn't certain) is that they were left there by a parasitoid.

Can anyone identify the caterpillars, confirm whether they are likely to have been left by a parasitoid and if so identify a likely culprit? The sample was from a forested area in Sabah, northern Borneo; I've requested a size from the person who posted the photos.


texts: I understand epiphytes are not parasitic. But how exactly are they helping the tree on which they grow?


texts: How many proteins on PDB have unknown function?

texts: I was wondering how many of the files in the Protein Data Bank (PDB) have unknown function. The only paper I can find from an internet search is this one from 2012, which I assume might be outdated. I’d welcome suggestions of how to find this information for myself.


texts: "selective pressure" or "selection pressure"?

texts:
Editing a manuscript of mine, a co-author changes "selection pressure" to "selective pressure". Are those two terms interchangeable? Or are there subtle differences that I'm not aware of?

The sentence under consideration: "In contrast, gene expression changes during development and tissue formation are under high selection/selective pressure."

FWIW, "selection pressure" is a bit more popular in the literature.


texts: Does the number of nodes determines the rate at which a neural signal is transmitted?

texts:
I know that the the bigger the neuron's diameter is, the faster the neuron signal is transmitted. This makes sense according to the proportionality of resistance to the inverse of area and thus, in physics, there is lower resistance in wires that have bigger diameters (cross-sectional areas). I can imagine that this is the same logic for our neurons as well because they are like wires. I also know that the more myelinated a neuron is, the faster the neuron signal travels too because myelination acts as an insulation that reduces resistance in signal transmission.

But then, my question is: does the number of nodes matter and affect the rate at which a neural signal is transmitted? Can you please help explain why or why not? Let's say for example, that two neurons have same amount of diameter and myelinated sheaths hypothetically, but one of them has more nodes. Does that number of nodes of ranvier make the saltatory conduction faster?


texts: I found him in a kitchen located in Toronto, Ontario, Canada.


texts:
I almost stepped on this little critter. It blended into my garage floor. It is about about the size of my hand, with huge bulbous eyes that immediately caught my attention. There was a distinct white bump below\between the eyes.  It froze when I turned on the light and did not move at all until I turned the light off. Then it moved faster than my eyes could follow in the direction of my garden.
I am on an island in the San Francisco Bay, California. The current temperature is ranging from 50 (night) to 65 degrees and rainy season has just started (late this year). It blended so well with the garage floor that my camera had problems focusing on it.


texts:
I am not talking about seeing in total darkness, which I understand is not possible. I am looking more about a question how far can a human see during starry night or with half moon/full moon. I tried googling for this, but found no useful results.

EDIT I think I need to clarify: I am thinking more in terms of immediate surroundings. I understand we can a source of light from afar, but what about a tree on a flat land - from how far would we see it in star light?


texts: How do DNA-binding proteins recognize the correct DNA base pairs?

texts:
My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?"

He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-T, T-A, C-G, and G-C base pairs. However, they are not always significantly different in some pairs (i.e. the minor groove of the C-G and G-C base pairs have the same acceptor - donor - acceptor pattern).

So how would a binding protein know the difference between C-G and G-C on the minor groove of a DNA base pair? How does a DNA binding protein know it's reached the right base pair, more generally?

Thank you!


texts: My family snapped this picture around Sydney, Australia. Could someone please advise what this tree is? Help! We are smittened with it :)


texts: Forensic genetics- why is mtDNA comparison sometimes better than nDNA comparison?

texts:
Why is (in forensic genetics) in some cases more appropriate comparison of nuclear DNA but in some other cases comparison of mitochondrial DNA?

Is it because geneticists are sometimes unable to find nDNA or if nDNA is too damaged? Also could it be because of the structure of mtDNA (it's more protected against degradation, which is good for identifying old biological material)? I can't see any other advantages, since mitochondrial DNA mutations occur frequently, due to the lack of the error checking, but are there any that I am missing?

Thank you in advance.


texts: Help me identify this caterpillar looking insect

texts:
Can someone please help me identify this caterpillar looking insect from the Caribbean?

Thanks.


texts: Are there any known rules that neurons always follow while transmitting/receiving signals?

texts:
I'm new to neurobiology so I don't know much about it. However, I have worked on artificial neural networks. Man-made AI networks all follow a handful of simple rules.
I was wondering if biological neurons also have a set of predictable rules?
E.g
What does a neuron do if it does not get stimulated/receives no signal for a long time. Will it die ... or try to find new connections that might send signals?
What does a neuron do if it is over-stimulated?
What does a neuron do if it receives a signal -> does it broadcast it to all of its connections, or only 1. Does it have a preferred output path for any incoming signals.
Can a neuron send out a new signal without having received a signal from anywhere else.
How does a neuron know if it has done his job "well". How does it get positive feedback.


texts: Has there ever been an experiment performed that demonstrated a form of 'spatial memory' in a unicellular organism?  I'm imagining something analogous to the classic 'rat in maze' experiments, but obviously on a much smaller scale.  Possibly even something as simple as following a concentration gradient, but choosing to go either upstream or downstream based on some sort of prior reward in a similar circumstance.


texts: I have to answer a few questions from an article I'm reading, and I am just really confused on defining "catalytic domain." I have to relate it to the antibiotic Teixobactin. Is catalytic domain the same as the enzyme's active site?


texts: What makes an E.coli an E.coli, genotype or phenotype?

texts:
According to this paper, among 61 strains of E. coli they studied only 6% of the genes are common in all. Which means that the overwhelming majority of the genes are not shared.

And wikipedia defines E. coli like this:

  ... is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).

Which is a phenotypic  definition. My question is: what defines E. coli as a species: its genotype or its phenotype?


texts: I’m afraid the quality of the television picture below isn’t very good, but can anyone identify this moth? It was one of those that invaded the pitch at the Euro Final in Paris on 10th July 2016.


texts: Possibility of orthogonal view for a creature?

texts: Just a pure curiosity: Does there exist a creature with an orthogonal view to the world instead of perspective? What would be an optical explanation for possibility/impossibility?


texts:
I read that NASA looks for water on Mars or other planets as a sign of a life.

I wonder why scientists look for water as proof of a life? isn't there any animal that drinks another liquid like alcohol or something?


texts: Why do larger diameter myelinated axons have greater conduction velocities than small diameter myelinated axons?

texts:
A canonical statement I have frequently read is that "large diameter axons conduct action potentials at faster velocities than small diameter axons". After recently learning the effect of increased capacitance on the cell membrane (namely, that more charge is required for depolarization to occur...Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?), I find this canon to be rather confusing.

I have attached a picture to make my question clearer:

In the above picture, both neurons have the same myelin spacing. So, my question is why should the action potential in Axon B traverse the distance X1 to X2 more quickly than in Axon A. Shouldn't the increased capacitance of Axon B (due to its increased diameter) increase the time it takes for the action potential to travel between the two points?


texts: why prokaryotic ribosomes have 30s and40s subunits and eukaryotic ribosomes have 40sand 60s subunits?

texts: Ribosomes are protein factories of cell and are composed of two subunits; one smaller and other larger unit I want to know that why ,ribosomes of eukaryotes have a 40s and 60s subunit and prokaryotic ribosomes have 30s and50s subunits ?If we combine 30s and 50s subunits shouldn't it be 80s ribosome instead of 70s ribosome .


texts: To what extent is prion aggregation responsible for Alzheimer's disease?

texts:
I was intrigued by a description of prions as a factor regarding 'Mad Cow Disease', the epizootic threatening the cattle stock of the United Kingdom and France predominantly.

Understandably, the prion, a misfolded protein causes neurodegenerative damage through inducing an aggregation of prions into a complex capable of converting functional proteins. Disregarding Creutzfeldt-Jacob disease, thus far believed to be a Dementia characterised by the accumulation of prions, I simply seek clarification as to whether the onset of Alzheimer's disease should have a direct correlation with an aggregate of misfolded proteins.

Nota Bene

Although the hypothesis regarding the accumulation of amyloid-derived diffusible ligands, toxic oligomers, may be associated with the prion causing Bovine Spongiform Encephalitis, if any further clarity regarding the direct correlation between these two events in humans would be appreciated.


texts: How to characterise a protein family in a putative genome island?

texts:
We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in some of these strains. Each strain has multiple copies separated in their genome. Genetic differences have been observed among the DNA sequence in the different strains. Since some mobile genetic elements are present near these genes, it is possible that they are playing a role in the molecular evolution of this protein family.

How could I add additional evidences that this is a putative genomic island?

Some references would be also appreciated.

Thanks

UPDATE: For each strain, I thought about extracting the genomic region were these genes are located, maybe 8 Kb up- and down-stream of the gene. Then, running a miriad of tools to try to predict some of these island-associated elements. However, assuming that these "sequence-based" tools need the entire genome sequence, is it possible that I run them using the whole genome sequence and then focus on certain selected genomic regions?


texts: What causes phospholipids to flow so quickly in cell membranes? In Biology by Cambell et al. they state that a phospholipids can travel up to 2 micrometers per second. Is that a random movement or has anyone found that phospholipids have a current?


texts: Rate of growth of an RNA or DNA sequence

texts: Given, e.g., a mixture of the necessary components in optimal conditions, what would be the average rate of attachment of nuceotides to ribose molecules?  This is related to the study of how long it would be expected take for a particular genome to evolve.


texts: Detailed working of the voltage-gated sodium channel

texts:
Hodgkin and Huxley formulated the ion currents through the three voltage-gated ion channels Na, K, and L as

$$\sum_{k}I_{k}=g_{\rm Na}\,m^{3}h\,(u-E_{\rm Na})+g_{\rm K}\,n^{4}\,(u-E_{\rm K%
})+g_{L}\,(u-E_{L}).$$

From Gerstner et al, Neuronal Dynamics, 2.2 Hodgkin-Huxley Model

What they probably didn't know - but is known today - is, that the sodium channel possesses four voltage-sensors (S4), opposed to one ball (IFM) which may close the channel and is described by $h$:

From Wikipedia, Ball and chain inactivation

Do I interpret Hodgkin and Huxley correctly, in that they found experimentally that three of the four voltage sensors must be in the up (= open) state for the pore to be open? Does this hold "exactly", or should the exponent in $m^3$ not be taken too "literally"? For example, the four voltage-sensors might be slightly different and have different deviations (when in their resp. up states), and only their "average" deviation counts, which is somehow reflected in the exponent $3$? The question then arises, why the exponent is an integer number. Couldn't it be any real number then?


texts: Which one is better to use for water stress experiment GWAS or RNASeq?

texts:
This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic diversity using DArT markers. Based on the charaterization result, i have selected 10 varieties to be subjected to water stress with the objective of identifying genes that are responsible for tolerance in this plant. My challenge now is:
1. bambara groundnut does not have a reference genome, so will i be able to use GWAS in getting these genes from the result of the DArTSeq.
2. Bearing in mind that the whole 95 varieties characterized were not subjected to water stress, do i need to set up another experiment entirely for the water stress and go ahead to make use of RNASeq to get the genes?
3. It is obvious that some genes will be upregulated and some will be downregulated, how do i identify these genes and how do i know if they are expressed at the onset of stress, during, or after stress?
4. when is the appropriate time to take my samples, i was considering taking at 50% flowering stage. Is this good?
Any help and insightful articles will be greatly appreciated.


texts: Does variation in human gut length vary predictably with diet of ancestors?

texts:
Background: Numerous online searches, textbooks and other sources seem to pin the average length of the human gut from mouth to anus (oroanal) between about 5-10m in length. To pick a reputable example, this page from Harvard suggests that the small intestine is typically 2.91m and the average large intestine is 1.90m. The paper they cite (Helander & Fändriks, 2014) suggests this makes up most of the ~5m of the average human gut. Helander & Fändriks (2014) performed a lit review to come to these numbers, so their average lengths are probably some of the best estimates we have. (Other sources can be seen here and here, and Raines et al. 2014 seem to suggest that intestines of living people are much longer).

Regardless, Helander & Fändriks (2014), similar to Raines et al. (2014) and other sources, comment that there is "considerable variation between individuals" throughout the literature they reviewed.

My question: is the length of a given human gut predictable by the diet of their ancestors? In other words, are gut lengths between individuals more similar between family members and their ancestors than for others whose ancestors lived elsewhere in the world (and presumably had an alternative diet)?

For example: Are the guts of people of western European descent more similar to each other than the gut lengths of those of East Asian descent (or Sub-saharan descent, etc.).

Reasoning: Gut length (& complexity) of different animals varies based on digestive needs (which are a result of the typical diet of the animal). The general assumption (with support) is that diets high in food with indigestible material results in increased gut dimensions.

See Naya et al., 2009 for a general discussion about "gut flexibility", list of review citations, and results indicating correlation of population (diet) with gut length in toads.
Davis et al. (2013) found strong evidence that diet and intestinal complexity were linked in terapontid fishes -- specifically, more complex guts seemed to be associated with shifts away from carnivorous diets.
Gut plasticity does not seem to be immediate. For example  Ferraris & Diamond (1993) found (unsurprisingly) that intestinal length was independent of diet in a week-long mouse study.
Discussion of variation in human diet can be found here.

I haven't been able to find any sources discussing this "gut flexibility" phenomenon in humans.


texts: Would it be more genetically efficient to have shorter lifespans?

texts:
If, for example, humans had an average lifespan of, say, 30 years, and we reached sexual maturity at age 10, then we could "evolve" more quickly and theoretically "weed-out" more genetic diseases because we would live for shorter times, hence more natural selection.

  Why don't we continually evolve for shorter lifespans (or do we)?


texts: Why are cancer rates low in large animals?

texts:
Large animals generally have more cells and live longer than smaller animals. For example, bowhead whales live up to 200 years and weigh up to 100 tonnes, as opposed to humans (living ~71 years and weigh ~75 kg) and mice (10–25 g, <1 year in the wild). Hence, whales have an immense number of cells and those cells are subjected to environmental carcinogenic influences (chemicals, UV) for a longer period of time.

Cancer is caused by random mutations and those random mutations are basically stochastic processes. Given their long life span and larger number of cells, shouldn't larger animals have a substantially higher chance to develop cancer? In fact, story goes that bowhead whales in fact only very rarely contract cancer, and less so compared to humans?


texts: Endogenous retroviral insertions as evidence for evolutionary relationships among primates

texts:
A synopsis of a 2005 paper in PlosBiology by Yohn et al. states that:

  Searching the genomes of a subset of apes and monkeys revealed that
  the retrovirus had integrated into the germline of African great apes
  and Old World monkeys—but did not infect humans and Asian apes
  (orangutan, siamang, and gibbon). This undermines the notion that an
  ancient infection invaded an ancestral primate lineage, since great
  apes (including humans) share a common ancestor with Old World
  monkeys.

Also, Micheal Lynch writes :

  "Remarkably, we have found many cases of parallel intron gains at
  essentially the same sites in independent genotypes," Lynch said.
  "This strongly argues against the common assumption that when two
  species share introns at the same site, it is always due to
  inheritance from a common ancestor."

Since shared ERVs in humans and chimps is touted as one of the proofs of humans and chimps sharing ancestry (like by Ken Miller here), does the above paper (and quote) undermine this line of reasoning?

Is there any good (recent) source which discusses proof of common descent using ERVs?


texts: What is the purpose of measuring both VS (volatile solid) and TS (total solid)?

texts:
In the biogas process you often measure Volatile solid and Total solids. Can any one explain these concepts more accurately and why it is interesting to look at these properties.

The biogas process I refer to is a process of fermenting waste food materials and slaugther house waste in to bio fuels, consisting largely of methane. The fermentation is conducted in anaerobic milieu in large plants.

Total solids and Volatile solid are measurements on the sludge the currently fermented waste,(the gooey stuff that is in the bio-reactor).


texts: Why are brightly coloured marine animals thought not to display aposematism?

texts:
There are many brightly coloured marine animals, such as fish, corals, sea stars, and octopodes. And yet Wikipaedia says it is thought that those colours don't serve to deter predators, while they do serve that purpose in insects and frogs. Why should bright colours not deter marine predators? And what, then, is their purpose?

Wikipaedia gives a few arguments, but some don't seem terribly strong, while others I don't quite understand:

  It has been proposed that aposematism and mimicry is less evident in marine invertebrates than terrestrial insects because predation is a more intense selective force for many insects, which also disperse as adults rather than as larvae and have much shorter generation times.[24] Further, there is evidence that fish predators such as blueheads may adapt to visual cues more rapidly than do birds, making aposematism less effective.[30]

I read what may be four different arguments, or perhaps some together constitute one argument:

predation is a more intense selective force for many insects

Is this really true? If so, what causes this stronger pressure on insects?

insects disperse as adults

By this I presume they compare insects, whose eggs are often found clumped together in large numbers, with marine animals whose eggs are fertilised while floating around dispersed; but why does that make aposematism less useful for those marine animals? And aren't there also many marine animals whose eggs are laid in clumps on solid sea floors? Is this related to the supposedly lower pressure of predation from 1?

insects have much shorter generation times

That's very interesting: do they really have much shorter times between generations? At least a reference is made, but it is inaccessible. But how does that make aposematism more beneficial? Is this, too, related to 1?

fish predators such as blueheads may adapt to visual cues more rapidly

This, too, refers to a scientific source. The experiment showed that fish can quickly overcome instinctive aversion from certain colours (mainly red) in food. At least I understand this argument (although I'm not sure I think it provides nearly enough evidence).

Some thoughts: marine animals often do exhibit camouflage and mimicry successfully, cf. angler fish and harmful parasitic fish that mimic cleaner fish; could it be that there is something different about the metabolism of marine animals?; or could it be that the three-dimensional environment makes other strategies more effective, such as flight—but then how about all the floor-bound animals, and the unmoving ones?


texts: Question regarding 2 constructs of tobacco plant

texts:
Six independent transformation experiments of tobacco leaf explants were carried out using
two different constructs - (1) construct I containing only a Hygromycin-resistance gene
$(HYG^R)$ as a selection marker and (2) construct II with the $(HYG^R)$ gene as a selection
marker and a passenger gene encoding a dephosphorylase enzyme $(DEP)$ that inhibits
phosphorylation in cells in which it is expressed. The marker as well as passenger genes
were placed under transcriptional control of a constitutive promoter $(CaMV35S)$, which
expresses in all cells/tissues. The results obtained are tabulated below.

Explain how The $HYG^R$ gene used in construct II lost its functionality probably due to
mutation(s) either in the gene or in the promoter.

My approach: There is a probability that Expression of the $DEP$ gene is lethal to the transformed cells.


texts: Interpretation of graph from evolutionary biology

texts:
I am studying evolutionary biology, and been presented with this graph:

I am having some difficulties understand its meaning. For a start, why is time measured as a fraction of the population size? Also, what does it mean by allele frequency? Does it mean the frequency of a single allele? But if the first caption it referred to 'frequencies'... Any help? :)


texts:
I spotted this millipede-like creature in Hervey Bay, Australia at low tide, just kind of hanging out at the bottom of a small saltwater tidepool.

It's several inches long, composed of a large number of segments, each of which appears to sport a pair of legs.

Hard to tell from the photos, but the creature is aquatic and in both instances was observed moving around under about an inch or so of water.  No specimens, alive or dead, were observed outside of the water.

They leave obvious trails behind them in the sand at the bottom of the tidepool as they move across it, and I assume they have some ability to burrow into the sand as I saw far more trails than I did creatures.

What are these things?