texts: What makes humans omnivores, and not herbivores?

texts:
Some vegans claim that humans are herbivores, not omnivores, and that we are not physiologically designed to eat meat (see here: http://www.peta.org/living/food/natural-human-diet/).

  "According to biologists and anthropologists who study our anatomy and our evolutionary history, humans are herbivores who are not well suited to eating meat. Humans lack both the physical characteristics of carnivores and the instinct that drives them to kill animals and devour their raw carcasses.
  Although many humans choose to eat a wide variety of plant and animal foods, earning us the dubious title of “omnivore,” we’re anatomically herbivorous."

They go onto claim that we don't have tiger claws and teeth for catching and eating meat, that our jaws and teeth are designed for grinding plants not meat, that our stomach acid is too week to break down meat, that our intestinal tract is long like a herbivore for digesting plants and that it takes so long for meat to pass through that it rots and poisons us causing cancer, that we lack a hunting drive, that meat with it's cholesterol and protein is the cause of all disease so obviously its poison that we are not supposed to eat, that we get food poisoning from meat (like that never happens with vegetables...) and that the only reason humans started eating meat was to survive in times when there was a lack of plant foods available but according to our anatomy it's clear we're actually herbivores not designed for eating meat.

Can this be debunked?


texts: Help identify the insects I keep finding at my house (Auburn, WA)

texts:
Could anyone tell me what is this living being is called? I keep finding his relatives flying/crawling in my house once in a while since late Summer this year. We live in Auburn, WA, in case it helps narrowing down the list of who it can be...

Knowing the name will help me figuring out:

whether it's dangerous for my wife, or our infant;
how to get rid of it (I start suspecting they either breed inside the house, or somewhere very close because I only find these insects when it's getting warmer outside).

Sorry for the low quality of the photo. By the way, this animal is about 15mm or 5/8" long (not measuring the legs).


texts: How is the effective dose calculated when only part of the body is irradiated?

texts:
For calculating the effective radiation dose in Sv, the equivalent dose absorbed by each body part is averaged according to tissue-specific weighting factors, which sum up to 1.

If not the whole body is irradiated, how are these factors used?


texts: Do antibodies to an arbovirus in a bloodmeal reduce vector competence?

texts: When we conduct mosquito infection studies we typically mix blood and virus rather than using viraemic blood from naturally infected hosts. I'm looking for a paper I read some years ago which demonstrated that virus mixed with blood containing antibodies to that virus (not to mosquito midgut or salivary gland antigens) resulted in a lower proportion of infectious vectors than virus mixed with blood that does not contain those antigens. Unfortunately I don't seem to have kept a copy and now every search I conduct only throws up results to the aforementioned studies of anti-midgut or anti-SG antibodies. The nearest thing I can find is this, which looks at inhibition during intrathoracic inoculation (a completely different route of infection which is not particularly realistic, although we sometimes use it to boost the infection rate).


texts: How do physics notions of fluid dynamics relate to pressure gradients in circulation?

texts:
I'm having a hard time comprehending why sometimes physiology notions seem to contradict each other and contradict physics teachings.
More specifically I don't understand why aortic coarctation causes the pressure gradient to increase. In this condition the radius of the blood vessel decreases which should mean that pressure decreases too. According to Bernoulli theorem ΔP+Δvp/2=o
where v is velocity and p density. This theorem and the fact that velocity has to increase to maintain a stable flow through the coarctation should mean that the pressure gradient drops. Moreover in every textbook I've found it is said that tension on the aortic wall increases too but this seems even more counterintuitive, because if the radius decreases due to La Place T=Pr tension (T) should decrease too.
Then the most puzzling thing to me is the pressure drop when there vasoconstriction of  the arterioles, this is fine according to my reasoning so far (except it seems to contradict aortic coarctation) but resistance is supposed to increase too with vasoconstriction, and because of this equation: ΔP=Q*R (where Q is flow and R is resistance) the pressure gradient should go up. Now I think I understand that it increases because of the successive drop in pressure, correct? What am I missing with aortic coarctation? I'm sure it has to do with confusing the PTM in that specific place and the pressure gradient but I can't figure it out.


texts: What kind of insect is this and what is it doing?

texts:
I live in Denmark and found these two insects on a tree. I'm interested in the big fly and have the following questions:

What kind of fly is it?
What is it doing with the little fly?


texts: What part of the skin is damaged under sun exposure?

texts: How exactly does extensive sun exposure lead to skin damage and increase cancer risk. In which part of the skin is the sun doing the most damage. Is it in the epidermis or beneath ? I would like to know if UV-protective tattoos would be possible.


texts: Biodiversity is restricted by genome combinatorics?

texts:
Me and some friends are interested in opinions for the following:

Conjecture

  The maximum number of species must be limited by the maximum
  combinatorial/permutational space that can be occupied by DNA. Thus if
  there is a maximum physical genome size this is what will determine
  the maximum number of species that can possibly exist.

Explanation

E.G. say maximum number of DNA base pairs able to fit in a genome was $3$, each base pair can be one of either ${A,G,T,C}$. Then there are $4^3 = 64$ possible combinations of genomes. Extrapolate to genome sizes of $x$ base pairs, then there are $4^x$ combinations.

Questions

Would it be possible to claim that the underlying "blueprint" that codes for living diversity sets the absolute maximum for the total "diversity space"?

**Does it make sense to define the total number of species life can achieve with the simple function:

$S < 4^x$, where X is the maximum genome size measured in DNA base pairs?**

Notable Comments

  @Shigeta: for $S<4^x$ the combinations involved quickly dwarf the
  number of atoms in the universe at ~10^80.

  @rg255: Even at this simplification of: $S<20^{x/3}$ there are
  $1.024e+13$ possible combinations with just 10 codons, many many more
  than there is likely species in the world.


texts:
I'm having a problem which has been troubling me for the second straight summer. Since 2014 I'm living in my parents attic. I had a very small bedroom and since I had my first girlfriend at that time I wanted a bigger bed. The first two years nothing seemed to be wrong. But last year around June when I came home and wanted to sleep I saw all these little insects on my bed. Pretty weird ofcourse, but since my room was a mess(food,clothes,etc.) I thought it was just because of my bad habits. Since then every day when the temperature was 25 degrees celcius or higher these insects appeared. They came from under my bed, they were in closets, they literally came from everywhere. Not during daytime, but around 10/11 am. Since our attic has this crawling space all around it in which we store stuff we almost never use I thought they had a nest there. But when I crawled through it I couldn't find anything. After some research I found out that this creature could be a mealworm beetle. I bought some insect spray and it all around the baseboard off my attic. I also sprayed some other places where they could be hiding. This worked for a day or two before they came again. The problem is that I never have established where they came from. So they just kept on coming until around September.

All of this kept me from sleeping a couple of hours every week, not to mention the graveyard off all these little creatures(I think I killed around 100 of them by directally spraying insect spray on them or other methods). Ofcourse I also found alot of them the morning after killed by the spray.

A couple of minutes ago I found the first one of this year. It was pretty high on a wall(Around two meters) and I killed it by spraying the insect spray on it. It fell down and after a couple of minutes it gave up. I will also include a picture of the dead insect. Some other interesting things about these creatures were that they actually made sound when walking around and falling down. Also when I tried to flat one it made a bit of a crunching sound and it was pretty hard too.

I live in the Netherlands in a remote village.

Can someone confirm me these are in fact mealworm beetles and what is the best way to make sure my attic is not filled with them this summer again. I have a cleaned up room now with no food leftovers but alot of cables everywhere


texts:
Which out of eagle, rat, duck or owl has the widest angle of binocular vision?

I am pretty sure it's not rat and duck but I am confused between owl and eagle. Can anybody help me figure out which one would have the widest angle of binocular vision?


texts: Total amount of CO₂ / Oxygen in Bloodstream in Humans

texts:
How much carbon dioxide and oxygen from/for respiration are in the bloodstream at any one time? (mass per litre of blood or similar)

And would there be much more aside from the blood in tissue, e.g. muscle, brain, etc.

So far the figures I have are as follows (please double check for me, I dont have a clue)

O₂ molecules per red blood cell: 1 billion. Red blood cells per micro litre of blood in males: 4.7 to 6.1 million. Molecules per mole: 6 x 10^23. Therefore moles of O2 per litre of blood: approx 0.01 (correct?) This seems quite low, since an inhalation is typically 0.5L and about a quarter of the oxygen is absorbed (oxygen by volume, 5% of the air) (1 thousandth of a mole of oxygen absorbed per inhalation?)

Thanks


texts: What happens when pure chlorophyll A absorbs blue light?

texts: When pure chlorophyll A is put in the presence of only blue light, what happens? My guess is that the extra energy is released as heat/kinetic energy, and then the electron has dropped to the lowest energy state above the state that would normally release red light when UV light is shone. Then, it would drop to ground state and release red light as normal. Is this correct? The reasoning behind this is that UV is even higher energy than violet/blue light, so the same phenomenon should happen, except with less kinetic energy added. On a side note, what is the next electron state after the one that sends out red light?


texts: Nomenclature for mutations at specific nucleotide positions

texts: I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of a nucleotide as location as  FGFR3:c.1843-35A>T. What does "1843-35" mean?


texts: What conditions should I use for Gel Red staining?

texts:
What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often indistinguishable. We have tried both pre- and post-staining, together with varying concentrations of Gel Red.

Any advice about how to fix this problem?


texts: Does the term "fitness advantage" or "fitness disadvantage" make sense?

texts: Same for the terms "selective advantage" and "selective disadvantage" which I intend to use synonymously.  There are usages of each on Google Scholar, but do evolutionary biologists understand what is meant?


texts: Are there animals that can deliberately manipulate their metabolism, apart from hibernation?

texts:
Are there animals that can slow down their metabolism deliberately? I know that hibernation would be one mechanism, and maybe being cold-blooded, but I was wondering if there was maybe an animal that could crank up or slow down metabolism based on food resources?

Are there chemical compounds that could have this effect?


texts:
As a caretaker of a turtle, I sometimes struggle understanding the logic behind the inclusion of corn, soybean, and wheat meals in reptile food, such ingredients seem truly aberrant from what a reptile would naturally be exposed to. Nevertheless I am aware of the biological and chemical similarity between most organisms, so I wonder whether that will help reptiles, especially omnivores with an eclectic digestive ability, to digest these compounds.

I'm looking for legitimate studies on reptile digestibility; anecdotal experience or advice is supplementary if present.


texts: Quick overview of how to capture microscope images of histology plate or fluorescent plate

texts:
I am looking at these two:

I would like to DIY take photographs of plant and animal cells using a cheap microscope such as this:

I don't know too much about microscopes or the techniques to do the staining, but that is what this question is about. I would like to know briefly what is required (tool-wise and material-wise) to capture images like the two above.

For fluorescent microscopy images, wondering if I actually need a fluorescent microscope, or if I can make do with a regular optical microscope. If I need a fluorescent one, wondering if there is anything else needed, like special lighting or special materials for tagging the cells, which seems like it might require extra stuff like centrifuge and who knows what else. In that case I would just like to get a sense for how complicated it is to do fluorescent microscopy.

For the histology slides, wondering generally what it takes to do that too, if I can get by with a regular microscope.

Generally wondering what equipment is required to accomplish these two images.

So far I have a DSLR camera and am imagining a basic optimal microscope with a DSLR adapter, and perhaps some basic dies that I would just drip into the slide (don't even need a pipette). That just shows my simplistic understanding, maybe fluorescent microscopy requires advanced biotechnology of some sort, which is sort of what I'm wondering, what the basics are.


texts: What is the name of the groove down the middle of an anther?

texts: I thought it had a name along the lines of interlocular groove, but I haven't been able to find that term anywhere.


texts: Found this colourful  insect in our garden. It measures about 1.5cm. I am from Kuching, Sarawak, Malaysiai


texts: Why is DNA Shuffling more efficient than Point Mutation?

texts:
In a related post on Biology-SE the following insightful comment was made:

  The advantage of DNA shuffling over introducing single mutations is
  that you have to screen fewer mutants and the activity/stability of
  the protein could be improved several hundred fold more.

Is there a mathematical argument as to why DNA Shuffling should be more efficient than introducing point mutations?

Even supposing each DNA Shuffling / Point Mutation step is equally "expensive"  (and in reality DNA shuffling seems much more work) they are both generating one variant per-step, right? So why is the variant in one case grossly better than the other?

Related Post: Directed evolution: Point mutation vs Insertion-Deletion vs Shuffling


texts: How do you merge SNP data with a reference genome?

texts:
My Data

I have a 23andMe file listing SNPs in the form:

rsid       chromosome      position        genotype
rsXXXXX         1           PPPPPP          CT
rsXXXXX         1           PPPPPP          GG

Fields are TAB-separated and each line corresponds to a single SNP. For each SNP, four fields of data are supplied.

An identifier (an rsid or an internal id)
Its location on the reference genome.

The chromosome it is located on.
The position within the chromosome is is located on.

The genotype call oriented with respect to the plus strand on the human reference sequence.

The reference genome is the human assembly build 37 (also known as Annotation Release 104).

My Question

How do I merge the SNPs into the reference genome?

For example, take the first line in my SNP file:

rsXXXXX        1           PPPPPP          CT

Part 1

I can see that I need to replace the nucleotide at position PPPPPP on chomosome 1 of the reference genome with a nucleotide from the genotype field, but which nucleotide am I supposed to use? C or T? And why?

Part 2

Where am I supposed to start counting from on the reference genome? Looking at chromosome 1 of the human assembly build 37, the first ~10,000 characters (excluding the first line description) are N. Is the first N number 1? eg. If PPPPPP was 100,000 would I replace the 100,000th character in the reference genome with the correct nucleotide from Part 1 of this question? Or should I start counting from the first non-N character in the fasta file?


texts: How many agarose gel bands are typical for circularised DNA

texts:
I am aware that circular DNA can be both relaxed and super coiled. However when running an agarose gel of the circular plasmid along with singly digested plasmid with BamHI and HindIII, I see 1 band for the linearized plasmid (lanes 2-5) (as expected) but 5 bands for the circular plasmid (lanes 6 and 7).

What are these various conformations?


texts: How to determine whether the energy of a stem-loop fold is significant or not?

texts: If I have a predicted RNA stem-loop of energy -0.30 kcal/mol, and another of -4.9 kcal/mol, how do I tell whether such a structure is a significantly stable structure or not? Our two competing hypotheses are that there is some structure with sufficient energetic stability to fold inside a cell, versus the one that there is not.


texts: Is there a conformal transformation that maps the skull of Panthera tigris to the one of Panthera leo?

texts: While visiting the Museum of Natural History in Rouen a few months ago, I was stunned by the similarity between the skulls of Panthera tigris and Panthera Leo: the overall shapes were very similar and only distances between homologous parts seemed to vary. As I'm into math, I wondered if this similarity could be explained by some conformal transformation mapping the skull of one species to the one of the other. Are there clues about such geometric correspondences between related species?


texts: Understanding ancestry testing mathematically

texts:
Forgive me if this question has been asked here before, because it is something which should be very easy to find, but I can't seem to find an answer no matter where I search.

The question is simply where to learn the mathematics that goes into things like popular ancestry tests, and also more academic things like determining ancestry components of historical groups (e.g. usage of the terms Ancient North Eurasian, Eastern European Hunter-Gatherers and all that).

It is clear that if someone gets an ancestry test saying say 32% Scandinavian, then of course that doesn't mean 32% of their base pairs have a convenient "Scandinavian" label attached to them, rather there is some statistical inference going on behind these percentages, and I would like to understand that.

Suppose I have the raw data of my own fully sequenced genome, and also a database of the genomes of many individuals from various populations (of course grouping them into populations is already something that involves some assumptions that I would like to learn more about). Where would I learn how to analyze that myself to produce something like the results of an ancestry test? Is there a textbook someone could recommend that gets into the actual algorithms used?


texts: Properly changing the time scale of a parameter in a growth model

texts:
I have a two-population model, where one of the populations is a bacterial culture with its growth described as a logistic growth, with a reported growth rate of $2 \log\hbox{bacteria hour}^{-1}$ and a death rate of $1.5 \log\hbox{bacteria hour}^{-1}$ and a carrying capacity of  $7 \log\hbox{bacteria}$. However, my model studies the interaction between bacteria and fungi in a time scale of days, but if I try to directly rescale these parameters, I get a growth rate of $48 \log\hbox{bacteria day}^{-1}$ and a death rate of $36 \log\hbox{bacteria day}^{-1}$, which is absurd, given the carrying capacity of bacteria.

Is there a standard method for properly rescaling these parameters for bacterial growth, without having to change the model? What alternatives do I have?


texts: Nutrient agar as the medium for antibiotic susceptibility testing

texts:
I couldn't get Mueller Hinton agar to conduct antibiotic susceptibility testing. I'm thinking of just choosing nutrient agar as the growth medium for the bacteria Staphylococcus epidermidis. Will there be any major issue in choosing nutrient agar as the growth medium?
Thanks in advance


texts: Is there an Exit site (E-site) on the eukaryotic ribosome?

texts:
One of my professors mentioned something about the e-site (the exit site for the t-RNA) on a eukaryotic ribosome.  There was a student in the class who objected, saying that there is no e-site on eukaryotic ribosomes; it only exists on prokaryotic ribosomes.  I've tried to find some reliable source to figure out who's right, but to date the only thing I've found is an obscure sentence in a wikipedia article, which doesn't look all that official.

Is there indeed an e-site on the eukaryotic ribosome?


texts: Why do palpitations happen when someone is nearing something rewarding?

texts:
When you are nearing something rewarding (IE: winning a prize, or winning a game), why do you experience tachycardia?

For example, if someone entered a raffle with the number 9284938, and the announcer was starting to announce 9..2..8..4, the closer the announcer gets when palpations would start to occur.

My guess this is something to do with dopamine since dopamine is a rewarding hormone and it gets metabolized directly into epinephrine, but I don't think I'm right.


texts: How sterile is sterile when working with nucleic acids to prevent contamination?

texts:
I am reading up on preparatory work on working with nucleic acids and a lot of the instructions speak on excessive procedures on cleaning environments with high %ethanol and making sure the equipment is nuclease free, and autoclaved.

Are these sterilization steps really necessary when doing research /running gels? Buying all of this equipment seems very excessive, and given that just one nuclease could compromise my results why bother?


texts: I heard that irises are different and unique for every person. According this link, probability of two irises having identical pattern is 1 in 10 to the 78th power. That's how iris scanners identify the identity of people. This technology is becoming very evident. So I ask, why are irises for each person different and unique?


texts: Why are cell lines frozen in vapor phase?

texts: For most of the cell lines I've come across, ATCC recommends storing them in the vapor phase of liquid nitrogen. I'm taking that to mean any place above the level of liquid in the nitrogen storage tank. What is the reason for this? Under what conditions/requirements would one store cells/tissue submerged in liquid?


texts: Mesoderm vs Mesenchyme- what's the difference?

texts:
My embryology textbook states that mesoderm can exist as Mesenchyme or Epithelium. I'm not sure what 'epithelium' means. Here is a quote for context:

  Somatic, splanchnic, and somite mesoderm can be temporarily an epithelium.
  The temporary epithelium transforms to a secondary mesenchyme

What does this quote mean?


texts: Does the metabolic rate determine how fast the telomeres shorten?

texts:
In many papers one can read that telomeres may play an important role in longevity. According to Calado et al.1 the telomeres of mice are much longer than the telomeres of humans. However, mice have an average life expectancy of about 2 years and humans about 80 years.

Does the metabolic rate therefore determine how fast the telomeres shorten? Can one say that the higher the metabolic rate, the faster the telomere shorten?

Telomere dynamics in mice and humans


texts: Why does black and yellow indicate danger?

texts:
It is a well-known fact that combination of black and yellow indicates danger or poisonousness.

In western society it seems obvious this comes from bees and wasps, but it seems like many tropical frogs use yellow and black. Black and yellow also indicates toxicity in some fish species and the order of the colors seems to communicate whether we see a harmless milk snake or a venomous coral snake.

So which came first: the fear of black and yellow or the color of bees? Are there any studies about the color combinations effect on human brain? Is it learned or congenital?


texts:
Why do some men have patchy beards? Or more specifically, why would some hair follicles lack sufficient 5-alpha reductase while others nearby don't when their genetic code is identical and they are both the same type of cell? (See below.)

(Though my actual question is more broad in nature, the answer to this particular example should give me what I'm looking for.)
On this website (http://beardcoach.com/2009/11/why-you-have-a-patchy-beard/) explaining why some men grow patchy beards it says:

  "When the dermal papillae of your beard follicles utilize testosterone, they actually metabolize it and create another androgen as a byproduct called dihydrotestosterone...To utilize testosterone and create dihydrotestosterone, your beard follicles need yet another substance, an enzyme called 5-alpha-reductase.  This enzyme is necessary for this conversion, and if you have low levels of it, then you have low levels of dihydrotestosterone.  More importantly to the topic at hand, if you don’t have enough 5-alpha-reductase, the dermal papillae of your beard follicles can’t properly use testosterone to tell your hair matrices to make hair.  And if your beard hair matrices aren’t making hair, you aren’t growing a beard."

What it doesn't explain is why certain hair follicles have sufficient hormone (or enzyme to utilize it) and others don't.


texts:
I read in a reference book on Google Books (Biology of Termites: a Modern Synthesis, eds. Bignell, Roisin, and Lo) that the termite Heterotermes perfidus found on the South Atlantic island of St Helena is a "valid species":

  Gay states definitively that "there is no doubt now, however, that H. perfidus is a valid species ..." (p. 537)

I don't understand what "valid species" means.


texts:
Does anyone know if saliva can stay viable for about 5 days, before it gets suspended into a DNA genealogy vial for testing?

Background: My brother wants to do a DNA genealogy test at a US testing facility. The country he lives in doesn't allow it, however. For some reason FedEx has no problem with shipping his saliva to me in the U.S. The fastest they can do is 4 days. Will it still be viable to test? Or will it have gone bad somehow? He wants to ship it tomorrow.


texts: Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?

texts:
It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ?

Here a wikipedia article with a link to a journal article which proposes a function of this enzyme. This article was written in 2002 but in most of the text books I have referred to ( written well after 2002 ), no function is mentioned.

MY QUESTION : What are the difficulties that are not allowing us to understand the precise role of this enzyme ?


texts:
My friend got stung by a stingray yesterday and the lifeguard quickly stuck her foot into hot water (she said the water burned slightly on contact) and remarkably, she was walking without pain in a hour. I have heard that rattlesnake's bites can be helped by applying heat to denature the proteins. I am assuming this is what happened here, please correct if wrong. Because I am often in areas where immediate help in cases of animal bites/stings is not available, this is important to me as a first response as I get the person to help.

What kinds of venom are susceptible to denaturing by heat? How do I know which the previous categories a given venom falls into?
Is there a rough temperature I should aim for to denature the venom?
How likely is it that I would end up doing more harm by applying heat out of ignorance than doing nothing till I get to help (could be a day or more depending on the location)?


texts:
I received this flower as a gift.

So far, I couldn't identify what flower it is. My family thinks it may be either some sort of Clematis or an Ipomoea purpurea.
The main reason I want to identify this flower is to know if it can live outside most of the year (I live in France).


texts: What is the role of Homocysteine in cognitive function?

texts:
I'm looking at this link : Homocysteine and cognitive impairments and am looking for more information on specific cognitive impairments associated with elevated levels Homocysteine. That article is not very clear on that point. I've seen some research papers about the study of this in elderly people and cardiovascular studies. I'm interested in average adults.

I've been fascinated with the effect/lack of thereof of vitamin B6 on dreaming and Homocysteine is the first thing that I've stumbled upon in quite some time that is directly related to the B family of vitamins. Has there been any research about what Homocysteine gets metabolized to if exposed to B-Complex vitamins versus Vitamin B6 alone?

Thank you for your input!


texts: Estimation of cases with dominant inheritance

texts:
I am reading [1] and I didn't understand this passage:

  All bilateral cases should be counted as hereditary because the proportion of affected offspring closely approximates the 50% expected with dominant inheritance.

Shouldn't the percentage be 75% with dominant inheritance?

[1]: Knudson, Alfred G. "Mutation and cancer: statistical study of retinoblastoma." Proceedings of the National Academy of Sciences 68.4 (1971): 820-823.


texts: What are some uses of oxidative/reductive power inside cells?

texts: I know respiration and photosynthesis are based on oxidation and reduction, and the formation of NADH and NADPH in them is very important for many cell processes. I know that NADPH, for example, is used in the CBB cycle to fix carbon. However where else are oxidation and reduction reactions needed in cells? I can think of an example for oxidation: getting rid of toxic products. For example, alcohol dehydrogenase in the liver oxidises alcohol to acetaldehyde. However I can't think of much else, and i'm especially stuck on ehy reductive power is useful in cells.


texts: Why can you graft two unrelated cacti successfully, but you cannot do this on garden trees?

texts: Any cactus can be grafted onto any other cactus, and even the most unlike of them grow together. My latest graft was a Schlumbergera truncata scion on an Opuntia microdasys rootstock. This kind of graft is always successful. Why can't garden trees be grafted in a similar way, between genera?


texts:
What are the basic differences between genbank, NCBI and entrez gene?
And please tell some books and webpages where I can get more about the databases .(currently I'm using Bioinformatics and functional Genomics by Pavsner)


texts: What is the adaptive significance of temperature dependent sex determination?

texts: Why do some reptiles have TDSD ?  Is it because one of the genders is healthier than the other that only they, can survive high temperatures?


texts: What is the outer boundary of oligodendrocyte myelination?

texts:
The sensory and motor neurons comprising the spinal cord and brain stem have the interesting property that different structural components belonging to the same neuron can occupy both the PNS and CNS.

Here are several examples:

Motor neurons' somas are in the CNS while the majority of their axonal projections are in the PNS
Sympathetic preganglionic neurons' somas are in the CNS while the majority of their axonal projections are in the PNS.
Pseuduniopolar sensory neurons' have part of their axons in the CNS, but their somas and other part of their axons are in the PNS.

The general dogma of myelinating cells states that Schwann cells myelinate the PNS axons while oligodendrocytes myelinate the CNS axons. However, I'd like to know which cells are responsible for myelinating the segments of axons that are just exiting or entering the spinal cord. Does there exist an abrupt demarcation point where the myelinating cells suddenly cease to operate / exist?

Referring to the provided picture below:

Does this picture reflect what is truly observed? Is there really a distinct "outer limit" of oligodendrocyte myelination?


texts:
While searching for literature on ketone bodies, I can only seem to find how they are synthesized, but not how they are broken down.
I'm looking for the series of events with enzyme names and intermediates. Does anyone have this?


texts: What is the definition of an opioid, beyond that it's something that stimulates opioid receptors?

texts:
At first glance, this looks like a circular definition.

Is there some way to definitively determine if a given molecule is or is not an opioid? (Medically or scientifically, not legally).

I'm hoping for something more scientific than "if it's on this list, it is; and if it's not, it isn't."

Wikipedia's article Opioid receptor:

  Opioid receptors are a group of inhibitory G protein-coupled receptors with opioids as ligands. The endogenous opioids are dynorphins, enkephalins, endorphins, endomorphins and nociceptin. The opioid receptors are ~40% identical to somatostatin receptors (SSTRs). Opioid receptors are distributed widely in the brain, and are also found in the spinal cord and digestive tract. (emphasis added)

Wikipedia's article on Opioid:

  Opioids are substances that act on opioid receptors to produce morphine-like effects. Medically they are primarily used for pain relief, including anesthesia. Other medical uses include suppression of diarrhea, treating addiction, reversing opioid overdose, suppressing cough, and suppressing opioid induced constipation. Extremely strong opioids are approved only for veterinary use such as immobilizing large mammals. Opioids are also frequently used non-medically for their euphoric effects or to prevent withdrawal. (emphasis added)


texts:
This question leads me to wonder about seeing in and through rain.

From visual point of view, rain is light-bending droplets moving downwards, unformly in steady rain, less uniformly if there's variable strong wind. At least human brain is pretty good at filtering out the rain and seeing the stationary background.

Is this ability just physics, and no special adaptation needed? Or is it a biological ability, our eyes and brain doing some "heavy lifting" to be able to see as far as possible in rain?

If it is biological, evolved ability, then is there difference between different animals on how well they see in rain, compared to how well they see in clear weather? Has the ability evolved rarely, or does it arise naturally and easily if it gives advantage to a species? I suppose the only interesting animals here are those, which see far in clear weather to begin with.

I'm obviously looking for some real research done on the subject, not just speculation.


texts: Are there any non-mammalian species known that lactate?

texts: Are there any non-mammalian animals that produce milk to feed their young, or are mammals the only milk-producing animals?


texts: What animal has the longest juvenile period?

texts:
I just heard the following complaint from a comedienne.

  Humans are the only animal that is completely useless for the first twenty five years of life.

Obviously this is just a joke but it is true that primates and especially humans do have profoundly long juvenile periods compared with most animals. It's got me wondering whether humans really do spend the most time in sexual immaturity.

Unfortunately I have found this question hard to search because Google thinks I'm asking about the longest gestation period (which seems to be a much more popular question). To be clear, I am not asking about the longest gestation period.


texts: Can I leave BL21(DE3) cells in room temperature?

texts: I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I wanted to do the large-scale inoculation a few (at least 7) hours from now instead of right away, but I do not want the cells to start dying. Can I take the cells out of the incubator and leave the cells in room temperature? I'm hesitant about this because even at room temperature, wouldn't cells still be growing, making it possible for cells to die as well? What extra steps, if any, should I take before using the cells?


texts: Why is thymidine incorporation (DPM) normalized to per mg protein content while testing for cell proliferation?

texts:
Sorry for this naive question. After performing the thymidine incorporation assay to test proliferation, many papers report normalization of disintegrations per minute (DPM) to per mg protein content? What does this normalization or ratio of DPM to cellular protein content exactly signify?
Thanks in advance.


texts: Why are urban birds still scared of humans?

texts: I understand that animals are naturally scared of humans because we basically slaughtered every living thing we found in our way for millennia. How long does it take for them to genetically 'forget' we are a threat?


texts: Using punnett squares to express sex/gene linkage and recombination frequency

texts:
I have been using punnett squares to visualize mating experiments. I am looking at a pairing which is known to have a crossover event occur. I know from empirically collected data the recombination frequency is ~3%. Can punnett squares be used to express the results bearing the recombination frequency in mind or should I consider a different visualisation technique?
The end result of what I want to achieve is the expected genotypic/phenotypic outcomes taking recombination into account.
In addition the pairing has a sex-linked mutation which further complicates things e.g. aB/Ab x Ab/Y
Here is an example punnett square:
 a-B/A-b x A-b/Y
 -------------------------
 | x   | A-b     | Y     |
 -------------------------
 | a-B | A-b/a-B | a-B/Y |
 -------------------------
 | A-b | A-b/A-b | A-b/Y |
 -------------------------

If a want to represent a recombination event in the punnett square (e.g. to produce a-b/A-b and a-b/Y does this mean I would  need to add a-b as an additional trait to the punnett square like so?
a-B/A-b/a-b x A-b/Y
 -------------------------
 | x   | A-b     | Y     |
 -------------------------
 | a-B | A-b/a-B | a-B/Y |
 -------------------------
 | A-b | A-b/A-b | A-b/Y |
 -------------------------
 | a-b | A-b/a-b | a-b/Y |
 -------------------------

If that is the case, that would give me a frequency of 16.666666% for each.


texts: More general usage of the term 'congener'

texts:
In taxonomy the term 'congener' refers to two species within the same genus. In more colloquial usage, it can refer to any two objects within the same category. Is there a way to refer to related species that is not specific to a particular taxonomic rank--as in, in the same order or family but not necessarily the same genus?

Update: I guess the term 'relative' works, but I still wonder if there's a better term.


texts: How can I test a germinating pea seed for the presence of maltose?

texts: I need to do a simple experiment to test whether germinating pea seeds produce maltose for the breakdown of starch into simple sugars.


texts: Minimal viable EEG equipment for dissertation research on BCI / BMI

texts:
I am planning out a dissertation study of Brain-computer Interface (a.k.a. Brain-machine Interface, BCI, BMI, etc) applications.

One of the 3 papers in that dissertation will involve collecting original data, analyzing it, and writing a biofeedback application based upon this data.

I'm in a Computer Science department at a university which does not have a med school, so as far as I know I'll have to purchase the equipment myself out of a very modest research budget.

Thus, my question is "what's the lowest-end (i.e. cheapest) kind of EEG machine which would still be considered modern and sophisticated enough to be publication worthy in journals?".

Of course, I've done a good bit of research on this by reading recently publications on Google Scholar and will continue to do more research, but there's a lot of information overload and I have no prior background with EEG equipment, so any insight would be greatly appreciated.

From what I can tell the main thing driving price is the number of leads or sensors. They seem to range from 1 lead in consumer EEG toys to 100 leads, with a lot of products being advertised that have 16 or 24 leads. There are of course a lot of other features, so feel free to answer using either specific products or in terms of whatever features you've found important.


texts: What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

texts:
First definition.
Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly defined and evidenced that in bacteria the positively charged residues more commonly were found on the "inside" of a membrane (the cytoplasm rather than the periplasm).
Recent Literature.
However it seems the field has moved away from the idea of "inside the compartment" to "inside the cytoplasm" as more data became available. In a 2006 review even von Heijne describes some transmembrane helices as abiding to the positive inside rule because their positively charged residues were inside the cytoplasm, although never explicitly backtracks on the original definition. A similar review in 2007 by von Heijne offers a more definitive refinement of the rule, however removes the concept from being applicable to subcellular membranes.

...the loops connecting the helices differ in amino acid composition, depending on whether they face the inside or outside of the cell (the “positive-inside” rule).

We are now faced with an awkward rule that doesn't account for proteins elsewhere in the secretory pathway or in the other organelles. All those proteins are inside the cell.
More recently still large-scale analysis of transmembrane helices from different biological membrane surfaces, Sharpe et al., 2010 and Baeza-Delgado et al., 2013, show the clustering of positive charge being cytosolic rather than discussing it in terms of the inside of the compartment. Both of these papers still say that they corroborate with the positive inside rule.
Question.
To me it seems that the definition is somewhat sloppy and can broadly be used to say "inside the cytoplasm", despite publications being reluctant to define the rule clearly. Has the definition ever explicitly been changed, or has the field silently changed what "inside" means? ... Or have I completely misinterpreted something? How do the organelles fit into any of these definitions?


texts: Found a larva in my broccoli, is it a Small White (Pieris rapae)?

texts:
Found this living larva in broccoli from a store. It was about 10 mm long. It was in july this year, and I don't remember the country of origin for the broccoli. A bit of googling makes me think it could be a Pieris rapae, but I don't know if there are any similar species.

edit: Even if I don't know the origin of the broccoli, I assume (and hope) it was grown in Europe since I got it in Sweden.


texts: Direction of impulse at Axo-axonic synapse and dendro-dendritic synapses

texts: Do axo-axonic and dendro-dendritic synapses show some different impulse conduction directions than the usual dendritic (of carrying impulse towards cyton) and axonal nature (of carrying impulse away from the cyton) ?


texts:
Hello I have been reading papers about the Goodwin oscillator and I found that the equations are kind of tricky. Specially the part of the hill coefficient. In his paper "An entrainment model for timed enzyme synthesis in bacteria" from 1966, in the part of the differential equation of the mRNA concentration Xi, there is the term Zi and this term also exists in other books that talk about this oscillator. However, I don't know what it means. Goodwin never mentioned what this term means. I'm guessing it is about the hill coefficient, but still I do not quite understand well.
I share the link of a chapter book that explains the equations of this oscillator (page 244):

Biochemical Oscillations

Thanks for your help.


texts:
In Life Ascending the author, Nick Lane, refers to an enzyme in his introduction:

'' It concerns an enzyme (a protein that catalyses a chemical reaction) that is so central to life that it is found in all living organisms, from bacteria to man. This enzyme has been compared in two different species of bacteria, one living in superhot hydrothermal vents, the other in the frozen Antarctic. The gene sequences that encode these enzymes are different; they have diverged to the point that they are now quite distinct. We know that they did diverge from a common ancestor, for we see a spectrum of intermediates in bacteria living in more temperate conditions. But from the gene sequences alone there is little more we can say. They diverged, surely because their living conditions are so different, but this is abstract theoretical knowledge, dry and two-dimensional.
But now look at the molecular structure of these two enzymes, pierced by an intense beam of X-rays and deciphered through the wonderful advances in crystallography. The two structures are superimposable, so similar to each other that each fold and crevice, each niche and protrusion, is faithfully replicated in the other, in all three dimensions. An untutored eye could not distinguish between them.....The building blocks bind tightly to each other, through internal bonds that work like cement, retaining the structure despite the buffeting of energy from the boiling vents..... In the ice, the picture is reversed. Now the building blocks are flexible, allowing movement despite the frost...... Compare their activity at 6°C, and the frosty enzyme is twenty-nine times as fast; but try at 100°C, and it falls to pieces.
The picture that emerges is colourful and three-dimensional. The changes in gene sequence now have meaning: they preserve the structure of the enzyme and its function, despite the need to operate under totally different conditions.''

Emphasis mine and .... indicates omitted text.

I would be very grateful if anyone could tell me what this enzyme is, and if possible point me to further information about it!

N. B. the enzyme is only mentioned in the introduction "... never found the opportunity for a mention in the book proper." There are no references for said introduction, only the chapters.

Thank you!


texts: What is the name of this big tree with look of banyan branches?

texts:
Location is India, Tree is so huge & some branches are hanging like Banyan.

Its Hanging Branches look:

& Finally its leaf:

So what is it then?


texts: Genetic expression in interspecific hybrids

texts:
Referring to interspecific hybrids, I have the following two questions:-

Quoting from wikipedia:-

  The offspring of an interspecific cross are very often sterile; thus,
  hybrid sterility prevents the movement of genes from one species to
  the other, keeping both species distinct. Sterility is often
  attributed to the different number of chromosomes the two species
  have, for example donkeys have 62 chromosomes, while horses have 64
  chromosomes, and mules and hinnies have 63 chromosomes. Mules,
  hinnies, and other normally sterile interspecific hybrids cannot
  produce viable gametes, because differences in chromosome structure
  prevent appropriate pairing and segregation during meiosis, meiosis is
  disrupted, and viable sperm and eggs are not formed. However,
  fertility in female mules has been reported with a donkey as the
  father.

1) The sterility of hybrids prevents interspecific gene exchange and is necessary in case the hybrid has odd number of total chromosomes (the hybridized species has odd and even pairs of chromosomes individually), where equal meiotic division would not be possible, and is also necessary to avoid sex determination problems that may arise from such hybridizations genetically. What is the molecular (genetic) reason behind the sterility? In other words, why is the expression of primary sexual organs and its further proliferation to effect reproduction not possible, although the genes required for it are already present in the hybrids? Is this due to epigenetic mechanisms or is the reason inherent in the hybrid nature of the genome?

2) This might probably sound a bit naive, but why are these hybrids viable? They have 2 non-homologous haploid pairs of chromosomes which have a huge variety(compared to two homologous pairs) of different non-allelic genes. Why are all the essential functions not hindered by the presence of such considerably unrelated set of chromosomes?

Probably related to the question is the fact that certain allopolyploids are viable and become an entirely new species, but others are not. Is it because here are 2 sets of each combining species' chromosomes (and hence allowing proper meiotic pairing) or is there some other reason pertaining to the nature of the combined sets of chromosome?


texts: Today while we're cleaning our storage room I saw this strange looking spider and I'm not even sure if this is a spider, it has two claws folding inward to its mouth and two long weird limbs, it is about 2 inch long and rarely move on its place. Is it poisonous or dangerous to us? What should I do with it?


texts:
Some sites say wolves can bite around 400 psi. But this site claims that when facing a peril they can deliver upto 1200 ?https://plexidors.com/myths-around-dog-bite-force/(skip to the 'How does that measure compared to cousins in the wild?' portion to save time)
  -That's a huge range, and could in theory put them on par with big cats.Is what the site says true?
-I looked online extensively in the internet but I only came across a reddit post where they discuss this and it wasn't conclusive.Why is there a maximum bite force of other animals like crocodiles,gorillas,hyenas etc but not for wolves?


texts:
How can you increase the pheomelanin production in your body, while decreasing the eumelanin production? In other words, shifting the balance towards pheomelanin.

From what I see, sulfur and cysteine can help with this. MSM and glutathione caps can be a good way to do this, since these are used for skin lightening.

But is there another way? Something more scientific? Like deactivating the MC1R? Is that even possible?

Thank you!


texts:
Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment.
We know that mtDNA inheritance is solely matrilineal.

So the question is, If your mitochondrial DNA is released to the extracellular environment (or into
cell cytoplasm) due to cellular and/or mitochondrial damage, what could be the
ramification of this released DNA if your immune system cells (such as macrophages,
dendritic cells or B cells) pick up and sense these DNA as a danger signal?
Is there any chance for mtDNA to survive by establishing a new mtDNA ?

I am thinking, macrophages engulf and destroy them but cannot provide sufficient evidence.


texts: If fish gills do not split H2O into H2 and O, and just take the dissolved oxygen what is left leaving the gills?

texts: Could you please explain to me the exact left overs after a fish takes oxygen out of H2O?


texts:
I read article about apoptosis on Wikipedia, but didn't understand, how exactly the organism learns that it is necessary to launch process of apoptosis in certain cell. In other words, on what signs the cell is marked as "necessary to destroy"? How exactly at the chemical/biological level process of apoptosis starts?
Also I am misled by the fact that apoptosis occurs by a row of strongly differing reasons - not only aging, functionality losing, chemical/radiation affection, but also process of apoptosis can start in absolutely normal cells (including just newly created ones - for example, during formation of an embryo). How in that case the embryo knows what cells need to be destroyed, and how exactly it does it?


texts: probability of hairpin vs self-dimer formation?

texts:
I have a linear ssDNA oligo that is designed such that the ends are complementary, and conducive to hairpin formation (see attached figure). My question is, which has a higher likelihood of formation, a hairpin, or a self-dimer? Would the likelihood of hairpin formation increase if I decrease the concentration of the ssDNA oligo during the annealing process? If I enter the sequence in IDT oligo analyzer, the gibbs free energy for formation of self-dimer is significantly lower compared to hairpin.
The melting temperature of the complementary part of my oligo is 50 deg. The annealing will be done in nuclease free water, without any Mg+.


texts: What were the main discoveries in Biology?

texts: What were the greatest achievements in Biology? Can you please provide a short list of discoveries that you would consider as being the most important discoveries of the history of Biology.


texts: All somatic cells contain the same genome, then how does it knows that it should develop into a specific organ?

texts:
All somatic cells contain the same genome, then how it knows that it should develop into a specific organ. In https://www.youtube.com/watch?v=aeAL6xThfL8, Joe Hanson says that each cell has the same book that each has 20,000 same instructions. And each cell has bookmarks, where it finds which instructions to read.

Can you tell me where these bookmarks are stored in the cells? Is it outside the chromosomes or outside nucleus?


texts: Because hydras have immune systems, telomerase activity, and Piwi-piRNA like cancer cells I wonder if they can get cancer?


texts: What are the fibers and small droplets on the surface of dividing HeLa cells in the figure?

texts:
I did some literature searching but could not find any info probably because I did not know how people name them.

The figure is from the wikipedia entry HeLa


texts: What are the most important differences between HSP70 and HSP90?

texts: Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?


texts: In general, when a limb dies, how long does it take before it falls off? Can you go years with a black and useless limb, or does it just.. fall off right away?


texts: Bundle of His and Atrioventricular Bundle difference

texts:
I see most definition using  Bundle of His and AV bundle interchangeable including the wikipedia when you do a Google search for AV bundle
But my text book treats as two different things.

The action potential is conducted to the ventricular side by the AVN and the AV bundle from where the bundle of His transmit it through the entire ventricular musculature

So is there any subtle particular difference here?


texts:
What are the popular theories regarding how our blood divided into 4 groups. Particularly I'm interested in whether this was originally linked to disease.

Thanks for your answers, useful articles and further reading would also appreciated.


texts: Questions regarding Scapulohumeral Rhythm

texts:
I'm actually an artist, but I wanted to ask this because it will help a lot in my figure drawings.

My artistic anatomy teacher taught me about the Scapulohumeral Rhythm. He said that in during the first 30 degree of rotation of the humerus, neither the scapula nor the clavicle moves. But after that, for the next 60 degree of rotation of the humerus, its rotation is distributed in a 2:1 ratio to the Scapulathoracic joint.
He said that beyond that, the Humerus is locked into the socket with Acromium and Coracoid Process. So the Glenohumeral Joint is frozen. Additional elevation comes from the Clavicle.

My first question is how true is that?
My second question is what happens to the Scapula after the 90 degrees rotation of the Humerus? I noticed that the Scapula keeps rotating even after the Humerus is rotated beyond 90 degrees, but is there any consistent ratio?
My third question is what is the maximum elevation of the Humerus in degrees?

Forgive me if I looked liked an annoying dumbass, I'm just an artist. So, please explain in a simple and understandable way.


texts: How do migrating birds know where to migrate?

texts:
Migrating birds return to the same spot, year after year. These locations are often thousands of kilometers apart. How do the birds know where to fly to?

So far I have found that the birds tend to follow a leader. Like Canadian Geese flying after one bird in a V shape. It seems that this leader is the one who 'knows' where to fly, but how?


texts: DAM enzyme distances move along the genome

texts:
I am fusing a protein with a Dam enzyme (http://en.wikipedia.org/wiki/Dam_(methylase)).  The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, thus helping identify the protein binding region (using DpnI later on, and microarray technology).  However, I have no idea, in theory, how many (bps) will the enzyme traverse across the genome from its starting location.  I.e., how far (in terms of bp) from its starting location will the enzyme methylate the GATC sites.

There are methods for finding protein binding regions along the genome that use such technology, such example here: http://www.nature.com/nbt/journal/v18/n4/abs/nbt0400_424.html


texts: How to troubleshoot in vitro formaldehyde fixation for nucleosomes?

texts:
For an experiment, I am trying to fix the mononucleosomes (100ng) using formaldehyde as crosslinking agent in HEPES buffer. I have been using 2% formaldehyde in a reaction buffer containing 1mM EDTA, 25mM NaCl and 50mM HEPES, pH 7.5 (same as nucleosomes suspension buffer) to fix mononucleosomes.

In my first reaction, I added 100ng of nucleosomes, 2% formaldehyde and incubated at 4degC, 30', then I added 0.4% SDS and incubated for 30' at RT. I observed less intense but equally sharp band for nucleosomes (less smear) as compared to unfixed nucleosomes.

When I performed the same reaction again, the gel showed a huge smear covering the entire lane instead of a sharp band.

I have been reading about the fixation reactions and encountered an emphasis on using methanol free formaldehyde (while I was using 10-15% methanol containing formaldehyde). Do you think that can be one factor for not being able to get similar results?


texts:
Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells?

It's an essential amino acid, so I cannot fathom why low concentrations as opposed to higher ones are best. Does it have to do with carcinogenesis or some other dangerous side effect I wonder?


texts: Why are there still useless traits/mutations in our body

texts: Why is it that through decades of evolution , some seemingly useless body traits such as earlobes and pubic/chest hair still remains while other traits are generally replaced through evolution?


texts: Chart of intra-species genetic diversity across species / phyla?

texts:
I am looking for information on how genetic diversity within a species (not between species) differs between taxa. In other words: Is the "spread" in the genetic pool, if measured, for instance, in terms of single-nucleotide polymorphism (SNP), generally bigger / smaller for some groups of species than for others?

My ad-hoc idea is that species with a stronger phenotypic difference between individuals, like homo, should probably have a higher genetic diversity (higher rate of SNP) than those with lesser phenotypic variation, like, say, Orthoptera (grasshoppers etc.). But I couldn't find any statistics or research on this topic.

I am especially interested in data on far-related taxa. Ideally this would be a chart with comparative data for Sponges, Annelids, Arthropoda, Fish, Mammals (single representatives of these groups), or even Plants, Fungi, Archeae, Bacteria …

I do not look for information on the actual genome sequences, nor on biodiversity, but specifically on the genetic diversity within species from different phyla.

This is my first question here, thanks for you help!


texts: Are there any parasites that alter human behavior in a self destructive way?

texts:
There seems to be quite a few examples of parasites taking over the behavior of insects in a way that leads to the death of the host.  A couple of examples include:

Spinochordodes tellinii:  A nematomorph hairworm that causes crickets and grasshoppers to jump into water, and likely drown, as
part of their life cycle.
Ophiocordyceps unilateralis: A fungus that causes ants to leave their desired habitat for the habitat required for the fungus
to reproduce while consuming the ants internal organs.

In mammals, a common example is:

Toxoplasma gondii: A single celled parasite that appears to make rats attracted to cat pee in an attempt to continue its life
cycle within the cat.  Additionally, humans can be infected with
Toxoplasma gondii via contaminated meat, vegetables, and cat feces.  In fact, there is a study of Danish medical records from 45,788
women in which the rate of self harm increased 50% for women
suffering from chronic toxoplasmosis and the rate of attempted
suicide was 80% higher.  However, direct correlation between the
increases could not be linked to the these higher rates due to the
possibility of other factors such as depression.

So it seems that there is some widespread evidence of parasites causing a host to act in a potentially lethal way, but the evidence that I could find for humans seems to be minimal and yet to be proven.  Are there any examples of parasites causing humans to act in a risky, potentially deadly, manner?


texts: Transfer of antibodies from mother to fetus

texts:
My questions: When does fetus begins to acquire antibodies from mother? Does it continue throughout the pregnancy?

From Wikipedia: http://en.wikipedia.org/wiki/Passive_immunity

  This occurs around the third month of gestation.

From Helena Curtis Biology :

  During the last month of pregnancy , the baby usually begins to acquire antibodies from its mother,....

I believe that both these sources are reliable but they contradict when the transfer of antibodies starts.


texts: Are “Rings” in fish like rings in a tree?

texts: A lot of fish have structures like the rings in a tree. Is the number of “rings” an indicator of age, as in a tree, or is it fixed?


texts: Why are there multiple sequences for the same segment for an individual "strain" of influenza?

texts:
I am looking at the genome of the influenza virus being used in the flu vaccine 2017-2018: A/Michigan/45/2015.

When I look below at the individual segments, there are 4 sequences for each segment - shouldn't there be only one for a single "strain"? Is this due to rapid mutation rates? Or is it that they are including both positive and negative sense of the virus?

Edit: sorry, link here:

https://www.fludb.org/brc/fluStrainDetails.spg?strainName=A/Michigan/45/2015(H1N1)&decorator=influenza


texts:
I was wondering, what are the humans needs to fulfill to achieve a human colonisation on mars ?

Let me explain, this is for role play game in a futuristic world where humans colonized mars.
That creates questions that needs answers for background purposes.
I saw like each another some scifi, read novels etc. But I'd like to know scientifically what could help us achieve that.

If this post doesnt have it's place here, do not hesitate to remove it.

In my mind :
breath
eat
drink
dont take radiations (at least not to much)
stay at the right pressure and temperature
any gravity issue on our body ?
try to avoid wandering naked in space

Any help is appreciated
thanks guys :)


texts: Critical discussion: Gene expression and systems biology allows us to understand the control of complex traits

texts: I'm having a bit of trouble tackling this question. Any help on what I should write about or the points I should mention would be much appreciated. I keep seeing articles about eQTL and QTL are these relevant as well?


texts: Which organisms require the least fluctuation in ambient temperature?

texts: Note that I am NOT asking "which organism can survive the most extreme temperatures." Many extremophiles like the tardigrade can survives extreme heat, but also extreme cold. Many heat adapted animals like the camel can also tolerate fairly cold conditions. I want to know what species that are adapted to hot climes are hot climate obligates (or the corollary for cold climate obligates) and which extreme temps-obligates have the narrowest tolerance.


texts:
How do we perceive weight of our own body or something we are holding?

It might turn out that we don't perceive weight so is it subjective? Is it similar to pain, or something different?


texts:
Some kinds of trauma can cause pain so severe that it makes you unable to move or do anything at all.
It may put you out of action and unable to help yourself because of how excruciating it is.

Although I understand that pain is necessary to alert the brain that something is wrong and need to be fixed, I imagine it like an alarm going off alerting about trauma. But a crippling pain would be like a deafening siren hooked up to your ear making you unable to do anything to correct the problem, instead it might send you into a shock. It would be total disaster which could prevent you from taking any step about it. So, why does excruciating pain exist? Or in other words, why has this feature not gone extinct during the course of evolution in spite of its harmful effects?


texts:
I've been trying to a good contrast for my DNA bands, however I haven't been so successful. I've been running the ladders only to make sure I get a good contrast before further experimentation.
I created the gel using 70mL 1X TAE buffer, 0.84g of agarose (so about 1.2% gel), and 28ul EtBr.
I set the electrophoresis box at 90V for about 1 hour hoping to get a better gel but the results came out looking the same as if I had ran it at 110V.
I've attached a picture of my gel. It was taken with a DSLR, no flash, 20 seconds exposure time.
Any tips would help. Thanks


texts: Can coding DNA be used for DNA fingerprinting?

texts: I am confused if coding DNA can be used for DNA fingerprinting because I have read that non-coding segments of DNA are used to identify and analyze DNA. I want to know if coding DNA segments are of equal length in all individuals?


texts:
In the European population, about 1 in 2500 people suffers from Cystic Fibrosis, a genetically determined (descared), autosomal disease. Healthy parents have a child suffering from Cystic Fibrosis. The woman remarries a healthy man. What is the chance of a child from this second marriage suffering from Cystic Fibrosis ?

My attempt

http://i.imgur.com/4mhU3Qh.jpg

But the answer given is 1/100


texts: Are there specific conditions that allow humans to see ultraviolet wavelengths

texts:
It is fairly common knowledge that the lens in its normal state absorbs ultraviolet (UV) radiation.  An interesting notion has come up from time to time in my reading that suggests there are a small number of conditions that result in humans being able to 'see' ultraviolet.

What conditions may cause this?  Also, those affected, would they 'see' it has a different shade of violet?


texts: Traceability of a mature tree to its original seed via DNA

texts: Is it possible to trace a specific seed to a fully mature tree?  For example, Can a seed be traced to the full-grown plant based on DNA?  Would it be possible for me to catalog a seed DNA and then years later be able to identify the full-grown plant to that seed that was cataloged?


texts: Trying to identify the tree in this picture. Shot from the Nepenthe restaurant, Big Sur, California

texts:
I'm trying to identify the tree in this picture. This was shot from the Nepenthe restaurant, Big Sur, California.
Any help is appreciated!
Thanks,
Robert


texts: What is the name of the machine used to measure optical density? We used it in a lab but I can't remember what they called it.


texts: Can C. elegans be raised on Lactobacillus as the only food source?

texts:
I'm interested in running some C. elegans experiments for educational purposes, but would like to avoid having to grow or handle E. coli.  I was wondering if C. elegans need E. coli specifically, or if they would grow well on most (non-pathogenic) kinds of bacteria.

In particular, I'm curious about whether C. elegans would grow on (either live or pasteurized) yoghurt, including strains such as Lactobacillus acidophilus and L. delbrueckii.

I did a quick literature search and found a few articles (like this) which talk about screening probiotics in C. elegans by adding them as part of their diet, but I haven't been able to find any reference to using them as the only food source.


texts:
I have found a diagram similar to the following one in my biology textbook. The diagram describes allosteric regulation.

However, I do not quite understand why the maximum reaction rate $V_{max}$ is still reached, even though I thought this is only possible for a competitive inhibition.

I think that the diagram should look something like this where the maximum reaction rate is not reached.

Is there simply an error in the diagram or have I misunderstood something here?


texts: Why it seems that principles of chemistry are not being applied in this biochemical process?

texts:
According to an answer in this question, my concept used below does not apply:

In the non-cyclic photophosphorylation, consider splitting of two water molecules, then 4 e- (electrons) and 4 H+ (protons) are generated in the lumen of the thylakoid. Due to quinone cycle 8 H+ are transferred from stroma to lumen. 4 e- will reduce 2 NADP+ to 2 NADPH, these H+ are taken from stroma so there is a net decrease of 8 + 2 = 10 H+ and a net increase of 4 + 8 = 12 H+ in the lumen. So if we apply principles of chemistry then to attain equilibrium there should be equal number of H+ on both side. Therefore 11 H+ must be transferred from lumen of thylakoid to stroma. Now there is 1 H+ on each side at equilibrium. We know that F0-F1 ATPase will produce 1 ATP for 3 H+ being transferred so in this process 11/3 ATP should produce but in books it is given that all 12 H+ are transported which is violating the principle of chemical equilibrium and produces 12/3=4 ATP.

So I basically want to ask: Why does it seem that in this process the principles of chemistry are violated?


texts: What is the name of the critter depicted in the attached image?

texts:
I found a critter on my bathroom towel. It's really tiny. Maybe 2 milimetres? I placed it on an envelope for the photograph.

Can someone identify what it is?


texts: What is the acceleration profile of a cheetah?

texts: I'm interested in the time it takes for a cheetah to reach maximum velocity as well as the acceleration over time that's typical of a cheetah prior to attaining this peak velocity.


texts: Does DNA react in all of the ways most other acids do?

texts:
As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of a state of equilibrium in water.

Do these reactions and equilibria occur to DNA (or, for that matter, RNA), which has only ever been described to me as an 'acid', and does this affect the processes DNA goes through, like replication and transcription?


texts: For the human head, which direction is anterior, and which direction is ventral?

texts:
I read the wikipedia entry and I am sort of confused.

In dog, the nose is toward the front. That's anterior. So I conclude that human nose is anterior.

In dog, the head is on the back. So that's dorsal. So I concluded that humans' top head is dorsal.

Yet that's not how things seem to work on anatomy.

We call humans' top head anterior. We also call human nose direction as ventral.

How could that be?

The whole system of anterior, dorsal, ventral, posterior is there so we can see humans like we see dogs (at least anatomically).

Yet it changes again.

So which one is right?

Let me put it this way

Dog's chin is ventral from the eye
In humans, is humans' chin ventral from the eye too? or posterior?

What about the nose? Dog's nose is it's anterior most organ.

In humans, is the nose anterior too?

I mean, if we're going to have different terms for humans and dogs, might as well use words like up, down, front, back right?


texts: How to set up a slow cooling on an AB Veriti thermal cycler?

texts: I want to incubate my sample at 50ºC and then slowly cool it down to 4ºC at a rate of 0.1ºC/s. I am using  AB Veriti thermal cycler. Does anyone know how to set up the rate of cooling? It has to do something with the ramp rate, which is given in % but I don't know how to convert this into a real rate.


texts: Organisms with one, two, or more than two biological parents

texts:
I am interested in the generic names of organisms with one, two, or more than two biological parents. I don't know if the latter possibility is possible in nature, but if it could be, it would certainly be interesting.

Thank you for your answers.


texts: What is a good list of unsolved protein structures?

texts:
I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein.

Things that I've been able to think of are low producing transcription factors and novel fusion proteins.


texts:
The problem is as following:

Primary Ciliary Dyskinesia (PCD) is caused by an autosomal recessive gene. 50% of patients with PCD also have Kartagener Syndrome. Josh has Kartagener Syndrome. What is the chance his brother or sister also have this syndrome?

A  0%
B  6.3%
C  12.5%
D  25%
E  50%

Is this problem actually solvable without knowing the alleles combination of the parents? The answer states C, but perhaps I´m missing something here.


texts: Is there evidence that children should play in dirt to get healthy?

texts:
I've heard it said many times, that we should let children play in the dirt as it builds up their immunity and prevents things like allergies in later life.

I have another suggestion which, to me, is equally plausible. In older times when families had lots of children, and they used to play in the dirt, those weaker children used to get ill and die. Leaving the `stronger' children who were less suceptible to allergies and diseases to grow to adulthood.

So in our cleaner lifestyles where we prevent our children from playing in the dirt, actually we are just letting children who would normally have died off early grow to adults. (Which is a good thing from a moral standpoint - although overall it means the human population as a whole grows weaker in the short term).

Therefor telling people to let their children play in the dirt is bad advice if this is true.

Which of these two options do you think is the truth?

(Mathematically, let us assume that by random chance 50% of babies have bad immunity, but that parents have an average of 4 children. This means if half the childen die in childhood, the adult population would be full of people with good immunity. This is my terrible conclusion which has no moral solution.)


texts: Is there any correlation between animal diet and blood pH?

texts:
The alkaline diet claim that as we humans have a slightly basic pH we shouldn't eat acidic food like meat (I think they claim that meat ashes are acid).
I was wondering that if carnivores animals share similar blood pH to humans and herbivores, that argument falls.
I did a google search, but I couldn't find the answer, even though it seems like basic data for a physiology textbook.
Similar questions have been posted here but without satisfactory answers.


texts: How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?

texts:
I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19.5 kDa) with an N-terminal His tag and a TEV cleavage site between the His tag and the N-terminus of the domain. The purpose is to study the properties of the domain in isolation, but without any tags that might interfere with its function. Using the His-tag will make for easy purification, after which the tag can be removed with TEV protease, leaving only a glycine at the N-terminus of the domain, which will not affect my experiments in an appreciable way.
The way I've gone about doing this is to use a forward primer that, after the restriction site and start codon, contains the sequence which codes for the his tag followed by the TEV cleavage sequence, followed by the first 6 codons of the domain sequence. The reverse primer contains the final 6 codons of the domain sequence followed by a stop codon and restriction site. These primers are used to amplify the target domain sequence from a plasmid that contains the full protein sequence, but with the N-terminal cleavable tag attached. The plan is then to clone this DNA insert into a pET21b vector to transform into DH5alpha / BL21 cells.
However, it seems like I'm having problems during PCR amplifying the sequence of the domain from the template DNA. After cloning my purified PCR product into the pET21b vector, and successfully transforming into DH5a cells, sequencing the section of the cloned plasmid with the insert revealed that the insert DNA consisted of only the forward and reverse primer sequences on the ends, sandwiching a single alanine codon. Put another way, the inserted sequence reads as (His-tag)-(TEV cleavage site)-(First 6 codons of domain)-(Single Ala Codon)-(Last 6 codons of domain). This would mean all my cloning steps were fine, but the insert DNA was copied incorrectly during PCR. If it were just the primer ends, I'd think there was some sort of overlap between the primer sequences, but there is that one alanine from the domain template DNA (alanine is the next residue after the first 6 in the domain sequence). A weird result, and I'm not sure where to begin troubleshooting.
My question is, is there anything that I'm doing in this procedure that might stand out as particularly problematic that would cause this issue? Or more generally, is there a better way to put a TEV protease-cleavable his tag on the N-terminus of a protein? Any advice would help, even if it's just to point in the direction of useful references or protocols, and I'm happy to clarify as needed. Thanks!


texts:
Since insects like mosquitos ingest only blood, and insects generally excrete their solid and liquid waste at the same time as frass, I was wondering: is mosquito defecation more like iron pellets or droplets of blood?

I've never seen a mosquito defecate, so I have no evidence. Do they defecate during flight? If so, are tiny little droplets of digested-blood falling from the sky?


texts: What would happen if we had a device that produced oxygen inside of our lungs?

texts:
Hypothetically speaking, suppose there is a device that produces a limitless supply of oxygen. The device is inhaled by a human and is resting inside the (a) lung.

What would hypothetically happen if this were possible?


texts: Why is iodine solution a very effective and with a broad spectrum, bactericide, fungicide and viricide?

texts: What is the similar property in each that allows a solution of iodine to deactivate and destroy so many species even from different kingdoms?


texts: Coordinates of amino acids in a protein sequence

texts: In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL... Where would I get the coordinates of M and K and L separately? Is there any method by which the coordinates of the amino acids can be calculated? I don't want the coordinates of the atoms, I want the absolute coordinate of each of the amino acid in a protein sequence as a whole...


texts: In biosynthesis of cysteine and methionine, where does the sulfur come from?

texts:
Methionine and Cysteine are the two amino acids containing sulfur. According to wikipedia, cysteine is built from methionine. However, the wikipedia also claims that methionine is synthesized from cysteine.
So, a chicken and egg problem (esp. since eggs are a rich source for those proteins). Where do living things get their sulfur to build these amino acids in the first place, in what forms is sulfur available biologically?


texts: What does "kcal/mol" mean when speaking of enzyme catalysis?

texts:
After thinking about it, I'm confused by what the reaction barrier of an enzyme actually means.

Imagine a reactor containing enzyme and substrate.

If the enzyme in the reactor has a reaction barrier of 15 kcal/mol,

a) then when 1 mole of product has formed, that means 15 kcal have been consumed, independent of how much enzyme is present in the reactor.

b) then when 1 mole of enzyme is present in the reactor and 1 mole of product is formed, 15 kcal have been consumed.

Is it option a), b) or otherwise?

Let us imagine two companies A and B.
Both companies use very similar technical equipment to carry out a biotechnological process where a chemical reaction is catalyzed by an enzyme.
Company A uses an enzyme with a reaction barrier of, say, 15 kcal/mol, while company B uses an enzyme to catalyze the same reaction but this enzyme has an activation energy of only, say 12 kcal/mol.
For every Mole of product, company B saves 3 kcal worth of energy needed to drive the factory.

Does that make sense?


texts: Transduction with P1 lysate prepared from strain that is proC::Tn10

texts: If I do a transduction with a P1 lysate prepared from a strain that is pro*C*::Tn10 and the recipient is wild type, will all my recombinants  be ProC- and Tet resistant since the Tn10 is in the proC gene?


texts: When did death due to aging first appear?

texts:
As I understand it, single-celled organisms that reproduce via mitosis essentially live forever. When a cell divides, one cannot say that either one of the new cells "is" the parent and the other the child, neither is older than the other, and we might say that the original cell is still alive as long as either of the cells resulting from the division is. With humans the pictures is very different, of course: we have no trouble telling parents and children apart and no one lives longer than about 120-something years.

When in evolutionary history did organisms stop living forever? Was it with the advent of multicellular life with differentiated cells? Sexual reproduction?


texts: What are the major causes of mutations in DNA?

texts: I know that point mutations can change the base sequence of a gene by altering a specific codon that codes for a particular amino acid. Are these mutations purely random events that occur when DNA is being copied into a cell? Furthermore, can environmental factors play a role in the amount of mutations that occur?


texts:
There are very goods in physics and mathematics (like Feynman lectures for exemple) that give an elementry but but broad view of their,therefore I'd like for help to find help to find a biology book that:
-Covers a variety of subject in an elementary fashion.
-Is written for the non-specialist.


texts: I'd be tempted to call nipples in men vestigial, but that suggests they have no modern function. They do have a function, of course, but only in women. So why do men (and all male mammals) have them?


texts: Cardiac pacemaker: how can different nodes have different frequencies?

texts: Primary SA node creates 70 beats per minute and secondary AV node 40-60 beats per minute. Is the AV node inactive (and other subsequent nodes) while the SA node is functional? If the primary, secondary and tertiary nodes are working simultaneously, wouldn't the difference in the beats per minute cause a mess?


texts:
Is it possible to surpass/decay cell death.  For example to disable the process muscles cells death, by tweaking the transduction pathways:

If it's not possible in our age Medicine, what it would take to do such thing in theory. The idea is to tweak the cell dying mechanisms for example to preserve neural and muscle cells for longer time. I am also curious how to disable a pathway or part of it.


texts: Why do dozens of preys run away from a clearly outnumbered predator? (e.g. zebras and lion)

texts:
We are all familiar with scenes where dozens (if not hundreds) of zebras, sheep, or other preys are chased by one lion, one wolf or other predator. Examples are all over youtube, but here is one of lion versus zebras. In that video you can count at least 30 zebras. Even more, zebras (particularly adult ones) are bigger than lions. There is also evidence of prey defending itself against predators, but this seems to be not the norm.

So my question is, why do high numbers of preys always run away from a clearly outnumbered predator?

Surely evolution would have already taught these animals that numbers can make a difference, so that coordinated defense strategies would be part of their natural repertoire, or of their social learning. Why nature seem to be so oddly incapable of making use of relative numbers as defense strategies?


texts: Retinal eccentricity to colour sensitivity

texts: Colour perception goes out to 50 degrees but is the sensitivity to RGB. Question is it the same in the four quadrants of the retinal field? That is if the red colour sensitivity eg is 30 temporal retina 50 degree nasal retina etc. And what are the eccentric limits for each colour [frequency]in the four quadrants.


texts: Cutting dna using restriction endonuclease

texts:
Genomic dna is digested with alu 1 which is a four base pair cutter. What is the frequency with wich it will cut the dna assuming a normal distribution of bases.

(this is not a homework)


texts: Are there "old" neuron types in the neocortex?

texts:
"Old" may mean a neuron type that appeared early in the tree of life, and it may mean – going together – that it comes early in the lineage tree of neuronal cells, rooted in the fertilized ovum:

[This is only for Schmidtea mediterranea. Could someone give me a link to a comparingly nice lineage tree for human neurons, please?]

My question is twofold:

Are there neuron types in the adult healthy brain co-present with some of their differentiated descendants?
Are there "old" neuron types in the neocortex, that either appeared early in the tree of life or come early in the lineage tree?


texts:
There is a lot of talk about inhumane treatment of animals and how we don't kill them in the proper way. I wonder how much research is done on this subject. What is the overall least painful way for an animal to die?

I also wonder if this would be the same for a human. It is often said that its least painful to die in ones sleep and i wonder if this is true. I wonder what is the most humane way to execute a capital punishment (if that is at all possible)


texts: Phylogeny: Hybridization between different species sharing same genus?

texts:
I am doing a cross-breeding project with Capsicum chinense x Capsicum baccatum. I'm planning to breed them until 6-8 gen.

My question: What will the completed breed be classified as? Would it be a new species or will it be considered as a strain of chinense or baccatum? Thanks.


texts: How do I cite a herbarium specimen that I have used to prepare a botanical description? Do I use the collector's name and number or the herbarium code and accession number? What if there is no record of the collector's name or number?


texts: What evolutionary mechanism caused felines to develop purring?

texts: And why can some felines roar while others meow?


texts: Anatomical Angle Made by the Fingers of an Extended Palm

texts:
Does the angle made by the fingers (excluding the thumb) of an extended palm (as shown in the figure below) have a name (such as the Lovibond or Cobb angle, for instance) ?

I have already checked Modeling the Constraints of Human Hand Motion, published by the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign, but it failed to provide any answers. (Perhaps there aren't any ?) Any input would be deeply appreciated.


texts:
So I'm sure you've all seen the dress photo where people see the dress as either White and Gold or Blue and Black.

It has essentially 'split' the internet because some people see the dress and they think that it is coloured blue and black, whereas the other half think that it is white and gold. It is trending on most social media sites as people fight about what the colour difference is.

So my question is why do different peoples eyes perceive different colours in this picture specifically?

For reference the photo with a color breakdown can be found here


texts: Are we naturally born right or left handed or ambidextrous?

texts:
Most of you here will be right or left handed. A few might be ambidextrous. But were we born that way?

I'm wondering if everyone was born ambidextrous, but as they grew up became more dependent on one hand, and that hand after more use now has stronger muscles, bones etc. Or were we naturally born with one hand stronger than the other?

I've heard somewhere that it has something to do with the brain, and which side which hemisphere is on. Not sure the validity of this statement. It's also been pointed out that chimps and apes show handedness, so this probably not just a human thing.

So, are we naturally born right or left handed? Or are we all born ambidextrous and does left or right handedness develops later?


texts: Would methamphetamine heal wounds, infections, and diseases?

texts:
Alright, so this sounds crazy but based on these research findings it is safe to assume that meth would allow wounds and diseases to heal faster by interleukin 6 . On the otherhand, using meth during illness would cause higher neurotoxicity due to extreme hyperthermia and fever.

Correct me if I'm wrong:

Firstly, dopamine increases interleukin 6 (IL-6) release and inhibits tumor necrosis factor release.
Interleukin-6 is the source of fevers and hyperthermia. Most importantly, IL-6 heals skin wounds. It's main goal is to regulate the immune system by raising and lowering temperature depending on if a person is sick or not. Raising body temperature will prevent a person from being sick and will make wounds heal faster, but will induce neurotoxicity, lowering it will prevent neurotoxicity but make someone vulnerable to infection. According to Wikipedia, IL-6 stimulates the inflammatory and auto-immune processes in many diseases such as diabetes, atherosclerosis, depression, Alzheimer's Disease (interestingly though, Alzheimer disease is reliant on dopamine depletion, and people with Alzheimer had significantly higher levels of IL-6, which is surprising. One possibility is due to the fact that dopamine increases interleukin 6 release, and without dopamine, IL-6 cant be released, meaning more IL-6 will be metabolized but not used).

IL-6 is also the main, and perhaps only, cause of meth-induced neurotoxicity. It is responsible for neurotoxicity by means including, but not limited to, cell death, ROS generation, and neuronal damage. Lowering enviromental temprature significantly prevents neurotoxicity. To verify this claim, I Googled "methamphetamine neurotoxicity interleukin-6", and came to this article, furthering the evidence that meth vastly potentiates IL-6 and IL-6 induced hyperthermia is the result of meth-induced neurotoxocity, as mice with a mutation for IL-6 blocked meth-induced neurotoxicity, which also means that these mice won't be able to reheal faster.

To bring an update to this post, I have found this paper that shows that happiness potentiates the immune system. But this is a very minor influence as meth produces >1000 "units" of dopamine, relative to 300 units which cocaine produces. Meth would be much more efficient.

To bring further updates, it seems that my assumptions were correct. By googling "site:nih.gov methamphetamine neuroprotective", I was led to the following: https://www.ncbi.nlm.nih.gov/pubmed/24333768 and https://www.ncbi.nlm.nih.gov/pubmed/25724762

Surprisingly it is neuroprotective following stroke.

So, putting all this into account, is it possible that meth actually heals wounds and diseases (while at the same time inducing neurotoxicity)?

This assumption came to me because I have an aggressive cat and whenever I'm high on meth I noticed how wounds from a cat scratch would heal within a day or two instead of a week.


texts: Changing genetic code of E. coli to accept synthetic amino acids?

texts: I read in my Biology textbook that an experiment has been done in which one of   E. coli's stop codon has been altered to accept a synthetic amino acid. I do not get how it can be done. Taking the fact into account that every permutation of the 4 natural nitrogenous bases codes for a particular amino acid means that if the stop codon, let's say UGA, is altered to UUA it will code for Leucine. How does this leave a possibility for the production of a codon which codes for a synthetic amino acid? I will appreciate your kind explanation. Thank you a lot.


texts: Which aspects of renal physiology are standing in the way of an artificial (mechanical) kidney?

texts:
Scientists have been able to create artificial organs with varying degrees of success.  The mechanical heart (in its various forms, e.g. ventricular assist) is able to sustain life for some period of time.

Efforts to grow whole organs in the lab will probably ultimately lead to a more pragmatic solution.  What aspects of the renal physiology are standing in the way of an implantable mechanical kidney (fashioned more so from tubules and membranes than simply being a shrunken down dialysis machine)?


texts:
I don't mean if a bacterium can be the cause of cancer inside a human. But can actually a bacterium changes in the way as normal cells change into tumor cells?
So gaining such characteristics of a tumor cell and if inside human body create a tumor mass?


texts: How did Rna replicate according to Rna World Hypothesis?

texts:
I was studying Rna World Hypothesis in Khan Academy, and there is a line.....

The RNA world hypothesis suggests that life on Earth began with a simple RNA molecule that could copy itself without help from other molecules.

Here, it's say that "without the help of other molecules" but doesn't enzyme like Rna Polymerase (protein)take part in Rna replication? So what is the meaning of this bold line?


texts: What is a good identification key for European mushrooms?

texts:
I live in the Netherlands, and I am looking for an identification key for mushrooms.
Are there any keys you could share?


texts: What have the L-systems (Lindenmayer systems) been actually used for in biology?

texts:
From Wikipedia:

An L-system or Lindenmayer system is a parallel rewriting system and a type of formal grammar.
L-systems were introduced and developed in 1968 by Aristid Lindenmayer, a Hungarian theoretical biologist and botanist at the University of Utrecht. Lindenmayer used L-systems to describe the behaviour of plant cells and to model the growth processes of plant development.

I tried to find biological research that has actually used this system but I could not find any. Perhaps this is because I do not know biology that well.
Are these models important? Still taught?
They do produce pretty pictures (again from Wikipedia)


texts: What microscope/magnification would I need to observe P. Acnes bacteria?

texts:
I am currently attempting to grow a culture of P. Acnes bacteria.  Right now, my only hope in identifying colonies of the bacteria in the culture is to use a black light to find colonies that glow orange.  I am not sure whether or not this will work since nutrient agar may not provide them with something that helps them produce porphyrins.  It's also entirely possible that another form of bacteria contaminating the culture would produce the same effect.

I would like to entertain the possibility of buying a microscope for this project.  I have never owned a quality microscope(just toy ones in the past), so I don't really know what type of microscope or what magnification I'll need in order to correctly identify and observe the P. Acnes bacteria.

What would be interesting is if I could turn this into a pharmacological project; if I can verify that I have the correct bacteria(to a fair degree of certainty, anyway), I can see how the bacteria reacts to different chemicals and environments.


texts: When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then?

texts:
I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and Zinc finger nucleases.

I understand that there may be a few metrics used for analyzing any genome editing system.  One is the efficiency, which could be measured perhaps in edits per time or edits per molecule.  Another metric might be error-rate.  What is the probability that a genome is altered in something other than the intended way?  Another metric might be the length of the genome that may be edited at once.

I've also read that CRISPR/Cas9 evolved in bacteria.  When did CRISPR/Cas9 evolve in the history of life on earth?

If CRISPR/Cas9 evolved in bacteria, and before other evolutionary advances, including some of those that may have enabled certain multiceullar forms of life, I have to wonder if other systems like CRISPR/Cas9 but superior to it in some metric evolved as well.

How does recombination in sexual reproduction work?  Might it involve biomolecular machinery like that of CRISPR/Cas9?

How does the adaptive immune system work?  How does VDJ recombination work?  Does it involve an advanced (relative to CRISPR/Cas9) genome editing system?

How might one estimate the probability that a system superior to CRISPR/Cas9 exists already?